Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01002592.1 Hibiscus syriacus cultivar Beakdansim tig00005246_pilon, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 72029
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:5192 original size:15 final size:14

Alignment explanation

Indices: 5183--5292 Score: 57 Period size: 14 Copynumber: 7.4 Consensus size: 14 5173 CTTTTAGTTG 5183 TTTTTATTTTATTA 1 TTTTTATTTTATTA * 5197 TTTTTAAGATTTA--A 1 TTTTT-A-TTTTATTA 5211 CTTTTTATTTTTATT- 1 -TTTTTA-TTTTATTA * 5226 TATTTATTTTATTTA 1 TTTTTATTTTA-TTA * 5241 TTTATTATTTTTTTA 1 TTT-TTATTTTATTA 5256 CCTCTTTTATTTTTATT- 1 --T-TTTTA-TTTTATTA * 5273 TTTTTATTTCATTTA 1 TTTTTATTTTA-TTA 5288 TTTTT 1 TTTTT 5293 TCTTTCTTTT Statistics Matches: 74, Mismatches: 8, Indels: 27 0.68 0.07 0.25 Matches are distributed among these distances: 13 9 0.12 14 25 0.34 15 17 0.23 16 11 0.15 17 4 0.05 18 8 0.11 ACGTcount: A:0.20, C:0.05, G:0.01, T:0.75 Consensus pattern (14 bp): TTTTTATTTTATTA Found at i:5229 original size:4 final size:4 Alignment explanation

Indices: 5220--5290 Score: 51 Period size: 4 Copynumber: 17.8 Consensus size: 4 5210 ACTTTTTATT * * 5220 TTTA TTTA TTTA TTTTA TTTA TTTA -TTA TTTT TTTA CCTCT- TTTA -TT- 1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA --TTTA TTTA TTTA * 5267 TTTA TTTT TTTA TTTCA TTTA TTT 1 TTTA TTTA TTTA TTT-A TTTA TTT 5291 TTTCTTTCTT Statistics Matches: 53, Mismatches: 6, Indels: 16 0.71 0.08 0.21 Matches are distributed among these distances: 3 9 0.17 4 34 0.64 5 8 0.15 6 2 0.04 ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76 Consensus pattern (4 bp): TTTA Found at i:5242 original size:17 final size:17 Alignment explanation

Indices: 5220--5312 Score: 61 Period size: 17 Copynumber: 5.5 Consensus size: 17 5210 ACTTTTTATT 5220 TTTATTTATTTATTTTA 1 TTTATTTATTTATTTTA 5237 TTTATTTA-TTATTTT- 1 TTTATTTATTTATTTTA * 5252 TTTACCTCT-TTTATTTTTA 1 TTTA--TTTATTTA-TTTTA * 5271 TTTTTTTATTTCA-TTTA 1 TTTATTTATTT-ATTTTA * * 5288 TTT-TTTCTTTCTTTTGA 1 TTTATTTATTTATTTT-A * 5305 TTCATTTA 1 TTTATTTA 5313 ACATTTATTT Statistics Matches: 59, Mismatches: 7, Indels: 19 0.69 0.08 0.22 Matches are distributed among these distances: 15 4 0.07 16 16 0.27 17 25 0.42 18 10 0.17 19 4 0.07 ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74 Consensus pattern (17 bp): TTTATTTATTTATTTTA Found at i:5275 original size:23 final size:22 Alignment explanation

Indices: 5213--5292 Score: 88 Period size: 23 Copynumber: 3.5 Consensus size: 22 5203 AGATTTAACT * * 5213 TTTTATTTTTATTTATTTATTT 1 TTTTATTTTTATTTTTTTATTC * 5235 TATTTATTTATTATTTTTTTACCTC 1 T-TTTATTT-TTATTTTTTTA-TTC 5260 TTTTATTTTTATTTTTTTATTTC 1 TTTTATTTTTATTTTTTTA-TTC * 5283 ATTTATTTTT 1 TTTTATTTTT 5293 TCTTTCTTTT Statistics Matches: 49, Mismatches: 6, Indels: 5 0.82 0.10 0.08 Matches are distributed among these distances: 22 1 0.02 23 29 0.59 24 17 0.35 25 2 0.04 ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78 Consensus pattern (22 bp): TTTTATTTTTATTTTTTTATTC Found at i:8225 original size:29 final size:27 Alignment explanation

Indices: 8187--8280 Score: 77 Period size: 27 Copynumber: 3.4 Consensus size: 27 8177 AGATCAAATC * * 8187 AGAACAAAAAGAGAAAAGAGAAAAAAA 1 AGAAGAAAAAAAGAAAAGAGAAAAAAA * 8214 ACGAAG-AAAAAAGCAAAGAGAAAATAAA 1 A-GAAGAAAAAAAGAAAAGAGAAAA-AAA * 8242 A-AAGAGAAACAAAAACAAAG-GAAAAAAA 1 AGAAGA-AAA-AAAGA-AAAGAGAAAAAAA * 8270 TGAAGAAAAAA 1 AGAAGAAAAAA 8281 GACAAGACGC Statistics Matches: 54, Mismatches: 6, Indels: 14 0.73 0.08 0.19 Matches are distributed among these distances: 26 3 0.06 27 19 0.35 28 16 0.30 29 12 0.22 30 4 0.07 ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02 Consensus pattern (27 bp): AGAAGAAAAAAAGAAAAGAGAAAAAAA Found at i:8255 original size:12 final size:12 Alignment explanation

Indices: 8200--8280 Score: 54 Period size: 13 Copynumber: 6.1 Consensus size: 12 8190 ACAAAAAGAG 8200 AAAAGAGAAAAA 1 AAAAGAGAAAAA * 8212 AAACGAAGAAAAA 1 AAAAG-AGAAAAA 8225 AGCAAAGAGAAAATAA 1 A--AAAGAG-AAA-AA 8241 AAAAGAGAAACAA 1 AAAAGAGAAA-AA * * 8254 AAACAAAGGAAAA 1 AAA-AGAGAAAAA * 8267 AAATGAAGAAAAA 1 AAAAG-AGAAAAA 8280 A 1 A 8281 GACAAGACGC Statistics Matches: 54, Mismatches: 8, Indels: 13 0.72 0.11 0.17 Matches are distributed among these distances: 12 4 0.07 13 28 0.52 14 13 0.24 15 6 0.11 16 3 0.06 ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02 Consensus pattern (12 bp): AAAAGAGAAAAA Found at i:9375 original size:32 final size:32 Alignment explanation

Indices: 9334--9409 Score: 89 Period size: 32 Copynumber: 2.4 Consensus size: 32 9324 GAATCTTTGA * * * 9334 AGATTCAACATCAAATGTTAGGGCATTTTTAG 1 AGATTCAACATCAAATATCAGGGCATATTTAG * * * 9366 AGATTCAACATCGAATATCGGGGCATATTTGG 1 AGATTCAACATCAAATATCAGGGCATATTTAG * 9398 GGATTCAACATC 1 AGATTCAACATC 9410 CTGATGCGAA Statistics Matches: 37, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 32 37 1.00 ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30 Consensus pattern (32 bp): AGATTCAACATCAAATATCAGGGCATATTTAG Found at i:10061 original size:21 final size:21 Alignment explanation

Indices: 10037--10095 Score: 67 Period size: 21 Copynumber: 3.1 Consensus size: 21 10027 ACAGTTTCTT 10037 TTAAAACAAATTTTGTCTCTC 1 TTAAAACAAATTTTGTCTCTC * 10058 TTAAGAC--A--TT-T-TCTC 1 TTAAAACAAATTTTGTCTCTC 10073 TTAAAACAAATTTTGTCTCTC 1 TTAAAACAAATTTTGTCTCTC 10094 TT 1 TT 10096 GAGACGGTTT Statistics Matches: 30, Mismatches: 2, Indels: 12 0.68 0.05 0.27 Matches are distributed among these distances: 15 10 0.33 16 1 0.03 17 3 0.10 19 3 0.10 20 1 0.03 21 12 0.40 ACGTcount: A:0.31, C:0.19, G:0.05, T:0.46 Consensus pattern (21 bp): TTAAAACAAATTTTGTCTCTC Found at i:10065 original size:36 final size:36 Alignment explanation

Indices: 10002--10118 Score: 162 Period size: 36 Copynumber: 3.2 Consensus size: 36 9992 TAATTTACTC * * 10002 AAAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTTTT 1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT * * 10039 AAAACAAATTTTGTCTCTCTTAAGACATTTTCTCTT 1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT * * 10075 AAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTT 1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT * 10111 GAAACAAA 1 AAAACAAA 10119 AACTTTGAAT Statistics Matches: 71, Mismatches: 9, Indels: 1 0.88 0.11 0.01 Matches are distributed among these distances: 36 63 0.89 37 8 0.11 ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38 Consensus pattern (36 bp): AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT Found at i:10204 original size:37 final size:36 Alignment explanation

Indices: 10141--10245 Score: 138 Period size: 37 Copynumber: 2.9 Consensus size: 36 10131 GTTTTCCTTG * ** 10141 AAACAAAGTTTTGTCTCTATTGAGACAGTTTCTTTTA 1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCGTA * * * 10178 GAACTAAATTTTGTCTCTCTTTAGACATTTTCTCGTA 1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCGTA 10215 AAACAAATTTTGTCTCTCTTGAGACAGTTTC 1 AAACAAATTTTGTCTCTCTTGAGACAGTTTC 10246 CCTTGAAACA Statistics Matches: 58, Mismatches: 9, Indels: 3 0.83 0.13 0.04 Matches are distributed among these distances: 36 25 0.43 37 30 0.52 38 3 0.05 ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43 Consensus pattern (36 bp): AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGTA Found at i:10341 original size:37 final size:36 Alignment explanation

Indices: 10280--10395 Score: 135 Period size: 37 Copynumber: 3.2 Consensus size: 36 10270 GTTTTCCTTT * * * 10280 AAACAAGTTTCGTCTCTCTTGAGACAATTTCTTTTA 1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTTTAA * * * 10316 GAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTAA 1 AAAC-AAATTTTGTCTCTCTTGAGACAATTTCT-TTAA * * 10354 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTTT-G 1 AAACAAATTTTGTCTCTCTTGAGACAATTTCTTTAA 10389 AAACAAA 1 AAACAAA 10396 ATATCTGAAT Statistics Matches: 68, Mismatches: 10, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 35 7 0.10 36 4 0.06 37 52 0.76 38 5 0.07 ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40 Consensus pattern (36 bp): AAACAAATTTTGTCTCTCTTGAGACAATTTCTTTAA Found at i:10391 original size:138 final size:139 Alignment explanation

Indices: 10003--10485 Score: 740 Period size: 138 Copynumber: 3.5 Consensus size: 139 9993 AATTTACTCA * * * 10003 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCTTTTAAAAC-AAATTTTGTCTCTCTTAAGACAT 1 AAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT * * * * 10067 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTGAAACAAAAACTTTGAATTTG 66 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG 10132 TTTTCCTTG 131 TTTTCCTTG * ** * 10141 AAACAAAGTTTTGTCTCTATTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTTAGACAT 1 AAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT 10206 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG 66 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG * 10271 TTTTCCTTT 131 TTTTCCTTG * * 10280 AAAC-AAGTTTCGTCTCTCTTGAGACAATTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT 1 AAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT * * * 10344 TTTCTCGTAAAAACAAATTTTGTCTCTCTTGAGACAGTTT-CTTTGAAACAAAATATCTGAATCT 66 TTTCTCGT-AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT 10408 GTTTTCCTTG 130 GTTTTCCTTG * * * * 10418 AAACAAA-TTGCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAATTTTGTCTATCTTGAGACAG 1 AAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT 10482 TTTC 66 TTTC 10486 CCTTGAACAA Statistics Matches: 319, Mismatches: 23, Indels: 6 0.92 0.07 0.02 Matches are distributed among these distances: 138 191 0.60 139 128 0.40 ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41 Consensus pattern (139 bp): AAACAAAGTTTCGTCTCCCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG TTTTCCTTG Found at i:10496 original size:101 final size:101 Alignment explanation

Indices: 10358--10553 Score: 304 Period size: 101 Copynumber: 1.9 Consensus size: 101 10348 TCGTAAAAAC * * 10358 AAATTTTGTCTCTCTTGAGACAGTTTCTTTGAAACAAAATATCTGAATCTGTTTTCCTTGAAACA 1 AAATTTTGTCTATCTTGAGACAGTTTCCTTGAAACAAAATATCTGAATCTGTTTTCCTTGAAACA * * 10423 AATTGCGTCTCCCTTGAGACAGTTTCTTTTGGAACT 66 AATTGCGTCTCACTCGAGACAGTTTCTTTTGGAACT * * * 10459 AAATTTTGTCTATCTTGAGACAGTTTCCCTTG-AACAAAATCTTTGAATCTGTTTTCCTTTAAAC 1 AAATTTTGTCTATCTTGAGACAGTTT-CCTTGAAACAAAATATCTGAATCTGTTTTCCTTGAAAC * 10523 AAATTTCGTCTCACTCGAGACAGTTTCTTTT 65 AAATTGCGTCTCACTCGAGACAGTTTCTTTT 10554 AAGACAATTT Statistics Matches: 86, Mismatches: 8, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 101 82 0.95 102 4 0.05 ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41 Consensus pattern (101 bp): AAATTTTGTCTATCTTGAGACAGTTTCCTTGAAACAAAATATCTGAATCTGTTTTCCTTGAAACA AATTGCGTCTCACTCGAGACAGTTTCTTTTGGAACT Found at i:11857 original size:25 final size:24 Alignment explanation

Indices: 11819--11865 Score: 60 Period size: 25 Copynumber: 1.9 Consensus size: 24 11809 TTTTACCTCT 11819 TTTTTTATTTTTTT-ATTTCATTCA 1 TTTTTTATTTTTTTGA-TTCATTCA * 11843 TTTTTTCTTTCTTTTGATTCATT 1 TTTTTTATTT-TTTTGATTCATT 11866 TAACATTTAT Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 24 9 0.45 25 10 0.50 26 1 0.05 ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74 Consensus pattern (24 bp): TTTTTTATTTTTTTGATTCATTCA Found at i:12077 original size:24 final size:24 Alignment explanation

Indices: 12045--12091 Score: 85 Period size: 24 Copynumber: 2.0 Consensus size: 24 12035 TAATCATTCC * 12045 TTGACCGTAACCGACTCCTGAACT 1 TTGACCGTAACCGACTCCCGAACT 12069 TTGACCGTAACCGACTCCCGAAC 1 TTGACCGTAACCGACTCCCGAAC 12092 CCGACACGTT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21 Consensus pattern (24 bp): TTGACCGTAACCGACTCCCGAACT Found at i:19343 original size:20 final size:20 Alignment explanation

Indices: 19318--19366 Score: 98 Period size: 20 Copynumber: 2.5 Consensus size: 20 19308 TTTTATTTAA 19318 TATACCCATGCTCCACTACC 1 TATACCCATGCTCCACTACC 19338 TATACCCATGCTCCACTACC 1 TATACCCATGCTCCACTACC 19358 TATACCCAT 1 TATACCCAT 19367 ACCCACTCAC Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 29 1.00 ACGTcount: A:0.27, C:0.43, G:0.04, T:0.27 Consensus pattern (20 bp): TATACCCATGCTCCACTACC Found at i:21557 original size:18 final size:18 Alignment explanation

Indices: 21536--21581 Score: 74 Period size: 18 Copynumber: 2.5 Consensus size: 18 21526 TTGGGTAGAA 21536 AAAAGATTTTGCCTATCC 1 AAAAGATTTTGCCTATCC * 21554 AAAAGATTTTGGCTATCC 1 AAAAGATTTTGCCTATCC 21572 AAAAGGATTT 1 AAAA-GATTT 21582 CCGTGGAAAA Statistics Matches: 26, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 18 21 0.81 19 5 0.19 ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33 Consensus pattern (18 bp): AAAAGATTTTGCCTATCC Found at i:22824 original size:91 final size:90 Alignment explanation

Indices: 22661--23387 Score: 963 Period size: 91 Copynumber: 8.0 Consensus size: 90 22651 GATAAACCAA * * * * 22661 TCAGTATTTCCAATGGAGAGATAATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATA 1 TCAG-ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * 22726 ATGAGAAGAACTTGTTCAACCTTGGC 65 ATAAGAAGAACTTGTTCAACCTTGGC * * 22752 TCAGCATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATA 1 TCAG-ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * 22817 ATAAGAAGAACTTGTTCAACCTTGGT 65 ATAAGAAGAACTTGTTCAACCTTGGC * ** * 22843 TCAAGATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAATGAGAAAAAGTTCATA 1 TC-AGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * 22908 ATAAGAAGAACTTGTTCAA-CTTATGC 65 ATAAGAAGAACTTGTTCAACCTT-GGC * * * * 22934 TCAATATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATA 1 TC-AGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * 22999 ATAAGAAGAACTTGTTCAACCTTGGT 65 ATAAGAAGAACTTGTTCAACCTTGGC * 23025 TCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAGAAGAAGTTCATA 1 TC-AGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * * * 23090 ATGAA-AAGAATTTGTTCAACTTTAGC 65 AT-AAGAAGAACTTGTTCAACCTTGGC * * * * * 23116 TCAACATTTCTAGTGGAGAGTTCATAATGAGAATAACTCATCCAACAAGGGAGAATAAGTTCATA 1 TC-AGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * * * 23181 TTGAGAAGAACTTGTTCAACCTTGGT 65 ATAAGAAGAACTTGTTCAACCTTGGC * * 23207 TCAAGATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACAAGGGAGAAGAAGTTCATA 1 TC-AGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * 23272 ATGAGAAGAACTTGTTCAACCTTGGC 65 ATAAGAAGAACTTGTTCAACCTTGGC * * * ** * * 23298 TCAACATTTCCATTGGAGAGTTTATAATGAGAAGAACTCATCCAATAAGGAAGAGGAAGTTCATA 1 TC-AGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA * * * 23363 GTAAAAAGAATTTGTTCAACCTTGG 65 ATAAGAAGAACTTGTTCAACCTTGG 23388 AGGAAAACGA Statistics Matches: 567, Mismatches: 64, Indels: 10 0.88 0.10 0.02 Matches are distributed among these distances: 90 4 0.01 91 556 0.98 92 7 0.01 ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26 Consensus pattern (90 bp): TCAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA TAAGAAGAACTTGTTCAACCTTGGC Found at i:23156 original size:273 final size:271 Alignment explanation

Indices: 22665--23385 Score: 1061 Period size: 273 Copynumber: 2.6 Consensus size: 271 22655 AACCAATCAG * * * 22665 TATTTCCAATGGAGAGATAATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATAATGA 1 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA 22730 GAAGAACTTGTTCAACCTTGGCTC-AGCATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATC 66 GAAGAACTTGTTCAACCTTGGCTCAAG-ATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATC * * * * * 22794 CAACGAGGGAGAAGAAGTTTATAATAAGAAGAACTTGTTCAACCTTGGTTCAAGATTTCTAGTGG 130 CAACGA-GGAGAAGAAGTTCATAATAA-AAGAATTTGTTCAACCTTAGCTCAACATTTCTAGTGG * 22859 AGAGTTCATAATGAGAAGAACTCATCCAACGAA-TGAGAAAAAGTTCATAATAAGAAGAACTTGT 193 AGAGTTCATAATGAGAAGAACTCATCCAAC-AAGGGAGAAAAAGTTCATAATAAGAAGAACTTGT * 22923 TCAA-CTTATGCTCAA 257 TCAACCTT-GGCTCAA * * * 22938 TATTTCCAATGGAGGGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTTATAATAA 1 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA * * 23003 GAAGAACTTGTTCAACCTTGGTTCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCC 66 GAAGAACTTGTTCAACCTTGGCTCAAGATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATCC * 23068 AACGAGAGAGAAGAAGTTCATAATGAAAAGAATTTGTTCAACTTTAGCTCAACATTTCTAGTGGA 131 AACGAG-GAGAAGAAGTTCATAAT-AAAAGAATTTGTTCAACCTTAGCTCAACATTTCTAGTGGA * * * * 23133 GAGTTCATAATGAGAATAACTCATCCAACAAGGGAGAATAAGTTCATATTGAGAAGAACTTGTTC 194 GAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATAAGAAGAACTTGTTC * 23198 AACCTTGGTTCAA 259 AACCTTGGCTCAA * * * * 23211 GATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCAACAAGGGAGAAGAAGTTCATAATGA 1 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA * * 23276 GAAGAACTTGTTCAACCTTGGCTCAACATTTCCATTGGAGAGTTTATAATGAGAAGAACTCATCC 66 GAAGAACTTGTTCAACCTTGGCTCAAGATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATCC ** * * 23341 AATAAGGAAGAGGAAGTTCATAGTAAAAAGAATTTGTTCAACCTT 131 AACGAGG-AGAAGAAGTTCATAAT-AAAAGAATTTGTTCAACCTT 23386 GGAGGAAAAC Statistics Matches: 404, Mismatches: 38, Indels: 12 0.89 0.08 0.03 Matches are distributed among these distances: 272 4 0.01 273 393 0.97 274 7 0.02 ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26 Consensus pattern (271 bp): TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGA GAAGAACTTGTTCAACCTTGGCTCAAGATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATCC AACGAGGAGAAGAAGTTCATAATAAAAGAATTTGTTCAACCTTAGCTCAACATTTCTAGTGGAGA GTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAAAAGTTCATAATAAGAAGAACTTGTTCAA CCTTGGCTCAA Found at i:23496 original size:15 final size:15 Alignment explanation

Indices: 23476--23504 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 23466 TACCGTTTCA 23476 CAGTAATGAGCAAAG 1 CAGTAATGAGCAAAG 23491 CAGTAATGAGCAAA 1 CAGTAATGAGCAAA 23505 AAGGGGCAGC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14 Consensus pattern (15 bp): CAGTAATGAGCAAAG Found at i:26514 original size:38 final size:37 Alignment explanation

Indices: 26472--26796 Score: 163 Period size: 36 Copynumber: 8.8 Consensus size: 37 26462 ACATTTTCGA * * 26472 AAAACGTATATCATATAGTTTTTAGAAAACGGTTATTG 1 AAAACATATAT-ATATAGTTTTTAAAAAACGGTTATTG ** * 26510 AAAACATATAATATATAGTTTTTAAAAAATCATTTTTTTG 1 AAAACATAT-ATATATAGTTTTTAAAAAA-C-GGTTATTG * * * * * * * 26550 AAAATATATATAATATGGTTTTGATAATAC-GAT-TTA 1 AAAACATATAT-ATATAGTTTTTAAAAAACGGTTATTG * 26586 AAAACATATAT-TATA-TATTTTAGAAAACGGTTATTG 1 AAAACATATATATATAGT-TTTTAAAAAACGGTTATTG * * 26622 AAAACATATAATATATAGTTTTTAAAAAATCGTTTTTTG 1 AAAACATAT-ATATATAGTTTTTAAAAAA-CGGTTATTG * * * * * 26661 AAAATATATATA-ATACGGTTTTGATAATAC-G--ATTT 1 AAAACATATATATATA--GTTTTTAAAAAACGGTTATTG * ** * 26696 AAAACATATATTATATA-TTTTT-GAAAACAATTTTTG 1 AAAACATATA-TATATAGTTTTTAAAAAACGGTTATTG * * * * 26732 AATATATATATTATATAGTTTTGAAAATAA---TTTTTG 1 AAAACATATA-TATATAGTTTTTAAAA-AACGGTTATTG * * 26768 AAAATATATATTATATAGTTTTGAAAAAA 1 AAAACATATA-TATATAGTTTTTAAAAAA 26797 ATATTTTTAA Statistics Matches: 224, Mismatches: 42, Indels: 45 0.72 0.14 0.14 Matches are distributed among these distances: 33 5 0.02 34 15 0.07 35 15 0.07 36 74 0.33 37 13 0.06 38 43 0.19 39 33 0.15 40 26 0.12 ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42 Consensus pattern (37 bp): AAAACATATATATATAGTTTTTAAAAAACGGTTATTG Found at i:26626 original size:36 final size:36 Alignment explanation

Indices: 26544--26794 Score: 181 Period size: 36 Copynumber: 6.9 Consensus size: 36 26534 AAAAATCATT * * * 26544 TTTTTGAAAATATATATAATATGGTTTTGATAATAC-G 1 TTTTTGAAAACATATATTATATAGTTTTGA-AA-ACGG * * 26581 -ATTTAAAAACATATATTATATA-TTTTAGAAAACGG 1 TTTTTGAAAACATATATTATATAGTTTT-GAAAACGG * * * * 26616 TTATTGAAAACATATAATATATAGTTTTTAAAAAATCGT 1 TTTTTGAAAACATATATTATATAG-TTTT-GAAAA-CGG * * ** 26655 TTTTTGAAAATATATATAATACGGTTTTGATAATAC-G 1 TTTTTGAAAACATATATTATATAGTTTTGA-AA-ACGG * * ** 26692 -ATTT-AAAACATATATTATATATTTTTGAAAACAA 1 TTTTTGAAAACATATATTATATAGTTTTGAAAACGG * * *** 26726 TTTTTGAATATATATATTATATAGTTTTGAAAATAA 1 TTTTTGAAAACATATATTATATAGTTTTGAAAACGG * 26762 TTTTTGAAAATATATATTATATAGTTTTGAAAA 1 TTTTTGAAAACATATATTATATAGTTTTGAAAA 26795 AAATATTTTT Statistics Matches: 171, Mismatches: 32, Indels: 23 0.76 0.14 0.10 Matches are distributed among these distances: 33 2 0.01 34 4 0.02 35 29 0.17 36 98 0.57 37 1 0.01 38 16 0.09 39 21 0.12 ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44 Consensus pattern (36 bp): TTTTTGAAAACATATATTATATAGTTTTGAAAACGG Found at i:26627 original size:112 final size:111 Alignment explanation

Indices: 26471--26791 Score: 452 Period size: 112 Copynumber: 2.9 Consensus size: 111 26461 AACATTTTCG * * 26471 AAAAACGTATATCATATAGTTTTTAGAAAACGGTTATTGAAAACATATAATATATAGTTTTTAAA 1 AAAAACATATATTATATA--TTTTAGAAAACGGTTATTGAAAACATATAATATATAGTTTTTAAA 26536 AAATCATTTTTTTGAAAATATATATAATATGGTTTTGATAATACGATTT 64 AAATCA-TTTTTTGAAAATATATATAATATGGTTTTGATAATACGATTT 26585 AAAAACATATATTATATATTTTAGAAAACGGTTATTGAAAACATATAATATATAGTTTTTAAAAA 1 AAAAACATATATTATATATTTTAGAAAACGGTTATTGAAAACATATAATATATAGTTTTTAAAAA * * 26650 ATCGTTTTTTGAAAATATATATAATACGGTTTTGATAATACGATTT 66 ATCATTTTTTGAAAATATATATAATATGGTTTTGATAATACGATTT * ** * * * * * 26696 -AAAACATATATTATATATTTTTGAAAACAATTTTTGAATATATATATTATATAG-TTTT-GAAA 1 AAAAACATATATTATATATTTTAGAAAACGGTTATTGAAAACATATAATATATAGTTTTTAAAAA * * * 26758 AT-AATTTTTGAAAATATATATTATATAGTTTTGA 66 ATCATTTTTTGAAAATATATATAATATGGTTTTGA 26792 AAAAAATATT Statistics Matches: 190, Mismatches: 17, Indels: 7 0.89 0.08 0.03 Matches are distributed among these distances: 107 27 0.14 108 5 0.03 109 4 0.02 110 47 0.25 111 41 0.22 112 50 0.26 114 16 0.08 ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43 Consensus pattern (111 bp): AAAAACATATATTATATATTTTAGAAAACGGTTATTGAAAACATATAATATATAGTTTTTAAAAA ATCATTTTTTGAAAATATATATAATATGGTTTTGATAATACGATTT Found at i:26908 original size:39 final size:38 Alignment explanation

Indices: 26831--26913 Score: 114 Period size: 39 Copynumber: 2.2 Consensus size: 38 26821 CGTTTGAAAT * 26831 ATATATATAATATGTAATTTAGAAAACATTTTCAAAAAA 1 ATATATATAATATATAATTTAGAAAACATTTTC-AAAAA ** 26870 ATATATATAATATATGAATTT-GAAAACATTTTTTAAAA 1 ATATATATAATATAT-AATTTAGAAAACATTTTCAAAAA 26908 ATATAT 1 ATATAT 26914 GTAAAATTTA Statistics Matches: 40, Mismatches: 3, Indels: 3 0.87 0.07 0.07 Matches are distributed among these distances: 38 10 0.25 39 25 0.62 40 5 0.12 ACGTcount: A:0.52, C:0.04, G:0.05, T:0.40 Consensus pattern (38 bp): ATATATATAATATATAATTTAGAAAACATTTTCAAAAA Found at i:33815 original size:21 final size:21 Alignment explanation

Indices: 33790--33831 Score: 75 Period size: 21 Copynumber: 2.0 Consensus size: 21 33780 TTAAAGAGTA * 33790 AAAATATGAGAACAAAACAAT 1 AAAATATAAGAACAAAACAAT 33811 AAAATATAAGAACAAAACAAT 1 AAAATATAAGAACAAAACAAT 33832 CCCACATGGC Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.69, C:0.10, G:0.07, T:0.14 Consensus pattern (21 bp): AAAATATAAGAACAAAACAAT Found at i:33982 original size:24 final size:24 Alignment explanation

Indices: 33948--34003 Score: 103 Period size: 24 Copynumber: 2.3 Consensus size: 24 33938 CTATTCTTTC 33948 GCTTCAATTGAGCTCAAATTTTAG 1 GCTTCAATTGAGCTCAAATTTTAG * 33972 GTTTCAATTGAGCTCAAATTTTAG 1 GCTTCAATTGAGCTCAAATTTTAG 33996 GCTTCAAT 1 GCTTCAAT 34004 CGAACTTCTA Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 24 30 1.00 ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39 Consensus pattern (24 bp): GCTTCAATTGAGCTCAAATTTTAG Found at i:47048 original size:5 final size:5 Alignment explanation

Indices: 47038--47066 Score: 58 Period size: 5 Copynumber: 5.8 Consensus size: 5 47028 AAAGCTACGA 47038 ACCTC ACCTC ACCTC ACCTC ACCTC ACCT 1 ACCTC ACCTC ACCTC ACCTC ACCTC ACCT 47067 ATTTTAAAAG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 24 1.00 ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21 Consensus pattern (5 bp): ACCTC Found at i:53420 original size:12 final size:12 Alignment explanation

Indices: 53403--53428 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 53393 GGAAATTGGT 53403 CCAAATTAGGCA 1 CCAAATTAGGCA 53415 CCAAATTAGGCA 1 CCAAATTAGGCA 53427 CC 1 CC 53429 GAATATACAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15 Consensus pattern (12 bp): CCAAATTAGGCA Found at i:56297 original size:13 final size:13 Alignment explanation

Indices: 56279--56315 Score: 56 Period size: 13 Copynumber: 2.8 Consensus size: 13 56269 CGACCCGTTT * 56279 ACCCGTTTACCCG 1 ACCCGTTGACCCG * 56292 ACCCGTTGATCCG 1 ACCCGTTGACCCG 56305 ACCCGTTGACC 1 ACCCGTTGACC 56316 GGTGCTATTA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 13 21 1.00 ACGTcount: A:0.16, C:0.43, G:0.19, T:0.22 Consensus pattern (13 bp): ACCCGTTGACCCG Found at i:56377 original size:29 final size:29 Alignment explanation

Indices: 56316--56382 Score: 89 Period size: 29 Copynumber: 2.3 Consensus size: 29 56306 CCCGTTGACC * *** * 56316 GGTGCTATTATGGGAATTAATTCGGTTTT 1 GGTGCTATTATGAGAATTAATTCGAAATG 56345 GGTGCTATTATGAGAATTAATTCGAAATG 1 GGTGCTATTATGAGAATTAATTCGAAATG 56374 GGTGCTATT 1 GGTGCTATT 56383 TTGGTAATTT Statistics Matches: 33, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 29 33 1.00 ACGTcount: A:0.25, C:0.07, G:0.27, T:0.40 Consensus pattern (29 bp): GGTGCTATTATGAGAATTAATTCGAAATG Found at i:56391 original size:29 final size:28 Alignment explanation

Indices: 56316--56391 Score: 80 Period size: 29 Copynumber: 2.6 Consensus size: 28 56306 CCCGTTGACC *** * 56316 GGTGCTATTATGGGAATTAATTCGGTTTT 1 GGTGCTATTAT-GGAATTAATTCGAAATG 56345 GGTGCTATTATGAGAATTAATTCGAAATG 1 GGTGCTATTATG-GAATTAATTCGAAATG * 56374 GGTGCTATTTTGGTAATT 1 GGTGCTATTATGG-AATT 56392 TTTTTAAAAA Statistics Matches: 40, Mismatches: 5, Indels: 4 0.82 0.10 0.08 Matches are distributed among these distances: 28 2 0.05 29 38 0.95 ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42 Consensus pattern (28 bp): GGTGCTATTATGGAATTAATTCGAAATG Found at i:63458 original size:10 final size:10 Alignment explanation

Indices: 63443--63487 Score: 58 Period size: 9 Copynumber: 4.6 Consensus size: 10 63433 AACGCTGGAA 63443 ACCGGTTTTG 1 ACCGGTTTTG * 63453 ACCGG-TTTA 1 ACCGGTTTTG 63462 ACCGGTTTTG 1 ACCGGTTTTG 63472 AACCGG-TTTG 1 -ACCGGTTTTG 63482 ACCGGT 1 ACCGGT 63488 CACGACCCGT Statistics Matches: 30, Mismatches: 2, Indels: 6 0.79 0.05 0.16 Matches are distributed among these distances: 9 13 0.43 10 12 0.40 11 5 0.17 ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33 Consensus pattern (10 bp): ACCGGTTTTG Found at i:63477 original size:11 final size:11 Alignment explanation

Indices: 63442--63480 Score: 57 Period size: 11 Copynumber: 3.8 Consensus size: 11 63432 GAACGCTGGA 63442 AACCGGTTTTG 1 AACCGGTTTTG 63453 -ACCGG-TTT- 1 AACCGGTTTTG 63461 AACCGGTTTTG 1 AACCGGTTTTG 63472 AACCGGTTT 1 AACCGGTTT 63481 GACCGGTCAC Statistics Matches: 25, Mismatches: 0, Indels: 6 0.81 0.00 0.19 Matches are distributed among these distances: 9 8 0.32 10 8 0.32 11 9 0.36 ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36 Consensus pattern (11 bp): AACCGGTTTTG Found at i:63478 original size:20 final size:19 Alignment explanation

Indices: 63442--63487 Score: 74 Period size: 20 Copynumber: 2.4 Consensus size: 19 63432 GAACGCTGGA 63442 AACCGGTTTTGACCGGTTT 1 AACCGGTTTTGACCGGTTT 63461 AACCGGTTTTGAACCGGTTT 1 AACCGGTTTTG-ACCGGTTT * 63481 GACCGGT 1 AACCGGT 63488 CACGACCCGT Statistics Matches: 25, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 19 11 0.44 20 14 0.56 ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33 Consensus pattern (19 bp): AACCGGTTTTGACCGGTTT Found at i:63508 original size:13 final size:13 Alignment explanation

Indices: 63490--63524 Score: 61 Period size: 13 Copynumber: 2.7 Consensus size: 13 63480 TGACCGGTCA * 63490 CGACCCGTTTACC 1 CGACCCGTTAACC 63503 CGACCCGTTAACC 1 CGACCCGTTAACC 63516 CGACCCGTT 1 CGACCCGTT 63525 GACCGTTGAC Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 13 21 1.00 ACGTcount: A:0.17, C:0.46, G:0.17, T:0.20 Consensus pattern (13 bp): CGACCCGTTAACC Found at i:63597 original size:29 final size:29 Alignment explanation

Indices: 63536--63602 Score: 89 Period size: 29 Copynumber: 2.3 Consensus size: 29 63526 ACCGTTGACC * *** * 63536 GGTGCTATTATGGGAATTAATTCGGTTTT 1 GGTGCTATTATGAGAATTAATTCGAAATG 63565 GGTGCTATTATGAGAATTAATTCGAAATG 1 GGTGCTATTATGAGAATTAATTCGAAATG 63594 GGTGCTATT 1 GGTGCTATT 63603 TTGGTAATTT Statistics Matches: 33, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 29 33 1.00 ACGTcount: A:0.25, C:0.07, G:0.27, T:0.40 Consensus pattern (29 bp): GGTGCTATTATGAGAATTAATTCGAAATG Found at i:63611 original size:29 final size:28 Alignment explanation

Indices: 63536--63611 Score: 80 Period size: 29 Copynumber: 2.6 Consensus size: 28 63526 ACCGTTGACC *** * 63536 GGTGCTATTATGGGAATTAATTCGGTTTT 1 GGTGCTATTAT-GGAATTAATTCGAAATG 63565 GGTGCTATTATGAGAATTAATTCGAAATG 1 GGTGCTATTATG-GAATTAATTCGAAATG * 63594 GGTGCTATTTTGGTAATT 1 GGTGCTATTATGG-AATT 63612 TTTTTTTAAA Statistics Matches: 40, Mismatches: 5, Indels: 4 0.82 0.10 0.08 Matches are distributed among these distances: 28 2 0.05 29 38 0.95 ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42 Consensus pattern (28 bp): GGTGCTATTATGGAATTAATTCGAAATG Found at i:67183 original size:64 final size:64 Alignment explanation

Indices: 67026--67184 Score: 200 Period size: 64 Copynumber: 2.5 Consensus size: 64 67016 TGGAACACTT * * * * * 67026 AGTGCATCGGTGCACTA-AGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAGCCTG 1 AGTGCATCGATGCA-TAGAATGTGCATCGATGCATCAAATACATTCGATGTTTTCAAAAAGCCCG * 67090 AGTGCATCGATGCATAGTATGTGCATCGATGCATCAAATACATTCGATGTTTTCATTAAAA-CCC 1 AGTGCATCGATGCATAGAATGTGCATCGATGCATCAAATACATTCGATGTTTTCA--AAAAGCCC 67154 G 64 G 67155 AGTGCATCGATGCAT-GAAT-TGCATTCGATG 1 AGTGCATCGATGCATAGAATGTGCA-TCGATG 67185 TTTAATTAAT Statistics Matches: 84, Mismatches: 7, Indels: 8 0.85 0.07 0.08 Matches are distributed among these distances: 63 6 0.07 64 56 0.67 65 18 0.21 66 4 0.05 ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30 Consensus pattern (64 bp): AGTGCATCGATGCATAGAATGTGCATCGATGCATCAAATACATTCGATGTTTTCAAAAAGCCCG Done.