Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold601

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1259944
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29

Warning! 136746 characters in sequence are not A, C, G, or T


File 4 of 5

Found at i:562720 original size:437 final size:438

Alignment explanation

Indices: 561946--562942 Score: 1631 Period size: 437 Copynumber: 2.3 Consensus size: 438 561936 TTTACAAACT * 561946 TATATTGTTACGATCAACAACTTTG-TATCTATAATGCATTACAAAATTTTGATAGTTTTTAAGT 1 TATATTGTTACGATCAACAACTTTGCT-TCTATAATGCATTACAAAATCTTGATAGTTTTTAAGT * 562010 TATTTGTAATAGAGTTTTCGAGTGTCTTGACCCCTAATTTAAGGGGCCAGCCCC-TTTTTCTTGA 65 TATTTGTAATAGAGTTTACGAGTGTCTTGACCCCTAATTTAAGGGGCCAGCCCCTTTTTTCTTGA * 562074 GTTCCTTCGAAAAGTCTAACTAATACTAACAATTTTTGTTCTTACACTTATGTAGAATTGTTGTT 130 GTTCATTCGAAAAGTCTAACTAATACTAACAATTTTTGTTCTTACACTTATGTAGAATTGTTGTT * 562139 CATATTTTAGATACAAATGATTGGATATTTAAGGGGCCAGCCCTCTAGATCCTTAATGAAAACAG 195 CATATTTTAGATACAAATGATTGAATATTTAAGGGGCCAGCCCTCTAGATCCTTAATGAAAACAG * * * * 562204 ACTTTGGTGATTTGATTAATGGAATTGGTTAGAATCATCAATGCAAACATTTTCTCTTCTACAAT 260 ACATTGGTGATTTGATAAATGGAACTGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAAT * * * 562269 ACTTAACAAAATATGTCTCCTTTTCTAGATATATTGCGTCAATGTTTAAGTACTTTGGCCCCTAA 325 ACTTAACAAAATATGTCTCCTTTTCTAAATATATTGCGTCAAAGTTTAAGAACTTTGGCCCCTAA 562334 AAATCCCTAATTACGTAATAAATGGGCGTGGCAATGATTTTACCTGATA 390 AAATCCCTAATTACGTAATAAATGGGCGTGGCAATGATTTTACCTGATA * * 562383 TATATTGTTACGATCAACAACGTTGCTTCTATAATGCATTACAAAATCTTGATAGTTTTTAAGGT 1 TATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTGATAGTTTTTAAGTT 562448 ATTTGTAATAGAGTTTACGAGTGTCTTGACCCCTAATTTAAGGGGCCAGCCCCTTTTTTCTTGAG 66 ATTTGTAATAGAGTTTACGAGTGTCTTGACCCCTAATTTAAGGGGCCAGCCCCTTTTTTCTTGAG * * * 562513 TTCATTCGAAAGGTTTCACTAATACTAACAATTTTTGTTCTTACACTTATGTAGAATTGTTGTTC 131 TTCATTCGAAAAGTCTAACTAATACTAACAATTTTTGTTCTTACACTTATGTAGAATTGTTGTTC * *** 562578 ATATTTTAGATACAAATGATTGAATATTTAAGGGGCCAG-CTTCTAGATCCTTAATGGGGACAGA 196 ATATTTTAGATACAAATGATTGAATATTTAAGGGGCCAGCCCTCTAGATCCTTAATGAAAACAGA * * * 562642 CATTGGTGTTTTGATAAATGGAACTGATTAGAATCATCAATGCAAACATTTTCTCTTCTATAATG 261 CATTGGTGATTTGATAAATGGAACTGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAATA * 562707 CTTTACAAAATATGTCTCCTTTTCTAAATATATTGCGTCAAAGTTTAAGAACTTTGGCCCCTAAA 326 CTTAACAAAATATGTCTCCTTTTCTAAATATATTGCGTCAAAGTTTAAGAACTTTGGCCCCTAAA * * 562772 ACTCCCTAATTACGTGATAAATGGGCGTGGCAATGATTTTACCTGATA 391 AATCCCTAATTACGTAATAAATGGGCGTGGCAATGATTTTACCTGATA * * * 562820 TATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTTATCGTCTTTAAGTT 1 TATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTGATAGTTTTTAAGTT * * * * * *** 562885 ATTTGTATTATAGTTTACAAGTGTCTTGGCCCTTAAAGAAAGGGGCCAGCCCCTTTTT 66 ATTTGTAATAGAGTTTACGAGTGTCTTGACCCCTAATTTAAGGGGCCAGCCCCTTTTT 562943 GTTGAATTTG Statistics Matches: 519, Mismatches: 39, Indels: 4 0.92 0.07 0.01 Matches are distributed among these distances: 437 408 0.79 438 111 0.21 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38 Consensus pattern (438 bp): TATATTGTTACGATCAACAACTTTGCTTCTATAATGCATTACAAAATCTTGATAGTTTTTAAGTT ATTTGTAATAGAGTTTACGAGTGTCTTGACCCCTAATTTAAGGGGCCAGCCCCTTTTTTCTTGAG TTCATTCGAAAAGTCTAACTAATACTAACAATTTTTGTTCTTACACTTATGTAGAATTGTTGTTC ATATTTTAGATACAAATGATTGAATATTTAAGGGGCCAGCCCTCTAGATCCTTAATGAAAACAGA CATTGGTGATTTGATAAATGGAACTGATTAGAATCATCAATGCAAACATTTTCTCTTCTACAATA CTTAACAAAATATGTCTCCTTTTCTAAATATATTGCGTCAAAGTTTAAGAACTTTGGCCCCTAAA AATCCCTAATTACGTAATAAATGGGCGTGGCAATGATTTTACCTGATA Found at i:565538 original size:437 final size:438 Alignment explanation

Indices: 564676--565963 Score: 1996 Period size: 437 Copynumber: 2.9 Consensus size: 438 564666 GTGTAAGAGC * * * 564676 TTTGTTCAACAAGTGTTTAGAAATTCGTCACCGTTCTTGAGATATCTCAGAAAGAATATTTTAGG 1 TTTGTTCAACAAGTGTTCAGAAATTCGTTACCATTCTTGAGATATCTCAGAAAGAATATTTTAGG * ** * * * * 564741 GGCCGG-ACCTTATCTCCTTATTGGGGCCGCTGAAAAAAAATTGTAAGGTTGCATGTTATTACAT 66 GGCCGGTCCCTTATCTCCTTATTGGGGCCGCTGAACCAAATTTTTTAGGTTGCATGTTGTT--A- * * * * 564805 GTAGGTACATTATTTTGAGCATCTTTTCCTTTATACTGCATTTCAAAATATTTTTTCTTTTTGAG 128 --AGGTACATCATTTTGAGCATCTTTTCTTTTATACTGCATTTCAAAATATTTTTCCGTTTTGAG ** * * * * * * 564870 ATATAGGTTATTACATTTTTGGACTTTTGACCCCTAAAAATCCTTAATTACGTAACACATGAGAA 191 ATATAGGTGGTCAAAGTTTTGGACTTCTGACCCCTAAAAATCCCTAATTACGTAACATATGAG-A * * * * * 564935 AAATCATTATAATG-TTAGGCTACACAACTGTTAGATAAACATATTTGCTTCTAT-ATTCTATTA 255 AAATCGTTATACTGCTT-GGCTTCATAACTGTAAGATAAACATATTTGCTTCTATAATT-TATTA * * * 564998 CGAAATACCCCTCGGTAAAGAACTATAGGAAAAAGACTTTAGAGCCCTCTAGGTCCCTAATATTA 318 CAAAATATCCCTCGGTAAAGAACTATAGTAAAAAGACTTTAGAGCCCTCTAGGTCCCTAATATTA * * * * 565063 GGGGCTAGCCCCTTTTTCATGGTATCAAATGAAAGGTCATTTGATTATAAAGATAT 383 GGGGCCAGCCCCTTTTTCTTGGTATCAAATGAAAGGTCATTTAATTATAAAGACAT * * 565119 TTTGTTCAACAAGTGTTCAGAAATCCGTTACCATTCTTCAGATATCTCAGAAAGAATATTTTAGG 1 TTTGTTCAACAAGTGTTCAGAAATTCGTTACCATTCTTGAGATATCTCAGAAAGAATATTTTAGG * 565184 GGCCGGTCCCTTATCTCCTTATTGGGGCCGCTGAACCAAATTTTTTAGGCTGCATGTTGTTAAGG 66 GGCCGGTCCCTTATCTCCTTATTGGGGCCGCTGAACCAAATTTTTTAGGTTGCATGTTGTTAAGG 565249 -ACATCATTTTGAGCATCTTTTCTTTTATACTGCATTTCAAAATATTTTTCCGTTTTGAGATATA 131 TACATCATTTTGAGCATCTTTTCTTTTATACTGCATTTCAAAATATTTTTCCGTTTTGAGATATA 565313 GGTGGTCAAAGTTTTGGACTTCTGACCCCTAAAAATCCCTAATTACGTAACATATGAGAAAATCG 196 GGTGGTCAAAGTTTTGGACTTCTGACCCCTAAAAATCCCTAATTACGTAACATATGAGAAAATCG 565378 TTATACTGCTTGGCTTCATAACTGTAAGATAAACATATTTGCTTCTATAATTTATTACAAAATAT 261 TTATACTGCTTGGCTTCATAACTGTAAGATAAACATATTTGCTTCTATAATTTATTACAAAATAT * 565443 CCCTCAGTAAAGAACTATAGTAAAAAGACTTTAGAGCCCTCTAGGTCCCTAATATTAGGGGCCAG 326 CCCTCGGTAAAGAACTATAGTAAAAAGACTTTAGAGCCCTCTAGGTCCCTAATATTAGGGGCCAG * 565508 CCCCTTGTTCTTGGTATCAAATGAAAGGTCATTTAATTATAAAGACAT 391 CCCCTTTTTCTTGGTATCAAATGAAAGGTCATTTAATTATAAAGACAT * 565556 TTTGTTCAACAAGTGTTCAGAAATTCGTTACCATTCTTGAGATATCTCAGAAAGAATGTTTTAGG 1 TTTGTTCAACAAGTGTTCAGAAATTCGTTACCATTCTTGAGATATCTCAGAAAGAATATTTTAGG * 565621 GGCCGGTCCCTTATCTCCTTATTGGGGCCGCTGAACCAAATTTTTTAGGTTGCATGGTGTT-AGG 66 GGCCGGTCCCTTATCTCCTTATTGGGGCCGCTGAACCAAATTTTTTAGGTTGCATGTTGTTAAGG 565685 TACATCATTTTGAGCATCTTTTCTTTTATACTGCATTTCAAAATATTTTTCCGTTTTGAGATATA 131 TACATCATTTTGAGCATCTTTTCTTTTATACTGCATTTCAAAATATTTTTCCGTTTTGAGATATA 565750 GGTGGTCAAAGTTTTGGACTTCTGACCCCTAAAAATCCCTAATTACGTAACATATGAGAAAATCG 196 GGTGGTCAAAGTTTTGGACTTCTGACCCCTAAAAATCCCTAATTACGTAACATATGAGAAAATCG * * 565815 TTATACTGCTTGGCTTCATATCTGTAAGATAAACATATTTGCTTATATAATTTATTACAAAATAT 261 TTATACTGCTTGGCTTCATAACTGTAAGATAAACATATTTGCTTCTATAATTTATTACAAAATAT * ** * * 565880 CACTCGGTAAAGAGTTATGGGTAAAAA-ACTTTAGAGCCCTCTAGGTCCCTTAT-TTGAGGGGCC 326 CCCTCGGTAAAGAACTAT-AGTAAAAAGACTTTAGAGCCCTCTAGGTCCCTAATATT-AGGGGCC * 565943 AGCCCCTTTTTCTTGATATCA 389 AGCCCCTTTTTCTTGGTATCA 565964 GCAGAAAGGT Statistics Matches: 785, Mismatches: 54, Indels: 18 0.92 0.06 0.02 Matches are distributed among these distances: 436 5 0.01 437 542 0.69 438 122 0.16 439 3 0.00 442 1 0.00 443 66 0.08 444 46 0.06 ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36 Consensus pattern (438 bp): TTTGTTCAACAAGTGTTCAGAAATTCGTTACCATTCTTGAGATATCTCAGAAAGAATATTTTAGG GGCCGGTCCCTTATCTCCTTATTGGGGCCGCTGAACCAAATTTTTTAGGTTGCATGTTGTTAAGG TACATCATTTTGAGCATCTTTTCTTTTATACTGCATTTCAAAATATTTTTCCGTTTTGAGATATA GGTGGTCAAAGTTTTGGACTTCTGACCCCTAAAAATCCCTAATTACGTAACATATGAGAAAATCG TTATACTGCTTGGCTTCATAACTGTAAGATAAACATATTTGCTTCTATAATTTATTACAAAATAT CCCTCGGTAAAGAACTATAGTAAAAAGACTTTAGAGCCCTCTAGGTCCCTAATATTAGGGGCCAG CCCCTTTTTCTTGGTATCAAATGAAAGGTCATTTAATTATAAAGACAT Found at i:567470 original size:437 final size:436 Alignment explanation

Indices: 566715--567724 Score: 1673 Period size: 437 Copynumber: 2.3 Consensus size: 436 566705 AATAAATGTG * * 566715 AGATGAACATTATTGCTTCCTAAACATATTACAAAATAATTT-TCAGTAAAGTGCTATGGAAGAA 1 AGATGAACATT-TTGCTTCTTAAACATATTACAAAAT-ATTTCTCAGTAAAGTGCTATAGAAGAA * * 566779 AGACTTTAGAGCCCTTTTGGTCCCTAAATTGAAGGGCCAGCCCCTTTTTCTTGGCATCATACGAA 64 AGACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGACCAGCCCCTTTTTCTTGGCATCATACGAA * 566844 AGTTCTTTTGATATTAAAAATATTTTGTTCAACAAGTGTTTAGAAATTCTTTGACGTTTAAGAGC 129 AGTTCTTTTGATATCAAAAATATTTTGTTCAACAAGTGTTTAGAAATTCTTTGACGTTTAAGAGC * * 566909 TATCTGGGATAGGACGTTTTAGGGGCCGACCCCTAATCTCCTTATTGGGGCCAGATAACAAATCT 194 TATCTGGGATAGGACATTTTAGGGGCCGACCCCTAATCTCCTTATTGGGGCCAGAAAACAAATCT * * * 566974 TTTATGATTGAATATTGTTTAAAACATTATTCTAAGCATCTTTTATTCTATATTGCTTTTCAAAA 259 TTTATGATTGAATATTGTTTAAAACATCATTCTAAGCATATTTTACTCTATATTGCTTTTCAAAA * * 567039 TATTTGTCCTTTTTGAGATATATTCGATCGAAGTTTTGGACTTCTGGCCCCTTGAAACCCCTTAT 324 TATTTGTCCTTTTTGAGATATATTCGATCGAAGTTTTGGACTTCTGGCCCCTTAAAACCCCTAAT * 567104 TACGTAACGCATTATAAAAATTTTATAATGTATAATTTTATTAGTGAA 389 TACGTAACGCATAATAAAAATTTTATAATGTATAATTTTATTAGTGAA * 567152 AGATGAACATGTTTGCTTCTTAAACTTATTACAAAATATTTCTCAGTAAAGTGCTATAGAAGAAA 1 AGATGAACAT-TTTGCTTCTTAAACATATTACAAAATATTTCTCAGTAAAGTGCTATAGAAGAAA * * 567217 GACTTTAGAGCCCTTTTAGCCCCTAAATTGAAGGCCCAGCCCCTTTTTCTTGGCATCATACGAAA 65 GACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGACCAGCCCCTTTTTCTTGGCATCATACGAAA * * * * * 567282 GTTCTTTTGATATCAAACATATTTTGTTCATCAAGTGTTTAGAAATTCTTTGCCGTTTTAGGGCT 130 GTTCTTTTGATATCAAAAATATTTTGTTCAACAAGTGTTTAGAAATTCTTTGACGTTTAAGAGCT * * 567347 ATCTGGGATATGACATTTTAGGGGCCGACCCCTAATCTCCTTATTGGGGCCAGAAAATGAAAT-T 195 ATCTGGGATAGGACATTTTAGGGGCCGACCCCTAATCTCCTTATTGGGGCCAGAAAA-CAAATCT 567411 TTTATGATTGAATATTGTTTAAAACATCATTCTAAGCATATTTTACTCTATATTGCTTTTCAAAA 259 TTTATGATTGAATATTGTTTAAAACATCATTCTAAGCATATTTTACTCTATATTGCTTTTCAAAA 567476 TATTTGTCCTTTTTGAGATATATTCGATCGAAGTTTTGGACTTCTGGCCCCTTAAAACCCCTAAT 324 TATTTGTCCTTTTTGAGATATATTCGATCGAAGTTTTGGACTTCTGGCCCCTTAAAACCCCTAAT * 567541 TACGTAACGCATAATAAAAATTTTATAATGTATAGTTTTATTAGTGAA 389 TACGTAACGCATAATAAAAATTTTATAATGTATAATTTTATTAGTGAA 567589 AGATGAACATCTTTGCTTCTTAAACATATTACAAAATATTTCTCAGTAAAGTGCTATAGAAGAAA 1 AGATGAACAT-TTTGCTTCTTAAACATATTACAAAATATTTCTCAGTAAAGTGCTATAGAAGAAA * * * * ** * 567654 GACTTTAAAGCCCTTTTGGCCCTTAATTTGAGGGACCAGCCCCTTTTTCTTGTTATCAAACGAAA 65 GACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGACCAGCCCCTTTTTCTTGGCATCATACGAAA * 567719 GCTCTT 130 GTTCTT 567725 GTAAATATTA Statistics Matches: 535, Mismatches: 35, Indels: 6 0.93 0.06 0.01 Matches are distributed among these distances: 436 4 0.01 437 526 0.98 438 5 0.01 ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37 Consensus pattern (436 bp): AGATGAACATTTTGCTTCTTAAACATATTACAAAATATTTCTCAGTAAAGTGCTATAGAAGAAAG ACTTTAGAGCCCTTTTGGCCCCTAAATTGAAGGACCAGCCCCTTTTTCTTGGCATCATACGAAAG TTCTTTTGATATCAAAAATATTTTGTTCAACAAGTGTTTAGAAATTCTTTGACGTTTAAGAGCTA TCTGGGATAGGACATTTTAGGGGCCGACCCCTAATCTCCTTATTGGGGCCAGAAAACAAATCTTT TATGATTGAATATTGTTTAAAACATCATTCTAAGCATATTTTACTCTATATTGCTTTTCAAAATA TTTGTCCTTTTTGAGATATATTCGATCGAAGTTTTGGACTTCTGGCCCCTTAAAACCCCTAATTA CGTAACGCATAATAAAAATTTTATAATGTATAATTTTATTAGTGAA Found at i:570180 original size:437 final size:437 Alignment explanation

Indices: 568530--570522 Score: 2799 Period size: 437 Copynumber: 4.6 Consensus size: 437 568520 CGGAATTGTC * * * * * 568530 CTCCATTTTGAGATATAGAGGATC-AAGTTTTGGACTTCTGGTCCCTTAAAATCCCAAATTACGT 1 CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT ** * ** ** * * * * 568594 AACGTAGGAGTAAAAGATTGCCATGTATTGGCAAATATCGTTAGTATAAACATAATTGCCTCTAC 66 AATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGCTTCTAT * * * * * * *** * 568659 AACGGATCAAAAAATATTTCACAGTAAATATTTATCATGAAAAGTCTTTAGAGCCCCCTCAGCCC 131 AACGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTTAGAGCCTTATCGGCCC * * * * * * * * * 568724 CTTATATGAAGGACCAGCCCCTTTTTCATGATCTCATACATGTAAGAATGTGTTTGTCAACTCAA 196 CTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCT--TAAATGAAAG-CT-CG--TGTCAATTCAA * * ** 568789 ACACATTTTGTTTAACAAGTGTTT-GAAATTCTGTACCGTACTGGAGATATCTGGTA-AGATTCG 255 ACACATTTTGTTCAACAAGTGTTTAGAAATTCTGTACCGTTCTGGAGATATCTGG-AGAGGGTCG * * * * * * * * 568852 TTTTAGGGGCCGACCCTGTTACTCCTTTTAAGGACCGTATCACACAGAGAA-TATGGTTACATAC 319 TTTTAGGGGCCGACCCTGTAACTCCTTTCAGGGACCGCATAACAAAGA-AATTATTG-T---TGC * * * * * * * * * 568916 TAGTATTGTTAAGCTTAATTTTTTTAGCTTCTTTTGTTCAAAATTGTTTTTC-ATA-GTTAT 379 -AG-ATTGATAAGCTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTT-T * * ** * 568976 CCTCCATTTTGAGATATTGAGGATCAAAGTGATGGACTTCTGGTCCCTTAAAATCCCTAATTACG 1 -CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACG * * 569041 TAATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGTTTTTA 65 TAATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGCTTCTA * * * *** * 569106 TAAGGTATCACAAAATATTTCACAGTGAAATGTTATCATCAAAAGACTTTAGAGCCCCCTCAGCC 130 TAACGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTTAGAGCCTTATCGGCC * * * * 569171 CCTTATTTGAAGGGCCAGTCCCTTTTTCTTGATCTCAAATGAAAGCTCTTGTCAATT------CA 195 CCTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTTAAATGAAAGCTCGTGTCAATTCAAACACA 569230 TTTTGTTCAACAAGTGTTTAGAAATTCTGTACCGTTCTGGAGATATCTGGAGAGGGTCGTTTTAG 260 TTTTGTTCAACAAGTGTTTAGAAATTCTGTACCGTTCTGGAGATATCTGGAGAGGGTCGTTTTAG ** 569295 GGGCCGACCCTGTATTTCCTTTCAGGGACCGCATAACAAAGAAATTATTGTTGCAGATTGATAAG 325 GGGCCGACCCTGTAACTCCTTTCAGGGACCGCATAACAAAGAAATTATTGTTGCAGATTGATAAG * 569360 CTTAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTTT 390 CTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTTT * 569408 CTCCATTTAGAGATATTAAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT 1 CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT * 569473 AATATAGGAGTAAATGATTGCCATGTACAGGTGAATAACGTTAGAAT-AACATAATTGCTTCTAT 66 AATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGCTTCTAT * * 569537 GACGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAGAGACTTTAGAGCCTTATCGGCCC 131 AACGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTTAGAGCCTTATCGGCCC 569602 CTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTTAAATGAAAGCTCGTGTCAATTCAAACACAT 196 CTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTTAAATGAAAGCTCGTGTCAATTCAAACACAT * * * 569667 TTTGTTCAACAAGTGTTGAGAAATTGTGTACCGTTCTGGAGATATCTTGAGAGGGTCGTTTTAGG 261 TTTGTTCAACAAGTGTTTAGAAATTCTGTACCGTTCTGGAGATATCTGGAGAGGGTCGTTTTAGG * * * 569732 GGCCGACCCTGTAACTCCTTTCAGCGACTGCATAACAAAGAAATAATTGTTGCAGATTGATAAGC 326 GGCCGACCCTGTAACTCCTTTCAGGGACCGCATAACAAAGAAATTATTGTTGCAGATTGATAAGC 569797 TCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTTT 391 TCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTTT 569844 CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT 1 CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT * ** 569909 AATATAGGAGTAAATGATTGACATGTTTAGGTGAATAACGTTAGAATAAACATAATTGCTTCTAT 66 AATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGCTTCTAT * * 569974 GACGTATCACAAAATATTTTACAGTAAAAAGTGT-TCATCAAAAGACTTTAGAGCCTTATCGGCC 131 AACGTATCACAAAATATTTCACAGTAAAAAGT-TATCATCAAAAGACTTTAGAGCCTTATCGGCC 570038 CCTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTTAAATGAAAGCTCGTGTCAATTCAAACACA 195 CCTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTTAAATGAAAGCTCGTGTCAATTCAAACACA * * * 570103 TTCTGTCCAACAAGTGTTTAGAAATTCTGTACCGTTCTGAAGATATCTGGAGAGGGTCGTTTTAG 260 TTTTGTTCAACAAGTGTTTAGAAATTCTGTACCGTTCTGGAGATATCTGGAGAGGGTCGTTTTAG * * 570168 GGGCCGACCCTGTAACTCCTTTCAGGGACCGCATTACAAAGAAATTATTGTTGCAGTTTGATAAG 325 GGGCCGACCCTGTAACTCCTTTCAGGGACCGCATAACAAAGAAATTATTGTTGCAGATTGATAAG 570233 CTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTTT 390 CTCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTTT 570281 CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT 1 CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT * * 570346 AATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGTTTTTAT 66 AATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGCTTCTAT * * * * 570411 AAGGTATCACAAAATATTTCACATTTAAAAGTTATTATCAAAAGACTTTAGAGCCTTATCGGCCC 131 AACGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTTAGAGCCTTATCGGCCC * 570476 CTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTCAAATGAAAGCTC 196 CTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTTAAATGAAAGCTC 570523 TTGTAAAAAT Statistics Matches: 1412, Mismatches: 119, Indels: 40 0.90 0.08 0.03 Matches are distributed among these distances: 430 123 0.09 431 146 0.10 432 5 0.00 433 5 0.00 436 304 0.22 437 615 0.44 438 1 0.00 442 7 0.00 445 1 0.00 446 7 0.00 447 23 0.02 448 175 0.12 ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34 Consensus pattern (437 bp): CTCCATTTAGAGATATTGAGCATCAAAGTTTTGGACTTCTGGCCCCTTAAAATCCCTAATTACGT AATATAGGAGTAAATGATTGCCATGTAGAGGTGAATAACGTTAGAATAAACATAATTGCTTCTAT AACGTATCACAAAATATTTCACAGTAAAAAGTTATCATCAAAAGACTTTAGAGCCTTATCGGCCC CTAATTTGAAGGGCCAGCCCCTTTTTCTTGATCTTAAATGAAAGCTCGTGTCAATTCAAACACAT TTTGTTCAACAAGTGTTTAGAAATTCTGTACCGTTCTGGAGATATCTGGAGAGGGTCGTTTTAGG GGCCGACCCTGTAACTCCTTTCAGGGACCGCATAACAAAGAAATTATTGTTGCAGATTGATAAGC TCAATATTTTGAGCATCTTTTGTTCAATATTGCTTATCAAAATGTTT Found at i:572002 original size:437 final size:437 Alignment explanation

Indices: 571254--573107 Score: 2596 Period size: 437 Copynumber: 4.2 Consensus size: 437 571244 CTAATCTAGC * * * * * 571254 CTTA-ATAACCTTTCACAAAAT-TGCTCTCATTAAAGGGCTATAGATAAAAGA-TTTAAGAGCTC 1 CTTATATAACATTTCACAAAATAT-CTCTCAGTAAAGGGCTACAGATTAAAGACTTT-AGAGCCC * * * * * 571316 TTTGATCCCCTAATTTAAGGGGCCAGTCCCTTTTTCTTGATATCAAATGAAAAGAT-ATTTAATT 64 TTTGGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAAT-AAAAGGTCATTTAATT * * * * * * * * * 571380 CTGAACACATTTTG-TCAACAAGTGTTGAGAAAATCGTTACTGTTCTGGAGATATATGAGATAGA 128 TTAAACACATGTTGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGAAAGA * 571444 AGGTTTTAGGGGCCGATCCCTTATCTCTTATCCCTTATAGGGGCCGTTTAGCGAAATTTTGAAGG 193 AGGTTTTAGGGGCCGATCCCTTA--TC-T-T--CTTTTAGGGGCCGTTTAGCGAAATTTTGAAGG * * 571509 TTGAATATTGTTAAGAACATTAATTTGAACAACTTTTATTCTGTATTGCATTTCAAATTATTTTT 252 TTGAATATTGTTAAGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTTCAAAATATTTTT * * * 571574 TCTTTCTGAGATATGGGTTATTGAAATTTTGGACTTTAGGCCCCTAAAAACCCTTAATTACGTAA 317 CCTTTCTGAGATATGGGTTATTGAAATTTTGGACTTTTGGCCCCTAATAACCCTTAATTACGTAA * 571639 CACATAATAAAATCATTACATTGCTTGGATACATATCTGTGAGATAAACATATTTG 382 CACATAATAAAATCACTACATTGCTTGGATACATATCTGTGAGATAAACATATTTG * * * 571695 CTTATATAACATTTCAAAAAATATCTCTCAGTAAAGGGCTACATATTTAAGACTTTAGAGCCCTT 1 CTTATATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTT * * * * 571760 TGGTCCCCTTATTTGAGGTGCCAGCCCCTTTTTCTTGATATTAAATGAAAGGTCATTCAATTTTA 66 TGGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTAATTTTA * * 571825 AACAAAT-TCTGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGATAGAAG 131 AACACATGT-TGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGAAAGAAG 571889 GTTTTAGGGGCCGATCCCTTATCTTCTTTTAGGGGCCGTTTAGCGAAATTTTGAAGGTTGAATAT 195 GTTTTAGGGGCCGATCCCTTATCTTCTTTTAGGGGCCGTTTAGCGAAATTTTGAAGGTTGAATAT 571954 TGTTAAGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTTCAAAATATTTTTCCTTTCTG 260 TGTTAAGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTTCAAAATATTTTTCCTTTCTG 572019 AGATATGGGTTATTGAAATTTTGGACTTTTGGCCCCTAATAACCCTTAATTACGTAACACATAAT 325 AGATATGGGTTATTGAAATTTTGGACTTTTGGCCCCTAATAACCCTTAATTACGTAACACATAAT * 572084 AAAATCACTACATTGCTTGGATACATAACTGTGAGATAAACATATTTG 390 AAAATCACTACATTGCTTGGATACATATCTGTGAGATAAACATATTTG * 572132 CTTCTATAACATTTCACAAAATATCTCTCAG-ATAAGGGCTACAGATTAAAGACTTTAGAGCCCT 1 CTTATATAACATTTCACAAAATATCTCTCAGTA-AAGGGCTACAGATTAAAGACTTTAGAGCCCT 572196 TTGGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTAATTTT 65 TTGGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTAATTTT * * 572261 GAACCCATGTTGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGAAAGAAG 130 AAACACATGTTGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGAAAGAAG * * 572326 GTTTTAGGGGCTGGTCCCTTATCTTCTTTTAGGGGCCGTTTAGCGAAATTTTGAAGGTTGAATAT 195 GTTTTAGGGGCCGATCCCTTATCTTCTTTTAGGGGCCGTTTAGCGAAATTTTGAAGGTTGAATAT 572391 TGTTAAGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTTCAAAATATTTTTCCTTTCTG 260 TGTTAAGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTTCAAAATATTTTTCCTTTCTG 572456 AGATATGGGTTATTGAAATTTTGGACTTTTGGCCCCTAATAACCCTTAATTACGTAACACATAAT 325 AGATATGGGTTATTGAAATTTTGGACTTTTGGCCCCTAATAACCCTTAATTACGTAACACATAAT 572521 AAAATCACTACATTGCTTGGATACAT-TACTGTGAGATAAACATATTTG 390 AAAATCACTACATTGCTTGGATACATAT-CTGTGAGATAAACATATTTG * 572569 CTTCTATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTT 1 CTTATATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTT 572634 TGGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTAATTTTA 66 TGGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTAATTTTA 572699 AACACATGTTGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGAAAGAAGG 131 AACACATGTTGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGAAAGAAGG * * 572764 TTTTAGGGGCCGGTCCCTTATCTTCTTTTAGGGGCCGTTTAACGAAATTTTG-AGAGTTGAATAT 196 TTTTAGGGGCCGATCCCTTATCTTCTTTTAGGGGCCGTTTAGCGAAATTTTGAAG-GTTGAATAT * * * * * ** * * * 572828 TGTTGAA-AAC-GTCATTCTAAACACCTTTTCTTTTACACTGC-TTATCAAAATATTTTTCATTA 260 TGTT-AAGAACATTAATT-TGAACAACTTTTCTTCTGTATTGCATT-TCAAAATATTTTTCCTTT ** * * * * * * * * * 572890 AGGAGATATAGATGA-TCAAAGTTTTGAACTTCTGACCCCTAAAAATCCC-TAATTACGTAACAT 322 CTGAGATATGGGTTATTGAAA-TTTTGGACTTTTGGCCCCTAATAA-CCCTTAATTACGTAACAC * * * ** * * * * 572953 ATGA-GAAATACATTTTATTG-TATGGGTACATAACAGTAAGATAAACA-ATTTTG 385 ATAATAAAAT-CACTACATTGCT-TGGATACATATCTGTGAGATAAACATA-TTTG * * * * * * * * 573006 CTTCTATGA-TTTATAACAAAATAACTCTCAGTAAAGAGCTACAAATCAAAGACTTTAGA-CCCA 1 CTTATATAACATT-TCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCC- * * 573069 TTTGGGT-CCCTAATTTTAGGGGCCAGCCCCTTTTTCTTG 64 TTT-GGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTG 573108 GTATTAAACG Statistics Matches: 1299, Mismatches: 91, Indels: 50 0.90 0.06 0.03 Matches are distributed among these distances: 436 24 0.02 437 1077 0.83 438 10 0.01 439 1 0.00 440 1 0.00 441 12 0.01 442 102 0.08 443 72 0.06 ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36 Consensus pattern (437 bp): CTTATATAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGAGCCCTT TGGTCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTAATTTTA AACACATGTTGTTCAACAAGTCTTTAGAAATTCGTTACCGTTTTGGAGATATATGAGAAAGAAGG TTTTAGGGGCCGATCCCTTATCTTCTTTTAGGGGCCGTTTAGCGAAATTTTGAAGGTTGAATATT GTTAAGAACATTAATTTGAACAACTTTTCTTCTGTATTGCATTTCAAAATATTTTTCCTTTCTGA GATATGGGTTATTGAAATTTTGGACTTTTGGCCCCTAATAACCCTTAATTACGTAACACATAATA AAATCACTACATTGCTTGGATACATATCTGTGAGATAAACATATTTG Found at i:573648 original size:63 final size:63 Alignment explanation

Indices: 573549--573680 Score: 246 Period size: 63 Copynumber: 2.1 Consensus size: 63 573539 AAAAAAAAAA * 573549 TAATAATAGGGAAAAAGAAACAAAGCAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT 1 TAATAAAAGGGAAAAAGAAACAAAGCAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT * 573612 TAATAAAAGGGAAAAAGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT 1 TAATAAAAGGGAAAAAGAAACAAAGCAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT 573675 TAATAA 1 TAATAA 573681 TAAGAAAAGT Statistics Matches: 67, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 63 67 1.00 ACGTcount: A:0.50, C:0.14, G:0.20, T:0.17 Consensus pattern (63 bp): TAATAAAAGGGAAAAAGAAACAAAGCAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCT Found at i:573709 original size:63 final size:62 Alignment explanation

Indices: 573558--573711 Score: 195 Period size: 63 Copynumber: 2.5 Consensus size: 62 573548 ATAATAATAG * * * 573558 GGAAAAAGAAACAAAGCAAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAA 1 GGAAAAAGAAAAAAAACAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAA * * 573620 GGGAAAAAGAAACAAAGCAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAATAA 1 -GGAAAAAGAAAAAAAACAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAA-AA * * 573684 -GAAAAGTGAAAAAGAAAC-ATTACAATAA 1 GGAAAA-AGAAAAA-AAACAATAACAATAA 573712 TAGAAGGGTC Statistics Matches: 83, Mismatches: 5, Indels: 6 0.88 0.05 0.06 Matches are distributed among these distances: 62 5 0.06 63 73 0.88 64 5 0.06 ACGTcount: A:0.53, C:0.13, G:0.19, T:0.16 Consensus pattern (62 bp): GGAAAAAGAAAAAAAACAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAA Found at i:576068 original size:22 final size:22 Alignment explanation

Indices: 576040--576086 Score: 85 Period size: 22 Copynumber: 2.1 Consensus size: 22 576030 TACATCAAAG 576040 CAAAGTACCAGTAGTTAGATTA 1 CAAAGTACCAGTAGTTAGATTA * 576062 CAAAGTACCAGTAGTTAGTTTA 1 CAAAGTACCAGTAGTTAGATTA 576084 CAA 1 CAA 576087 TGTAAATATA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28 Consensus pattern (22 bp): CAAAGTACCAGTAGTTAGATTA Found at i:580657 original size:21 final size:21 Alignment explanation

Indices: 580631--580678 Score: 96 Period size: 21 Copynumber: 2.3 Consensus size: 21 580621 GGCGTGCGGC 580631 CAGTAAACACATATTGTGTTA 1 CAGTAAACACATATTGTGTTA 580652 CAGTAAACACATATTGTGTTA 1 CAGTAAACACATATTGTGTTA 580673 CAGTAA 1 CAGTAA 580679 CTAGCTAGAG Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 27 1.00 ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31 Consensus pattern (21 bp): CAGTAAACACATATTGTGTTA Found at i:583149 original size:26 final size:26 Alignment explanation

Indices: 583120--583173 Score: 108 Period size: 26 Copynumber: 2.1 Consensus size: 26 583110 AAGATTCGTT 583120 AAAAAATACTCTGTAACACCTTGACC 1 AAAAAATACTCTGTAACACCTTGACC 583146 AAAAAATACTCTGTAACACCTTGACC 1 AAAAAATACTCTGTAACACCTTGACC 583172 AA 1 AA 583174 TATTTGAAAA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22 Consensus pattern (26 bp): AAAAAATACTCTGTAACACCTTGACC Found at i:594856 original size:14 final size:14 Alignment explanation

Indices: 594837--594866 Score: 60 Period size: 14 Copynumber: 2.1 Consensus size: 14 594827 CTGCTATCAC 594837 CGACAGCCCATACA 1 CGACAGCCCATACA 594851 CGACAGCCCATACA 1 CGACAGCCCATACA 594865 CG 1 CG 594867 TAAGTTTGTG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.33, C:0.43, G:0.17, T:0.07 Consensus pattern (14 bp): CGACAGCCCATACA Found at i:599913 original size:161 final size:161 Alignment explanation

Indices: 599508--600170 Score: 956 Period size: 161 Copynumber: 4.1 Consensus size: 161 599498 AACATCCACA * * ** ** ** * 599508 AAGAAAATGAACGTAAACTGCAAATAACTGGAATTTCACTATGTCCAAGGGGTATAACTCTGTTG 1 AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACATCCAAGGGCCATAACTCTGTCG * * * 599573 AAAATTGCTCGATCGTACCCAATATCGAACTTGACCTA-AATATTATCATGATAAACATGTACAC 66 AAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGAA-ATTATCATGATAAACCTGTATAC ** 599637 AAAATTTCATTCCAATATGTAGATCCTCTGCG 130 AAAATTTCATTCCAATATGTTCATCCTCTGCG * 599669 AAG-AAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACATCCAAGGGCCATAACTCTGTTG 1 AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACATCCAAGGGCCATAACTCTGTCG * * * * * 599733 AAAATTGCTCGAACGTACCCAGTATCGAACTTGATCTAGAAATTATCATGATTAACCTGTATACA 66 AAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATTATCATGATAAACCTGTATACA * 599798 AAATTTCATTCCAATATGTTGATCCTCTGCG 131 AAATTTCATTCCAATATGTTCATCCTCTGCG * ** 599829 AAGAAAATGAGCGGAAACTGCAAATAACTTGAATTTTTCTAGGTCCAAGGGCCATAACTCTGTCG 1 AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACATCCAAGGGCCATAACTCTGTCG * * * 599894 AAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAAGCTGTATACC 66 AAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATTATCATGATAAACCTGTATACA 599959 AAATTTCATTCCTAA-ATGTTCATCCTCTGCG 131 AAATTTCATTCC-AATATGTTCATCCTCTGCG * * * 599990 AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCAACATCCAAGGGCCATAACTCTGTCA 1 AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACATCCAAGGGCCATAACTCTGTCG * * * 600055 AAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAATCTGTATACC 66 AAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATTATCATGATAAACCTGTATACA 600120 AAATTTCA-TCTCAATATGTTCATCCTCTGCG 131 AAATTTCATTC-CAATATGTTCATCCTCTGCG ** 600151 AAGAAAATGAATGGAAACTG 1 AAGAAAATGAGCGGAAACTG 600171 TTAGTGGACC Statistics Matches: 461, Mismatches: 36, Indels: 10 0.91 0.07 0.02 Matches are distributed among these distances: 160 146 0.32 161 313 0.68 162 2 0.00 ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29 Consensus pattern (161 bp): AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACATCCAAGGGCCATAACTCTGTCG AAAATTGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATTATCATGATAAACCTGTATACA AAATTTCATTCCAATATGTTCATCCTCTGCG Found at i:600194 original size:8 final size:8 Alignment explanation

Indices: 600181--600215 Score: 52 Period size: 8 Copynumber: 4.4 Consensus size: 8 600171 TTAGTGGACC 600181 GACCGACA 1 GACCGACA * 600189 GACCGACC 1 GACCGACA * 600197 GACCGACC 1 GACCGACA 600205 GACCGACA 1 GACCGACA 600213 GAC 1 GAC 600216 AGCAGCAAAG Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 8 25 1.00 ACGTcount: A:0.31, C:0.43, G:0.26, T:0.00 Consensus pattern (8 bp): GACCGACA Found at i:600194 original size:12 final size:12 Alignment explanation

Indices: 600177--600215 Score: 69 Period size: 12 Copynumber: 3.2 Consensus size: 12 600167 ACTGTTAGTG 600177 GACCGACCGACA 1 GACCGACCGACA * 600189 GACCGACCGACC 1 GACCGACCGACA 600201 GACCGACCGACA 1 GACCGACCGACA 600213 GAC 1 GAC 600216 AGCAGCAAAG Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 12 25 1.00 ACGTcount: A:0.31, C:0.44, G:0.26, T:0.00 Consensus pattern (12 bp): GACCGACCGACA Found at i:600217 original size:4 final size:4 Alignment explanation

Indices: 600177--600211 Score: 61 Period size: 4 Copynumber: 8.8 Consensus size: 4 600167 ACTGTTAGTG * 600177 GACC GACC GACA GACC GACC GACC GACC GACC GAC 1 GACC GACC GACC GACC GACC GACC GACC GACC GAC 600212 AGACAGCAGC Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 4 29 1.00 ACGTcount: A:0.29, C:0.46, G:0.26, T:0.00 Consensus pattern (4 bp): GACC Found at i:603230 original size:40 final size:40 Alignment explanation

Indices: 603181--603258 Score: 131 Period size: 41 Copynumber: 1.9 Consensus size: 40 603171 CGATTATATA * 603181 TTAAAACTGAACAG-TTTTTAAAAATGAACTACATGTACT 1 TTAAAACTGAACAGTTTTTTAAAAATGAAATACATGTACT 603220 TTAAAGACTGAACAGTTTTTTAAAAATGAAATACATGTA 1 TTAAA-ACTGAACAGTTTTTTAAAAATGAAATACATGTA 603259 ATGGTATGGG Statistics Matches: 36, Mismatches: 1, Indels: 2 0.92 0.03 0.05 Matches are distributed among these distances: 39 5 0.14 40 9 0.25 41 22 0.61 ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33 Consensus pattern (40 bp): TTAAAACTGAACAGTTTTTTAAAAATGAAATACATGTACT Found at i:612663 original size:79 final size:79 Alignment explanation

Indices: 612532--612688 Score: 278 Period size: 79 Copynumber: 2.0 Consensus size: 79 612522 ATGATTTGTG * 612532 CTTAGGTCCAAACAATGTTTCACTTCCGGTTTGCCCGAGTAACTGCATAGGAGAGTTGATAAAAA 1 CTTAGGTCCAAACAATGTTTCACTTCCGGTTTGCCCGAGTAACTGCATAGGAGAGCTGATAAAAA 612597 TCAACTCCCAAAAC 66 TCAACTCCCAAAAC * * * 612611 CTTAGGTCCAAACACTGTTTCACTTCCGGTTTGCCCGAGTAACTGCATAGGAGAGCTGTTTAAAA 1 CTTAGGTCCAAACAATGTTTCACTTCCGGTTTGCCCGAGTAACTGCATAGGAGAGCTGATAAAAA 612676 TCAACTCCCAAAA 66 TCAACTCCCAAAA 612689 ACCAATTGAA Statistics Matches: 74, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 79 74 1.00 ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26 Consensus pattern (79 bp): CTTAGGTCCAAACAATGTTTCACTTCCGGTTTGCCCGAGTAACTGCATAGGAGAGCTGATAAAAA TCAACTCCCAAAAC Found at i:618310 original size:49 final size:50 Alignment explanation

Indices: 618216--618312 Score: 133 Period size: 49 Copynumber: 2.0 Consensus size: 50 618206 AGCACTGTGG ** * * * 618216 CAACACACTTTGAAAAACTTTTTCAAATTGCTTTAACTTTGGGACCAAAT 1 CAACACACTTTGAAAAACAATTTCAAAGTGCGTTAAATTTGGGACCAAAT * 618266 CAACACACTTTGAAAAA-AATTTCATAGTGCGTTAAATTTGGGACCAA 1 CAACACACTTTGAAAAACAATTTCAAAGTGCGTTAAATTTGGGACCAA 618313 GTTATAACCC Statistics Matches: 41, Mismatches: 6, Indels: 1 0.85 0.12 0.02 Matches are distributed among these distances: 49 24 0.59 50 17 0.41 ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31 Consensus pattern (50 bp): CAACACACTTTGAAAAACAATTTCAAAGTGCGTTAAATTTGGGACCAAAT Found at i:628882 original size:4 final size:4 Alignment explanation

Indices: 628867--628921 Score: 92 Period size: 4 Copynumber: 13.8 Consensus size: 4 628857 TTTTGTTATA * * 628867 AAAT ATAT AAAT AAAT AAAT AAAT AGAT AAAT AAAT AAAT AAAT AAAT 1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT 628915 AAAT AAA 1 AAAT AAA 628922 CCATGAAGTA Statistics Matches: 47, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 4 47 1.00 ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25 Consensus pattern (4 bp): AAAT Found at i:630393 original size:19 final size:19 Alignment explanation

Indices: 630366--630405 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 630356 TGTATTGATA * * 630366 TATTGAATGCTTGTGTGTT 1 TATTCAATGATTGTGTGTT 630385 TATTCAATGATTGTGTGTT 1 TATTCAATGATTGTGTGTT 630404 TA 1 TA 630406 AGTTTTACTT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.20, C:0.05, G:0.23, T:0.53 Consensus pattern (19 bp): TATTCAATGATTGTGTGTT Found at i:636245 original size:261 final size:260 Alignment explanation

Indices: 635781--636301 Score: 1024 Period size: 261 Copynumber: 2.0 Consensus size: 260 635771 TAACATCCAC 635781 ATTGTCTGATAGTCCTCATGGTTTCATAAACAGATCAAGAAATTGTGTGAGAATCTGCCATCCTG 1 ATTGTCTGATAGTCCTCATGGTTTCATAAACAGATCAAGAAATTGTGTGAGAATCTGCCATCCTG 635846 CTGCATACAGAGGATTGTTGACTGATTTTTACAAAATCTTCACTCATTTTAGACCATGAAGGACG 66 CTGCATACAGAGGATTGTTGACTGATTTTTACAAAATCTTCACTCATTTTAGACCATGAAGGACG 635911 TGCAGTTTTATCGCTTACTTAAATGTATATTATTTCAGTCAGAAACGTTTAGTTGCATCGTTTAC 131 TGCAGTTTTATCGCTTACTTAAATGTATATTATTTCAGTCAGAAACGTTTAGTTGCATCGTTTAC 635976 ACGTATATTGTTATAGTCAGATTTAAATAAAAATGTGTGTTTAGTTTTTTAGGTTGAAAAAAAAA 196 ACGTATATTGTTATAGTCAGATTTAAATAAAAATGTGTGTTTAGTTTTTTAGGTTGAAAAAAAAA 636041 NATTGTCTGATAGTCCTCATGGTTTCATAAACAGATCAAGAAATTGTGTGAGAATCTGCCATCCT 1 -ATTGTCTGATAGTCCTCATGGTTTCATAAACAGATCAAGAAATTGTGTGAGAATCTGCCATCCT * 636106 GCTGCATACAGGGGATTGTTGACTGATTTTTACAAAATCTTCACTCATTTTAGACCATGAAGGAC 65 GCTGCATACAGAGGATTGTTGACTGATTTTTACAAAATCTTCACTCATTTTAGACCATGAAGGAC 636171 GTGCAGTTTTATCGCTTACTTAAATGTATATTATTTCAGTCAGAAACGTTTAGTTGCATCGTTTA 130 GTGCAGTTTTATCGCTTACTTAAATGTATATTATTTCAGTCAGAAACGTTTAGTTGCATCGTTTA 636236 CACGTATATTGTTATAGTCAGATTTAAATAAAAATGTGTGTTTAGTTTTTTAGGTTGAAAAAAAA 195 CACGTATATTGTTATAGTCAGATTTAAATAAAAATGTGTGTTTAGTTTTTTAGGTTGAAAAAAAA 636301 A 260 A 636302 TTGAATTTCA Statistics Matches: 259, Mismatches: 1, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 261 259 1.00 ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37 Consensus pattern (260 bp): ATTGTCTGATAGTCCTCATGGTTTCATAAACAGATCAAGAAATTGTGTGAGAATCTGCCATCCTG CTGCATACAGAGGATTGTTGACTGATTTTTACAAAATCTTCACTCATTTTAGACCATGAAGGACG TGCAGTTTTATCGCTTACTTAAATGTATATTATTTCAGTCAGAAACGTTTAGTTGCATCGTTTAC ACGTATATTGTTATAGTCAGATTTAAATAAAAATGTGTGTTTAGTTTTTTAGGTTGAAAAAAAAA Found at i:637141 original size:2 final size:2 Alignment explanation

Indices: 637134--637165 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 637124 TAATTAACCT 637134 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 637166 TTTCAAATAT Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:637739 original size:15 final size:17 Alignment explanation

Indices: 637719--637751 Score: 52 Period size: 15 Copynumber: 2.1 Consensus size: 17 637709 GCCATGATTT 637719 TATATC-TAAA-AATTA 1 TATATCTTAAATAATTA 637734 TATATCTTAAATAATTA 1 TATATCTTAAATAATTA 637751 T 1 T 637752 TGTCCTCTGA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 6 0.38 16 4 0.25 17 6 0.38 ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45 Consensus pattern (17 bp): TATATCTTAAATAATTA Found at i:648942 original size:2 final size:2 Alignment explanation

Indices: 648935--648966 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 648925 CAAACAAGTC 648935 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 648967 GTGTGTGTGT Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:648971 original size:2 final size:2 Alignment explanation

Indices: 648966--649007 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 648956 TATATATATA 648966 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 649008 CGAGAATTAT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50 Consensus pattern (2 bp): TG Found at i:659361 original size:44 final size:43 Alignment explanation

Indices: 659296--659384 Score: 160 Period size: 44 Copynumber: 2.0 Consensus size: 43 659286 GGAAAAGTAG * 659296 CACGCTGGGTTGACCGTAATCGTGCTACGGACACAATTCAACA 1 CACGCTGGGTTGACCGCAATCGTGCTACGGACACAATTCAACA 659339 CNACGCTGGGTTGACCGCAATCGTGCTACGGACACAATTCAACA 1 C-ACGCTGGGTTGACCGCAATCGTGCTACGGACACAATTCAACA 659383 CA 1 CA 659385 AAATTTGATA Statistics Matches: 44, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 43 2 0.05 44 42 0.95 ACGTcount: A:0.28, C:0.29, G:0.22, T:0.19 Consensus pattern (43 bp): CACGCTGGGTTGACCGCAATCGTGCTACGGACACAATTCAACA Found at i:666309 original size:3 final size:3 Alignment explanation

Indices: 666237--666290 Score: 72 Period size: 3 Copynumber: 18.0 Consensus size: 3 666227 AATAAACAAA * * * * 666237 AAT AAT AAT AAT AAT GAT AAT AAT GAT AAT CAT GAT AAT AAT AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 666285 AAT AAT 1 AAT AAT 666291 TTAAATAAAA Statistics Matches: 44, Mismatches: 7, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 3 44 1.00 ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33 Consensus pattern (3 bp): AAT Found at i:686788 original size:30 final size:31 Alignment explanation

Indices: 686729--686788 Score: 86 Period size: 30 Copynumber: 2.0 Consensus size: 31 686719 TGATTACCGT * 686729 TCCATCAAGTTTGGGAATGGATTGATTTTAA 1 TCCATCAAGTTTGGGAATGCATTGATTTTAA * * 686760 TCCATCAAG-TTGGGAATTCATTGGTTTTA 1 TCCATCAAGTTTGGGAATGCATTGATTTTA 686789 TTTAAAATAT Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 30 17 0.65 31 9 0.35 ACGTcount: A:0.27, C:0.12, G:0.22, T:0.40 Consensus pattern (31 bp): TCCATCAAGTTTGGGAATGCATTGATTTTAA Found at i:698897 original size:16 final size:16 Alignment explanation

Indices: 698876--698906 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 698866 AAATTACTTG * 698876 ACTACTTCTAAAAAAA 1 ACTACTACTAAAAAAA 698892 ACTACTACTAAAAAA 1 ACTACTACTAAAAAA 698907 CGATATTAAG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23 Consensus pattern (16 bp): ACTACTACTAAAAAAA Found at i:700975 original size:4 final size:4 Alignment explanation

Indices: 700945--700996 Score: 59 Period size: 4 Copynumber: 13.0 Consensus size: 4 700935 GCTGCTTTGC * * * * * 700945 GTGT GTAT GTAT GTAT GTAT GTAT GTGT GTGT GTGT GTGT GTGT GTGT 1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT 700993 GTGT 1 GTGT 700997 CCATGGTCAG Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 4 46 1.00 ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50 Consensus pattern (4 bp): GTGT Found at i:714194 original size:134 final size:134 Alignment explanation

Indices: 713954--714201 Score: 487 Period size: 134 Copynumber: 1.9 Consensus size: 134 713944 TAAATTATCG 713954 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC 1 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC * 714019 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTATATGCAACAATAA 66 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTATATGCAACAATAA 714084 ATCA 131 ATCA 714088 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC 1 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC 714153 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACC 66 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACC 714202 ATTTTGGCAG Statistics Matches: 113, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 134 113 1.00 ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25 Consensus pattern (134 bp): GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCCTATATGCAACAATAA ATCA Found at i:720445 original size:21 final size:21 Alignment explanation

Indices: 720393--720473 Score: 119 Period size: 21 Copynumber: 3.9 Consensus size: 21 720383 TCATGCTACA * * 720393 TGTATGCTATGGTATGCGATT 1 TGTATGCTATGCTATGAGATT * 720414 T-TAATGATATGCTATGAGATT 1 TGT-ATGCTATGCTATGAGATT 720435 TGTATGCTATGCTATGAGATT 1 TGTATGCTATGCTATGAGATT 720456 TGTATGCTATGCTATGAG 1 TGTATGCTATGCTATGAG 720474 GAATTGAAAT Statistics Matches: 54, Mismatches: 4, Indels: 4 0.87 0.06 0.06 Matches are distributed among these distances: 20 1 0.02 21 52 0.96 22 1 0.02 ACGTcount: A:0.25, C:0.09, G:0.25, T:0.42 Consensus pattern (21 bp): TGTATGCTATGCTATGAGATT Found at i:720697 original size:10 final size:10 Alignment explanation

Indices: 720678--720717 Score: 53 Period size: 10 Copynumber: 4.0 Consensus size: 10 720668 AAATAATGTT 720678 GTATGCTATG 1 GTATGCTATG * * 720688 CTATGGTATG 1 GTATGCTATG 720698 GTATGCTATG 1 GTATGCTATG * 720708 GTATGATATG 1 GTATGCTATG 720718 ACGAATGCGA Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 10 25 1.00 ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40 Consensus pattern (10 bp): GTATGCTATG Found at i:720702 original size:15 final size:15 Alignment explanation

Indices: 720678--720717 Score: 62 Period size: 15 Copynumber: 2.7 Consensus size: 15 720668 AAATAATGTT * 720678 GTATGCTATGCTATG 1 GTATGATATGCTATG * 720693 GTATGGTATGCTATG 1 GTATGATATGCTATG 720708 GTATGATATG 1 GTATGATATG 720718 ACGAATGCGA Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 15 23 1.00 ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40 Consensus pattern (15 bp): GTATGATATGCTATG Found at i:720768 original size:21 final size:21 Alignment explanation

Indices: 720742--720817 Score: 107 Period size: 21 Copynumber: 3.6 Consensus size: 21 720732 ATGAGATTGT * 720742 ATGCTATGGTATGAGATTCCA 1 ATGCTATGCTATGAGATTCCA * 720763 ATGCTATGGTATGAGATTCCA 1 ATGCTATGCTATGAGATTCCA * * * 720784 ATACTATGCTATGATATTTCA 1 ATGCTATGCTATGAGATTCCA 720805 ATGCTATGCTATG 1 ATGCTATGCTATG 720818 CTATGGTGTA Statistics Matches: 50, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 21 50 1.00 ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37 Consensus pattern (21 bp): ATGCTATGCTATGAGATTCCA Found at i:744060 original size:21 final size:21 Alignment explanation

Indices: 744016--744114 Score: 141 Period size: 21 Copynumber: 4.9 Consensus size: 21 744006 AGTTCCAACG * 744016 ACTACCACTACGACA--A-CG 1 ACTACCACTACGACACCACCA 744034 ACTACCACTACGACACCACCA 1 ACTACCACTACGACACCACCA 744055 ACTACCACTACGACACCACCA 1 ACTACCACTACGACACCACCA * * * 744076 ACTACCACCACGACACCAACT 1 ACTACCACTACGACACCACCA 744097 ACTACCACTACGACACCA 1 ACTACCACTACGACACCA 744115 ACTAAACCTC Statistics Matches: 73, Mismatches: 5, Indels: 3 0.90 0.06 0.04 Matches are distributed among these distances: 18 15 0.21 20 1 0.01 21 57 0.78 ACGTcount: A:0.38, C:0.45, G:0.06, T:0.10 Consensus pattern (21 bp): ACTACCACTACGACACCACCA Found at i:750707 original size:1 final size:1 Alignment explanation

Indices: 750703--750825 Score: 129 Period size: 1 Copynumber: 123.0 Consensus size: 1 750693 AAAAAAATGC ** ** ** 750703 AAAAAAAAAACCAAAAAAAAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * * * *** * 750768 AAAAAAAAAAAAAATAAATAAAATAAAAATGCAAAAAAAAAAATAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 750826 TAATGCAATC Statistics Matches: 103, Mismatches: 19, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 1 103 1.00 ACGTcount: A:0.89, C:0.05, G:0.02, T:0.04 Consensus pattern (1 bp): A Found at i:750743 original size:36 final size:35 Alignment explanation

Indices: 750703--750825 Score: 165 Period size: 36 Copynumber: 3.5 Consensus size: 35 750693 AAAAAAATGC ** * 750703 AAAAAAAAAACCAAAAAAAAAAACCAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAGC-AAAAAAAAAA 750739 AAAAAAAAAAAAAAAAAAAAAAAGCAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAGCAAAAAAAAAA * * * 750774 AAAAAAAATAAATAAAATAAAAATGCAAAAAAAAAA 1 AAAAAAAA-AAAAAAAAAAAAAAAGCAAAAAAAAAA * 750810 ATAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAA 750826 TAATGCAATC Statistics Matches: 78, Mismatches: 8, Indels: 3 0.88 0.09 0.03 Matches are distributed among these distances: 35 25 0.32 36 53 0.68 ACGTcount: A:0.89, C:0.05, G:0.02, T:0.04 Consensus pattern (35 bp): AAAAAAAAAAAAAAAAAAAAAAAGCAAAAAAAAAA Found at i:752122 original size:11 final size:11 Alignment explanation

Indices: 752106--752185 Score: 87 Period size: 11 Copynumber: 7.6 Consensus size: 11 752096 TTATTATTTT 752106 TTTTTTTTGCA 1 TTTTTTTTGCA 752117 TTTTTTTTGCA 1 TTTTTTTTGCA 752128 TTTTTTTTGCA 1 TTTTTTTTGCA * ** 752139 TTTTTATTGTT 1 TTTTTTTTGCA ** 752150 TTTTTTTTTTA 1 TTTTTTTTGCA 752161 -TTTTTTT--- 1 TTTTTTTTGCA 752168 TTTTTTTTGCA 1 TTTTTTTTGCA 752179 TTTTTTT 1 TTTTTTT 752186 GTTAAGTTTA Statistics Matches: 59, Mismatches: 6, Indels: 8 0.81 0.08 0.11 Matches are distributed among these distances: 8 7 0.12 10 7 0.12 11 45 0.76 ACGTcount: A:0.07, C:0.05, G:0.06, T:0.81 Consensus pattern (11 bp): TTTTTTTTGCA Found at i:752134 original size:22 final size:20 Alignment explanation

Indices: 752102--752185 Score: 91 Period size: 20 Copynumber: 4.2 Consensus size: 20 752092 ATTATTATTA 752102 TTTT-TTTTTTTTGCATTTT 1 TTTTGTTTTTTTTGCATTTT 752121 TTTTGCATTTTTTTTGCATTTT 1 TTTTG--TTTTTTTTGCATTTT * ** 752143 TATTGTTTTTTTT-TTTTATT 1 TTTTGTTTTTTTTGCATT-TT * 752163 TTTTTTTTTTTTTGCATTTT 1 TTTTGTTTTTTTTGCATTTT 752183 TTT 1 TTT 752186 GTTAAGTTTA Statistics Matches: 53, Mismatches: 7, Indels: 9 0.77 0.10 0.13 Matches are distributed among these distances: 19 6 0.11 20 26 0.49 21 2 0.04 22 19 0.36 ACGTcount: A:0.07, C:0.05, G:0.06, T:0.82 Consensus pattern (20 bp): TTTTGTTTTTTTTGCATTTT Found at i:752166 original size:15 final size:16 Alignment explanation

Indices: 752139--752174 Score: 65 Period size: 15 Copynumber: 2.3 Consensus size: 16 752129 TTTTTTTGCA 752139 TTTTTATTGTTTTTTT 1 TTTTTATTGTTTTTTT 752155 TTTTTATT-TTTTTTT 1 TTTTTATTGTTTTTTT 752170 TTTTT 1 TTTTT 752175 TGCATTTTTT Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 15 12 0.60 16 8 0.40 ACGTcount: A:0.06, C:0.00, G:0.03, T:0.92 Consensus pattern (16 bp): TTTTTATTGTTTTTTT Found at i:753692 original size:21 final size:21 Alignment explanation

Indices: 753654--753694 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 753644 CCAAGACGCT * 753654 ACTTATTCATGTCGACATGCA 1 ACTTATTCATGTCAACATGCA * * 753675 ACTTATTTATGTTAACATGC 1 ACTTATTCATGTCAACATGC 753695 GAGATAAATA Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39 Consensus pattern (21 bp): ACTTATTCATGTCAACATGCA Found at i:753839 original size:63 final size:63 Alignment explanation

Indices: 753742--753872 Score: 163 Period size: 63 Copynumber: 2.1 Consensus size: 63 753732 TGTCAATATC * * * * * * 753742 CAACTTGTTTATGTTCACATGCAAGATAAATATGTTGACATGCAACATATTTATGTTGACATG 1 CAACTTATTTATATTAACATGCAACATAAATATGTCGACATGCAACATAATTATGTTGACATG ** * * * 753805 CAACTTATTTATATTAACATGCAACATATCTATGTCGACATGCAACTTAATTGTGTTTACATG 1 CAACTTATTTATATTAACATGCAACATAAATATGTCGACATGCAACATAATTATGTTGACATG 753868 CAACT 1 CAACT 753873 GAATTACAAC Statistics Matches: 57, Mismatches: 11, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 63 57 1.00 ACGTcount: A:0.34, C:0.17, G:0.13, T:0.37 Consensus pattern (63 bp): CAACTTATTTATATTAACATGCAACATAAATATGTCGACATGCAACATAATTATGTTGACATG Found at i:753851 original size:42 final size:42 Alignment explanation

Indices: 753779--753871 Score: 132 Period size: 42 Copynumber: 2.2 Consensus size: 42 753769 AAATATGTTG * * * 753779 ACATGCAACATATTTATGTTGACATGCAACTTATTTATATTA 1 ACATGCAACATATCTATGTCGACATGCAACTTAATTATATTA * * * 753821 ACATGCAACATATCTATGTCGACATGCAACTTAATTGTGTTT 1 ACATGCAACATATCTATGTCGACATGCAACTTAATTATATTA 753863 ACATGCAAC 1 ACATGCAAC 753872 TGAATTACAA Statistics Matches: 45, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 42 45 1.00 ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35 Consensus pattern (42 bp): ACATGCAACATATCTATGTCGACATGCAACTTAATTATATTA Found at i:753872 original size:21 final size:21 Alignment explanation

Indices: 753750--753878 Score: 116 Period size: 21 Copynumber: 6.1 Consensus size: 21 753740 TCCAACTTGT * ** 753750 TTATGTTCACATGCAAGATAA 1 TTATGTTGACATGCAACTTAA * * * 753771 ATATGTTGACATGCAACATAT 1 TTATGTTGACATGCAACTTAA * 753792 TTATGTTGACATGCAACTTAT 1 TTATGTTGACATGCAACTTAA * * * 753813 TTATATTAACATGCAACAT-A 1 TTATGTTGACATGCAACTTAA * 753833 TCTATGTCGACATGCAACTTAA 1 T-TATGTTGACATGCAACTTAA * * * 753855 TTGTGTTTACATGCAACTGAA 1 TTATGTTGACATGCAACTTAA 753876 TTA 1 TTA 753879 CAACGGTATA Statistics Matches: 87, Mismatches: 19, Indels: 4 0.79 0.17 0.04 Matches are distributed among these distances: 20 1 0.01 21 84 0.97 22 2 0.02 ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36 Consensus pattern (21 bp): TTATGTTGACATGCAACTTAA Found at i:755982 original size:16 final size:16 Alignment explanation

Indices: 755963--756014 Score: 86 Period size: 16 Copynumber: 3.2 Consensus size: 16 755953 GCGTCCGTCA 755963 GTCCGTCCGTCTGTCC 1 GTCCGTCCGTCTGTCC 755979 GTCCGTCCGTCTGTCC 1 GTCCGTCCGTCTGTCC * * 755995 GTCCGTCCGTATGTCT 1 GTCCGTCCGTCTGTCC 756011 GTCC 1 GTCC 756015 CACTTCAGTT Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 34 1.00 ACGTcount: A:0.02, C:0.40, G:0.25, T:0.33 Consensus pattern (16 bp): GTCCGTCCGTCTGTCC Found at i:756013 original size:4 final size:4 Alignment explanation

Indices: 755954--756004 Score: 75 Period size: 4 Copynumber: 12.8 Consensus size: 4 755944 CTTTCCTCTG * * * 755954 CGTC CGTC AGTC CGTC CGTC TGTC CGTC CGTC CGTC TGTC CGTC CGTC 1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC 756002 CGT 1 CGT 756005 ATGTCTGTCC Statistics Matches: 41, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 4 41 1.00 ACGTcount: A:0.02, C:0.43, G:0.25, T:0.29 Consensus pattern (4 bp): CGTC Found at i:758931 original size:22 final size:21 Alignment explanation

Indices: 758869--758931 Score: 58 Period size: 22 Copynumber: 2.9 Consensus size: 21 758859 TAATTATTAT * 758869 ATTCATTCATAAATTTAAAACA 1 ATTCATTC-TAAATTTTAAACA 758891 ATTC-TT-TAAATTACCTTAAACA 1 ATTCATTCTAAATT---TTAAACA 758913 ATTCATTCTAGAATTTTAA 1 ATTCATTCTA-AATTTTAA 758932 TTTGGGCATT Statistics Matches: 34, Mismatches: 1, Indels: 12 0.72 0.02 0.26 Matches are distributed among these distances: 19 6 0.18 21 2 0.06 22 18 0.53 23 2 0.06 24 2 0.06 25 4 0.12 ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41 Consensus pattern (21 bp): ATTCATTCTAAATTTTAAACA Found at i:761105 original size:42 final size:42 Alignment explanation

Indices: 761058--761140 Score: 112 Period size: 42 Copynumber: 2.0 Consensus size: 42 761048 CAAATGAACC * * 761058 CCGATAAAACCAAATAGTACTACATTTAAACCAGATGATACT 1 CCGATAAAACCAAATAGTACTACAGTAAAACCAGATGATACT * * * * 761100 CCGATAAAATCAAATGGTACTCCAGTAAAACCCGATGATAC 1 CCGATAAAACCAAATAGTACTACAGTAAAACCAGATGATAC 761141 CCCTTAAACC Statistics Matches: 35, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 42 35 1.00 ACGTcount: A:0.43, C:0.23, G:0.12, T:0.22 Consensus pattern (42 bp): CCGATAAAACCAAATAGTACTACAGTAAAACCAGATGATACT Found at i:768980 original size:2 final size:2 Alignment explanation

Indices: 768973--768999 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 768963 ACAGTCATGA 768973 AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT A 769000 NNNNNNNNNN Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:775022 original size:21 final size:21 Alignment explanation

Indices: 774998--775461 Score: 287 Period size: 21 Copynumber: 22.2 Consensus size: 21 774988 ACCATCATCA * * 774998 ACACCACGAACTGCAACAACG 1 ACACCACGAACTACCACAACG * ** 775019 ACACCGCGAACTACCAGGACG 1 ACACCACGAACTACCACAACG * 775040 ACACCACCAACTACCACAACG 1 ACACCACGAACTACCACAACG ** * * 775061 ACACTGCCAACTACCACTACG 1 ACACCACGAACTACCACAACG * * 775082 ACACCACCAACTACCACTACG 1 ACACCACGAACTACCACAACG * 775103 ACACCTAC-AACTACCACTACG 1 ACACC-ACGAACTACCACAACG * * * 775124 ACACCGCCAACTACCACTACG 1 ACACCACGAACTACCACAACG * ** 775145 ACCCCTAC-AACTACCACTTCG 1 ACACC-ACGAACTACCACAACG * ** 775166 ACACCGCGAACTACCAGGACG 1 ACACCACGAACTACCACAACG * * * * 775187 ACCCCCCCAACTCCCACAACG 1 ACACCACGAACTACCACAACG ** * * 775208 ACACTGCCAACTACCACTACG 1 ACACCACGAACTACCACAACG * 775229 ACACCTAC-AACTACCACTACG 1 ACACC-ACGAACTACCACAACG * ** 775250 ACACCGCGAACTACCAGGACG 1 ACACCACGAACTACCACAACG * * * 775271 ACACCGCCAACTACCACTACG 1 ACACCACGAACTACCACAACG * * * 775292 ACACCGCTAACTACCACTACG 1 ACACCACGAACTACCACAACG * * * * * 775313 GCACC-TGCAACAACCACTACT 1 ACACCACG-AACTACCACAACG * 775334 ACA-C-CG-ACTACCACTACG 1 ACACCACGAACTACCACAACG * 775352 AAACCAAC-AACTACCACAACG 1 ACACC-ACGAACTACCACAACG * * * 775373 ACACCACCAACAACCACTACG 1 ACACCACGAACTACCACAACG * * * 775394 ACACCACCAACAACCACTACG 1 ACACCACGAACTACCACAACG * * 775415 ACACCACCAACTACCACTACG 1 ACACCACGAACTACCACAACG * * * * * 775436 ATATCACCAAGTACCACTACG 1 ACACCACGAACTACCACAACG 775457 ACACC 1 ACACC 775462 GGCAACTTCA Statistics Matches: 368, Mismatches: 63, Indels: 24 0.81 0.14 0.05 Matches are distributed among these distances: 18 12 0.03 19 1 0.00 20 7 0.02 21 344 0.93 22 4 0.01 ACGTcount: A:0.37, C:0.44, G:0.09, T:0.10 Consensus pattern (21 bp): ACACCACGAACTACCACAACG Found at i:775097 original size:63 final size:63 Alignment explanation

Indices: 775016--775549 Score: 472 Period size: 63 Copynumber: 8.5 Consensus size: 63 775006 AACTGCAACA * * ** * * 775016 ACGACACCGCGAACTACCAGGACGACACCACCAACTACCACAACGACACTGCCAACTACCACT 1 ACGACACCACCAACTACCACTACGACACCACCAACTACCACTACGACACCGCCAACTACCACT 775079 ACGACACCACCAACTACCACTACGACACCTA-CAACTACCACTACGACACCGCCAACTACCACT 1 ACGACACCACCAACTACCACTACGACACC-ACCAACTACCACTACGACACCGCCAACTACCACT * * * * ** * * * * 775142 ACGACCCCTA-CAACTACCACTTCGACACCGCGAACTACCAGGACGACCCCCCCAACTCCCACA 1 ACGACACC-ACCAACTACCACTACGACACCACCAACTACCACTACGACACCGCCAACTACCACT ** * ** 775205 ACGACACTGCCAACTACCACTACGACACCTA-CAACTACCACTACGACACCGCGAACTACCAGG 1 ACGACACCACCAACTACCACTACGACACC-ACCAACTACCACTACGACACCGCCAACTACCACT * * * * * 775268 ACGACACCGCCAACTACCACTACGACACCGCTAACTACCACTACGGCACCTG-CAACAACCACT 1 ACGACACCACCAACTACCACTACGACACCACCAACTACCACTACGACACC-GCCAACTACCACT * * * * * * * 775331 AC--TA-CACCGACTACCACTACGAAACCAACAACTACCACAACGACACCACCAACAACCACT 1 ACGACACCACCAACTACCACTACGACACCACCAACTACCACTACGACACCGCCAACTACCACT * * * * * 775391 ACGACACCACCAACAACCACTACGACACCACCAACTACCACTACGATATCACCAAGTACCACT 1 ACGACACCACCAACTACCACTACGACACCACCAACTACCACTACGACACCGCCAACTACCACT ** * * * * * * * * * * * * 775454 ACGACACCGGCAACTTCAATTACGACACTACTAACCATCA-AACCAACACCACAAACTATCACT 1 ACGACACCACCAACTACCACTACGACACCACCAACTACCACTA-CGACACCGCCAACTACCACT * * * 775517 ACGACACAACTAACTACTACTACGACACCACCA 1 ACGACACCACCAACTACCACTACGACACCACCA 775550 CCAACCACCA Statistics Matches: 375, Mismatches: 84, Indels: 24 0.78 0.17 0.05 Matches are distributed among these distances: 60 48 0.13 61 1 0.00 62 2 0.01 63 321 0.86 64 3 0.01 ACGTcount: A:0.37, C:0.43, G:0.09, T:0.11 Consensus pattern (63 bp): ACGACACCACCAACTACCACTACGACACCACCAACTACCACTACGACACCGCCAACTACCACT Found at i:775523 original size:21 final size:21 Alignment explanation

Indices: 775499--775549 Score: 57 Period size: 21 Copynumber: 2.4 Consensus size: 21 775489 CATCAAACCA * * 775499 ACACCACAAACTATCACTACG 1 ACACCACCAACTACCACTACG * * * 775520 ACACAACTAACTACTACTACG 1 ACACCACCAACTACCACTACG 775541 ACACCACCA 1 ACACCACCA 775550 CCAACCACCA Statistics Matches: 24, Mismatches: 6, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.43, C:0.39, G:0.04, T:0.14 Consensus pattern (21 bp): ACACCACCAACTACCACTACG Found at i:775545 original size:42 final size:42 Alignment explanation

Indices: 775027--775549 Score: 434 Period size: 42 Copynumber: 12.5 Consensus size: 42 775017 CGACACCGCG ** * * 775027 AACTACCAGGACGACACCACCAACTACCACAACGACACTGCC 1 AACTACCACTACGACACCACCAACTACCACTACGACACTACC 775069 AACTACCACTACGACACCACCAACTACCACTACGACACCTA-C 1 AACTACCACTACGACACCACCAACTACCACTACGACA-CTACC * * 775111 AACTACCACTACGACACCGCCAACTACCACTACGACCCCTA-C 1 AACTACCACTACGACACCACCAACTACCACTACGA-CACTACC * * * ** * ** 775153 AACTACCACTTCGACACCGCGAACTACCAGGACGACCCCCCC 1 AACTACCACTACGACACCACCAACTACCACTACGACACTACC * * ** 775195 AACTCCCACAACGACACTGCCAACTACCACTACGACACCTA-C 1 AACTACCACTACGACACCACCAACTACCACTACGACA-CTACC * * ** ** 775237 AACTACCACTACGACACCGCGAACTACCAGGACGACACCGCC 1 AACTACCACTACGACACCACCAACTACCACTACGACACTACC * * * * 775279 AACTACCACTACGACACCGCTAACTACCACTACGGCACCT-GC 1 AACTACCACTACGACACCACCAACTACCACTACGACA-CTACC * * * * * * 775321 AACAACCACTAC--TA-CACCGACTACCACTACGAAACCAAC 1 AACTACCACTACGACACCACCAACTACCACTACGACACTACC * * * 775360 AACTACCACAACGACACCACCAACAACCACTACGACACCACC 1 AACTACCACTACGACACCACCAACTACCACTACGACACTACC * * 775402 AACAACCACTACGACACCACCAACTACCACTACGATA-TCACC 1 AACTACCACTACGACACCACCAACTACCACTACGACACT-ACC * ** * * * * 775444 AAGTACCACTACGACACCGGCAACTTCAATTACGACACTACT 1 AACTACCACTACGACACCACCAACTACCACTACGACACTACC * * * * * * * * 775486 AACCATCA-AACCAACACCACAAACTATCACTACGACACAACT 1 AACTACCACTA-CGACACCACCAACTACCACTACGACACTACC * 775528 AACTACTACTACGACACCACCA 1 AACTACCACTACGACACCACCA 775550 CCAACCACCA Statistics Matches: 382, Mismatches: 85, Indels: 28 0.77 0.17 0.06 Matches are distributed among these distances: 38 1 0.00 39 26 0.07 40 1 0.00 41 6 0.02 42 341 0.89 43 7 0.02 ACGTcount: A:0.37, C:0.43, G:0.08, T:0.11 Consensus pattern (42 bp): AACTACCACTACGACACCACCAACTACCACTACGACACTACC Found at i:776621 original size:11 final size:11 Alignment explanation

Indices: 776605--776632 Score: 56 Period size: 11 Copynumber: 2.5 Consensus size: 11 776595 TATGGTTCAT 776605 GTACATGTAAA 1 GTACATGTAAA 776616 GTACATGTAAA 1 GTACATGTAAA 776627 GTACAT 1 GTACAT 776633 TGACAATGTA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 17 1.00 ACGTcount: A:0.43, C:0.11, G:0.18, T:0.29 Consensus pattern (11 bp): GTACATGTAAA Found at i:791691 original size:2 final size:2 Alignment explanation

Indices: 791684--791723 Score: 71 Period size: 2 Copynumber: 20.0 Consensus size: 2 791674 AATTTTTATC * 791684 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 791724 ATTGCACACT Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (2 bp): TA Found at i:794088 original size:1 final size:1 Alignment explanation

Indices: 794082--794136 Score: 101 Period size: 1 Copynumber: 55.0 Consensus size: 1 794072 TGTGTGTGTG * 794082 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 794137 GTCAGCTATT Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 1 52 1.00 ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98 Consensus pattern (1 bp): T Found at i:794148 original size:11 final size:11 Alignment explanation

Indices: 794134--794158 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 794124 TTTTTTTTGT 794134 TTTGTCAGCTA 1 TTTGTCAGCTA 794145 TTTGTCAGCTA 1 TTTGTCAGCTA 794156 TTT 1 TTT 794159 AAACCGCAAC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52 Consensus pattern (11 bp): TTTGTCAGCTA Found at i:805108 original size:99 final size:98 Alignment explanation

Indices: 805005--807122 Score: 2092 Period size: 99 Copynumber: 21.4 Consensus size: 98 804995 GAAACGACCA * * * 805005 CACTGTAGAACTTTTATTAGATAATA-AAGCAGATATTAATTCATGTGACACTAACAGAA-AAAC 1 CACTGTACAACTTTTATTAGATAA-AGGAGCAGATATTAATTCATGTGACACAAACA-AAGAAAC * * * * 805068 TCCTCTACATAAAGCAATTACATGTGGACGTGAAAG 64 TCCTCTACATAAAGCCAGTA-ATGGGGACATGAAAG ** * 805104 CACTGTACGGCTTTTATTAGA-AAGAGGAGCAGATATTAATTCATGTGACACAAAAAAAGAAACT 1 CACTGTACAACTTTTATTAGATAA-AGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACT * * * * 805168 CCCCTTCATAAAGCCAGTAAATTGGGACATGATAG 65 CCTCTACATAAAGCCAGT-AATGGGGACATGAAAG * ** * 805203 CATTGTACGGCTTTTATTAGA-AAGAAGAGCAGATATTAATTCATGTGACACAAACAAAGAAACT 1 CACTGTACAACTTTTATTAGATAA-AGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACT * * * * 805267 CCCCTTCATAAAGCCAGTAAATGGGGACATTATAG 65 CCTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * * * 805302 CACTGTACAATTTTTATTAGATGAAGGTGCAGATATTAATTCATGTGACGCAAACAAAGAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * * 805367 CTCTACATAAAGCAAGTGAA-GAAGGACATAAAAG 66 CTCTACATAAAGCCAGT-AATG-GGGACATGAAAG * * * * * * * 805401 TACCGTGCAACTTTTATTAGAAAAAAGAGCAGACATTGATTCATGTGACACAAACAAAGAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * 805466 CTCTACAAAAAGCCAGTGAA-GGAGGACATAAAAG 66 CTCTACATAAAGCCAGT-AATGG-GGACATGAAAG * * * * * 805500 AACTGTGCAACTTTTATTCA-AAAAAGGAGCAAATATTAATTCATGTGACACAAAAAAAGAAACT 1 CACTGTACAACTTTTATT-AGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACT * ** * * 805564 CCCCTTTATAAAGCCAGTAAGTTGGGACATGATAG 65 CCTCTACATAAAGCCAGTAA-TGGGGACATGAAAG * * * ** * * * 805599 CACTGTACAATTTTTATTAGATGAAGGTGCATCTATTAATTTAAGTGACACAAACAAAGTAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * * 805664 CTCTACATAAGGCCAGTGAATGTGGACATGAATG 66 CTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * 805698 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTTATGTGATACAAACAAAGAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC ** * * ** * ** 805763 CTCTTGATAAAGCAATTAAATATGGACAAGGCAG 66 CTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * * * * * * * * 805797 TACGGTACAACGTTTATTAGATTACGGGGCAGACATTAATTCATGTGACACAAACAAGGAAAATC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * * * * ** 805862 ATCTAAATTATGCCAGTGAAT-GGGACCTTGCTAG 66 CTCTACATAAAGCCAGT-AATGGGGA-CATGAAAG * * * 805896 CACAGTACAA-TTATTATTAGATAAAGGAGCAAATATAAATTCATGTGACACAAACAAAGAAACT 1 CACTGTACAACTT-TTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACT * * ** 805960 CCTCTACATAAAGCCAGTGGACGGGGACATTG-CTG 65 CCTCTACATAAAGCCAGT-AATGGGGACA-TGAAAG * * * * * * 805995 CACTGTACAACTTTTATTAGATAAAGGAGCAGATGTTAATTTATGTGATATAAATAAAAAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * * 806060 CTCTACATAAAGCAAGTAAAGGAGGACATCAAAG 66 CTCTACATAAAGCCAGTAATGG-GGACATGAAAG * * 806094 CACGGTGCAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC 806159 CTCTACATAAAGCCAGTAAATGGGGACATGAAAG 66 CTCTACATAAAGCCAGT-AATGGGGACATGAAAG * 806193 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAATGAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * 806258 CTCTA-ATAAAAGCCAGTAAATGGGGACATGATAG 66 CTCTACAT-AAAGCCAGT-AATGGGGACATGAAAG * ** * 806292 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTGATTCATGTGACGGAAACGGAA-AAACT 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAAC-AAAGAAACT ** ** 806356 CCTCTACATAAAGCCAGTCTTTGGGGACATGTCAG 65 CCTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * * * ** * * * 806391 CACTGTAAAACTCTTATTAGATGAAGGAGCAAATACCAATT-ATGATGATATAAACAATGAAACT 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATG-TGACACAAACAAAGAAACT * * * * ** * 806455 CCTCTTCATGAAGCCATTGAAAGGGGATGTGAAAA 65 CCTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * * ** * * * ** 806490 CACAGTGCAACTTTTGTTAGATAAAGGAGCAGATACCAATT-ATTGTGATATAAACAATGAATTT 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCA-TGTGACACAAACAAAGAAACT * ** * 806554 CCTCTACATAAAGCCAGTGAAAGGGGATGTGAAAA 65 CCTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * * * *** * * 806589 CA-TAGTGCAACTTTTATTAGATAAAGGAGCATATATTAATGCATGCGACTTTAACGGAA-CAAC 1 CACT-GTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAAC-AAAGAAAC * 806652 TCCTCTACATAAAGCCAGTAAATGGGGACATAAAAG 64 TCCTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * *** * 806688 CATTGTGCAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACGTCGAAACAC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * * 806753 CTTTACACAAAGCCAGTGAATGGGGAGATGAAAG 66 CTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * * * * * 806787 CTCTGTACAGCTTTTATTAGATAAAGGAGCGGATGTTAATTCATGTGACACAAACGAAGAAACAC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * * * * 806852 CTTTACATAAAGCCAGTAAAGAAGGAGAGGAAAG 66 CTCTACATAAAGCCAGTAATG-GGGACATGAAAG * * * * 806886 CACTGTACAACTTTTATTAGATAACGGAGCAAATATTGATTCATGTGACGCAAACAAAGAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * * 806951 CTCTACATAAAGCCAGTGGACGGGGACATGAAAG 66 CTCTACATAAAGCCAGT-AATGGGGACATGAAAG * * * 806985 CACTGTACAACTTTTATTAGATGAAGGAGCAGATATTAATTCATATGACACAAATAAAGAAACTC 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC ** 807050 CTCTACATAAAGCCAGTGAGA-AAGGACATGAAAG 66 CTCTACATAAAGCCAGT-A-ATGGGGACATGAAAG * * 807084 CACTGTACAACTTTTATTAAAAAAAGGAGCAGATATTAA 1 CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAA 807123 GGAGGAGGAA Statistics Matches: 1687, Mismatches: 299, Indels: 66 0.82 0.15 0.03 Matches are distributed among these distances: 98 27 0.02 99 1631 0.97 100 29 0.02 ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25 Consensus pattern (98 bp): CACTGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC CTCTACATAAAGCCAGTAATGGGGACATGAAAG Found at i:807257 original size:99 final size:97 Alignment explanation

Indices: 807130--807515 Score: 389 Period size: 99 Copynumber: 3.9 Consensus size: 97 807120 TAAGGAGGAG * * * * * * 807130 GAAAGCACTGTGCAACGTTTATTAGATAAAGGAGGAAATAGTAATTCATGCGACACAAATAAAGA 1 GAAAGCACTGTACAACTTTTATTAGATAAAGGAGCAAATATTAATTCATGTGACACAAACAAAGA 807195 AACTCCTCTACATAAAGTCAATGAAGAAGGACAT 66 AACTCCTCTACATAAAG-CAA-GAAGAAGGACAT * * * * 807229 GAAAGCACTGTGCAACTTTTATAAGATAAGGGAGCAACTATTAATTCATGTGACACAAACAAAGA 1 GAAAGCACTGTACAACTTTTATTAGATAAAGGAGCAAATATTAATTCATGTGACACAAACAAAGA * * * 807294 AACTCCTCTACATAAAGCAAGTATACTGCGA-ACT 66 AACTCCTCTACATAAAGCAAGAAGA-AG-GACA-T * * * * * * 807328 GAGAGCACTTTACAACTTTTATTAGATAAAGGAGCAAATATTAATTTATGTGATATAAACAATGA 1 GAAAGCACTGTACAACTTTTATTAGATAAAGGAGCAAATATTAATTCATGTGACACAAACAAAGA * * * 807393 AACTCCTATACATAAAGCCAAGGAATG-GGGACGT 66 AACTCCTCTACATAAAG-CAA-GAA-GAAGGACAT * * * * 807427 GAAAGCACTGTACATCTATTATTACATGTAGATAAAGAAGCATATATTAATTCATGTGACACCAA 1 GAAAGCACTGTACAAC--TT-TT--AT-TAGATAAAGGAGCAAATATTAATTCATGTGACACAAA * 807492 CAAAGAAACTCCTCTATATAAAGC 60 CAAAGAAACTCCTCTACATAAAGC 807516 CAGTGAATGC Statistics Matches: 236, Mismatches: 38, Indels: 21 0.80 0.13 0.07 Matches are distributed among these distances: 97 3 0.01 98 5 0.02 99 164 0.69 100 4 0.02 101 4 0.02 102 2 0.01 104 3 0.01 105 51 0.22 ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25 Consensus pattern (97 bp): GAAAGCACTGTACAACTTTTATTAGATAAAGGAGCAAATATTAATTCATGTGACACAAACAAAGA AACTCCTCTACATAAAGCAAGAAGAAGGACAT Found at i:807263 original size:150 final size:150 Alignment explanation

Indices: 806980--807272 Score: 421 Period size: 150 Copynumber: 2.0 Consensus size: 150 806970 ACGGGGACAT * * * * * 806980 GAAAGCACTGTACAACTTTTATTAGATGAAGGAGCAGATATTAATTCATATGACACAAATAAAGA 1 GAAAGCACTGTACAACGTTTATTAGATAAAGGAGCAAATAGTAATTCATACGACACAAATAAAGA * 807045 AACTCCTCTACATAAAGCCAGTGAGAAAGGACATGAAAGCACTGTACAACTTTTATTAAAAAAAG 66 AACTCCTCTACATAAAGCCAATGAGAAAGGACATGAAAGCACTGTACAACTTTTATTAAAAAAAG 807110 GAGCAGA-TATTAAGGAGGAG 131 GAGCA-ACTATTAAGGAGGAG * * * 807130 GAAAGCACTGTGCAACGTTTATTAGATAAAGGAGGAAATAGTAATTCATGCGACACAAATAAAGA 1 GAAAGCACTGTACAACGTTTATTAGATAAAGGAGCAAATAGTAATTCATACGACACAAATAAAGA * * * 807195 AACTCCTCTACATAAAGTCAATGA-AGAAGGACATGAAAGCACTGTGCAACTTTTA-TAAGATAA 66 AACTCCTCTACATAAAGCCAATGAGA-AAGGACATGAAAGCACTGTACAACTTTTATTAA-AAAA * 807258 GGGAGCAACTATTAA 129 AGGAGCAACTATTAA 807273 TTCATGTGAC Statistics Matches: 127, Mismatches: 13, Indels: 6 0.87 0.09 0.04 Matches are distributed among these distances: 149 5 0.04 150 122 0.96 ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23 Consensus pattern (150 bp): GAAAGCACTGTACAACGTTTATTAGATAAAGGAGCAAATAGTAATTCATACGACACAAATAAAGA AACTCCTCTACATAAAGCCAATGAGAAAGGACATGAAAGCACTGTACAACTTTTATTAAAAAAAG GAGCAACTATTAAGGAGGAG Found at i:807344 original size:249 final size:248 Alignment explanation

Indices: 806873--807371 Score: 675 Period size: 249 Copynumber: 2.0 Consensus size: 248 806863 GCCAGTAAAG * * * * * * 806873 AAGGAGAGGAAAGCACTGTACAACTTTTATTAGATAACGGAGCAAATATTGATTCATGTGACGCA 1 AAGGAGAGGAAAGCACTGTACAACGTTTATTAGATAAAGGAGCAAATAGTAATTCATGCGACACA * * * * 806938 AACAAAGAAACTCCTCTACATAAAGCCAGTGGACGGGGACATGAAAGCACTGTACAACTTTTATT 66 AACAAAGAAACTCCTCTACATAAAGCCAATGGAAGAGGACATGAAAGCACTGTACAACTTTTATA * * 807003 AGATGAAGGAGCAGATATTAATTCATATGACACAAATAAAGAAACTCCTCTACATAAAGCCAGTG 131 AGATGAAGGAGCAGATATTAATTCATATGACACAAACAAAGAAACTCCTCTACATAAAGCAAGTG * 807068 AGAAAGGACATGAAAGCACTGTACAACTTTTATTAAAAAAAGGAGCAGATATT 196 AGAAAGGACATGAAAGCACTGTACAACTTTTATTAAAAAAAGGAGCAAATATT * * 807121 AAGGAGGAGGAAAGCACTGTGCAACGTTTATTAGATAAAGGAGGAAATAGTAATTCATGCGACAC 1 AAGGA-GAGGAAAGCACTGTACAACGTTTATTAGATAAAGGAGCAAATAGTAATTCATGCGACAC * * * 807186 AAATAAAGAAACTCCTCTACATAAAGTCAAT-GAAGAAGGACATGAAAGCACTGTGCAACTTTTA 65 AAACAAAGAAACTCCTCTACATAAAGCCAATGGAAG-AGGACATGAAAGCACTGTACAACTTTTA * 807250 TAAGAT-AAGGGAGCA-ACTATTAATTCATGTGACACAAACAAAGAAACTCCTCTACATAAAGCA 129 TAAGATGAA-GGAGCAGA-TATTAATTCATATGACACAAACAAAGAAACTCCTCTACATAAAGCA * ** * * * * 807313 AGT-ATACTGCGA-ACTGAGAGCACTTTACAACTTTTATTAGATAAAGGAGCAAATATT 192 AGTGAGAAAG-GACA-TGAAAGCACTGTACAACTTTTATTAAAAAAAGGAGCAAATATT 807370 AA 1 AA 807372 TTTATGTGAT Statistics Matches: 219, Mismatches: 26, Indels: 11 0.86 0.10 0.04 Matches are distributed among these distances: 248 15 0.07 249 204 0.93 ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23 Consensus pattern (248 bp): AAGGAGAGGAAAGCACTGTACAACGTTTATTAGATAAAGGAGCAAATAGTAATTCATGCGACACA AACAAAGAAACTCCTCTACATAAAGCCAATGGAAGAGGACATGAAAGCACTGTACAACTTTTATA AGATGAAGGAGCAGATATTAATTCATATGACACAAACAAAGAAACTCCTCTACATAAAGCAAGTG AGAAAGGACATGAAAGCACTGTACAACTTTTATTAAAAAAAGGAGCAAATATT Found at i:807436 original size:348 final size:348 Alignment explanation

Indices: 806799--807450 Score: 882 Period size: 348 Copynumber: 1.9 Consensus size: 348 806789 CTGTACAGCT * * * * 806799 TTTATTAGATAAAGGAGCGGATGTTAATTCATGTGACACAAACGAAGAAACACCTTTACATAAAG 1 TTTATTAGATAAAGGAGCGAATGTTAATTCATGCGACACAAACAAAGAAACACCTCTACATAAAG * * * * 806864 CCAGTAAAGAAGGAGAGGAAAGCACTGTACAACTTTTATTAGATAACGGAGCAAATATTGATTCA 66 CCAATAAAGAAGGACAGGAAAGCACTGTACAACTTTTATAAGATAACGGAGCAAATATTAATTCA * * * * * 806929 TGTGACGCAAACAAAGAAACTCCTCTACATAAAGCCAGTGGACGGGGACATGAAAGCACTGTACA 131 TGTGACACAAACAAAGAAACTCCTCTACATAAAGCAAGTAGACGCGAACATGAAAGCACTGTACA * * * * 806994 ACTTTTATTAGATGAAGGAGCAGATATTAATTCATATGACACAAATAAAGAAACTCCTCTACATA 196 ACTTTTATTAGATAAAGGAGCAAATATTAATTCATATGACACAAACAAAGAAACTCCTATACATA * 807059 AAGCCAGTGAGAAAGGACATGAAAGCACTGTACAACTTTTATTAAAAAAAGGAGCAGATATTAAG 261 AAGCCAGTGAGAAAGGACATGAAAGCACTGTACAACTATTATTAAAAAAAGGAGCAGATATTAAG 807124 GAGGAGGAAAGCACTGTGCAACG 326 GAGGAGGAAAGCACTGTGCAACG * * 807147 TTTATTAGATAAAGGAG-GAAATAG-TAATTCATGCGACACAAATAAAGAAACTCCTCTACATAA 1 TTTATTAGATAAAGGAGCG-AAT-GTTAATTCATGCGACACAAACAAAGAAACACCTCTACATAA * * * * * * 807210 AGTCAATGAAGAAGGACATGAAAGCACTGTGCAACTTTTATAAGATAAGGGAGCAACTATTAATT 64 AGCCAATAAAGAAGGACAGGAAAGCACTGTACAACTTTTATAAGATAACGGAGCAAATATTAATT * * * 807275 CATGTGACACAAACAAAGAAACTCCTCTACATAAAGCAAGTATACTGCGAAC-TGAGAGCACTTT 129 CATGTGACACAAACAAAGAAACTCCTCTACATAAAGCAAGTAGAC-GCGAACATGAAAGCACTGT * * * * * 807339 ACAACTTTTATTAGATAAAGGAGCAAATATTAATTTATGTGATATAAACAATGAAACTCCTATAC 193 ACAACTTTTATTAGATAAAGGAGCAAATATTAATTCATATGACACAAACAAAGAAACTCCTATAC ** * * 807404 ATAAAGCCAAG-GA-ATGGGGACGTGAAAGCACTGTACATCTATTATTA 258 ATAAAGCC-AGTGAGA-AAGGACATGAAAGCACTGTACAACTATTATTA 807451 CATGTAGATA Statistics Matches: 261, Mismatches: 38, Indels: 10 0.84 0.12 0.03 Matches are distributed among these distances: 347 2 0.01 348 252 0.97 349 7 0.03 ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23 Consensus pattern (348 bp): TTTATTAGATAAAGGAGCGAATGTTAATTCATGCGACACAAACAAAGAAACACCTCTACATAAAG CCAATAAAGAAGGACAGGAAAGCACTGTACAACTTTTATAAGATAACGGAGCAAATATTAATTCA TGTGACACAAACAAAGAAACTCCTCTACATAAAGCAAGTAGACGCGAACATGAAAGCACTGTACA ACTTTTATTAGATAAAGGAGCAAATATTAATTCATATGACACAAACAAAGAAACTCCTATACATA AAGCCAGTGAGAAAGGACATGAAAGCACTGTACAACTATTATTAAAAAAAGGAGCAGATATTAAG GAGGAGGAAAGCACTGTGCAACG Found at i:807538 original size:105 final size:98 Alignment explanation

Indices: 807132--807610 Score: 367 Period size: 99 Copynumber: 4.8 Consensus size: 98 807122 AGGAGGAGGA * * * * * * * 807132 AAGCACTGTGCAACGTTTATTAGATAAAGGAGGAAATAGTAATTCATGCGACACAAATAAAGAAA 1 AAGCACTGTACAACTTTTATTAGATAAAGAAGCAAATATTAATTCATGTGACACAAACAAAGAAA * * * * * 807197 CTCCTCTACATAAAGTCAATGAA-GAAGGACATGA 66 CTCCTCTACATAAAGCCAGTGAATG--CGACCTGG * * * * * 807231 AAGCACTGTGCAACTTTTATAAGATAAGGGAGCAACTATTAATTCATGTGACACAAACAAAGAAA 1 AAGCACTGTACAACTTTTATTAGATAAAGAAGCAAATATTAATTCATGTGACACAAACAAAGAAA * * 807296 CTCCTCTACATAAAGCAAGT-ATACTGCGAACT-G 66 CTCCTCTACATAAAGCCAGTGA-A-TGCGACCTGG * * * * * * 807329 AGAGCACTTTACAACTTTTATTAGATAAAGGAGCAAATATTAATTTATGTGATATAAACAATGAA 1 A-AGCACTGTACAACTTTTATTAGATAAAGAAGCAAATATTAATTCATGTGACACAAACAAAGAA * * * * 807394 ACTCCTATACATAAAGCCAAG-GAATGGGGACGTGA 65 ACTCCTCTACATAAAGCC-AGTGAAT-GCGACCTGG * * * 807429 AAGCACTGTACATCTATTATTACATGTAGATAAAGAAGCATATATTAATTCATGTGACACCAACA 1 AAGCACTGTACAAC--TT-TT--AT-TAGATAAAGAAGCAAATATTAATTCATGTGACACAAACA * 807494 AAGAAACTCCTCTATATAAAGCCAGTGAATGCTGACCTGG 60 AAGAAACTCCTCTACATAAAGCCAGTGAATGC-GACCTGG * * * * * * * * * * * 807534 AAGCAATATTCAACTGTTACTAGTTAAAGGAGCAGATATTAACTT-TTGTGACA-ATAAGAAACA 1 AAGCACTGTACAACTTTTATTAGATAAAGAAGCAAATATTAA-TTCATGTGACACA-AACAAAGA * 807597 AACTCCTTTACATA 64 AACTCCTCTACATA 807611 TCGCCGGTTA Statistics Matches: 303, Mismatches: 59, Indels: 36 0.76 0.15 0.09 Matches are distributed among these distances: 98 3 0.01 99 208 0.69 100 7 0.02 101 3 0.01 102 4 0.01 103 1 0.00 104 5 0.02 105 72 0.24 ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25 Consensus pattern (98 bp): AAGCACTGTACAACTTTTATTAGATAAAGAAGCAAATATTAATTCATGTGACACAAACAAAGAAA CTCCTCTACATAAAGCCAGTGAATGCGACCTGG Found at i:812872 original size:20 final size:21 Alignment explanation

Indices: 812830--812873 Score: 72 Period size: 21 Copynumber: 2.1 Consensus size: 21 812820 AGACTATAGG * 812830 TACATTATGTCAAATTACCAT 1 TACATTATGTCAAAGTACCAT 812851 TACATTATGTCAAAGT-CCAT 1 TACATTATGTCAAAGTACCAT 812871 TAC 1 TAC 812874 GTGGTGTGAA Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 20 7 0.32 21 15 0.68 ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36 Consensus pattern (21 bp): TACATTATGTCAAAGTACCAT Found at i:813115 original size:84 final size:82 Alignment explanation

Indices: 813027--813197 Score: 182 Period size: 84 Copynumber: 2.1 Consensus size: 82 813017 CAACCAAAGG * * * * * ** * 813027 TCAATACATCATGACATTAT-TTCGACACTGTATTACATGGGGCGAATGTATCCTTACATTATGT 1 TCAATACATCATGACATTATATT-AACACCGCAGTACATAGCACGAATCTATCCTTACA-T-TGT 813091 CAACATTTTATTACATGATA 63 CAACATTTTATTACATGATA * * * * * * 813111 TCAATATATCCTTACATTATATTAACACCGCAGTACGTATCACGATTCTATCCTTACATTGTCAA 1 TCAATACATCATGACATTATATTAACACCGCAGTACATAGCACGAATCTATCCTTACATTGTCAA 813176 CATTTTATTACATGATA 66 CATTTTATTACATGATA 813193 TCAAT 1 TCAAT 813198 GCATTTTTAC Statistics Matches: 72, Mismatches: 14, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 82 28 0.39 83 1 0.01 84 41 0.57 85 2 0.03 ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37 Consensus pattern (82 bp): TCAATACATCATGACATTATATTAACACCGCAGTACATAGCACGAATCTATCCTTACATTGTCAA CATTTTATTACATGATA Found at i:813121 original size:42 final size:42 Alignment explanation

Indices: 813075--813197 Score: 112 Period size: 42 Copynumber: 3.0 Consensus size: 42 813065 GGGGCGAATG 813075 TATCCTTACATTATGTCAACATTTTATTACATGATATCAATA 1 TATCCTTACATTATGTCAACATTTTATTACATGATATCAATA * * **** * * 813117 TATCCTTACATTATATTAACACCGCAGTAC--G-TATCACGATTC 1 TATCCTTACATTATGTCAACATTTTATTACATGATATCA--A-TA 813159 TATCCTTACA-T-TGTCAACATTTTATTACATGATATCAAT 1 TATCCTTACATTATGTCAACATTTTATTACATGATATCAAT 813198 GCATTTTTAC Statistics Matches: 60, Mismatches: 15, Indels: 14 0.67 0.17 0.16 Matches are distributed among these distances: 39 5 0.08 40 12 0.20 41 3 0.05 42 35 0.58 43 5 0.08 ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40 Consensus pattern (42 bp): TATCCTTACATTATGTCAACATTTTATTACATGATATCAATA Found at i:819289 original size:21 final size:22 Alignment explanation

Indices: 819260--819305 Score: 76 Period size: 21 Copynumber: 2.1 Consensus size: 22 819250 AATAGCAACG 819260 TTTACTTTTAACTACTAAATAC 1 TTTACTTTTAACTACTAAATAC * 819282 TTTA-TTTTATCTACTAAATAC 1 TTTACTTTTAACTACTAAATAC 819303 TTT 1 TTT 819306 GAGACTAAAT Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 21 19 0.83 22 4 0.17 ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52 Consensus pattern (22 bp): TTTACTTTTAACTACTAAATAC Found at i:820146 original size:21 final size:21 Alignment explanation

Indices: 820122--820182 Score: 50 Period size: 21 Copynumber: 2.9 Consensus size: 21 820112 TACTGCGGTG * 820122 TTGATATAATGTAAGGATATA 1 TTGAAATAATGTAAGGATATA ** ** * * 820143 TTGAAAGCATGTAATAAAATG 1 TTGAAATAATGTAAGGATATA * 820164 TTGACATAATGTAAGGATA 1 TTGAAATAATGTAAGGATA 820183 CATTCGCCCC Statistics Matches: 27, Mismatches: 13, Indels: 0 0.68 0.32 0.00 Matches are distributed among these distances: 21 27 1.00 ACGTcount: A:0.44, C:0.03, G:0.20, T:0.33 Consensus pattern (21 bp): TTGAAATAATGTAAGGATATA Found at i:820196 original size:42 final size:42 Alignment explanation

Indices: 820066--820200 Score: 119 Period size: 42 Copynumber: 3.2 Consensus size: 42 820056 GCATTGATAT * * * 820066 CATGTAATAAAATGTTGACATAATGTAAGGATAGAATCGCGA 1 CATGTAATAAAATGTTGACATAATGTAAGGATACATTCGCAA * * * **** * * * 820108 TACGTACTGCGGTGTTGATATAATGTAAGGATATATT-GAAA 1 CATGTAATAAAATGTTGACATAATGTAAGGATACATTCGCAA ** 820149 GCATGTAATAAAATGTTGACATAATGTAAGGATACATTCGCCC 1 -CATGTAATAAAATGTTGACATAATGTAAGGATACATTCGCAA 820192 CATGTAATA 1 CATGTAATA 820201 CAGTGTCGAA Statistics Matches: 67, Mismatches: 24, Indels: 4 0.71 0.25 0.04 Matches are distributed among these distances: 41 2 0.03 42 64 0.96 43 1 0.01 ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30 Consensus pattern (42 bp): CATGTAATAAAATGTTGACATAATGTAAGGATACATTCGCAA Found at i:820409 original size:20 final size:21 Alignment explanation

Indices: 820384--820427 Score: 63 Period size: 21 Copynumber: 2.1 Consensus size: 21 820374 TTCACACCAC * 820384 GTAATG-GACTTTGACATAAT 1 GTAATGAGAATTTGACATAAT * 820404 GTAATGATAATTTGACATAAT 1 GTAATGAGAATTTGACATAAT 820425 GTA 1 GTA 820428 CCTATAGTAT Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 20 6 0.29 21 15 0.71 ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36 Consensus pattern (21 bp): GTAATGAGAATTTGACATAAT Found at i:822765 original size:18 final size:19 Alignment explanation

Indices: 822742--822784 Score: 61 Period size: 21 Copynumber: 2.2 Consensus size: 19 822732 CATATTTTGA 822742 AATATCTAT-GAGTTTATC 1 AATATCTATAGAGTTTATC 822760 AATATCTATGAAGAGTTTATC 1 AATATCTAT--AGAGTTTATC 822781 AATA 1 AATA 822785 AAACATTCCG Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 18 9 0.41 21 13 0.59 ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40 Consensus pattern (19 bp): AATATCTATAGAGTTTATC Found at i:826096 original size:99 final size:98 Alignment explanation

Indices: 825986--829876 Score: 3894 Period size: 99 Copynumber: 39.4 Consensus size: 98 825976 ACGACCACAT * * * 825986 TGTAGAACTTTTACTA-AGTAAAGGAGCAGATATTAATTCATGTAAC-CTAAGA-AAAGAAACTC 1 TGTACAACTTTTATTAGA-TAAAGGAGCAGATATTAATTCATGTGACAC-AA-ACAAAGAAACTC * 826048 CTCTACATAAAGCCAGTGGAAAGGGACATGTAAG-AGC 63 CTCTACATAAAGCCAGT-GAAAGGGACATGAAAGCA-C * * 826085 TGTACAACTTTTATTAGATAAAGGAGCAAATATCAATTCATGTGACACAAACAAAGAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * * 826150 TACTTAAAG-CAAT-AAGAGGAGGA-AGGGAAAGCAC 66 TACATAAAGCCAGTGAA-A-G-GGACA-TGAAAGCAC * * * * 826184 TGCACAGCTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACA-AATATAATGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAA-ACAAAGAAACTCCT * * * 826248 GTACATAAAGCAAGTGGAAAGGGACATGTAAG-AGC 65 CTACATAAAGCCAGT-GAAAGGGACATGAAAGCA-C * * 826283 TGTACAGCTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGAC-CTAAAGAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACAC-AAACAAAGAAACTCCT * * 826347 CTACATAAAGCCAGTGAAGGAGGACATAAAAGCAC 65 CTACATAAAGCCAGTGAAAG-GGACATGAAAGCAC * * * 826382 TGTGCAACTTTTATTAGAAAAAGGAGCAGATATTAATTCATGTGACA-ATTACAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACA-AACAAAGAAACTCCT * * * * 826446 CTACATAAAGCCAGTGAAGAAGGTCAGGAAAGTAC 65 CTACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * 826481 TGTACAACTTTTATTAGAAAAAGGAGCAAATATTAATTCATGTGAC-CTAAAGAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACAC-AAACAAAGAAACTCCT * * 826545 CTACATAAAGCCAGTGAAGGAGGACATAAAAGCAC 65 CTACATAAAGCCAGTGAAAG-GGACATGAAAGCAC * * * 826580 TGTGCAACTTTTATTAGAAAAAGGAGCAGATATTAATTCATGTGACA-ATTACAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACA-AACAAAGAAACTCCT * * * * 826644 CTACATAAAGCCAGTGAAGAAGGTCAGGAAAGTAC 65 CTACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * 826679 TGTACAACTTTTATTAGAAAAAGGAGCAAATATTAATTCATGTGAC-CTAAAGAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACAC-AAACAAAGAAACTCCT * * 826743 CTACATAAAGCCAGTGAAGGAGGACATAAAAGCAC 65 CTACATAAAGCCAGTGAAAG-GGACATGAAAGCAC * * * * * 826778 TGTGCAACTTTTATTACAAAAAGGAGCAAATATTAATTCATGTGAC-CTTAACAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACAC-AAACAAAGAAACTCCT ** * 826842 CTACATAAAGCCAGTAGACGGGGACATGAGAGCAC 65 CTACATAAAGCCAGT-GAAAGGGACATGAAAGCAC * * * * 826877 TGTGCAACTTTTATTAGAAAAAGGAGCAAATATTAATTCATGTGACACAAAGAAAGAAAC-CTCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC-CT * * * * 826941 CTGCA-AAAGGCCTGTGAAAGAGGACTTGAAAGAAC 65 CTACATAAA-GCCAGTGAAAG-GGACATGAAAGCAC * * * 826976 TGTGCAACTTTTATTAGAAAAAGGAGGAGCAAATATTAATTCATGTGACACAAACAAAGAAACTC 1 TGTACAACTTTTATTAG-ATAA--AGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTC * 827041 CTCTACATAAAGCCAGT-AAATGGGGACATGATAGCAC 63 CTCTACATAAAGCCAGTGAAA--GGGACATGAAAGCAC * * * * * 827078 GGTACAACTTGTGTTAGATAAAGGGGCAGATATTAATTCATGTGACACAAACAAAAAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * ** * 827143 TACATAAAGCCAGTGAATGGGGATGTGATAGCAC 66 TACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * 827177 GGTACAACTTTTATTAGATAAAGGGGCAGATATTAATTCATGTGACACAAACAAAAAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * ** * 827242 TACATAAAGCCAGTGAATGGGGATGTGATAGCAC 66 TACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * * 827276 GGTACAACTTTTATTAGATAAAGGGGCAGATATTAATTCATGTGACACAAGCAAAAAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * 827341 TACATAAAGCCAGT-AAATGGAGAAATGATAGCA- 66 TACATAAAGCCAGTGAAA-GG-GACATGAAAGCAC * * * * * 827374 TGGTACAACTTTTATTAGAAAAAGGAGCGGATGTTAATTCATGGGAC-CTTAACAAAGAAACTCC 1 T-GTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACAC-AAACAAAGAAACTCC * * ** * 827438 TCTAGATAATGCCAGTAGACGGGGAAATGAAAGCAC 64 TCTACATAAAGCCAGT-GAAAGGGACATGAAAGCAC * * * * 827474 TGTGCAACTTATATTAGAAAAAGGAGCAAATATTAATTCATGTGACACAAACAAAGAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * * 827539 TACATAAAGCCAGTGAATGGGGACATTATAGCAC 66 TACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * * 827573 GGTGCAACTTTTATTAGATAAAGGGGCAGATATTAATTCATGTGACACAAACAAAAAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * * * 827638 TACATAAAGCCATTGAACGTGGACATGATAGTA- 66 TACATAAAGCCAGTGAAAG-GGACATGAAAGCAC * * * 827671 TGTACAAGTTTTATTAGATAATGGAGCAGATATTAATAT-ATGTAACACAAACAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAAT-TCATGTGACACAAACAAAGAAACTCCT * * * 827735 CTACATAAAGCCATTGAACGTGGACATGATAGCAC 65 CTACATAAAGCCAGTGAAAG-GGACATGAAAGCAC * * * * 827770 TGTGCAACGTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACGAACAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * * * * * * 827835 TACAAAAAGCAATTAAATATGGACGTAAAAGCAC 66 TACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * * * * * 827869 TGTACAGCTTTTATTAGATAAAGTAGCAGATATTGA-TC-TGTGTAAAACAAACAATGAAACACT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTG--ACACAAACAAAGAAACTCC * * * * * * 827932 TCTCCATTATGCCAGTCAATGGGGACTTGATAA-CAC 64 TCTACATAAAGCCAGTGAA-AGGGACATGA-AAGCAC * * 827968 TGTACAACTTTTATTAGATAAAGGGGCAGATATTGATTCATGTGACACAAACAAAGAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * 828033 TACATAAAGCTAGTG-AAGGAAGGCATGAAAGCAC 66 TACATAAAGCCAGTGAAAGG--GACATGAAAGCAC * * * * * * 828067 TGTACAAGTTTAATTATATAATGGAGCAGATATTAATAT-ATGTAACACAAACAAAGAAACCCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAAT-TCATGTGACACAAACAAAGAAACTCCT * * * * 828131 CTGCATAAAGCAAGTGAATGGGGA-AGTGAAAGAAC 65 CTACATAAAGCCAGTGAA-AGGGACA-TGAAAGCAC * * * 828166 TGTACAACTTTTATTAGATAAAGGAGCAGCTATTAATTTATGTGACATAAACAAAGAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * * 828231 TACATAAATCCAGTAAAATGGGATAT-AAAGGCAC 66 TACATAAAGCCAGTGAAA-GGGACATGAAA-GCAC * * 828265 CGTACAACTTTTATTAGAAAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * 828330 TACATAAAGCCAGT-AAATGGGGACGTGAAAGCAC 66 TACATAAAGCCAGTGAAA--GGGACATGAAAGCAC * * * * * * * * 828364 TGTACAGCTTTTATTAGATAAAGGAGCAAATGTAAATTCATGTGACACATATAAAGAAACCCCTT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * * ** * 828429 TACACAAAGTCAGTGAAATGGGACAACAAAGCAT 66 TACATAAAGCCAGTGAAA-GGGACATGAAAGCAC 828463 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * 828528 TACATAAAGCCAGTGAATGTGGA-AGTGAAAGCAC 66 TACATAAAGCCAGTGAAAG-GGACA-TGAAAGCAC * * * 828562 TGTACAGCTTTTATTAGATAAAGGAGCAAATATTAATTTAT-TAGACACAAACAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGT-GACACAAACAAAGAAACTCCT * * * * * * 828626 CTACATACAG-CAATTAAATGTGGAGAGGAAATCAC 65 CTACATAAAGCCAGTGAAA-G-GGACATGAAAGCAC * * * 828661 TGTACAGCTTTTATTAGATAAAGGAGCAAATATT-ATTCTATGTGACACAAACAAAGAAACTCTT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTC-ATGTGACACAAACAAAGAAACTCCT * * * * ** * * 828725 CTCCATTATGCCAGTCTATGGGGACTTAAAAGCAC 65 CTACATAAAGCCAGT-GAAAGGGACATGAAAGCAC * * * * 828760 TGTACAACGTTTATTAGGA-AAAGGAACAGATATTAATTCATATGACA-AATACAATGAAACTCC 1 TGTACAACTTTTATTA-GATAAAGGAGCAGATATTAATTCATGTGACACAA-ACAAAGAAACTCC * * 828823 TCTACATAAAGCCAGTGAATCGGGACATGAAAGAAC 64 TCTACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * 828859 TGTACAGCTTTTATTAGATAACGGAGCAGATATTAATTCATGTGACGA-AAACAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGAC-ACAAACAAAGAAACTCCT * * 828923 CTGCATAAAGCCAGTGGAAAGGGACGTGAAAGCAC 65 CTACATAAAGCCAGT-GAAAGGGACATGAAAGCAC * * 828958 TGTACAACTTTTATTAGATAAAGGTGCAGATATTAATTTATGTGACACAAACAAAGAAACTCCTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * ** * 829023 TACATAAAGCCTGTGATTGGGGACATGATAGCAC 66 TACATAAAGCCAGTGA-AAGGGACATGAAAGCAC * * * * * 829057 TGTACAACTTTTATTAGATAAAGGATCAAACATTAATTCATTTGACA-AATACAATGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAA-ACAAAGAAACTCCT * * * 829121 CTACATAAAGCCAGTGAATCGGGACATAAAAGAAC 65 CTACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * * 829156 AGTGCAACTTTTATTACATAAAGGAGCAGATATTAATTCCTGTGACGA-AAACAAAGAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGAC-ACAAACAAAGAAACTCCT * * 829220 CTGCATAAAGCCAGTGCAAAGGGACGTGAAAGCAC 65 CTACATAAAGCCAGTG-AAAGGGACATGAAAGCAC * * 829255 TGTACAACTTTTATTAGATAAAGGAGCAAATATTAATTCATGTGACGA-AAACAAACAAACTCCT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGAC-ACAAACAAAGAAACTCCT * * * 829319 CTGCATAAAGCCAGTGGAAAGGGACGTAAAAGCAC 65 CTACATAAAGCCAGT-GAAAGGGACATGAAAGCAC * 829354 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACA-AATACAATGAAAC-CTC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAA-ACAAAGAAACTC-C * * * ** * 829417 TTTACATAGAGCCAAACT-ACTGGGACATGAAAACAC 64 TCTACATAAAGCC--AGTGAAAGGGACATGAAAGCAC * * * 829453 TGTACAACTTTTATCAGATAAAGG-GCAGATATTAATTCATGAGACACAAACAAATAAA-----C 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC * 829512 T-C-----G--AGTGAACAGGGATATGAAAGCAC 66 TACATAAAGCCAGTGAA-AGGGACATGAAAGCAC * * * * * * * * * 829538 TGCACATCATTTACTAAATAAATGAGCAGATATTAATTTACATGAGACACAAACAAAGACACTAC 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAA-TT-CATGTGACACAAACAAAGAAACTCC * * * * * 829603 TCTACGTTAAGCAAG-GAAACCGGGAC-TAAAAAGAAC 64 TCTACATAAAGCCAGTGAAA--GGGACAT-GAAAGCAC * * * * 829639 TGTACACATTTTTATT-GAATAAAGGAGCAGATATTAATTCATGTGGCAGAAACAACGACAA-TC 1 TGTACA-ACTTTTATTAG-ATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGA-AACTC * * * * * * ** 829702 CTCTCCAAAAAGCCAATAAAAGGGGACCTAAAAGCGT 63 CTCTACATAAAGCCAGTGAAA-GGGACATGAAAGCAC ** * * ** ** * * * * 829739 TACACAACTTCTATTGGATAAAAAAAAAACATACTAATCCATGTTACGA-AAACAAAGAAACTCC 1 TGTACAACTTTTATTAGAT-AAAGGAGCAGATATTAATTCATGTGAC-ACAAACAAAGAAACTCC * 829803 TCTACATAAAGCCTGTGAAAGAGGACATGAAAGCAC 64 TCTACATAAAGCCAGTGAAAG-GGACATGAAAGCAC **** * * 829839 TGTATTTTTTTTATTTGATCAAGGAGCAGATATTAATT 1 TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATT 829877 TTTTGACAAT Statistics Matches: 3192, Mismatches: 464, Indels: 272 0.81 0.12 0.07 Matches are distributed among these distances: 83 2 0.00 84 1 0.00 85 30 0.01 86 11 0.00 87 3 0.00 88 19 0.01 92 1 0.00 93 3 0.00 94 1 0.00 96 2 0.00 97 7 0.00 98 185 0.06 99 2607 0.82 100 174 0.05 101 43 0.01 102 98 0.03 103 5 0.00 ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24 Consensus pattern (98 bp): TGTACAACTTTTATTAGATAAAGGAGCAGATATTAATTCATGTGACACAAACAAAGAAACTCCTC TACATAAAGCCAGTGAAAGGGACATGAAAGCAC Found at i:836213 original size:69 final size:69 Alignment explanation

Indices: 836119--836356 Score: 404 Period size: 69 Copynumber: 3.4 Consensus size: 69 836109 CCATTCCCAT * * 836119 TTAAATACTCGTGCACTTAGTGTACACTAATTACATTAAAGGTTCCGGATGTAGGTTACTCATTC 1 TTAAATACTCGTGCACTCAGTGTACACTAATTACATTAAAGGTTCAGGATGTAGGTTACTCATTC 836184 ATTC 66 ATTC * 836188 TTAAATACTCGTGCACTCAGTGTACACTAATTACATTAAAGGTTCAGGATGTAGGTTTCTCATTC 1 TTAAATACTCGTGCACTCAGTGTACACTAATTACATTAAAGGTTCAGGATGTAGGTTACTCATTC 836253 ATTC 66 ATTC ** * * * 836257 TTAAATACTCGTGCACTCAGTGTTTACTAATTACATTAAAGGTTCTGGGTGTAGGCTACTCATTC 1 TTAAATACTCGTGCACTCAGTGTACACTAATTACATTAAAGGTTCAGGATGTAGGTTACTCATTC 836322 ATTC 66 ATTC 836326 TTAAATACTCGTGCACTCAGTGTACACTAAT 1 TTAAATACTCGTGCACTCAGTGTACACTAAT 836357 ACACTACCAG Statistics Matches: 158, Mismatches: 11, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 69 158 1.00 ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36 Consensus pattern (69 bp): TTAAATACTCGTGCACTCAGTGTACACTAATTACATTAAAGGTTCAGGATGTAGGTTACTCATTC ATTC Found at i:838217 original size:2 final size:2 Alignment explanation

Indices: 838206--838250 Score: 81 Period size: 2 Copynumber: 22.5 Consensus size: 2 838196 GGAAAAAAAA * 838206 AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 838248 AG A 1 AG A 838251 TTGAAGTTCA Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02 Consensus pattern (2 bp): AG Found at i:839860 original size:2 final size:2 Alignment explanation

Indices: 839853--839916 Score: 110 Period size: 2 Copynumber: 32.0 Consensus size: 2 839843 CTATCATTTT * * 839853 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA CA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 839895 GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA 839917 TTATTTTACA Statistics Matches: 59, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 59 1.00 ACGTcount: A:0.52, C:0.02, G:0.47, T:0.00 Consensus pattern (2 bp): GA Found at i:842260 original size:14 final size:14 Alignment explanation

Indices: 842254--842290 Score: 74 Period size: 14 Copynumber: 2.6 Consensus size: 14 842244 TTCGAGATTG 842254 GAGATTCGAAATAC 1 GAGATTCGAAATAC 842268 GAGATTCGAAATAC 1 GAGATTCGAAATAC 842282 GAGATTCGA 1 GAGATTCGA 842291 GATTCNNNNN Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 23 1.00 ACGTcount: A:0.41, C:0.14, G:0.24, T:0.22 Consensus pattern (14 bp): GAGATTCGAAATAC Found at i:842293 original size:7 final size:7 Alignment explanation

Indices: 842243--842295 Score: 61 Period size: 7 Copynumber: 7.6 Consensus size: 7 842233 GAGAAGGATC 842243 ATTCGAG 1 ATTCGAG * 842250 ATTGGAG 1 ATTCGAG * 842257 ATTCGAA 1 ATTCGAG * 842264 ATACGAG 1 ATTCGAG * 842271 ATTCGAA 1 ATTCGAG * 842278 ATACGAG 1 ATTCGAG 842285 ATTCGAG 1 ATTCGAG 842292 ATTC 1 ATTC 842296 NNNNNNNNNN Statistics Matches: 36, Mismatches: 10, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 7 36 1.00 ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26 Consensus pattern (7 bp): ATTCGAG Found at i:844636 original size:2 final size:2 Alignment explanation

Indices: 844629--844668 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 844619 GAGTTTATAC 844629 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 844669 CGATTGCATT Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:845239 original size:142 final size:141 Alignment explanation

Indices: 844963--845227 Score: 338 Period size: 142 Copynumber: 1.9 Consensus size: 141 844953 ATATAATAGC * * * 844963 TACTGTACACAGCCCTTCTTGACAATTTGCAGTTCACGGTAGCGAGATAGGTAAAAAGAGATGAA 1 TACTGTACACAGCCCTTCTTGACAATTTGCAGTGCACGGTAGCCAGATAGGGAAAAAGAGATGAA * * * * * 845028 AGACACACGTGTACACGTATATATACACACACTTCCTCAGATCTGAATGGTCGGTCAGTGATTAT 66 AGACACACGTGTA-ACGTATATATACACACACGTCCTCAGATCTGAATGCTCGGTCAATGATCAA 845093 ATAATAGCTATA 130 ATAATAGCTATA * * * 845105 TACTGTATACAGCCCTTCTTGACAATTTGCAGTGCACGGTAGCCAGACT-GGGAACAATGAGGTG 1 TACTGTACACAGCCCTTCTTGACAATTTGCAGTGCACGGTAGCCAGA-TAGGGAA-AAAGAGATG * * * * * 845169 ACAGACACACGTGT-ACTTGTATATACACACACGTCCTCAGGTCTGGATGCTCGGT-AATG 64 AAAGACACACGTGTAACGTATATATACACACACGTCCTCAGATCTGAATGCTCGGTCAATG 845228 CTACACAATA Statistics Matches: 107, Mismatches: 14, Indels: 6 0.84 0.11 0.05 Matches are distributed among these distances: 140 3 0.03 141 35 0.33 142 48 0.45 143 21 0.20 ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26 Consensus pattern (141 bp): TACTGTACACAGCCCTTCTTGACAATTTGCAGTGCACGGTAGCCAGATAGGGAAAAAGAGATGAA AGACACACGTGTAACGTATATATACACACACGTCCTCAGATCTGAATGCTCGGTCAATGATCAAA TAATAGCTATA Found at i:845735 original size:2 final size:2 Alignment explanation

Indices: 845728--845764 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 845718 GAAAAATCAG 845728 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 845765 ATGATTTATA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:846332 original size:20 final size:20 Alignment explanation

Indices: 846307--846383 Score: 75 Period size: 20 Copynumber: 3.9 Consensus size: 20 846297 AGGGGCATGC * 846307 ACAGGGGCAGACAGTGGCTT 1 ACAGGGGCAGACAGGGGCTT * * 846327 ACA-GGGTATGACAGGGGCGT 1 ACAGGGGCA-GACAGGGGCTT ** 846347 ACAGGGGGTGACAGGGGCTT 1 ACAGGGGCAGACAGGGGCTT * * 846367 ACAGTGGCACACAGGGG 1 ACAGGGGCAGACAGGGG 846384 TTGTGTACAG Statistics Matches: 45, Mismatches: 10, Indels: 4 0.76 0.17 0.07 Matches are distributed among these distances: 19 4 0.09 20 38 0.84 21 3 0.07 ACGTcount: A:0.25, C:0.18, G:0.44, T:0.13 Consensus pattern (20 bp): ACAGGGGCAGACAGGGGCTT Found at i:846366 original size:40 final size:41 Alignment explanation

Indices: 846284--846370 Score: 104 Period size: 40 Copynumber: 2.1 Consensus size: 41 846274 TTAAAGACCG * * 846284 TACAGGGGATGTCAGGGGCATGCACAGGGGCAGACAGTGGCT 1 TACAGGGGATGACAGGGGCA-GCACAGGGGCAGACAGGGGCT * * ** 846326 TACAGGGTATGACAGGGGC-GTACAGGGGGTGACAGGGGCT 1 TACAGGGGATGACAGGGGCAGCACAGGGGCAGACAGGGGCT 846366 TACAG 1 TACAG 846371 TGGCACACAG Statistics Matches: 39, Mismatches: 6, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 40 22 0.56 42 17 0.44 ACGTcount: A:0.24, C:0.17, G:0.44, T:0.15 Consensus pattern (41 bp): TACAGGGGATGACAGGGGCAGCACAGGGGCAGACAGGGGCT Found at i:846445 original size:23 final size:22 Alignment explanation

Indices: 846366--846456 Score: 82 Period size: 23 Copynumber: 4.2 Consensus size: 22 846356 GACAGGGGCT * 846366 TACAGTGGCACACAGGGGTTGTG 1 TACAGTGGCACACAGGGG-TATG * * 846389 TACAGGGGCGCACAGGGG-ATG 1 TACAGTGGCACACAGGGGTATG * * * 846410 -ACAG-GGTATACAGGGGCTCTG 1 TACAGTGGCACACAGGGG-TATG 846431 TACAGTGGCACACAGGGG-ATG 1 TACAGTGGCACACAGGGGTATG 846452 TACAG 1 TACAG 846457 GGGATGACAG Statistics Matches: 54, Mismatches: 10, Indels: 10 0.73 0.14 0.14 Matches are distributed among these distances: 19 9 0.17 20 4 0.07 21 11 0.20 22 4 0.07 23 26 0.48 ACGTcount: A:0.25, C:0.19, G:0.40, T:0.16 Consensus pattern (22 bp): TACAGTGGCACACAGGGGTATG Found at i:846445 original size:42 final size:43 Alignment explanation

Indices: 846307--846458 Score: 127 Period size: 42 Copynumber: 3.6 Consensus size: 43 846297 AGGGGCATGC * * * 846307 ACAGGGGCAGACAGTGGCT-TACAGGGTATGACAGGGG--C-GT 1 ACAGGGGCACACAGGGGATGTACAGGGTAT-ACAGGGGCTCTGT *** * * * * * 846347 ACAGGGGGTGACAGGGGCT-TACAGTGGCACACAGGGGTTGTGT 1 ACAGGGGCACACAGGGGATGTACAG-GGTATACAGGGGCTCTGT * 846390 ACAGGGGCGCACAGGGGATG-ACAGGGTATACAGGGGCTCTGT 1 ACAGGGGCACACAGGGGATGTACAGGGTATACAGGGGCTCTGT * 846432 ACAGTGGCACACAGGGGATGTACAGGG 1 ACAGGGGCACACAGGGGATGTACAGGG 846459 GATGACAGTG Statistics Matches: 90, Mismatches: 16, Indels: 9 0.78 0.14 0.08 Matches are distributed among these distances: 40 28 0.31 41 3 0.03 42 32 0.36 43 27 0.30 ACGTcount: A:0.24, C:0.18, G:0.43, T:0.15 Consensus pattern (43 bp): ACAGGGGCACACAGGGGATGTACAGGGTATACAGGGGCTCTGT Found at i:846458 original size:11 final size:10 Alignment explanation

Indices: 846442--846502 Score: 50 Period size: 10 Copynumber: 5.9 Consensus size: 10 846432 ACAGTGGCAC 846442 ACAGGGGATG 1 ACAGGGGATG 846452 TACAGGGGATG 1 -ACAGGGGATG ** ** 846463 ACAGTGAAAAC 1 ACAG-GGGATG * 846474 ACAGGGGGTG 1 ACAGGGGATG * 846484 ACAGGGGAAG 1 ACAGGGGATG 846494 ACAGGGGAT 1 ACAGGGGAT 846503 TTTCATACGG Statistics Matches: 37, Mismatches: 12, Indels: 3 0.71 0.23 0.06 Matches are distributed among these distances: 10 21 0.57 11 16 0.43 ACGTcount: A:0.34, C:0.11, G:0.44, T:0.10 Consensus pattern (10 bp): ACAGGGGATG Found at i:850158 original size:2 final size:2 Alignment explanation

Indices: 850151--850185 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 850141 TATGATACTG 850151 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 850186 AATCTATGAA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:855948 original size:9 final size:9 Alignment explanation

Indices: 855934--855963 Score: 51 Period size: 9 Copynumber: 3.2 Consensus size: 9 855924 GTATTTGCCT 855934 ATGGATGGC 1 ATGGATGGC 855943 ATGGATGGC 1 ATGGATGGC 855952 TATGGATGGC 1 -ATGGATGGC 855962 AT 1 AT 855964 TTCGAACACA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 9 11 0.55 10 9 0.45 ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27 Consensus pattern (9 bp): ATGGATGGC Found at i:855958 original size:10 final size:10 Alignment explanation

Indices: 855932--855961 Score: 53 Period size: 10 Copynumber: 3.1 Consensus size: 10 855922 CAGTATTTGC 855932 CTATGGATGG 1 CTATGGATGG 855942 C-ATGGATGG 1 CTATGGATGG 855951 CTATGGATGG 1 CTATGGATGG 855961 C 1 C 855962 ATTTCGAACA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 9 9 0.47 10 10 0.53 ACGTcount: A:0.20, C:0.13, G:0.40, T:0.27 Consensus pattern (10 bp): CTATGGATGG Found at i:858015 original size:85 final size:83 Alignment explanation

Indices: 857831--858027 Score: 226 Period size: 81 Copynumber: 2.4 Consensus size: 83 857821 ACCAACTTTG * ** 857831 TTGTTGATATCGACGATATCG-ACACCAAAA-TGACGATATCAACATCGATATCGAATTTTGAGA 1 TTGTCGATATCGACGATATCGTACA-CAAAATTGACGATATCAACATCGATATCGAATACTGAGA * 857894 AATGCTAATCCAATTATGA 65 AATGCAAATCCAATTATGA * 857913 -TGTCGATATCGACGATATCGTACA-AAAATTGACGATATCGACATCGATATCGACATACACTGA 1 TTGTCGATATCGACGATATCGTACACAAAATTGACGATATCAACATCGATATCGA-AT--ACTGA * * 857976 TGAAGTTGCAAAT-CAATT-TTA 63 -GAA-ATGCAAATCCAATTATGA * 857997 TTGTCGATATCGACGATATCGTACATAAAAT 1 TTGTCGATATCGACGATATCGTACACAAAAT 858028 AAAATGTCGA Statistics Matches: 99, Mismatches: 7, Indels: 14 0.82 0.06 0.12 Matches are distributed among these distances: 80 4 0.04 81 42 0.42 82 5 0.05 84 5 0.05 85 32 0.32 86 11 0.11 ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29 Consensus pattern (83 bp): TTGTCGATATCGACGATATCGTACACAAAATTGACGATATCAACATCGATATCGAATACTGAGAA ATGCAAATCCAATTATGA Found at i:858653 original size:78 final size:78 Alignment explanation

Indices: 858551--858713 Score: 193 Period size: 78 Copynumber: 2.1 Consensus size: 78 858541 ACCGTATCGT * * * * 858551 CGATATCGACGTTGAATATAGACAGAT-TGAGTTCTGTACCTACACAAATCGATATCGATACAAT 1 CGATATCAACGTTAAATATAGACAGCTGT-AGTTCTGTACATACACAAATCGATATCGATACAAT ** 858615 ATTGTCGATAACGA 65 ATCCTCGATAACGA * * ** * * 858629 CGATATCAACGTTAAATATGGACAGCTGTAGTTGTGTACATATGCAACTCGATATCGATACGATA 1 CGATATCAACGTTAAATATAGACAGCTGTAGTTCTGTACATACACAAATCGATATCGATACAATA * 858694 TCCTCGATATCGA 66 TCCTCGATAACGA 858707 CGATATC 1 CGATATC 858714 GACATGAATA Statistics Matches: 71, Mismatches: 13, Indels: 2 0.83 0.15 0.02 Matches are distributed among these distances: 78 70 0.99 79 1 0.01 ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29 Consensus pattern (78 bp): CGATATCAACGTTAAATATAGACAGCTGTAGTTCTGTACATACACAAATCGATATCGATACAATA TCCTCGATAACGA Found at i:858711 original size:18 final size:19 Alignment explanation

Indices: 858676--858713 Score: 60 Period size: 20 Copynumber: 2.0 Consensus size: 19 858666 ACATATGCAA 858676 CTCGATATCGATACGATATC 1 CTCGATATCGA-ACGATATC 858696 CTCGATATCG-ACGATATC 1 CTCGATATCGAACGATATC 858714 GACATGAATA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 18 8 0.44 20 10 0.56 ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29 Consensus pattern (19 bp): CTCGATATCGAACGATATC Found at i:858787 original size:18 final size:19 Alignment explanation

Indices: 858753--858790 Score: 60 Period size: 18 Copynumber: 2.0 Consensus size: 19 858743 TCAAAGAAAT 858753 TCGATATCGATACGATATCG 1 TCGATATCGA-ACGATATCG 858773 TCGATATCG-ACGATATCG 1 TCGATATCGAACGATATCG 858791 ACGTTGAATA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 18 9 0.50 20 9 0.50 ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29 Consensus pattern (19 bp): TCGATATCGAACGATATCG Found at i:858791 original size:9 final size:9 Alignment explanation

Indices: 858754--858793 Score: 53 Period size: 9 Copynumber: 4.2 Consensus size: 9 858744 CAAAGAAATT 858754 CGATATCGATA 1 CGATATCG--A * 858765 CGATATCGT 1 CGATATCGA 858774 CGATATCGA 1 CGATATCGA 858783 CGATATCGA 1 CGATATCGA 858792 CG 1 CG 858794 TTGAATATGA Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 9 19 0.70 11 8 0.30 ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25 Consensus pattern (9 bp): CGATATCGA Found at i:866111 original size:18 final size:21 Alignment explanation

Indices: 866080--866121 Score: 54 Period size: 20 Copynumber: 2.1 Consensus size: 21 866070 ATTTTCAATA 866080 TTTTCTGTTCGAAA-ATTATT 1 TTTTCTGTTCGAAAGATTATT 866100 TTTTCTG-T-GAAAGTATTATT 1 TTTTCTGTTCGAAAG-ATTATT 866120 TT 1 TT 866122 CCTATCGGAT Statistics Matches: 20, Mismatches: 0, Indels: 4 0.83 0.00 0.17 Matches are distributed among these distances: 18 4 0.20 19 1 0.05 20 15 0.75 ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57 Consensus pattern (21 bp): TTTTCTGTTCGAAAGATTATT Found at i:873935 original size:2 final size:2 Alignment explanation

Indices: 873928--873972 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 873918 TCCATAATAT 873928 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 873970 GA G 1 GA G 873973 NNNNNNNNNN Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:881725 original size:2 final size:2 Alignment explanation

Indices: 881718--881748 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 881708 CAATTATTAT 881718 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 881749 CAACTCTAGG Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:882272 original size:2 final size:2 Alignment explanation

Indices: 882265--882305 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 882255 AGTTCGCTCT 882265 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 882306 CACAGTCAAT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:883729 original size:25 final size:25 Alignment explanation

Indices: 883695--883743 Score: 89 Period size: 25 Copynumber: 2.0 Consensus size: 25 883685 AGCCTACTAG 883695 TATATAGTATACATGTACATGTCTC 1 TATATAGTATACATGTACATGTCTC * 883720 TATATAGTATATATGTACATGTCT 1 TATATAGTATACATGTACATGTCT 883744 ATATTTTGTC Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 23 1.00 ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43 Consensus pattern (25 bp): TATATAGTATACATGTACATGTCTC Found at i:890181 original size:78 final size:78 Alignment explanation

Indices: 889997--890672 Score: 911 Period size: 78 Copynumber: 8.6 Consensus size: 78 889987 AATGGCAAAT * * ** * * ** * * 889997 TTACCTGTCAGTTACTAGTAGGACACTCTTTGTAAATTTGCTGTCATGGGATGTAATCATATAAT 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAAT--TACATT * * 890062 ATTGTAATATCATGG 64 ATTGTAATACCAAGG * * * * * * * * * 890077 TTACCTGTAAGTTACTAGTTGTACACTCATGGTGGAATTGCTGTCATATAATGTAATTACATCAC 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT * * * 890142 TGTAAAATCATGG 66 TGTAATACCAAGG ** * * * * * 890155 TTACCTGTTTGTTACAAGTAGAACACTTTTGGTGGTCTTGCTGTCATATAATGTAATTACATTAT 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT * ** 890220 TGTAATATCAAAC 66 TGTAATACCAAGG 890233 TTACCTGTCAGTGTCTGTAACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTA 1 TTACCTGTCA--G--T-T-ACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTA 890298 CATTATTGTAATACCAAGG 60 CATTATTGTAATACCAAGG * 890317 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATCAT 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT * 890382 TGTAATACCAAGA 66 TGTAATACCAAGG * * 890395 TTACCTGTCTGTAACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT 890460 TGTAATACCAAGG 66 TGTAATACCAAGG 890473 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT 890538 TGTAATACCAAGG 66 TGTAATACCAAGG 890551 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT * 890616 TGTAATACCAAGA 66 TGTAATACCAAGG * * 890629 TTACCTGTCTGTAACTAGTAGAACACTCTTGGTGGACTTGCTGT 1 TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGT 890673 CTCCAATGAT Statistics Matches: 538, Mismatches: 52, Indels: 14 0.89 0.09 0.02 Matches are distributed among these distances: 78 419 0.78 79 1 0.00 80 48 0.09 82 2 0.00 83 1 0.00 84 67 0.12 ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37 Consensus pattern (78 bp): TTACCTGTCAGTTACTAGTAGAACACTCTTGGTGGACTTGCTGTTATGTAATGTAATTACATTAT TGTAATACCAAGG Found at i:895521 original size:23 final size:23 Alignment explanation

Indices: 895485--895528 Score: 61 Period size: 23 Copynumber: 1.9 Consensus size: 23 895475 CAAGCCTGCA ** * 895485 AAATACAGGCAAACAATATACAG 1 AAATACAGAAAAACAAAATACAG 895508 AAATACAGAAAAACAAAATAC 1 AAATACAGAAAAACAAAATAC 895529 TGAACACTTC Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.64, C:0.16, G:0.09, T:0.11 Consensus pattern (23 bp): AAATACAGAAAAACAAAATACAG Found at i:899198 original size:169 final size:168 Alignment explanation

Indices: 898244--899164 Score: 1283 Period size: 168 Copynumber: 5.5 Consensus size: 168 898234 CCAATGTCCT * * * * ** * 898244 GAACCCCTGACCCAGGGGCCATGAACTTCACAATTTAGGTAAAGGAG-ATTGTGGATATCATAAC 1 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGG-GCCTCATGGACATCATAAC * * ** ** * * * * * 898308 CATGTATTCAGTTTTTTGCCCACATGTGTGGGAGTACAGAAGAAGATTTTCTTAGATTTAATACA 65 CATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA * 898373 TTTTTACTATTTAGCCATATTGGCCCCACCCTAGAG-CA 130 TTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCA * * ** * 898411 TGAACACCTAACAAAGGGGTCATGAATTTCACAAATTTA-GTAGAGAGCCTCATGGACATCATAA 1 -GAACCCCTGACCCAGGGGTCATGAATTTCAC-AATTTAGGTAGAGGGCCTCATGGACATCATAA * * * * 898475 TCATGCATTTAGTTTTTAACATATATATATAGGAGTAGAGAAGAAGATTTTCTAAGATCTAATAC 64 CCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATAC * 898540 ATTTTTACTATTTGGCCATATCGGCCCCACCCTAGAG-CA 129 ATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCA * * * * * 898579 TGAACCCCTGACCGAGGGGTCGTGAATTTCACAATTAAGGTAGAGAGCCTCATGGACATCATAAA 1 -GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCCTCATGGACATCATAAC * * 898644 CATGCATTTAGTTTTTAACAAATATATAAGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATATA 65 CATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA * * 898709 TTTTTACTATTTGGCCATATTGGCCCCACCCTAGTGCCT 130 TTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCA * * 898748 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAATC 1 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCCTCATGGACATCATAACC * * 898813 ATGCATTTAGTATTTAACAAATATATATGAGAGTAGAGAAGAAGATTTTCTAAGATTTAATACAT 66 ATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACAT * * 898878 TTTTACTATTTGGCCATATTAGCCCCACCCTAGAGCCT 131 TTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCA ** * * 898916 GAACCCCTGACCCAGGGGTTTTGAATTTCACAATTAAGGTAGAGGGCTTCATGGACATCATAACC 1 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCCTCATGGACATCATAACC 898981 ATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTTAATACA 66 ATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGA-TTTAATACA * * 899046 TTTTTACTATATGGCCATATTGGCCCAACCCTAGAGCCA 130 TTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCA * * * 899085 GAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATAACC 1 GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCCTCATGGACATCATAACC * 899150 ATGCATTCAGTTTTT 66 ATGCATTTAGTTTTT 899165 TCCTCACATG Statistics Matches: 675, Mismatches: 73, Indels: 9 0.89 0.10 0.01 Matches are distributed among these distances: 167 6 0.01 168 546 0.81 169 123 0.18 ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30 Consensus pattern (168 bp): GAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGCCTCATGGACATCATAACC ATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACAT TTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCA Found at i:899379 original size:7 final size:7 Alignment explanation

Indices: 899369--899406 Score: 58 Period size: 7 Copynumber: 5.4 Consensus size: 7 899359 AAAATTGTTA 899369 ACGCACG 1 ACGCACG 899376 ACGCACG 1 ACGCACG * 899383 GCGCACG 1 ACGCACG * 899390 ACGCACA 1 ACGCACG 899397 ACGCACG 1 ACGCACG 899404 ACG 1 ACG 899407 ACGGACGAAG Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 7 27 1.00 ACGTcount: A:0.29, C:0.42, G:0.29, T:0.00 Consensus pattern (7 bp): ACGCACG Found at i:900161 original size:14 final size:14 Alignment explanation

Indices: 900142--900172 Score: 62 Period size: 14 Copynumber: 2.2 Consensus size: 14 900132 TACTTATTAG 900142 TCTCTCTCTCTCTT 1 TCTCTCTCTCTCTT 900156 TCTCTCTCTCTCTT 1 TCTCTCTCTCTCTT 900170 TCT 1 TCT 900173 GCAACTTTGC Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 17 1.00 ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58 Consensus pattern (14 bp): TCTCTCTCTCTCTT Found at i:901236 original size:4 final size:4 Alignment explanation

Indices: 901227--901279 Score: 106 Period size: 4 Copynumber: 13.2 Consensus size: 4 901217 TGTAAATCAC 901227 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 901275 AGAT A 1 AGAT A 901280 CCTTGTGATG Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 49 1.00 ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25 Consensus pattern (4 bp): AGAT Found at i:901804 original size:25 final size:25 Alignment explanation

Indices: 901775--901824 Score: 64 Period size: 25 Copynumber: 2.0 Consensus size: 25 901765 AACAATAATT * 901775 TCTCAAAATTTCAATTATCCAGACA 1 TCTCAAAATTTCAATTATACAGACA *** 901800 TCTCAGTCTTTCAATTATACAGACA 1 TCTCAAAATTTCAATTATACAGACA 901825 CATCAACAAT Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 25 21 1.00 ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34 Consensus pattern (25 bp): TCTCAAAATTTCAATTATACAGACA Found at i:902802 original size:2 final size:2 Alignment explanation

Indices: 902795--902820 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 902785 ATTTTCACTC 902795 CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT 902821 NNNNNNNNNN Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:910859 original size:2 final size:2 Alignment explanation

Indices: 910852--910890 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 910842 CTGACAATGG 910852 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 910891 GAGCAGCGAT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:916909 original size:168 final size:165 Alignment explanation

Indices: 916527--917021 Score: 663 Period size: 168 Copynumber: 3.0 Consensus size: 165 916517 TGCCCACATG * * * * 916527 TATGGAAGTAGAGAAGTAGATTTTTTAAGATTTAAAACATTTTTACTATATGGCCATATTGGCCC 1 TATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCC * * ** * * 916592 CACCCTGGAGCCTGAACCCCTAACAAAGAGGTCATGAATTTCACAATTTTGGTAGAGGGTTTCAT 66 CACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAA-TTTGGTAGAGGGCTTCAT * 916657 GGAC---TAACCAGGCATTTAGTTTTAAACAAATATA 130 GGACATATAAACA-GCATTTAGTTTTAAACAAATATA * * * 916691 TATGGGAGCAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATAGCCATAATGGCCC 1 TATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCC * * 916756 CATCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTATGGTAGAGGGCCTCAT 66 CACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATT-TGGTAGAGGGCTTCAT * 916821 AGACATGATAAACAGCCATTTAGTTTTAAACAAATATA 130 GGACAT-ATAAACAG-CATTTAGTTTTAAACAAATATA * * * 916859 TATGGGAGTAGAGAAGAAGATTTTCTAAAATTTAATACATTTTAACTATATGGCCATATTTGCCC 1 TATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCC * * * 916924 CACCCTAGAGCCTGAACCCCTGACCCAGGGGACATGAAGTTCACAATTTAGGTAGAGGACTTCAT 66 CACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTT-GGTAGAGGGCTTCAT * * * 916989 GGACATCATAATCATGCACTTAGTTTAAAACAA 130 GGACAT-ATAAACA-GCATTTAGTTTTAAACAA 917022 CAAGATATCT Statistics Matches: 290, Mismatches: 33, Indels: 12 0.87 0.10 0.04 Matches are distributed among these distances: 163 2 0.01 164 115 0.40 167 2 0.01 168 170 0.59 169 1 0.00 ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29 Consensus pattern (165 bp): TATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCC CACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTGGTAGAGGGCTTCATG GACATATAAACAGCATTTAGTTTTAAACAAATATA Found at i:917504 original size:166 final size:166 Alignment explanation

Indices: 917079--918038 Score: 1451 Period size: 166 Copynumber: 5.8 Consensus size: 166 917069 GTGAATATGC * * * * * * * * * 917079 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATTCCACA 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * * * * 917144 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATACATAGCTGCTGAGA 66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 917209 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCT- 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA * * 917244 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * * * 917309 ATATGGCATGCCTTAACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAAAAGCTGCTGAGA 66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * 917374 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA * 917410 AAAATAAACAAAGTAC-TCATTAAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC 1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC * * * 917474 GATATGGCATGCCTAAACAAACACTGTGTAAAAATTTCAAGCATCTGCAATATATAGTTGCTGAG 65 GATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG * 917539 AAATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA 130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA * * * * 917576 AAAATAAACAAAGTAC-TCATTAAACAGGAAGTTAACGTCTGATTGGTACAAAAATACATCCCAC 1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC ** * * * 917640 GATAAAGCATGCCTATACATATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGA- 65 GATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG * 917704 AAATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA 130 AAA-TCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA * * 917742 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATACATCCCACG 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * * * 917807 ATATGGTATGCCTATACAAATATTGTGTAAAAATTTGAAGCATCTGCGATAAATAGTTGCTGAGA 66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * 917872 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCT-A * 917909 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG 1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * 917974 ATATGGCATGCCTAAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 918039 TAAATGCGAC Statistics Matches: 732, Mismatches: 57, Indels: 10 0.92 0.07 0.01 Matches are distributed among these distances: 165 153 0.21 166 452 0.62 167 127 0.17 ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29 Consensus pattern (166 bp): AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA Found at i:918071 original size:4 final size:4 Alignment explanation

Indices: 918062--918107 Score: 56 Period size: 4 Copynumber: 11.5 Consensus size: 4 918052 AATTTTTGTT * * * * 918062 ACGG ACGG ACAG ACAG ACAG ACAG ACGG ACGG ACGG ACGG ACGG AC 1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG AC 918108 AGACAGACAG Statistics Matches: 40, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 4 40 1.00 ACGTcount: A:0.35, C:0.26, G:0.39, T:0.00 Consensus pattern (4 bp): ACGG Found at i:918112 original size:4 final size:4 Alignment explanation

Indices: 918069--918120 Score: 59 Period size: 4 Copynumber: 13.0 Consensus size: 4 918059 GTTACGGACG * * * * * 918069 GACA GACA GACA GACA GACG GACG GACG GACG GACG GACA GACA GACA 1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA 918117 GACA 1 GACA 918121 CACAAGGGTA Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 4 46 1.00 ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00 Consensus pattern (4 bp): GACA Found at i:927818 original size:12 final size:12 Alignment explanation

Indices: 927801--927831 Score: 53 Period size: 12 Copynumber: 2.6 Consensus size: 12 927791 TAAAAAGTTT 927801 ACAGACGGACAG 1 ACAGACGGACAG 927813 ACAGACGGACAG 1 ACAGACGGACAG * 927825 ACGGACG 1 ACAGACG 927832 ACGGACAACG Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00 Consensus pattern (12 bp): ACAGACGGACAG Found at i:928009 original size:32 final size:32 Alignment explanation

Indices: 927968--928035 Score: 109 Period size: 32 Copynumber: 2.1 Consensus size: 32 927958 ATCATGTGCA 927968 CAGATTTAGAGAAGGGGTGGGAGTGAGGGGTC 1 CAGATTTAGAGAAGGGGTGGGAGTGAGGGGTC * ** 928000 CAGATTTAGAGAAGGGTTGGGAGTGATTGGTC 1 CAGATTTAGAGAAGGGGTGGGAGTGAGGGGTC 928032 CAGA 1 CAGA 928036 CCCGACCCCC Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 32 33 1.00 ACGTcount: A:0.26, C:0.07, G:0.44, T:0.22 Consensus pattern (32 bp): CAGATTTAGAGAAGGGGTGGGAGTGAGGGGTC Found at i:942964 original size:2 final size:2 Alignment explanation

Indices: 942957--943015 Score: 100 Period size: 2 Copynumber: 29.5 Consensus size: 2 942947 ATAAGGGAAT * 942957 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA * 942999 GA GA GA GA AA GA GA GA G 1 GA GA GA GA GA GA GA GA G 943016 GATCATTATG Statistics Matches: 53, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00 Consensus pattern (2 bp): GA Found at i:943122 original size:2 final size:2 Alignment explanation

Indices: 943115--943164 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 943105 AGGGAAAAAT 943115 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 943157 GA GA GA GA 1 GA GA GA GA 943165 ACAAGTCCAT Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:951576 original size:4 final size:4 Alignment explanation

Indices: 951567--951624 Score: 107 Period size: 4 Copynumber: 14.5 Consensus size: 4 951557 TAAACTTCGC * 951567 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTGT CTTT 1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT 951615 CTTT CTTT CT 1 CTTT CTTT CT 951625 CAACATATCT Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 4 52 1.00 ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72 Consensus pattern (4 bp): CTTT Found at i:953211 original size:11 final size:11 Alignment explanation

Indices: 953197--953319 Score: 108 Period size: 11 Copynumber: 11.2 Consensus size: 11 953187 AACTGATGGG * 953197 TGACTGAAAAA 1 TGACTGAAAGA 953208 TGACTGAAAGA 1 TGACTGAAAGA * 953219 TGATTGAAAGA 1 TGACTGAAAGA 953230 TGACTGAAAGA 1 TGACTGAAAGA * * 953241 TGTCAGAAA-A 1 TGACTGAAAGA * 953251 -GTAATAGAAAGA 1 TG-ACT-GAAAGA * * * 953263 TAACTG-ATGTG 1 TGACTGAAAG-A 953274 TGACTGAAAGA 1 TGACTGAAAGA 953285 TGACTGAAAGA 1 TGACTGAAAGA * * 953296 TGATTGAAAAA 1 TGACTGAAAGA 953307 TGACTGAAAGA 1 TGACTGAAAGA 953318 TG 1 TG 953320 TCAGAAAAGT Statistics Matches: 87, Mismatches: 19, Indels: 12 0.74 0.16 0.10 Matches are distributed among these distances: 9 1 0.01 10 3 0.03 11 78 0.90 12 5 0.06 ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22 Consensus pattern (11 bp): TGACTGAAAGA Found at i:953234 original size:33 final size:33 Alignment explanation

Indices: 953197--953319 Score: 122 Period size: 33 Copynumber: 3.7 Consensus size: 33 953187 AACTGATGGG 953197 TGACTGAAAAATGACTGAAAGATGATTGAAAGA 1 TGACTGAAAAATGACTGAAAGATGATTGAAAGA * * * * * 953230 TGACTGAAAGATGTCAGAAA-AGTAATAGAAAGA 1 TGACTGAAAAATGACTGAAAGA-TGATTGAAAGA * **** * 953263 TAACTGATGTGTGACTGAAAGATGACTGAAAGA 1 TGACTGAAAAATGACTGAAAGATGATTGAAAGA * 953296 TGATTGAAAAATGACTGAAAGATG 1 TGACTGAAAAATGACTGAAAGATG 953320 TCAGAAAAGT Statistics Matches: 67, Mismatches: 21, Indels: 4 0.73 0.23 0.04 Matches are distributed among these distances: 32 1 0.01 33 65 0.97 34 1 0.01 ACGTcount: A:0.46, C:0.07, G:0.25, T:0.22 Consensus pattern (33 bp): TGACTGAAAAATGACTGAAAGATGATTGAAAGA Found at i:953240 original size:77 final size:77 Alignment explanation

Indices: 953128--953360 Score: 344 Period size: 77 Copynumber: 3.0 Consensus size: 77 953118 ATTGGATTAG * * * * * * * * 953128 AAATGACTTAAAGGTGACT-AAAATATGACTAAAAGATTTAAGAAAAGTGATAGAAATATAACTG 1 AAATGACTGAAAGATGATTGAAAA-ATGACTGAAAGATGTCAGAAAAGTAATAGAAAGATAACTG * 953192 ATGGGTGACTGAA 65 ATGTGTGACTGAA * 953205 AAATGACTGAAAGATGATTGAAAGATGACTGAAAGATGTCAGAAAAGTAATAGAAAGATAACTGA 1 AAATGACTGAAAGATGATTGAAAAATGACTGAAAGATGTCAGAAAAGTAATAGAAAGATAACTGA 953270 TGTGTGACTGAA 66 TGTGTGACTGAA * 953282 AGATGACTGAAAGATGATTGAAAAATGACTGAAAGATGTCAGAAAAGTAATAGAAAGATAACTGA 1 AAATGACTGAAAGATGATTGAAAAATGACTGAAAGATGTCAGAAAAGTAATAGAAAGATAACTGA 953347 TGTGTGACT-AA 66 TGTGTGACTGAA 953358 AAA 1 AAA 953361 GTGAATGATG Statistics Matches: 142, Mismatches: 13, Indels: 3 0.90 0.08 0.02 Matches are distributed among these distances: 76 4 0.03 77 135 0.95 78 3 0.02 ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23 Consensus pattern (77 bp): AAATGACTGAAAGATGATTGAAAAATGACTGAAAGATGTCAGAAAAGTAATAGAAAGATAACTGA TGTGTGACTGAA Done.