14 11.19 0.00 6.45 corrected_mouse_rDNA_unit_Feb2013_IGS 279 311 (33053) (GGC)n#Simple_repeat 1 31 (0) m_b1s252i0 1 corrected_mou 279 GGCGGAGGAGGGGGATCGGCGGCGGCGGCGGCG 311 v v v -- (GGC)n#Simple 1 GGCGGCGGCGGCGG--CGGCGGCGGCGGCGGCG 31 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.06 (2 / 32), avg. gap size = 1.00 (2 / 2) 22 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 668 691 (32673) (C)n#Simple_repeat 1 24 (0) m_b1s252i1 2 corrected_mou 668 CCCCCCCCCCCCCCCCCCCCCCCC 691 (C)n#Simple_r 1 CCCCCCCCCCCCCCCCCCCCCCCC 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 910 927 (32437) (T)n#Simple_repeat 1 18 (0) m_b1s252i2 3 corrected_mou 910 TTTTTTTTTTTTTTTTTT 927 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0) 22 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 1124 1147 (32217) (T)n#Simple_repeat 1 24 (0) m_b1s252i3 4 corrected_mou 1124 TTTTTTTTTTTTTTTTTTTTTTTT 1147 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTT 24 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0) 56 1.96 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 1686 1737 (34746) (TG)n#Simple_repeat 1 52 (0) c_b1s251i0 5 corrected_mou 1686 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTG 1735 i (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 corrected_mou 1736 TG 1737 (TG)n#Simple_ 51 TG 52 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 307 22.33 17.48 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 1802 1898 (31567) C SVA_B#Retroposon/SVA (1076) 307 193 m_b1s502i0 6 corrected_mou 1802 CTGTAATTCCAGCAC-TCCAGAGGCAGAGGCAGGCAGACTTCT------- 1843 i i i - vi v ? iiv ------- C SVA_B#Retropo 307 CTGCAATCCCGGCACCTCGGGAGGCCGAGGCNGGCAGATCACTCGCGGTC 258 corrected_mou 1844 --GAGTTCGAGGCCAGCCTGGTC--TACAGAGGAACCCTGTCT----CGA 1885 -- i v i i i --i i v i i ---- i C SVA_B#Retropo 257 AGGAGCTGGAGACCAGCCCGGCCAACACGGCGAAACCCCGTCTCCACCAA 208 corrected_mou 1886 AAAAT--GAAAATAA 1898 -- iv C SVA_B#Retropo 207 AAAATACGAAAACCA 193 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 22.64 Transitions / transversions = 2.67 (16/6) Gap_init rate = 0.06 (6 / 96), avg. gap size = 3.00 (18 / 6) 57 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 1899 1949 (34534) (ATAC)n#Simple_repeat 1 51 (0) c_b1s251i1 7 corrected_mou 1899 ATACATACATACATACATACATACATACATACATACATACATACATACAT 1948 (ATAC)n#Simpl 1 ATACATACATACATACATACATACATACATACATACATACATACATACAT 50 corrected_mou 1949 A 1949 (ATAC)n#Simpl 51 A 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 23 16.31 2.08 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 1999 2046 (31419) (GATA)n#Simple_repeat 1 49 (0) m_b1s252i4 8 corrected_mou 1999 GATAGAGAGATAGATA-ATAGATAGATGGATAGAGTGATACAAATATAG 2046 v - i vv v v v (GATA)n#Simpl 1 GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG 49 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.02 (1 / 47), avg. gap size = 1.00 (1 / 1) 51 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 2220 2265 (34218) (TTGC)n#Simple_repeat 1 46 (0) c_b1s251i2 9 corrected_mou 2220 TTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTT 2265 (TTGC)n#Simpl 1 TTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTTGCTT 46 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 45), avg. gap size = 0.0 (0 / 0) 19 12.84 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 2420 2453 (31057) (ATT)n#Simple_repeat 1 34 (0) m_b1s252i5 10 corrected_mou 2420 ATTATTATCATTATCATTATTAATTTTATTATTA 2453 i i v v (ATT)n#Simple 1 ATTATTATTATTATTATTATTATTATTATTATTA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 21 15.46 0.00 2.27 corrected_mouse_rDNA_unit_Feb2013_IGS 2679 2723 (30787) (TTTC)n#Simple_repeat 1 44 (0) m_b1s252i6 11 corrected_mou 2679 TTTCATTGCTTCATTTCTATTTCTCTTTCTTTCTTTCTTTCTTTC 2723 - v iv v i i (TTTC)n#Simpl 1 TTTC-TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 44 Matrix = Unknown Transitions / transversions = 1.00 (3/3) Gap_init rate = 0.02 (1 / 44), avg. gap size = 1.00 (1 / 1) 12 12.52 5.13 5.13 corrected_mouse_rDNA_unit_Feb2013_IGS 2939 2977 (30533) (GCTTT)n#Simple_repeat 1 39 (0) m_b1s252i7 12 corrected_mou 2939 GCTTTGCTTTGTTTTG--TTGTTTTTCTTTTGGTTTTGCTT 2977 i -- i v - - i (GCTTT)n#Simp 1 GCTTTGCTTTGCTTTGCTTTGCTTTGC-TTT-GCTTTGCTT 39 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.33 (4 / 3) 13 15.83 2.70 2.70 corrected_mouse_rDNA_unit_Feb2013_IGS 2941 2977 (30533) (TTTGCT)n#Simple_repeat 1 37 (0) m_b1s252i8 12 corrected_mou 2941 TTTGC-TTTGTTTTGTTGTTTTTCTTTTGGTTTTGCTT 2977 - i - vv v v (TTTGCT)n#Sim 1 TTTGCTTTTGCTTT-TGCTTTTGCTTTTGCTTTTGCTT 37 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.06 (2 / 36), avg. gap size = 1.00 (2 / 2) 22 2.94 5.71 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 3148 3182 (30328) (CCTC)n#Simple_repeat 1 37 (0) m_b1s252i9 13 corrected_mou 3148 CCTCCCT-CC-CCCTCCCTCCCTCCCTCCCTCCTTCC 3182 - - i (CCTC)n#Simpl 1 CCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCC 37 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.06 (2 / 34), avg. gap size = 1.00 (2 / 2) 40 6.26 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 3194 3244 (33239) (AATAA)n#Simple_repeat 1 51 (0) c_b1s251i3 14 corrected_mou 3194 AATAAAATAAAATAAAATAAGATAAGATAAGATAAAATAAAATAAAATAA 3243 i i i (AATAA)n#Simp 1 AATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAA 50 corrected_mou 3244 A 3244 (AATAA)n#Simp 51 A 51 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 54 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 3505 3553 (32930) (CACT)n#Simple_repeat 1 49 (0) c_b1s251i4 15 corrected_mou 3505 CACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTC 3553 (CACT)n#Simpl 1 CACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTC 49 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 21 19.73 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 3637 3683 (29925) (TTTTTG)n#Simple_repeat 1 47 (0) m_b1s252i10 16 corrected_mou 3637 TTTTGGTTTTGGTTTTGGTGGTTTTTTGTTTTTTTGTTTTTGTTTTT 3683 v v v vv v v v (TTTTTG)n#Sim 1 TTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTT 47 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 38 0.00 2.56 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 3844 3882 (32601) (TATG)n#Simple_repeat 1 40 (0) c_b1s251i5 17 corrected_mou 3844 TATGTATGTAT-TATGTATGTATGTATGTATGTATGTATG 3882 - (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATG 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 38), avg. gap size = 1.00 (1 / 1) 16 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 3883 3901 (29745) (CATG)n#Simple_repeat 4 22 (1) m_b1s252i11 18 corrected_mou 3883 CATGCATGCATGCATGCAT 3901 (CATG)n#Simpl 4 CATGCATGCATGCATGCAT 22 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0) 13 12.91 5.56 2.70 corrected_mouse_rDNA_unit_Feb2013_IGS 3900 3935 (29711) (ATTT)n#Simple_repeat 1 37 (0) m_b1s252i12 19 corrected_mou 3900 ATTT-TTTTTTTA-AGATTTATTTATTTATTATATGTA 3935 - v -vv - v (ATTT)n#Simpl 1 ATTTATTTATTTATTTATTTATTTATTTATT-TATTTA 37 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.09 (3 / 35), avg. gap size = 1.00 (3 / 3) 14 8.13 3.85 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 4356 4381 (29265) (AAC)n#Simple_repeat 1 27 (0) m_b1s252i13 20 corrected_mou 4356 AACCACAA-AACAACAGCAACAACAAC 4381 v - i (AAC)n#Simple 1 AACAACAACAACAACAACAACAACAAC 27 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1) 13 9.26 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 4395 4417 (29229) (TGTT)n#Simple_repeat 1 23 (0) m_b1s252i14 21 corrected_mou 4395 TGTTTGTTTGTTTGTTTATGTGT 4417 i v (TGTT)n#Simpl 1 TGTTTGTTTGTTTGTTTGTTTGT 23 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0) 69 3.37 2.00 4.08 corrected_mouse_rDNA_unit_Feb2013_IGS 4421 4520 (31963) (TATT)n#Simple_repeat 1 98 (0) c_b1s251i6 22 corrected_mou 4421 TATTTATTTATTTACTTACTTACATTTATTTATTTATTTA-TT-TTTATT 4468 i - -i - - (TATT)n#Simpl 1 TATTTATTTATTTATTTA-TT-TATTTATTTATTTATTTATTTATTTATT 48 corrected_mou 4469 TATTCATCTGTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 4518 i - - (TATT)n#Simpl 49 TATTTAT-T-TATTTATTTATTTATTTATTTATTTATTTATTTATTTATT 96 corrected_mou 4519 TA 4520 (TATT)n#Simpl 97 TA 98 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.06 (6 / 99), avg. gap size = 1.00 (6 / 6) 25 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 4521 4551 (29194) (CTTA)n#Simple_repeat 1 31 (0) m_b1s252i15 23 corrected_mou 4521 CTTACTTACTTACTTACTTACTTACTTACTT 4551 (CTTA)n#Simpl 1 CTTACTTACTTACTTACTTACTTACTTACTT 31 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 33 0.00 2.27 4.65 corrected_mouse_rDNA_unit_Feb2013_IGS 4614 4657 (31826) (CAAAA)n#Simple_repeat 1 43 (0) c_b1s251i7 24 corrected_mou 4614 CAAAA-AAAACAAAACAAAACAAAACAAAACAACAACAACAACAA 4657 - - - (CAAAA)n#Simp 1 CAAAACAAAACAAAACAAAACAAAACAAAACAA-AACAA-AACAA 43 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.07 (3 / 43), avg. gap size = 1.00 (3 / 3) 18 15.51 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 4775 4804 (28984) (AT)n#Simple_repeat 1 30 (0) m_b1s252i16 25 corrected_mou 4775 ATACATATACATGTATATGTATATATATAT 4804 i i i i (AT)n#Simple_ 1 ATATATATATATATATATATATATATATAT 30 Matrix = Unknown Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 121 4.07 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 4858 4985 (31498) (TCTT)n#Simple_repeat 1 128 (0) c_b1s251i8 26 corrected_mou 4858 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 4907 (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 50 corrected_mou 4908 TTTCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 4957 i i i i (TCTT)n#Simpl 51 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 100 corrected_mou 4958 TCTTTCTTTCTTTCTTTCTTTCTCTCTT 4985 i (TCTT)n#Simpl 101 TCTTTCTTTCTTTCTTTCTTTCTTTCTT 128 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.00 (0 / 127), avg. gap size = 0.0 (0 / 0) 97 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 5187 5271 (31212) (GAA)n#Simple_repeat 1 85 (0) c_b1s251i9 27 corrected_mou 5187 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 5236 (GAA)n#Simple 1 GAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 50 corrected_mou 5237 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 5271 (GAA)n#Simple 51 AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG 85 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 84), avg. gap size = 0.0 (0 / 0) 26 6.26 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 5430 5463 (31020) (AATA)n#Simple_repeat 1 34 (0) c_b1s251i10 28 corrected_mou 5430 AATAAATAAATAAACAAACAAATAAATAAATAAA 5463 i i (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAATAAA 34 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 46 18.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 5466 5551 (28481) (GAAGAG)n#Simple_repeat 1 86 (0) m_b1s252i17 29 corrected_mou 5466 GAAGAAAAAGAAGAAGAAGAAGAAGAAGAGGAGGAGGAGGAGGAGGAGGA 5515 ii i i i i i i (GAAGAG)n#Sim 1 GAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGA 50 corrected_mou 5516 GGAGGAAGAGGAGGAGGGGGAGGAGGAGGAAGAGGA 5551 i i ii i (GAAGAG)n#Sim 51 AGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGA 86 Matrix = Unknown Transitions / transversions = 1.00 (13/0) Gap_init rate = 0.00 (0 / 85), avg. gap size = 0.0 (0 / 0) 49 12.93 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 5475 5553 (28479) (GAG)n#Simple_repeat 1 79 (0) m_b1s252i18 29 corrected_mou 5475 GAAGAAGAAGAAGAAGAAGAGGAGGAGGAGGAGGAGGAGGAGGAGGAAGA 5524 i i i i i i i (GAG)n#Simple 1 GAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGA 50 corrected_mou 5525 GGAGGAGGGGGAGGAGGAGGAAGAGGAGG 5553 i i (GAG)n#Simple 51 GGAGGAGGAGGAGGAGGAGGAGGAGGAGG 79 Matrix = Unknown Transitions / transversions = 1.00 (9/0) Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0) 38 1.99 7.84 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 5611 5661 (30822) (TA)n#Simple_repeat 1 55 (0) c_b1s251i11 30 corrected_mou 5611 TATATATATA-ATATATATA-ATATATATATA-AT-TAAATATATATATA 5656 - - - - v (TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50 corrected_mou 5657 TATAT 5661 (TA)n#Simple_ 51 TATAT 55 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.08 (4 / 50), avg. gap size = 1.00 (4 / 4) 28 17.37 2.99 1.47 corrected_mouse_rDNA_unit_Feb2013_IGS 5687 5753 (28329) (GTTT)n#Simple_repeat 1 68 (0) m_b1s252i19 31 corrected_mou 5687 GTTTGTCTG-CTGTTTGTTTGTTTGTTTGTTTGCTTGCTTGATTTCTTGC 5735 i -i i i v vi i (GTTT)n#Simpl 1 GTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGT 50 corrected_mou 5736 TTGCTTTTTTTCTTT-TTT 5753 - v v - (GTTT)n#Simpl 51 TTG-TTTGTTTGTTTGTTT 68 Matrix = Unknown Transitions / transversions = 1.50 (6/4) Gap_init rate = 0.05 (3 / 66), avg. gap size = 1.00 (3 / 3) 55 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 5872 5920 (30563) (TTA)n#Simple_repeat 1 49 (0) c_b1s251i12 32 corrected_mou 5872 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 5920 (TTA)n#Simple 1 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT 49 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 48), avg. gap size = 0.0 (0 / 0) 17 20.15 2.08 2.08 corrected_mouse_rDNA_unit_Feb2013_IGS 5980 6027 (28103) (TTTA)n#Simple_repeat 1 48 (0) m_b1s252i20 33 corrected_mou 5980 TTTCTTTCTTT-TTTTTTTTTTTAAAGATTTATTTATTTATTATATGTA 6027 v v - v v vvv - v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT-TATTTA 48 Matrix = Unknown Transitions / transversions = 0.00 (0/8) Gap_init rate = 0.04 (2 / 47), avg. gap size = 1.00 (2 / 2) 12 25.56 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 7132 7168 (26962) (GGGAGG)n#Simple_repeat 1 37 (0) m_b1s252i22 34 corrected_mou 7132 GGGTGGGGCTGGGGGAGGGGTGGGGTGGGGGGCAGGG 7168 v vv vi v i v (GGGAGG)n#Sim 1 GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGG 37 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 16 21.71 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 7132 7163 (26967) (G)n#Simple_repeat 1 32 (0) m_b1s252i23 34 corrected_mou 7132 GGGTGGGGCTGGGGGAGGGGTGGGGTGGGGGG 7163 v vv i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 32 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 523 20.09 10.13 2.35 corrected_mouse_rDNA_unit_Feb2013_IGS 7553 7710 (26420) C AluJb#SINE/Alu (6) 306 137 m_b1s357i0 35 corrected_mou 7553 TTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTTTCTCTGTATAGCCCT 7602 i v v i v v C AluJb#SINE/Al 306 TTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTCTGTCGCCCA 257 corrected_mou 7603 GGCT---GTCC--TGG---------AACTCACTTTGTAGACCAGGCTGGC 7638 --- v -- ---------ii -- i v iv i i--i C AluJb#SINE/Al 256 GGCTGGAGTGCAGTGGCGCGATCACGGCTCAC--TGCAGCCTCGACC--T 211 corrected_mou 7639 CTCGAACTC-AGAAATACGCCTGCCTCTGCCTCCCGAGT-GCTGTGATTA 7686 i ii - vi v v i v - v i C AluJb#SINE/Al 210 CCCGGGCTCAAGCGATCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTA 161 corrected_mou 7687 AAGGCGTGCACCACCACGCCAGGC 7710 v i i v C AluJb#SINE/Al 160 CAGGCGCGCGCCACCACGCCCGGC 137 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 19.62 Transitions / transversions = 1.21 (17/14) Gap_init rate = 0.06 (9 / 157), avg. gap size = 2.22 (20 / 9) 17 11.43 5.00 2.44 corrected_mouse_rDNA_unit_Feb2013_IGS 7906 7945 (26185) (ATAA)n#Simple_repeat 1 41 (0) m_b1s252i25 36 corrected_mou 7906 ATAAATAAA-AAATAAATAAA-ACATTCAAAAATAAAGTAAA 7945 - - v vv v - (ATAA)n#Simpl 1 ATAAATAAATAAATAAATAAATAAATAAATAAATAAA-TAAA 41 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.08 (3 / 39), avg. gap size = 1.00 (3 / 3) 16 7.54 0.00 3.45 corrected_mouse_rDNA_unit_Feb2013_IGS 7970 7999 (26131) (ATTTT)n#Simple_repeat 1 29 (0) m_b1s252i26 37 corrected_mou 7970 ATTTTAATTTTATTTTATTGTATTGTATTT 7999 - v v (ATTTT)n#Simp 1 ATTTT-ATTTTATTTTATTTTATTTTATTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/2) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 21 3.96 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 8000 8025 (26105) (CA)n#Simple_repeat 1 26 (0) m_b1s252i27 38 corrected_mou 8000 CACACACACACACACACACACAGACA 8025 v (CA)n#Simple_ 1 CACACACACACACACACACACACACA 26 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 25), avg. gap size = 0.0 (0 / 0) 271 20.30 0.93 22.47 corrected_mouse_rDNA_unit_Feb2013_IGS 8198 8305 (25825) C SVA_A#Retroposon/SVA (1079) 308 220 m_b1s502i2 39 corrected_mou 8198 AATCCCAGCACTTC-GGAGGCAGAGGCAGGCAGATTTCTGAATTGGAGGC 8246 i - v i i iv ----- v C SVA_A#Retropo 308 AATCCCAGCACCTCGGGAGGCCGAGGCGGGCGGATCGC-----TCGAGGC 264 corrected_mou 8247 CAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCCAGGCTACACAGAGAA 8296 --------------- i ?v iv i ? v i v i C SVA_A#Retropo 263 CAG---------------GAGCTNGAGACCAGCCCGGNCAACACGGCGAG 229 corrected_mou 8297 ACCCTGTCT 8305 i C SVA_A#Retropo 228 ACCCCGTCT 220 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 14.88 Transitions / transversions = 1.43 (10/7) Gap_init rate = 0.20 (21 / 107), avg. gap size = 1.00 (21 / 21) 282 20.29 14.49 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 8198 8266 (25864) C SVA_B#Retroposon/SVA (1080) 303 225 m_b1s502i1 39 corrected_mou 8198 AATCCCAGCACTTCGG-AGGCAGAGGCAGGCAGATTTCT---------GA 8237 i i - v ? iv --------- C SVA_B#Retropo 303 AATCCCGGCACCTCGGGAGGCCGAGGCNGGCAGATCACTCGCGGTCAGGA 254 corrected_mou 8238 ATTGGAGGCCAGCCTGGTCTACAGAGTGA 8266 ii i i i v vi i C SVA_B#Retropo 253 GCTGGAGACCAGCCCGGCCAACACGGCGA 225 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 17.32 Transitions / transversions = 2.50 (10/4) Gap_init rate = 0.03 (2 / 68), avg. gap size = 5.00 (10 / 2) 18 7.14 0.00 3.23 corrected_mouse_rDNA_unit_Feb2013_IGS 8310 8341 (25789) (AAAC)n#Simple_repeat 1 31 (0) m_b1s252i28 40 corrected_mou 8310 AAACAAACAAACAGACAAACAAACCAAGCAAA 8341 i - i (AAAC)n#Simpl 1 AAACAAACAAACAAACAAACAAA-CAAACAAA 31 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 54 4.57 1.43 1.43 corrected_mouse_rDNA_unit_Feb2013_IGS 8466 8535 (27948) (TACA)n#Simple_repeat 1 70 (0) c_b1s251i13 41 corrected_mou 8466 TACAAACATACAAACATACCA-AAATACATACATACATACATACATACAT 8514 v v - - v (TACA)n#Simpl 1 TACATACATACATACATA-CATACATACATACATACATACATACATACAT 49 corrected_mou 8515 ACATACATACATACATACATA 8535 (TACA)n#Simpl 50 ACATACATACATACATACATA 70 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.03 (2 / 69), avg. gap size = 1.00 (2 / 2) 12 3.97 3.12 10.00 corrected_mouse_rDNA_unit_Feb2013_IGS 8649 8680 (25519) (TGTCT)n#Simple_repeat 1 30 (0) m_b1s252i29 42 corrected_mou 8649 TGTCTTGT-TTGTTTTTGTCTTGTACTTTGTCT 8680 - - i - - (TGTCT)n#Simp 1 TGTCTTGTCTTG-TCTTGTCTTGT-C-TTGTCT 30 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.13 (4 / 31), avg. gap size = 1.00 (4 / 4) 37 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 8903 8936 (27547) (CTGC)n#Simple_repeat 1 34 (0) c_b1s251i14 43 corrected_mou 8903 CTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCT 8936 (CTGC)n#Simpl 1 CTGCCTGCCTGCCTGCCTGCCTGCCTGCCTGCCT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 55 13.67 1.52 6.35 corrected_mouse_rDNA_unit_Feb2013_IGS 8988 9119 (25113) (TCTTTT)n#Simple_repeat 1 126 (0) m_b1s252i30 44 corrected_mou 8988 TCTTTTTCTCTTCCTTTTTCTTTTTCTTTCATTTTCTTTCTCTTTCTTTT 9037 i i -- i i i (TCTTTT)n#Sim 1 TCTTTTTCTTTTTCTTTTTCTTTTTCTTT--TTCTTTTTCTTTTTCTTTT 48 corrected_mou 9038 TCTCTTTC--TTTCTCTTTCTCTTTCTTTTTCATTTTCTCTCTCTCTCTT 9085 i -- i i - - i i i (TCTTTT)n#Sim 49 TCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTC-TTTT-TCTTTTTCTTTT 96 corrected_mou 9086 CCTTTTTTTCTTTCTTTCTTACATTTATTCTTTT 9119 i i i - - - - (TCTTTT)n#Sim 97 TCTTTTTCTTTTTCTTT-TT-C-TTT-TTCTTTT 126 Matrix = Unknown Transitions / transversions = 1.00 (14/0) Gap_init rate = 0.07 (9 / 131), avg. gap size = 1.11 (10 / 9) 66 4.12 0.00 1.32 corrected_mouse_rDNA_unit_Feb2013_IGS 9126 9202 (27281) (TATTT)n#Simple_repeat 1 76 (0) c_b1s251i15 45 corrected_mou 9126 TATTTTATTTCATTTCATTTGACTTTTATTTTATTTTATTTTATTTTATT 9175 i i v - (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTA-TTTTATTTTATTTTATTTTATTTTATT 49 corrected_mou 9176 TTATTTTATTTTATTTTATTTTATTTT 9202 (TATTT)n#Simp 50 TTATTTTATTTTATTTTATTTTATTTT 76 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.01 (1 / 76), avg. gap size = 1.00 (1 / 1) 512 22.81 3.20 15.90 corrected_mouse_rDNA_unit_Feb2013_IGS 9286 9370 (24966) C AluSx#SINE/Alu (116) 196 120 m_b1s357i1 46 corrected_mou 9286 ATCCTCCCATCTCTGCCTCCCTAGT-GTTGGGATTAAAGACATGGGCCAC 9334 i iii v v - i v i ii v C AluSx#SINE/Al 196 ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCAC 147 corrected_mou 9335 CAC-TCTGGCTACTTTTTAATTTTTTAATTTTTATTT 9370 -i i ------- vv --- C AluSx#SINE/Al 146 CACGCCCGGCTA-------ATTTTTGTATTTTTA--- 120 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 22.13 Transitions / transversions = 1.67 (10/6) Gap_init rate = 0.14 (12 / 84), avg. gap size = 1.00 (12 / 12) 31 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 9371 9399 (27084) (TTTTTG)n#Simple_repeat 1 29 (0) c_b1s251i16 47 corrected_mou 9371 TTTTTGTTTTTGTTTTTGTTTTTGTTTTT 9399 (TTTTTG)n#Sim 1 TTTTTGTTTTTGTTTTTGTTTTTGTTTTT 29 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 512 22.81 3.20 15.90 corrected_mouse_rDNA_unit_Feb2013_IGS 9400 9532 (24804) C AluSx#SINE/Alu (193) 119 3 m_b1s357i1 46 corrected_mou 9400 TCGAGACAGGGTTTCTCTGTATAACTCTGGCTGTCCTGGAACTCACTTCA 9449 v i v ii i vivi v vi v ------ C AluSx#SINE/Al 119 TAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTC------ 76 corrected_mou 9450 TAGACCAGGCTGGCCTTGAACTCAGA-AATCCGCCTGCCTCTGCCTCCC- 9497 ---------------i v i-i i v - C AluSx#SINE/Al 75 ---------------CTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCA 41 corrected_mou 9498 AAGTGCTGGGATTAAAGGTGTG---CTTTACGCCCGGC 9532 v i --- viii C AluSx#SINE/Al 40 AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGC 3 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 22.13 Transitions / transversions = 1.36 (15/11) Gap_init rate = 0.17 (23 / 132), avg. gap size = 1.13 (26 / 23) 16 12.48 9.09 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 9533 9576 (24760) (TTTTA)n#Simple_repeat 1 48 (0) m_b1s252i31 48 corrected_mou 9533 TTTTA-TTT-TTAAATTTTA-TTTA-TTTAATTTATTTTTGTTTATTT 9576 - - vv - - v vv (TTTTA)n#Simp 1 TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 48 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.09 (4 / 43), avg. gap size = 1.00 (4 / 4) 302 25.32 1.23 2.50 corrected_mouse_rDNA_unit_Feb2013_IGS 9651 9731 (24605) SVA_A#Retroposon/SVA 137 216 (1171) m_b1s502i3 49 corrected_mou 9651 TAATCTGTCTGCCTCTGCTTCCCAAATGC-TGGGATTAAAAGCATCTGCC 9699 i ivi v i i i - iv i iivi SVA_A#Retropo 137 TGATCCTCCTGCCTCGGCCTCCCGAGTGCCTGGGATTGCAGGCGCGCGCC 186 corrected_mou 9700 ACCACTGCCCTGACTAATTTTTTTTTTTTTGG 9731 i - - ii v v SVA_A#Retropo 187 GCCAC-GCCC-GACTGGTTTTTGTATTTTTGG 216 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 23.14 Transitions / transversions = 2.33 (14/6) Gap_init rate = 0.04 (3 / 80), avg. gap size = 1.00 (3 / 3) 51 6.54 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 9738 9801 (26682) (CCTT)n#Simple_repeat 1 64 (0) c_b1s251i17 50 corrected_mou 9738 CCTTTCTTCCTACCTTCCTTTCTTCCTTCCTTCCTTCCTTCATTCCTTCC 9787 i v i v (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 50 corrected_mou 9788 TTCCTTCCTTCCTT 9801 (CCTT)n#Simpl 51 TTCCTTCCTTCCTT 64 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 63), avg. gap size = 0.0 (0 / 0) 17 10.01 3.12 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 9802 9833 (24566) (TCTT)n#Simple_repeat 1 33 (0) m_b1s252i33 51 corrected_mou 9802 TCTTTCTTTCTTTCATTATTT-TTTCTTTTTTT 9833 v v - i (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 33 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1) 29 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 10059 10093 (24306) (AATA)n#Simple_repeat 1 35 (0) m_b1s252i34 52 corrected_mou 10059 AATAAATAAATAAATAAATAAATAAATAAATAAAT 10093 (AATA)n#Simpl 1 AATAAATAAATAAATAAATAAATAAATAAATAAAT 35 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 34), avg. gap size = 0.0 (0 / 0) 52 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 10094 10140 (26343) (AAGA)n#Simple_repeat 1 47 (0) c_b1s251i18 53 corrected_mou 10094 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 10140 (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 47 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0) 65 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 10457 10511 (25972) (TG)n#Simple_repeat 1 55 (0) c_b1s251i19 54 corrected_mou 10457 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 10506 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50 corrected_mou 10507 TGTGT 10511 (TG)n#Simple_ 51 TGTGT 55 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 40 17.32 3.45 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 10558 10644 (23855) (CTTT)n#Simple_repeat 1 90 (0) m_b1s252i35 55 corrected_mou 10558 CTTTAATTCTTTCTTTC-TTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 10606 vv - i i i i i i i (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50 corrected_mou 10607 TCCTTCCTTCCTTTCTTTC--TCTTTCTTTCTCTCTTTCT 10644 i i i -- i (CTTT)n#Simpl 51 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 90 Matrix = Unknown Transitions / transversions = 5.50 (11/2) Gap_init rate = 0.02 (2 / 86), avg. gap size = 1.50 (3 / 2) 31 0.00 3.03 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 10646 10678 (25805) (TTTTTTG)n#Simple_repeat 1 34 (0) c_b1s251i20 56 corrected_mou 10646 TTTTTT-TTTTTTGTTTTTTGTTTTTTGTTTTTT 10678 - (TTTTTTG)n#Si 1 TTTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTT 34 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.03 (1 / 32), avg. gap size = 1.00 (1 / 1) 18 18.05 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 10806 10843 (23688) (ATGT)n#Simple_repeat 1 38 (0) m_b1s252i36 57 corrected_mou 10806 ATGTGTGTGTGTATGTTTCTATGTATATATGTATATAT 10843 i i v v i i (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 38 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 28 25.44 3.45 1.12 corrected_mouse_rDNA_unit_Feb2013_IGS 10890 10976 (23555) (TCTC)n#Simple_repeat 1 89 (0) m_b1s252i37 58 corrected_mou 10890 TCTTTCTCTCTCTCTTTCT-TCTTTC-CTTTCTTTCTTTCTTTTTGCTTT 10937 i i - i - i i i i i - i (TCTC)n#Simpl 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT-CTCT 49 corrected_mou 10938 CTCTTTCT-TTTTTCTCTCTTTCTCCTTTTCTCTCTTTCT 10976 i - i i i ii i i (TCTC)n#Simpl 50 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 89 Matrix = Unknown Transitions / transversions = 1.00 (17/0) Gap_init rate = 0.05 (4 / 86), avg. gap size = 1.00 (4 / 4) 20 14.87 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 11124 11161 (23370) (ATGT)n#Simple_repeat 1 38 (0) m_b1s252i38 59 corrected_mou 11124 ATGTGTGTGTGTATGTTTGTATGTATATATGTATATAT 11161 i i v i i (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 38 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 94 4.36 3.36 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 11393 11511 (24972) (TCTT)n#Simple_repeat 1 123 (0) c_b1s251i21 60 corrected_mou 11393 TCTTTCTTTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 11442 i (TCTT)n#Simpl 1 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 50 corrected_mou 11443 TTTCTTTCTTTCTCTCTTTCTTTCTTTCTTT-TTACTTTC--TCTTTCTT 11489 i - v -- (TCTT)n#Simpl 51 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 100 corrected_mou 11490 T-TTTCTCTCTTTCTCTCTTTCT 11511 - i i (TCTT)n#Simpl 101 TCTTTCTTTCTTTCTTTCTTTCT 123 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.03 (3 / 118), avg. gap size = 1.33 (4 / 3) 18 18.05 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 11659 11696 (22953) (ATGT)n#Simple_repeat 1 38 (0) m_b1s252i39 61 corrected_mou 11659 ATGTGTGTGTGTATGTTTCTATGTATATATGTATATAT 11696 i i v v i i (ATGT)n#Simpl 1 ATGTATGTATGTATGTATGTATGTATGTATGTATGTAT 38 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 71 0.00 1.56 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 11743 11806 (24677) (TC)n#Simple_repeat 1 65 (0) c_b1s251i22 62 corrected_mou 11743 TCTCTCT-TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 11791 - (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 corrected_mou 11792 TCTCTCTCTCTCTCT 11806 (TC)n#Simple_ 51 TCTCTCTCTCTCTCT 65 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 15 22.09 2.04 2.04 corrected_mouse_rDNA_unit_Feb2013_IGS 12127 12175 (22537) (TTATTAT)n#Simple_repeat 1 49 (0) m_b1s252i40 63 corrected_mou 12127 TTA-TATTTTTCATTTATTATGCATTTTTTTAAGATTTATTTATTATTAT 12175 - v i vi - v vv vv (TTATTAT)n#Si 1 TTATTATTTATTATTTATTATTTA-TTATTTATTATTTATTATTTATTAT 49 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.04 (2 / 48), avg. gap size = 1.00 (2 / 2) 108 1.98 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 12968 13070 (23413) (AAGA)n#Simple_repeat 1 103 (0) c_b1s251i23 64 corrected_mou 12968 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 13017 (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50 corrected_mou 13018 GAAAGGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 13067 ii (AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 100 corrected_mou 13068 AAG 13070 (AAGA)n#Simpl 101 AAG 103 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 102), avg. gap size = 0.0 (0 / 0) 17 22.70 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 13150 13185 (21629) (T)n#Simple_repeat 1 36 (0) m_b1s252i41 65 corrected_mou 13150 TTTTTGTTTTTTGTTTTTTTGCTTGTTTTGGTTTTT 13185 v v vi v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 36 Matrix = Unknown Transitions / transversions = 0.17 (1/6) Gap_init rate = 0.00 (0 / 35), avg. gap size = 0.0 (0 / 0) 46 4.35 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 13245 13292 (23191) (GT)n#Simple_repeat 1 48 (0) c_b1s251i24 66 corrected_mou 13245 GTGTGTGTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 13292 ii (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 48 Matrix = Unknown Transitions / transversions = 1.00 (2/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 410 26.64 3.57 21.61 corrected_mouse_rDNA_unit_Feb2013_IGS 13358 13387 (21522) C AluJb#SINE/Alu (0) 312 285 m_b1s357i2 67 corrected_mou 13358 TTTTTTCTAATTCTTTTTCATTTCTATTTC 13387 i -- i iv i v i C AluJb#SINE/Al 312 TTTTTTTT--TTTTTTTTTTTTTTTTTTTT 285 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 27.21 Transitions / transversions = 2.50 (5/2) Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2) 36 2.08 6.12 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 13388 13436 (23047) (TTATT)n#Simple_repeat 1 52 (0) c_b1s251i25 68 corrected_mou 13388 TTATTTTATTTTATTTTATTTTATTTTA-TTTATTTTGTTTT-TTTT-TT 13434 - i - - (TTATT)n#Simp 1 TTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATT 50 corrected_mou 13435 TT 13436 (TTATT)n#Simp 51 TT 52 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.00 (3 / 3) 410 26.64 3.57 21.61 corrected_mouse_rDNA_unit_Feb2013_IGS 13437 13769 (21140) C AluJb#SINE/Alu (28) 284 4 m_b1s357i2 67 corrected_mou 13437 CGAGACAGGGTTTCTCCCTATAGCCCTGGCTGTTCTGGAACTCACTTTGC 13486 i i v i i v v ----- iiv -v v C AluJb#SINE/Al 284 TGAGACAGGGTCTCGCTCTGTCGCCCAGG-----CTGGAGTGCA-GTGGC 241 corrected_mou 13487 -CGACCATGGC-CATGGTGGCCTTGAATTC---------AGAAATCCTCC 13525 - i i - iv ii i vi --------- vi C AluJb#SINE/Al 240 GCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGCGATCCTCC 191 corrected_mou 13526 CATCCCTGCCTCCCTAGGA-CTGGGAATAAAGGCTTGAGCCACCACTCCC 13574 ii i v v v - v v vi v v C AluJb#SINE/Al 190 CGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCACCACGCCC 141 corrected_mou 13575 GGGTATATTTAATTTTTTTAATTTTTAAATTTTATTTGTTTTATTTATTT 13624 ------i v ------------------------------ C AluJb#SINE/Al 140 GG------CTAATTTTTGTA------------------------------ 127 corrected_mou 13625 TTCTTTTTTTTCAAGATGTGGTTTCTCTGTGTAACCCTGGCTGTCCTGGA 13674 --- v vi i v v ii vi v vi v C AluJb#SINE/Al 126 ---TTTTTTGTAGAGACGGGGTTTCGCCATGTTGCCCAGGCTGGTCTCGA 80 corrected_mou 13675 ACTCACTCTGTAGACCAGGCTGGCCTTGAACCATTAATCTGAACGTTTTT 13724 --------------- v ii i ----i i?vv ii iv C AluJb#SINE/Al 79 ACTC---------------CTGGGCTCAAGC----GATCCNCCCGCCTCG 49 corrected_mou 13725 GCTTCCCAAA-TGCTGGGATTAGAGGCATGTGACACCACTGCCCGG 13769 i - v i v v i - C AluJb#SINE/Al 48 GCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC-GCCCGG 4 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 27.21 Transitions / transversions = 1.09 (36/33) Gap_init rate = 0.21 (70 / 332), avg. gap size = 1.11 (78 / 70) 20 3.45 3.33 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 13794 13823 (21086) (CCTT)n#Simple_repeat 1 31 (0) m_b1s252i42 69 corrected_mou 13794 CCTTCCTTCCTTCC-TCCTTCCTTCCTCCCT 13823 - i (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 80 3.53 1.14 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 13824 13911 (22572) (TTTC)n#Simple_repeat 1 89 (0) c_b1s251i26 70 corrected_mou 13824 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 13873 (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 corrected_mou 13874 TCTTTCTTTCTTT-TTTCTCTCTCTCTTTCTCTCTTTCT 13911 - i i i (TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 89 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1) 19 11.70 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 13917 13944 (21052) (T)n#Simple_repeat 1 28 (0) m_b1s252i43 71 corrected_mou 13917 TTTTTTTTTTGTTTTGTTTTGTTTTTTT 13944 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 69 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 14012 14072 (22411) (TTCT)n#Simple_repeat 1 61 (0) c_b1s251i27 72 corrected_mou 14012 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 14061 (TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50 corrected_mou 14062 CTTTCTTTCTT 14072 (TTCT)n#Simpl 51 CTTTCTTTCTT 61 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 48 2.13 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 14223 14270 (22213) (CTCA)n#Simple_repeat 1 48 (0) c_b1s251i28 73 corrected_mou 14223 CTCACTCACTCACTCACTCACTCACTCACTCACTCACTCATTCACTCA 14270 i (CTCA)n#Simpl 1 CTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCA 48 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 17 14.46 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 14373 14403 (20700) (TCC)n#Simple_repeat 1 31 (0) m_b1s252i44 74 corrected_mou 14373 TCCTCCTCCTCCCCCTCCTCCCCCTTCTGCT 14403 i i i v (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 12 25.56 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 14783 14819 (20284) (GGGAGG)n#Simple_repeat 1 37 (0) m_b1s252i45 75 corrected_mou 14783 GGGTGGGGCTGGGGGAGGGGTGGGGTGGGGGGCAGGG 14819 v vv vi v i v (GGGAGG)n#Sim 1 GGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGG 37 Matrix = Unknown Transitions / transversions = 0.33 (2/6) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 16 21.71 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 14783 14814 (20289) (G)n#Simple_repeat 1 32 (0) m_b1s252i46 75 corrected_mou 14783 GGGTGGGGCTGGGGGAGGGGTGGGGTGGGGGG 14814 v vv i v v (G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 32 Matrix = Unknown Transitions / transversions = 0.20 (1/5) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 15200 15239 (21244) (T)n#Simple_repeat 1 40 (0) c_b1s251i29 76 corrected_mou 15200 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 15239 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 53 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 15301 15345 (21138) (TG)n#Simple_repeat 1 45 (0) c_b1s251i30 77 corrected_mou 15301 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 15345 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 546 18.45 10.27 6.25 corrected_mouse_rDNA_unit_Feb2013_IGS 15409 15435 (19801) C AluJb#SINE/Alu (1) 311 288 m_b1s357i3 78 corrected_mou 15409 TTTTTTTCTAATTCTTTTTCCTTTTTA 15435 i -- i ii - C AluJb#SINE/Al 311 TTTTTTTTT--TTTTTTTTTTTTTTT- 288 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 17.33 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.12 (3 / 26), avg. gap size = 1.00 (3 / 3) 56 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 15436 15486 (20997) (TATTT)n#Simple_repeat 1 51 (0) c_b1s251i31 79 corrected_mou 15436 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 15485 (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 50 corrected_mou 15486 T 15486 (TATTT)n#Simp 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 546 18.45 10.27 6.25 corrected_mouse_rDNA_unit_Feb2013_IGS 15487 15643 (19593) C AluJb#SINE/Alu (25) 287 120 m_b1s357i3 78 corrected_mou 15487 GGTTTTTGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCA 15536 -- i v v i v v ----- iiv C AluJb#SINE/Al 287 --TTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTG-----GAGTGCA 245 corrected_mou 15537 GTTTGCA-GACCA-GGCT------GGCCTAGAACTC---------AGAAA 15569 v- i- i - ------i v v --------- vi C AluJb#SINE/Al 244 GTG-GCGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGCGA 196 corrected_mou 15570 TCCTCCCATCTCTGCCTCCCGAGT-GCTGAGATTAAAGGCGTGCACCACC 15618 ii v - i i v i i C AluJb#SINE/Al 195 TCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCACC 146 corrected_mou 15619 ACACCCGGCT-ATTTTTAAATTTTTT 15643 i - iv C AluJb#SINE/Al 145 ACGCCCGGCTAATTTTTGTATTTTTT 120 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 17.33 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.09 (14 / 156), avg. gap size = 1.93 (27 / 14) 23 15.69 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 15655 15697 (19539) (TTTA)n#Simple_repeat 1 43 (0) m_b1s252i48 80 corrected_mou 15655 TTTATTTTTATTTTTATTTATTTATTTATTTATTTTTGTTTTT 15697 v v v v v v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 477 22.45 7.41 5.73 corrected_mouse_rDNA_unit_Feb2013_IGS 15779 15967 (19269) C AluSx#SINE/Alu (116) 196 5 m_b1s357i4 81 corrected_mou 15779 ATCCGCCTGCCTCTGCCTCCCAAGT-GCTGGGATTAAAGGTGTGCTTTAC 15827 i v v i - v i i vii C AluSx#SINE/Al 196 ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCAC 147 corrected_mou 15828 ---GCCCGGCTTTTATTTTTAAATTTTATTTATTTAATTTATTTTTGTTT 15874 --- v-- i----- -- i vv vvivv v C AluSx#SINE/Al 146 CACGCCCGGCTA--ATTTTTG-----TATTT--TTAGTAGAGACGGGGTT 106 corrected_mou 15875 ATCACTGTGTAGACCAGGCTGGCCTTGAAC-----ACTTTA----ATCTG 15915 - ii v i i i ----- i i ---- i C AluSx#SINE/Al 105 -TCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCG 57 corrected_mou 15916 TCTGCCTCTGCTTCCCAAA-TGCTGGGATTAAAAGCATCTGCCACCACTG 15964 i i v i - v i i vv i - C AluSx#SINE/Al 56 CCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC-G 8 corrected_mou 15965 CCC 15967 C AluSx#SINE/Al 7 CCC 5 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 20.55 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.09 (16 / 188), avg. gap size = 1.56 (25 / 16) 20 26.09 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 15975 16003 (19284) (TTTT)n#Simple_repeat 1 29 (31) m_b1s252i49 82 corrected_mou 15975 TTTTTTTTTTTTTTTTTTTTTAGAAAATA 16003 vvvvvv v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 42 6.04 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 16004 16055 (20428) (CCTT)n#Simple_repeat 1 52 (0) c_b1s251i32 83 corrected_mou 16004 CCTTTCTTCCTACCTTCCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 16053 i v i (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 50 corrected_mou 16054 TT 16055 (CCTT)n#Simpl 51 TT 52 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 20 26.09 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 16056 16085 (19202) (TTTT)n#Simple_repeat 30 59 (1) m_b1s252i49 84 corrected_mou 16056 TCTTTCTTTCATTATTTTTTTCTTTTTTTT 16085 i i iv v i (TTTT)n#Simpl 30 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 59 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 14 25.97 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 16215 16255 (19032) (TATG)n#Simple_repeat 1 41 (0) m_b1s252i51 85 corrected_mou 16215 TATGTGTCTTTGTATGTATGTATATATCGAAGTATTCATGT 16255 i v v i vv v vi (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGT 41 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 16309 16325 (18962) (A)n#Simple_repeat 1 17 (0) m_b1s252i52 86 corrected_mou 16309 AAAAAAAAAAAAAAAAA 16325 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 41 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 16326 16363 (20120) (AAAG)n#Simple_repeat 1 38 (0) c_b1s251i33 87 corrected_mou 16326 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 16363 (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 47 5.80 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 16472 16525 (19958) (GT)n#Simple_repeat 1 54 (0) c_b1s251i34 88 corrected_mou 16472 GTGTGTGTGTATGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAT 16521 i v i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 corrected_mou 16522 GTGT 16525 (GT)n#Simple_ 51 GTGT 54 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 17803 17844 (18639) (ACAG)n#Simple_repeat 1 42 (0) c_b1s251i35 89 corrected_mou 17803 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 17844 (ACAG)n#Simpl 1 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 17940 17971 (18512) (GTCT)n#Simple_repeat 1 32 (0) c_b1s251i36 90 corrected_mou 17940 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 17971 (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 17 4.13 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 17999 18023 (17426) (TGCC)n#Simple_repeat 1 25 (0) m_b1s252i53 91 corrected_mou 17999 TGGCTGCCTGCCTGCCTGCCTGCCT 18023 v (TGCC)n#Simpl 1 TGCCTGCCTGCCTGCCTGCCTGCCT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 65 15.19 0.83 0.83 corrected_mouse_rDNA_unit_Feb2013_IGS 18074 18193 (17256) (CTTT)n#Simple_repeat 1 120 (0) m_b1s252i54 92 corrected_mou 18074 CTTTTTTCTCTTTCTTTATCTTTTTCTTT-TTTCTTTTCTTCTTCCTTCC 18122 i - v i i - ii i i (CTTT)n#Simpl 1 CTTTCTT-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 49 corrected_mou 18123 TTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTACTTTCTTTCTT 18172 i i i v (CTTT)n#Simpl 50 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 99 corrected_mou 18173 TCTTTCTTACATTTATTCTTT 18193 v v iv (CTTT)n#Simpl 100 TCTTTCTTTCTTTCTTTCTTT 120 Matrix = Unknown Transitions / transversions = 2.20 (11/5) Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.00 (2 / 2) 57 6.68 0.00 1.25 corrected_mouse_rDNA_unit_Feb2013_IGS 19110 19190 (16259) (AAGA)n#Simple_repeat 1 80 (0) m_b1s252i55 93 corrected_mou 19110 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAA 19159 i (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50 corrected_mou 19160 GGAAGGAAGGAAGAAAGAAAGGAACGAAAGA 19190 i i i - v (AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAA-GAAAGAAAGA 80 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.01 (1 / 80), avg. gap size = 1.00 (1 / 1) 23 23.36 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 19256 19305 (16144) (T)n#Simple_repeat 1 50 (0) m_b1s252i56 94 corrected_mou 19256 TTTTTGTTTCTTGGTTTTTTTTTTTTTTTTGTTCGTTTGTTTTGGTTTTT 19305 v i vv v iv v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 53 4.37 1.41 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 19570 19640 (15809) (AAGA)n#Simple_repeat 1 72 (0) m_b1s252i57 95 corrected_mou 19570 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG-AAGAGA 19618 - i (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50 corrected_mou 19619 GAAAGAGAGAAAGAAATAAAGA 19640 i v (AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAAGA 72 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.01 (1 / 70), avg. gap size = 1.00 (1 / 1) 56 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 19681 19730 (16753) (AGGC)n#Simple_repeat 1 50 (0) c_b1s251i37 96 corrected_mou 19681 AGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAG 19730 (AGGC)n#Simpl 1 AGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAG 50 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 16 5.20 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 19939 19958 (15540) (GT)n#Simple_repeat 1 20 (0) m_b1s252i58 97 corrected_mou 19939 GTCTGTGTGTGTGTGTGTGT 19958 v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 25 6.39 8.16 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 20044 20092 (15406) (TTTAG)n#Simple_repeat 1 53 (0) m_b1s252i59 98 corrected_mou 20044 TTTATTTTA-TATA-TTT--TTTAGTTTAGTTTAGTTTAATTTAGTTTAG 20089 v - v - -- i (TTTAG)n#Simp 1 TTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAG 50 corrected_mou 20090 TTT 20092 (TTTAG)n#Simp 51 TTT 53 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.33 (4 / 3) 300 28.09 3.37 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 20156 20244 (15254) SVA_A#Retroposon/SVA 123 214 (1173) m_b1s502i4 99 corrected_mou 20156 GCCTCAAACTC-AGAAATCCTCCCATCTCTGCCTGAAGAGAGC-TGGGAT 20203 iii - vi iii v vvv v - SVA_A#Retropo 123 GCCTCGGGCTCCAGTGATCCTCCTGCCTCGGCCTCCCGAGTGCCTGGGAT 172 corrected_mou 20204 TAAAGACATGCGCCATCACTCCCGGCT-ATTTTTAAATTTTT 20244 iv i ii ii v i -i iv SVA_A#Retropo 173 TGCAGGCGCGCGCCGCCACGCCCGACTGGTTTTTGTATTTTT 214 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.53 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.00 (3 / 3) 262 19.77 1.33 5.56 corrected_mouse_rDNA_unit_Feb2013_IGS 20361 20435 (15063) SVA_E#Retroposon/SVA 139 210 (1172) m_b1s502i5 100 corrected_mou 20361 CTGCCTCTGCTTCCCTAATGC-TGCGATTAAAGGCATGTGCCACCACTGC 20409 v i v v i - iv ii i i - SVA_E#Retropo 139 CTGCCTCAGCCTGCCGAGTGCCTGCGATTGCAGGCGCGCGCCGCCAC-GC 187 corrected_mou 20410 CCGGACTGATTTCTTCTTTTTTTTTT 20435 i- i -- v SVA_E#Retropo 188 CT-GACTGGTT--TTCGTTTTTTTTT 210 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.38 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5) 50 12.37 2.11 2.11 corrected_mouse_rDNA_unit_Feb2013_IGS 20449 20543 (14955) (CTTT)n#Simple_repeat 1 95 (0) m_b1s252i60 101 corrected_mou 20449 CTTTCTTTC-TT-TTTCTCTCTCTCTTTCTTCCTTCCTTCCTTCCTTCCT 20496 - - i i i i i i i (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50 corrected_mou 20497 TTCTTTCTATTTCTTTTTTTCTTTCTTTCTTTCTTTCTTTTTTTTTT 20543 -- i i i (CTTT)n#Simpl 51 TTCTTTC--TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 95 Matrix = Unknown Transitions / transversions = 1.00 (10/0) Gap_init rate = 0.04 (4 / 94), avg. gap size = 1.00 (4 / 4) 20 3.45 3.33 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 20562 20591 (14907) (CCTT)n#Simple_repeat 1 31 (0) m_b1s252i61 102 corrected_mou 20562 CCTTCCTTCCTTCC-TCCTTCCTTCCTCCCT 20591 - i (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCT 31 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.03 (1 / 29), avg. gap size = 1.00 (1 / 1) 80 3.53 1.14 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 20592 20679 (15804) (TTTC)n#Simple_repeat 1 89 (0) c_b1s251i38 103 corrected_mou 20592 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 20641 (TTTC)n#Simpl 1 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 50 corrected_mou 20642 TCTTTCTTTCTTT-TTTCTCTCTCTCTTTCTCTCTTTCT 20679 - i i i (TTTC)n#Simpl 51 TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 89 Matrix = Unknown Transitions / transversions = 1.00 (3/0) Gap_init rate = 0.01 (1 / 87), avg. gap size = 1.00 (1 / 1) 19 11.70 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 20685 20712 (14873) (T)n#Simple_repeat 1 28 (0) m_b1s252i62 104 corrected_mou 20685 TTTTTTTTTTGTTTTGTTTTGTTTTTTT 20712 v v v (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 28 Matrix = Unknown Transitions / transversions = 0.00 (0/3) Gap_init rate = 0.00 (0 / 27), avg. gap size = 0.0 (0 / 0) 68 0.00 1.56 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 20780 20843 (15640) (TTCT)n#Simple_repeat 1 65 (0) c_b1s251i39 105 corrected_mou 20780 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC-TT 20828 - (TTCT)n#Simpl 1 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT 50 corrected_mou 20829 CTTTCTTTCTTTCTT 20843 (TTCT)n#Simpl 51 CTTTCTTTCTTTCTT 65 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1) 48 2.13 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 20994 21041 (15442) (CTCA)n#Simple_repeat 1 48 (0) c_b1s251i40 106 corrected_mou 20994 CTCACTCACTCACTCACTCACTCACTCACTCACTCACTCATTCACTCA 21041 i (CTCA)n#Simpl 1 CTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCACTCA 48 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0) 17 14.46 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 21144 21174 (14521) (TCC)n#Simple_repeat 1 31 (0) m_b1s252i63 107 corrected_mou 21144 TCCTCCTCCTCCCCCTCCTCCCCCTTCTGCT 21174 i i i v (TCC)n#Simple 1 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT 31 Matrix = Unknown Transitions / transversions = 3.00 (3/1) Gap_init rate = 0.00 (0 / 30), avg. gap size = 0.0 (0 / 0) 44 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 21972 22011 (14472) (T)n#Simple_repeat 1 40 (0) c_b1s251i41 108 corrected_mou 21972 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 22011 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 40 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 39), avg. gap size = 0.0 (0 / 0) 53 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 22073 22117 (14366) (TG)n#Simple_repeat 1 45 (0) c_b1s251i42 109 corrected_mou 22073 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 22117 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 44), avg. gap size = 0.0 (0 / 0) 546 18.45 10.27 6.25 corrected_mouse_rDNA_unit_Feb2013_IGS 22181 22207 (13621) C AluJb#SINE/Alu (1) 311 288 m_b1s357i5 110 corrected_mou 22181 TTTTTTTCTAATTCTTTTTCCTTTTTA 22207 i -- i ii - C AluJb#SINE/Al 311 TTTTTTTTT--TTTTTTTTTTTTTTT- 288 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 17.33 Transitions / transversions = 1.00 (4/0) Gap_init rate = 0.12 (3 / 26), avg. gap size = 1.00 (3 / 3) 56 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 22208 22258 (14225) (TATTT)n#Simple_repeat 1 51 (0) c_b1s251i43 111 corrected_mou 22208 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 22257 (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 50 corrected_mou 22258 T 22258 (TATTT)n#Simp 51 T 51 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0) 546 18.45 10.27 6.25 corrected_mouse_rDNA_unit_Feb2013_IGS 22259 22415 (13413) C AluJb#SINE/Alu (25) 287 120 m_b1s357i5 110 corrected_mou 22259 GGTTTTTGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCA 22308 -- i v v i v v ----- iiv C AluJb#SINE/Al 287 --TTTTTGAGACAGGGTCTCGCTCTGTCGCCCAGGCTG-----GAGTGCA 245 corrected_mou 22309 GTTTGCA-GACCA-GGCT------GGCCTAGAACTC---------AGAAA 22341 v- i- i - ------i v v --------- vi C AluJb#SINE/Al 244 GTG-GCGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGCGA 196 corrected_mou 22342 TCCTCCCATCTCTGCCTCCCGAGT-GCTGAGATTAAAGGCGTGCACCACC 22390 ii v - i i v i i C AluJb#SINE/Al 195 TCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCACC 146 corrected_mou 22391 ACACCCGGCT-ATTTTTAAATTTTTT 22415 i - iv C AluJb#SINE/Al 145 ACGCCCGGCTAATTTTTGTATTTTTT 120 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 17.33 Transitions / transversions = 1.33 (16/12) Gap_init rate = 0.09 (14 / 156), avg. gap size = 1.93 (27 / 14) 23 15.69 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 22427 22469 (13359) (TTTA)n#Simple_repeat 1 43 (0) m_b1s252i64 112 corrected_mou 22427 TTTATTTTTATTTTTATTTATTTATTTATTTATTTTTGTTTTT 22469 v v v v v v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTT 43 Matrix = Unknown Transitions / transversions = 0.00 (0/6) Gap_init rate = 0.00 (0 / 42), avg. gap size = 0.0 (0 / 0) 477 22.45 7.41 5.73 corrected_mouse_rDNA_unit_Feb2013_IGS 22551 22739 (13089) C AluSx#SINE/Alu (116) 196 5 m_b1s357i6 113 corrected_mou 22551 ATCCGCCTGCCTCTGCCTCCCAAGT-GCTGGGATTAAAGGTGTGCTTTAC 22599 i v v i - v i i vii C AluSx#SINE/Al 196 ATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCAC 147 corrected_mou 22600 ---GCCCGGCTTTTATTTTTAAATTTTATTTATTTAATTTATTTTTGTTT 22646 --- v-- i----- -- i vv vvivv v C AluSx#SINE/Al 146 CACGCCCGGCTA--ATTTTTG-----TATTT--TTAGTAGAGACGGGGTT 106 corrected_mou 22647 ATCACTGTGTAGACCAGGCTGGCCTTGAAC-----ACTTTA----ATCTG 22687 - ii v i i i ----- i i ---- i C AluSx#SINE/Al 105 -TCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCG 57 corrected_mou 22688 TCTGCCTCTGCTTCCCAAA-TGCTGGGATTAAAAGCATCTGCCACCACTG 22736 i i v i - v i i vv i - C AluSx#SINE/Al 56 CCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGC-G 8 corrected_mou 22737 CCC 22739 C AluSx#SINE/Al 7 CCC 5 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 20.55 Transitions / transversions = 1.35 (23/17) Gap_init rate = 0.09 (16 / 188), avg. gap size = 1.56 (25 / 16) 20 26.09 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 22747 22775 (13104) (TTTT)n#Simple_repeat 1 29 (31) m_b1s252i65 114 corrected_mou 22747 TTTTTTTTTTTTTTTTTTTTTAGAAAATA 22775 vvvvvv v (TTTT)n#Simpl 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT 29 Matrix = Unknown Transitions / transversions = 0.00 (0/7) Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0) 42 6.04 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 22776 22827 (13656) (CCTT)n#Simple_repeat 1 52 (0) c_b1s251i44 115 corrected_mou 22776 CCTTTCTTCCTACCTTCCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 22825 i v i (CCTT)n#Simpl 1 CCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCC 50 corrected_mou 22826 TT 22827 (CCTT)n#Simpl 51 TT 52 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0) 20 26.09 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 22828 22857 (13022) (TTTT)n#Simple_repeat 30 59 (1) m_b1s252i65 116 corrected_mou 22828 TCTTTCTTTCATTATTTTTTTCTTTTTTTT 22857 i i iv v i (TTTT)n#Simpl 30 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 59 Matrix = Unknown Transitions / transversions = 2.00 (4/2) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 14 25.97 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 22987 23027 (12852) (TATG)n#Simple_repeat 1 41 (0) m_b1s252i67 117 corrected_mou 22987 TATGTGTCTTTGTATGTATGTATATATCGAAGTATTCATGT 23027 i v v i vv v vi (TATG)n#Simpl 1 TATGTATGTATGTATGTATGTATGTATGTATGTATGTATGT 41 Matrix = Unknown Transitions / transversions = 0.50 (3/6) Gap_init rate = 0.00 (0 / 40), avg. gap size = 0.0 (0 / 0) 16 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 23081 23097 (12782) (A)n#Simple_repeat 1 17 (0) m_b1s252i68 118 corrected_mou 23081 AAAAAAAAAAAAAAAAA 23097 (A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0) 41 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 23098 23135 (13348) (AAAG)n#Simple_repeat 1 38 (0) c_b1s251i45 119 corrected_mou 23098 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 23135 (AAAG)n#Simpl 1 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 38 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0) 37 9.94 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 23244 23297 (13186) (GT)n#Simple_repeat 1 54 (0) c_b1s251i46 120 corrected_mou 23244 GTGTGTGTGTGTGTGTTTCCATGTGTGTGTGTGTGTGTGTGTGTGTGTAT 23293 v vii i (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50 corrected_mou 23294 GTGT 23297 (GT)n#Simple_ 51 GTGT 54 Matrix = Unknown Transitions / transversions = 1.50 (3/2) Gap_init rate = 0.00 (0 / 53), avg. gap size = 0.0 (0 / 0) 46 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 24590 24631 (11852) (ACAG)n#Simple_repeat 1 42 (0) c_b1s251i47 121 corrected_mou 24590 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 24631 (ACAG)n#Simpl 1 ACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGAC 42 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 41), avg. gap size = 0.0 (0 / 0) 34 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 24728 24759 (11724) (GTCT)n#Simple_repeat 1 32 (0) c_b1s251i48 122 corrected_mou 24728 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 24759 (GTCT)n#Simpl 1 GTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCT 32 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0) 17 4.13 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 24787 24811 (11230) (TGCC)n#Simple_repeat 1 25 (0) m_b1s252i69 123 corrected_mou 24787 TGGCTGCCTGCCTGCCTGCCTGCCT 24811 v (TGCC)n#Simpl 1 TGCCTGCCTGCCTGCCTGCCTGCCT 25 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 67 14.19 0.83 0.83 corrected_mouse_rDNA_unit_Feb2013_IGS 24862 24981 (11060) (CTTT)n#Simple_repeat 1 120 (0) m_b1s252i70 124 corrected_mou 24862 CTTTTTTCTCTTTCTTTATCTTTTTCTTT-TTTCTTTTCTTCTTCCTTCC 24910 i - v i i - ii i i (CTTT)n#Simpl 1 CTTTCTT-TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC 49 corrected_mou 24911 TTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 24960 i i i (CTTT)n#Simpl 50 TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT 99 corrected_mou 24961 TCTTTCTTACATTTATTCTTT 24981 v v iv (CTTT)n#Simpl 100 TCTTTCTTTCTTTCTTTCTTT 120 Matrix = Unknown Transitions / transversions = 2.75 (11/4) Gap_init rate = 0.02 (2 / 119), avg. gap size = 1.00 (2 / 2) 60 6.35 0.00 1.19 corrected_mouse_rDNA_unit_Feb2013_IGS 25898 25982 (10059) (AAGA)n#Simple_repeat 1 84 (0) m_b1s252i71 125 corrected_mou 25898 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 25947 (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50 corrected_mou 25948 GGAAGGAAGGAAGGAAGAAAGAAAGGAACGAAAGA 25982 i i i i - v (AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAAGAAA-GAAAGAAAGA 84 Matrix = Unknown Transitions / transversions = 4.00 (4/1) Gap_init rate = 0.01 (1 / 84), avg. gap size = 1.00 (1 / 1) 25 20.64 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 26048 26097 (9944) (T)n#Simple_repeat 1 50 (0) m_b1s252i72 126 corrected_mou 26048 TTTTTGTTTCTTGTTTTTTTTTTTTTTTTTGTTCGTTTGTTTTGGTTTTT 26097 v i v v iv v vv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 Matrix = Unknown Transitions / transversions = 0.29 (2/7) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 38 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 26160 26192 (10291) (TG)n#Simple_repeat 1 33 (0) c_b1s251i49 127 corrected_mou 26160 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 26192 (TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 33 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 32), avg. gap size = 0.0 (0 / 0) 416 16.70 3.14 17.14 corrected_mouse_rDNA_unit_Feb2013_IGS 26253 26279 (9854) C BC200#SINE/Alu (1) 144 122 m_b1s357i7 128 corrected_mou 26253 TTTTTTTCCAATTTTTTTTCCTTTTTA 26279 ---- i C BC200#SINE/Al 144 TTTTTTT----TTTTTTTTCCTTTTTG 122 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 16.02 Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.15 (4 / 26), avg. gap size = 1.00 (4 / 4) 68 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 26280 26340 (10143) (TATTT)n#Simple_repeat 1 61 (0) c_b1s251i50 129 corrected_mou 26280 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 26329 (TATTT)n#Simp 1 TATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTT 50 corrected_mou 26330 TATTTTATTTT 26340 (TATTT)n#Simp 51 TATTTTATTTT 61 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0) 416 16.70 3.14 17.14 corrected_mouse_rDNA_unit_Feb2013_IGS 26341 26471 (9662) C BC200#SINE/Alu (24) 121 6 m_b1s357i7 128 corrected_mou 26341 G-AGA-CAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTG 26388 - - i i v i v v v vi v ------ C BC200#SINE/Al 121 GGAGAACGGGGTCTCGCTATATTGCCCAGGCAGGTCTCGAACTC------ 78 corrected_mou 26389 CAGACCAGGCTGGCCACAAACTCAGAAATCCTCCCATCCCT--GCCTCCC 26436 --------- v v i ----- ii i -- C BC200#SINE/Al 77 ---------CTGGGCTCAAGCT-----ATCCTCCCGCCTCTCGGCCTCCC 42 corrected_mou 26437 TAGG-GCTGGGATTAAAGGCTTGAGCCACCACTCCC 26471 i - v v i v C BC200#SINE/Al 41 TAAGAGCTGGGATTACAGGCGTGAGCCACCGCGCCC 6 Matrix = 18p43g.matrix Kimura (with divCpGMod) = 16.02 Transitions / transversions = 0.91 (10/11) Gap_init rate = 0.18 (24 / 130), avg. gap size = 1.04 (25 / 24) 17 22.74 1.89 1.89 corrected_mouse_rDNA_unit_Feb2013_IGS 26475 26527 (9606) (TATT)n#Simple_repeat 1 53 (0) m_b1s252i73 130 corrected_mou 26475 TATTTTTTAATTTTTTAATTGTATTTATTTAATTCATT-TTTGTTTGTTT 26523 v v v v - v vv - i i (TATT)n#Simpl 1 TATTTATTTATTTATTTATT-TATTTATTTATTTATTTATTTATTTATTT 49 corrected_mou 26524 TTTT 26527 v (TATT)n#Simpl 50 ATTT 53 Matrix = Unknown Transitions / transversions = 0.25 (2/8) Gap_init rate = 0.04 (2 / 52), avg. gap size = 1.00 (2 / 2) 96 1.05 2.08 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 26688 26783 (9700) (CTTT)n#Simple_repeat 1 98 (0) c_b1s251i51 131 corrected_mou 26688 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 26737 (CTTT)n#Simpl 1 CTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 50 corrected_mou 26738 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC--TCTTTCTATCTTTCT 26783 -- v (CTTT)n#Simpl 51 TTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 98 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.01 (1 / 95), avg. gap size = 2.00 (2 / 1) 16 16.57 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 26785 26811 (9417) (T)n#Simple_repeat 1 27 (0) m_b1s252i74 132 corrected_mou 26785 TTTTTCTATTTTTTTTTTTCGTTTTTT 26811 i v iv (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (2/2) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 17 15.19 2.50 2.50 corrected_mouse_rDNA_unit_Feb2013_IGS 26942 26981 (9247) (TGTA)n#Simple_repeat 1 40 (0) m_b1s252i76 133 corrected_mou 26942 TGTGTGTGTGTATGTATGTATATACGTATATATAGTA-GTA 26981 i i i i i - - (TGTA)n#Simpl 1 TGTATGTATGTATGTATGTATGTATGTATGTAT-GTATGTA 40 Matrix = Unknown Transitions / transversions = 1.00 (5/0) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 43 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 27020 27056 (9427) (TC)n#Simple_repeat 1 37 (0) c_b1s251i52 134 corrected_mou 27020 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 27056 (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 37 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 36), avg. gap size = 0.0 (0 / 0) 17 14.64 2.50 2.50 corrected_mouse_rDNA_unit_Feb2013_IGS 27240 27279 (8985) (TTTA)n#Simple_repeat 1 40 (0) m_b1s252i77 135 corrected_mou 27240 TTTATTT-TTTTTTTAAAGATTTATTTATTTATTATATGTA 27279 - v vvv - v (TTTA)n#Simpl 1 TTTATTTATTTATTTATTTATTTATTTATTTATT-TATTTA 40 Matrix = Unknown Transitions / transversions = 0.00 (0/5) Gap_init rate = 0.05 (2 / 39), avg. gap size = 1.00 (2 / 2) 32 3.01 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 27469 27502 (8981) (GTG)n#Simple_repeat 1 34 (0) c_b1s251i53 136 corrected_mou 27469 GTGGTGGTGGTGGTGGTGGTGGTGTTGGTGGTGG 27502 v (GTG)n#Simple 1 GTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGG 34 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 60 3.91 1.27 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 28234 28312 (7985) (AAGA)n#Simple_repeat 1 80 (0) m_b1s252i78 137 corrected_mou 28234 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 28283 (AAGA)n#Simpl 1 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAA 50 corrected_mou 28284 G-AAGAGAGAAAGAGAGAAAGAAATAAAGA 28312 - i i v (AAGA)n#Simpl 51 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGA 80 Matrix = Unknown Transitions / transversions = 2.00 (2/1) Gap_init rate = 0.01 (1 / 78), avg. gap size = 1.00 (1 / 1) 56 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 28353 28402 (8081) (AGGC)n#Simple_repeat 1 50 (0) c_b1s251i54 138 corrected_mou 28353 AGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAG 28402 (AGGC)n#Simpl 1 AGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAG 50 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 49), avg. gap size = 0.0 (0 / 0) 16 5.20 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 28611 28630 (7716) (GT)n#Simple_repeat 1 20 (0) m_b1s252i79 139 corrected_mou 28611 GTCTGTGTGTGTGTGTGTGT 28630 v (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 Matrix = Unknown Transitions / transversions = 0.00 (0/1) Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) 25 6.39 8.16 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 28716 28764 (7582) (TTTAG)n#Simple_repeat 1 53 (0) m_b1s252i80 140 corrected_mou 28716 TTTATTTTA-TATA-TTT--TTTAGTTTAGTTTAGTTTAATTTAGTTTAG 28761 v - v - -- i (TTTAG)n#Simp 1 TTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAGTTTAG 50 corrected_mou 28762 TTT 28764 (TTTAG)n#Simp 51 TTT 53 Matrix = Unknown Transitions / transversions = 0.50 (1/2) Gap_init rate = 0.06 (3 / 48), avg. gap size = 1.33 (4 / 3) 300 28.09 3.37 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 28828 28916 (7430) SVA_A#Retroposon/SVA 123 214 (1173) m_b1s502i6 141 corrected_mou 28828 GCCTCAAACTC-AGAAATCCTCCCATCTCTGCCTGAAGAGAGC-TGGGAT 28875 iii - vi iii v vvv v - SVA_A#Retropo 123 GCCTCGGGCTCCAGTGATCCTCCTGCCTCGGCCTCCCGAGTGCCTGGGAT 172 corrected_mou 28876 TAAAGACATGCGCCATCACTCCCGGCT-ATTTTTAAATTTTT 28916 iv i ii ii v i -i iv SVA_A#Retropo 173 TGCAGGCGCGCGCCGCCACGCCCGACTGGTTTTTGTATTTTT 214 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 29.53 Transitions / transversions = 1.78 (16/9) Gap_init rate = 0.03 (3 / 88), avg. gap size = 1.00 (3 / 3) 262 19.77 1.33 5.56 corrected_mouse_rDNA_unit_Feb2013_IGS 29033 29107 (7239) SVA_E#Retroposon/SVA 139 210 (1172) m_b1s502i7 142 corrected_mou 29033 CTGCCTCTGCTTCCCTAATGC-TGCGATTAAAGGCATGTGCCACCACTGC 29081 v i v v i - iv ii i i - SVA_E#Retropo 139 CTGCCTCAGCCTGCCGAGTGCCTGCGATTGCAGGCGCGCGCCGCCAC-GC 187 corrected_mou 29082 CCGGACTGATTTCTTCTTTTTTTTTT 29107 i- i -- v SVA_E#Retropo 188 CT-GACTGGTT--TTCGTTTTTTTTT 210 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 16.38 Transitions / transversions = 1.80 (9/5) Gap_init rate = 0.07 (5 / 74), avg. gap size = 1.00 (5 / 5) 29 15.55 7.06 2.25 corrected_mouse_rDNA_unit_Feb2013_IGS 29124 29208 (7138) (TCTTTC)n#Simple_repeat 1 89 (0) m_b1s252i82 143 corrected_mou 29124 TCTTTCTTTTTCTCTCTCTCTTTCTTCCTTC-C-TTC-CTTCCTTCCTT- 29169 i i - i - - - i - i - (TCTTTC)n#Sim 1 TCTTTCTCTTTCTCTTTCTCTTTC-TCTTTCTCTTTCTCTTTC-TCTTTC 48 corrected_mou 29170 TCTTTCT-ATTCTTTTTTTCTTTCT-TTTTTCTTTTTTTTT 29208 -v i i - i i i (TCTTTC)n#Sim 49 TCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTTCTCTTT 89 Matrix = Unknown Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.10 (8 / 84), avg. gap size = 1.00 (8 / 8) 18 14.91 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 29276 29305 (7041) (A)n#Simple_repeat 1 30 (0) m_b1s252i83 144 corrected_mou 29276 AAAAAAAAACAAACAAAAAAAAAACCAAAA 29305 v v vv (A)n#Simple_r 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 30 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.00 (0 / 29), avg. gap size = 0.0 (0 / 0) 65 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 29528 29582 (6901) (AC)n#Simple_repeat 1 55 (0) c_b1s251i55 145 corrected_mou 29528 ACACACACACACACACACACACACACACACACACACACACACACACACAC 29577 (AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50 corrected_mou 29578 ACACA 29582 (AC)n#Simple_ 51 ACACA 55 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0) 13 20.58 10.61 1.39 corrected_mouse_rDNA_unit_Feb2013_IGS 29766 29831 (6569) (GAGC)n#Simple_repeat 1 72 (0) m_b1s252i84 146 corrected_mou 29766 GAGTGAG-G-GCGAGCGAGC-AGACGGGCGGGCGGGCGGGTGAGTG-GCC 29811 i - - - - i i i i i i - v (GAGC)n#Simpl 1 GAGCGAGCGAGCGAGCGAGCGAG-CGAGCGAGCGAGCGAGCGAGCGAGCG 49 corrected_mou 29812 GGCGGGCG-GTG-GC-AGCGAGC 29831 i i - i - - (GAGC)n#Simpl 50 AGCGAGCGAGCGAGCGAGCGAGC 72 Matrix = Unknown Transitions / transversions = 10.00 (10/1) Gap_init rate = 0.12 (8 / 65), avg. gap size = 1.00 (8 / 8) 13 14.03 7.32 2.33 corrected_mouse_rDNA_unit_Feb2013_IGS 30150 30190 (6210) (GTGC)n#Simple_repeat 1 43 (0) m_b1s252i85 147 corrected_mou 30150 GTG-GTGGGTGGGTACGCTGC-TCCGT-CGTGCGTGCGTGAGTG 30190 - v v i - - v - v (GTGC)n#Simpl 1 GTGCGTGCGTGCGTGCG-TGCGTGCGTGCGTGCGTGCGTGCGTG 43 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.10 (4 / 40), avg. gap size = 1.00 (4 / 4) 26 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 30718 30742 (5741) (T)n#Simple_repeat 1 25 (0) c_b1s251i56 148 corrected_mou 30718 TTTTTTTTTTTTTTTTTTTTTTTTT 30742 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTT 25 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 24), avg. gap size = 0.0 (0 / 0) 28 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 30859 30885 (5598) (T)n#Simple_repeat 1 27 (0) c_b1s251i57 149 corrected_mou 30859 TTTTTTTTTTTTTTTTTTTTTTTTTTT 30885 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTT 27 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 26), avg. gap size = 0.0 (0 / 0) 19 0.00 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 31635 31655 (4795) (T)n#Simple_repeat 1 21 (0) m_b1s252i86 150 corrected_mou 31635 TTTTTTTTTTTTTTTTTTTTT 31655 (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21 Matrix = Unknown Transitions / transversions = 1.00 (0/0) Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0) 18 4.77 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 32167 32188 (4262) (T)n#Simple_repeat 1 22 (0) m_b1s252i87 151 corrected_mou 32167 TTTTTTTTTTTTTTTCTTTTTT 32188 i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTT 22 Matrix = Unknown Transitions / transversions = 1.00 (1/0) Gap_init rate = 0.00 (0 / 21), avg. gap size = 0.0 (0 / 0) 26 6.13 0.00 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 32890 32923 (3560) (T)n#Simple_repeat 1 34 (0) c_b1s251i58 152 corrected_mou 32890 TTTTTGTTTTTTTTCTTTTTTTTTTTTTTTTTTT 32923 v i (T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34 Matrix = Unknown Transitions / transversions = 1.00 (1/1) Gap_init rate = 0.00 (0 / 33), avg. gap size = 0.0 (0 / 0) 601 20.16 1.54 5.88 corrected_mouse_rDNA_unit_Feb2013_IGS 33103 33297 (3186) FordPrefect#DNA/hAT-Tip100 769 955 (728) m_b1s502i8 153 corrected_mou 33103 CTCCCGATTGCGCGTCGTTGCTCACTCTTAGATCGATGTGGTGCTCCGGA 33152 i i -ii v iv ii - iv v-- vv FordPrefect#D 769 CTTCCGATCG-ATGTCCTCTCTTGC-CTCCGATCGATGTGGTGA--CGTC 814 corrected_mou 33153 GTTCTCTTC-GGGCCAGGGCCAAGCCGCGCCAGGCGAGGGACGGACATTC 33201 v i - i i vvii i i i FordPrefect#D 815 GTGCTCTCCCGGGTCGGTCTTAAGCCGTGCCGGACGAGGGACGGACATTC 864 corrected_mou 33202 AT-G-GCGAATGGCGGCCGCTCTTCTCGTTCTGCCAGCGGGCCCCTCGTC 33249 v - - - i i i vi i FordPrefect#D 865 CTTGCGCGAATGG-GACCGCTCTTCTCGCTCCGCCCACGGGCCCCTCGCC 913 corrected_mou 33250 TCTCCACCCCATCCGTCTGCCGGTGGTGTGTGGAAGGCAGGGGTGCGG 33297 v v i----- -i i FordPrefect#D 914 TATCCTCCCCG-----CTG-TGGCGGTGTGTGGAAGGCAGGGGTGCGG 955 Matrix = 20p43g.matrix Kimura (with divCpGMod) = 19.74 Transitions / transversions = 1.85 (24/13) Gap_init rate = 0.07 (14 / 194), avg. gap size = 1.00 (14 / 14) 12 15.77 2.56 5.26 corrected_mouse_rDNA_unit_Feb2013_IGS 34475 34513 (1970) (GTGCTGT)n#Simple_repeat 1 38 (0) m_b1s252i88 154 corrected_mou 34475 GTGGTGCGTGCTGTGTGCTTCTCGGGCTGTGTGGT-TGTG 34513 v i - v - v v - (GTGCTGT)n#Si 1 GTGCTGTGTGCTGTGTGC-TGT-GTGCTGTGTGCTGTGTG 38 Matrix = Unknown Transitions / transversions = 0.25 (1/4) Gap_init rate = 0.08 (3 / 38), avg. gap size = 1.00 (3 / 3) 12 19.46 2.86 0.00 corrected_mouse_rDNA_unit_Feb2013_IGS 34737 34771 (1712) (GTGTCG)n#Simple_repeat 1 36 (0) m_b1s252i89 155 corrected_mou 34737 GTGTCGGCATCGGTCTCTCTCTC-GTGTCGGTGTCG 34771 ii v vv v - (GTGTCG)n#Sim 1 GTGTCGGTGTCGGTGTCGGTGTCGGTGTCGGTGTCG 36 Matrix = Unknown Transitions / transversions = 0.50 (2/4) Gap_init rate = 0.03 (1 / 34), avg. gap size = 1.00 (1 / 1) 13 15.42 0.00 3.33 corrected_mouse_rDNA_unit_Feb2013_IGS 36397 36427 (56) (CTC)n#Simple_repeat 1 30 (0) m_b1s252i90 156 corrected_mou 36397 CTCCGCCGCCGCCGCCTCCTCCTCCTCTCTC 36427 v v v v - (CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTC-CTC 30 Matrix = Unknown Transitions / transversions = 0.00 (0/4) Gap_init rate = 0.03 (1 / 30), avg. gap size = 1.00 (1 / 1)