Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_D11

Parameters: 2 7 7 80 10 50 1000

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

Length: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33

Warning! 408745 characters in sequence are not A, C, G, or T


File 161 of 226

Found at i:49817430 original size:17 final size:17

Alignment explanation

Indices: 49817408--49817442 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 17 49817398 TTTATATACA * * 49817408 TATATATATTTACATTT 1 TATATACATATACATTT 49817425 TATATACATATACATTT 1 TATATACATATACATTT 49817442 T 1 T 49817443 TTATTTCCTA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54 Consensus pattern (17 bp): TATATACATATACATTT Found at i:49817634 original size:30 final size:31 Alignment explanation

Indices: 49817600--49817657 Score: 82 Period size: 31 Copynumber: 1.9 Consensus size: 31 49817590 TATTTGTTTT * * 49817600 TATATTTATGTA-ATTATCTTTTTTATAATC 1 TATATATATGTAGATAATCTTTTTTATAATC * 49817630 TATATATATGTAGATAATTTTTTTTATA 1 TATATATATGTAGATAATCTTTTTTATA 49817658 TATGTACATG Statistics Matches: 24, Mismatches: 3, Indels: 1 0.86 0.11 0.04 Matches are distributed among these distances: 30 11 0.46 31 13 0.54 ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59 Consensus pattern (31 bp): TATATATATGTAGATAATCTTTTTTATAATC Found at i:49818629 original size:13 final size:13 Alignment explanation

Indices: 49818611--49818636 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 49818601 ACTAAGGATA 49818611 GTATTTATTAACT 1 GTATTTATTAACT 49818624 GTATTTATTAACT 1 GTATTTATTAACT 49818637 CTCGACATTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54 Consensus pattern (13 bp): GTATTTATTAACT Found at i:49819440 original size:8 final size:8 Alignment explanation

Indices: 49819427--49819451 Score: 50 Period size: 8 Copynumber: 3.1 Consensus size: 8 49819417 GTTTTTTTAA 49819427 ATTAAAAT 1 ATTAAAAT 49819435 ATTAAAAT 1 ATTAAAAT 49819443 ATTAAAAT 1 ATTAAAAT 49819451 A 1 A 49819452 ATTTTTAATA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 17 1.00 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (8 bp): ATTAAAAT Found at i:49821554 original size:9 final size:9 Alignment explanation

Indices: 49821540--49821565 Score: 52 Period size: 9 Copynumber: 2.9 Consensus size: 9 49821530 GGATTAAATT 49821540 GTAAAAGTA 1 GTAAAAGTA 49821549 GTAAAAGTA 1 GTAAAAGTA 49821558 GTAAAAGT 1 GTAAAAGT 49821566 TAATCACTAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 17 1.00 ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23 Consensus pattern (9 bp): GTAAAAGTA Found at i:49824153 original size:2 final size:2 Alignment explanation

Indices: 49824148--49824173 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 49824138 TATTATATAC 49824148 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 49824174 ACACTTTATT 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:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:49849652 original size:220 final size:219 Alignment explanation

Indices: 49849356--49849800 Score: 651 Period size: 220 Copynumber: 2.0 Consensus size: 219 49849346 AATGCTACGA * * * 49849356 TTAAAAGAAGGTAGCTTAGCATGTATAATGAAGGTAAGTAGAGCTGATTATGGGACAAGCTTGAT 1 TTAAAAGAAAGTAGCTTAGCATGTATAATAAAGGTAACTAGAGCTGATTATGGGACAAGCTTGAT * * * * 49849421 CCATGCAAGGTATTTAGATTAATTTTTTAAGTTTGAGTTCGATCTGAT-TTGAAAAATGGATTTA 66 CCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTTCGACCCGATCCT-AAAAATGGATTTA * * * 49849485 ATTTTTTGTTTACGTTTGGTCCAATTTAAGAAAGGTAAATTC-GGCCCAACCCGGTCCACCCATA 130 ATTTTTTGTTTACGTTCGATCCAATTTAAGAAAGGTAAATCCGGGCCCAACCCGGTCCACCCATA 49849549 TTTAATTTTTTAGATTAGTTTTTAT 195 TTTAATTTTTTAGATTAGTTTTTAT * * * * 49849574 TTAAAAGAAAGTAGCTTAGCATGTATATAATAAAGGTAACTAGAGGTGATTATGGGCCGAGTTTG 1 TTAAAAGAAAGTAGCTTAGCATG--TATAATAAAGGTAACTAGAGCTGATTATGGGACAAGCTTG * * * * 49849639 ATTCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTTCTACCCGATCCTAGAAATGGGTTT 64 ATCCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTTCGACCCGATCCTAAAAATGGATTT * * * 49849704 AATTTTTTGTTTACGTTCGATCCGATTTAAGAAAGGTAAATCCGGGCCTAACCCGGTCCACTCAT 129 AATTTTTTGTTTACGTTCGATCCAATTTAAGAAAGGTAAATCCGGGCCCAACCCGGTCCACCCAT * 49849769 ATTTGATTTTTTAGATTAGTTTTTAT 194 ATTTAATTTTTTAGATTAGTTTTTAT 49849795 TTAAAA 1 TTAAAA 49849801 TCATTTAAAA Statistics Matches: 201, Mismatches: 22, Indels: 5 0.88 0.10 0.02 Matches are distributed among these distances: 218 22 0.11 220 128 0.64 221 51 0.25 ACGTcount: A:0.31, C:0.12, G:0.20, T:0.38 Consensus pattern (219 bp): TTAAAAGAAAGTAGCTTAGCATGTATAATAAAGGTAACTAGAGCTGATTATGGGACAAGCTTGAT CCATGCAAGGTATTTAGATTAACTTTTTAAGTTTGAGTTCGACCCGATCCTAAAAATGGATTTAA TTTTTTGTTTACGTTCGATCCAATTTAAGAAAGGTAAATCCGGGCCCAACCCGGTCCACCCATAT TTAATTTTTTAGATTAGTTTTTAT Found at i:49857706 original size:13 final size:14 Alignment explanation

Indices: 49857677--49857709 Score: 50 Period size: 13 Copynumber: 2.4 Consensus size: 14 49857667 TATGATTAGT * 49857677 GTTAATTAGGCTTA 1 GTTAATTAAGCTTA 49857691 GTTAATTAAG-TTA 1 GTTAATTAAGCTTA 49857704 GTTAAT 1 GTTAAT 49857710 ATTAATTTTA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 13 9 0.50 14 9 0.50 ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45 Consensus pattern (14 bp): GTTAATTAAGCTTA Found at i:49859713 original size:23 final size:21 Alignment explanation

Indices: 49859687--49859749 Score: 56 Period size: 24 Copynumber: 2.9 Consensus size: 21 49859677 ATATGAAATA 49859687 TAACATACAAAATAATATATAC 1 TAACATA-AAAATAATATATAC * * * 49859709 TTAACCTAAATAAATATTACATAC 1 -TAACAT-AA-AAATAATATATAC 49859733 TAA-ATAAAAATAATATA 1 TAACATAAAAATAATATA 49859750 AAACCAACAA Statistics Matches: 32, Mismatches: 6, Indels: 7 0.71 0.13 0.16 Matches are distributed among these distances: 20 8 0.25 21 2 0.06 22 1 0.03 23 9 0.28 24 12 0.38 ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30 Consensus pattern (21 bp): TAACATAAAAATAATATATAC Found at i:49859944 original size:3 final size:3 Alignment explanation

Indices: 49859936--49859982 Score: 60 Period size: 3 Copynumber: 15.7 Consensus size: 3 49859926 ATAATCAGAT * * 49859936 ATA ATA ATA ATA ACA ATA ATAA ATA GTA A-A ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA 49859981 AT 1 AT 49859983 TAAGTGATTA Statistics Matches: 38, Mismatches: 4, Indels: 4 0.83 0.09 0.09 Matches are distributed among these distances: 2 2 0.05 3 33 0.87 4 3 0.08 ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30 Consensus pattern (3 bp): ATA Found at i:49861162 original size:44 final size:44 Alignment explanation

Indices: 49861101--49861372 Score: 329 Period size: 44 Copynumber: 6.2 Consensus size: 44 49861091 TTCGATCTGC * 49861101 TCCACTACTGCTT-AGGGAGACAGGA-TCTACAATCTTCAACCTAT 1 TCCACTGCTG-TTCAGGGAGACAGGACT-TACAATCTTCAACCTAT * * * * 49861145 TACACTGCTGTTCAGGGAGATAGGACATACAATCTTCCACCTAT 1 TCCACTGCTGTTCAGGGAGACAGGACTTACAATCTTCAACCTAT * 49861189 TCCACTGCTGTTCAGGGAG-CTAGGACTTACAATCTTCCACCTAT 1 TCCACTGCTGTTCAGGGAGAC-AGGACTTACAATCTTCAACCTAT * * * 49861233 TCCACTACTGTTCAGGGAG-CTAGGACTTGCAATCTTCCACCTAT 1 TCCACTGCTGTTCAGGGAGAC-AGGACTTACAATCTTCAACCTAT * * * * 49861277 TCCACTGCTGGTCAGGGAGATAGGACTTGCAATCTTTAACCTAT 1 TCCACTGCTGTTCAGGGAGACAGGACTTACAATCTTCAACCTAT * * 49861321 TCCACTGCTGGTT-AGGGAGATAGGACTTGCAATCTTCAACCTAT 1 TCCACTGCT-GTTCAGGGAGACAGGACTTACAATCTTCAACCTAT 49861365 TCCACTGC 1 TCCACTGC 49861373 CGTCTAAGGA Statistics Matches: 206, Mismatches: 17, Indels: 10 0.88 0.07 0.04 Matches are distributed among these distances: 43 2 0.01 44 202 0.98 45 2 0.01 ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29 Consensus pattern (44 bp): TCCACTGCTGTTCAGGGAGACAGGACTTACAATCTTCAACCTAT Found at i:49861206 original size:88 final size:88 Alignment explanation

Indices: 49861101--49861372 Score: 372 Period size: 88 Copynumber: 3.1 Consensus size: 88 49861091 TTCGATCTGC * * 49861101 TCCACTACTGCTT-AGGGAGACAGGA-TCTACAATCTTCAACCTATTACACTGCTGTTCAGGGAG 1 TCCACTGCTG-TTCAGGGAGACAGGACT-TACAATCTTCAACCTATTCCACTGCTGTTCAGGGAG * * 49861164 ATAGGACATACAATCTTCCACCTAT 64 ATAGGACTTGCAATCTTCCACCTAT * * * 49861189 TCCACTGCTGTTCAGGGAG-CTAGGACTTACAATCTTCCACCTATTCCACTACTGTTCAGGGAGC 1 TCCACTGCTGTTCAGGGAGAC-AGGACTTACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGA 49861253 TAGGACTTGCAATCTTCCACCTAT 65 TAGGACTTGCAATCTTCCACCTAT * * * * 49861277 TCCACTGCTGGTCAGGGAGATAGGACTTGCAATCTTTAACCTATTCCACTGCTGGTT-AGGGAGA 1 TCCACTGCTGTTCAGGGAGACAGGACTTACAATCTTCAACCTATTCCACTGCT-GTTCAGGGAGA * 49861341 TAGGACTTGCAATCTTCAACCTAT 65 TAGGACTTGCAATCTTCCACCTAT 49861365 TCCACTGC 1 TCCACTGC 49861373 CGTCTAAGGA Statistics Matches: 164, Mismatches: 15, Indels: 10 0.87 0.08 0.05 Matches are distributed among these distances: 87 3 0.02 88 157 0.96 89 4 0.02 ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29 Consensus pattern (88 bp): TCCACTGCTGTTCAGGGAGACAGGACTTACAATCTTCAACCTATTCCACTGCTGTTCAGGGAGAT AGGACTTGCAATCTTCCACCTAT Found at i:49861326 original size:132 final size:132 Alignment explanation

Indices: 49861101--49861370 Score: 377 Period size: 132 Copynumber: 2.0 Consensus size: 132 49861091 TTCGATCTGC * 49861101 TCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTATTACACTGCTGTTCAGGGAGAT 1 TCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTATTACACTGCTGGTCAGGGAGAT * * * 49861166 AGGACATACAATCTTCCACCTATTCCACTGCT-GTTCAGGGAGCTAGGACTTACAATCTTCCACC 66 AGGACATACAATCTTCAACCTATTCCACTGCTGGTT-AGGGAGATAGGACTTACAATCTTCAACC 49861230 TAT 130 TAT * * * 49861233 TCCACTACTG-TTCAGGGAG-CTAGGA-CTTGCAATCTTCCACCTATTCCACTGCTGGTCAGGGA 1 TCCACTACTGCTT-AGGGAGAC-AGGATC-TACAATCTTCAACCTATTACACTGCTGGTCAGGGA * * * * 49861295 GATAGGACTTGCAATCTTTAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTGCAATCTTCAA 63 GATAGGACATACAATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTACAATCTTCAA 49861360 CCTAT 128 CCTAT 49861365 TCCACT 1 TCCACT 49861371 GCCGTCTAAG Statistics Matches: 123, Mismatches: 11, Indels: 8 0.87 0.08 0.06 Matches are distributed among these distances: 131 4 0.03 132 116 0.94 133 3 0.02 ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29 Consensus pattern (132 bp): TCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTATTACACTGCTGGTCAGGGAGAT AGGACATACAATCTTCAACCTATTCCACTGCTGGTTAGGGAGATAGGACTTACAATCTTCAACCT AT Found at i:49861384 original size:44 final size:44 Alignment explanation

Indices: 49861130--49861389 Score: 362 Period size: 44 Copynumber: 5.9 Consensus size: 44 49861120 ACAGGATCTA * * * 49861130 CAATCTTCAACCTATTACACTGCTGTTCAGGGAGATAGGACATA 1 CAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTG * * * 49861174 CAATCTTCCACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTA 1 CAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTG * * * 49861218 CAATCTTCCACCTATTCCACTACTGTTCAGGGAGCTAGGACTTG 1 CAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTG * * 49861262 CAATCTTCCACCTATTCCACTGCTGGTCAGGGAGATAGGACTTG 1 CAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTG * 49861306 CAATCTTTAACCTATTCCACTGCTGGTT-AGGGAGATAGGACTTG 1 CAATCTTCAACCTATTCCACTGCT-GTTCAGGGAGATAGGACTTG * * 49861350 CAATCTTCAACCTATTCCACTGCCG-TCTAAGGAGATAGGA 1 CAATCTTCAACCTATTCCACTGCTGTTC-AGGGAGATAGGA 49861390 ATAGTGGCTT Statistics Matches: 198, Mismatches: 15, Indels: 6 0.90 0.07 0.03 Matches are distributed among these distances: 42 1 0.01 43 1 0.01 44 194 0.98 45 2 0.01 ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28 Consensus pattern (44 bp): CAATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTG Found at i:49861541 original size:44 final size:44 Alignment explanation

Indices: 49861440--49861541 Score: 118 Period size: 44 Copynumber: 2.3 Consensus size: 44 49861430 AAGATTTGCC * * 49861440 ATCTTTGATCTGCTCCACTACTGCTTAGGAAGATAAGATCTGTA 1 ATCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAGAGCTGTA * * * * 49861484 ATTTTCAACCTGCTCCACTACTGCTTAGGGAGATAAG-GCT-TACA 1 ATCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAGAGCTGT--A 49861528 ATCTTCGATCTGCT 1 ATCTTCGATCTGCT 49861542 TCACCGTTAG Statistics Matches: 47, Mismatches: 9, Indels: 4 0.78 0.15 0.07 Matches are distributed among these distances: 42 1 0.02 43 2 0.04 44 44 0.94 ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33 Consensus pattern (44 bp): ATCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAGAGCTGTA Found at i:49861611 original size:89 final size:88 Alignment explanation

Indices: 49861474--49861667 Score: 192 Period size: 88 Copynumber: 2.2 Consensus size: 88 49861464 TTAGGAAGAT * * ** * * * 49861474 AAGATCTGTAATTTTCAACCTGCTCCACTACTGCTTAGGGAGATAAGGCTTACAATCTTCGATCT 1 AAGATCTGTTATTTTCAACCTGCTCCACTACTACCCAAGGAGACAAGGCTGAC-ATCTTCGATCT * * * 49861539 GCTTCACCGTTAGTACAGGGAGGC 65 GCTTCACCGTCAGTACAAGAAGGC * * * * 49861563 AAGATCTGTTATTTTCAACCTGCTCCGCTA-TAACCCAAGGAGGCAAGGCTGGCGTCTTCGATCT 1 AAGATCTGTTATTTTCAACCTGCTCCACTACT-ACCCAAGGAGACAAGGCTGACATCTTCGATCT * * * * 49861627 GCTTCGCTGTCGGTGCAAGAAGGC 65 GCTTCACCGTCAGTACAAGAAGGC * 49861651 AAGATCTGTTATCTTCA 1 AAGATCTGTTATTTTCA 49861668 CTGATCTGTT Statistics Matches: 85, Mismatches: 19, Indels: 3 0.79 0.18 0.03 Matches are distributed among these distances: 88 44 0.52 89 41 0.48 ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29 Consensus pattern (88 bp): AAGATCTGTTATTTTCAACCTGCTCCACTACTACCCAAGGAGACAAGGCTGACATCTTCGATCTG CTTCACCGTCAGTACAAGAAGGC Found at i:49868082 original size:31 final size:31 Alignment explanation

Indices: 49868009--49868085 Score: 91 Period size: 31 Copynumber: 2.5 Consensus size: 31 49867999 ACTAGAATGA * * * 49868009 GTATGATATGAACTACTAATTGACATGTGAT 1 GTATGATATGAATTGCTAAATGACATGTGAT * * * 49868040 ATGTGATATGAATTGCTAAATGATATGTGAT 1 GTATGATATGAATTGCTAAATGACATGTGAT * 49868071 GTATGAAATGAATTG 1 GTATGATATGAATTG 49868086 ATGATGAGAT Statistics Matches: 37, Mismatches: 9, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 31 37 1.00 ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36 Consensus pattern (31 bp): GTATGATATGAATTGCTAAATGACATGTGAT Found at i:49869784 original size:25 final size:25 Alignment explanation

Indices: 49869750--49869803 Score: 108 Period size: 25 Copynumber: 2.2 Consensus size: 25 49869740 ATGAAAGGAA 49869750 TGTACCAACGTATTACAGATCAAGT 1 TGTACCAACGTATTACAGATCAAGT 49869775 TGTACCAACGTATTACAGATCAAGT 1 TGTACCAACGTATTACAGATCAAGT 49869800 TGTA 1 TGTA 49869804 GTCAAGCAAG Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 29 1.00 ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30 Consensus pattern (25 bp): TGTACCAACGTATTACAGATCAAGT Found at i:49871021 original size:46 final size:45 Alignment explanation

Indices: 49870925--49871026 Score: 123 Period size: 46 Copynumber: 2.2 Consensus size: 45 49870915 TTTTCATAAC * * * 49870925 ATATGATTCAATACTAAAATCATTCCAAACTAACATGATAAGCAAT 1 ATATGA-TCAATACTAAAATCATTCCAAACTAACATAACAAGCAAA * ** * 49870971 ATATGACTCAATACTAAAATCATTCCCAACTAGTATAACAAGTAAA 1 ATATGA-TCAATACTAAAATCATTCCAAACTAACATAACAAGCAAA 49871017 ATATGATCAA 1 ATATGATCAA 49871027 AATTGTAACA Statistics Matches: 48, Mismatches: 8, Indels: 1 0.84 0.14 0.02 Matches are distributed among these distances: 45 4 0.08 46 44 0.92 ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27 Consensus pattern (45 bp): ATATGATCAATACTAAAATCATTCCAAACTAACATAACAAGCAAA Found at i:49874146 original size:84 final size:84 Alignment explanation

Indices: 49874032--49874367 Score: 564 Period size: 84 Copynumber: 4.0 Consensus size: 84 49874022 CGTAAAAAAT * * 49874032 AAAACACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTTGTGGCATTTTTGGTCTAGCGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874097 AATGGTCTGCGTTTTTAGC 66 AATGGTCTGTGTTTTTAGC * * * * 49874116 AAAATACAATGGCGTCGTTTATTGGCCTTCGGTGGCCTTAGTGGCGTTTTTTGTCTAGCGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874181 AATGGTCTATGTTTTTAGC 66 AATGGTCTGTGTTTTTAGC * * 49874200 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCACCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT 49874265 AATGGTCTGTGTTTTTAGC 66 AATGGTCTGTGTTTTTAGC * 49874284 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGTGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874349 AATGGTATGTGTTTTTAGC 66 AATGGTCTGTGTTTTTAGC 49874368 GGCGTTTTAA Statistics Matches: 235, Mismatches: 17, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 84 235 1.00 ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35 Consensus pattern (84 bp): AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT AATGGTCTGTGTTTTTAGC Found at i:49874499 original size:84 final size:84 Alignment explanation

Indices: 49874397--49874564 Score: 309 Period size: 84 Copynumber: 2.0 Consensus size: 84 49874387 CGCAAAAAAT * * 49874397 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGTCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCAGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT * 49874462 AATGGTCTGTGTTTTTAGC 66 AATGGTATGTGTTTTTAGC 49874481 AAAATACAACGGCGTCGTTTAGTGGCCTTCAGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCAGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT 49874546 AATGGTATGTGTTTTTAGC 66 AATGGTATGTGTTTTTAGC 49874565 GGCGTTTTAA Statistics Matches: 81, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 84 81 1.00 ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35 Consensus pattern (84 bp): AAAATACAACGGCGTCGTTTAGTGGCCTTCAGTGGCCTTAGTGGCGTTTTTGGTCTAGCGCCGCT AATGGTATGTGTTTTTAGC Found at i:49874535 original size:197 final size:198 Alignment explanation

Indices: 49874200--49875062 Score: 1410 Period size: 198 Copynumber: 4.4 Consensus size: 198 49874190 TGTTTTTAGC * * 49874200 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCACCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874265 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCA 66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG * 49874330 TTTTTGGTCTAGTGCCGCTAATGGTATGTGTTTTTAGCGGCGTTTT-AAAAAAAACGCCGCAAAA 131 TTTTTGGTCTAGCGCCGCTAATGGTATGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAAA 49874394 AAT 196 AAT * * 49874397 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGTCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874462 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCAGTGGCCTTAGTGGCG 66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG * 49874527 TTTTTGGTCTAGCGCCGCTAATGGTATGTGTTTTTAGCGGCGTTTT-AAAAAAAACGCCG-TAAA 131 TTTTTGGTCTAGCGCCGCTAATGGTATGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAAA 49874590 AAT 196 AAT * 49874593 AAAATACAACGGCGTTGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874658 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCTTAGTGGCG 66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG * * * * 49874723 TTTTTGGTCTAGGGCCACTAATGGTTTGTGTTTTTAGCGGCGTTTTCATAAAAAACGCCGCAAAA 131 TTTTTGGTCTAGCGCCGCTAATGGTATGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAAA * 49874788 ATT 196 AAT * 49874791 AAAATACCACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874856 AATGGTCTGTATTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG 66 AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG * * * * * 49874921 TTTTTGGTCTAGCGTCGCTAATGGTCTGTATTTGTAGCGGCGTTTTCAGAAAAAACGCCGCAAAA 131 TTTTTGGTCTAGCGCCGCTAATGGTATGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAAA 49874986 AAT 196 AAT * * * 49874989 AAAATATAACGTCGTCGTTTA----------GTGGCCTTAGTGGCATTTTTGGTCTAGCACCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT 49875044 AATGGTCTGTGTTTTTAGC 66 AATGGTCTGTGTTTTTAGC 49875063 GGCGTTTTTA Statistics Matches: 630, Mismatches: 34, Indels: 13 0.93 0.05 0.02 Matches are distributed among these distances: 188 51 0.08 196 174 0.28 197 196 0.31 198 209 0.33 ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33 Consensus pattern (198 bp): AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT AATGGTCTGTGTTTTTAGCAAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCG TTTTTGGTCTAGCGCCGCTAATGGTATGTGTTTTTAGCGGCGTTTTCAAAAAAAACGCCGCAAAA AAT Found at i:49874734 original size:84 final size:84 Alignment explanation

Indices: 49874593--49874760 Score: 282 Period size: 84 Copynumber: 2.0 Consensus size: 84 49874583 CCGTAAAAAT ** * 49874593 AAAATACAACGGCGTTGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT 1 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCACT 49874658 AATGGTCTGTGTTTTTAGC 66 AATGGTCTGTGTTTTTAGC * * 49874677 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGGGCCACT 1 AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCACT * 49874742 AATGGTTTGTGTTTTTAGC 66 AATGGTCTGTGTTTTTAGC 49874761 GGCGTTTTCA Statistics Matches: 78, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 84 78 1.00 ACGTcount: A:0.17, C:0.18, G:0.29, T:0.36 Consensus pattern (84 bp): AAAATACAACGGCGTCATTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCACT AATGGTCTGTGTTTTTAGC Found at i:49874887 original size:84 final size:84 Alignment explanation

Indices: 49874791--49874958 Score: 300 Period size: 84 Copynumber: 2.0 Consensus size: 84 49874781 CGCAAAAATT * 49874791 AAAATACCACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT * 49874856 AATGGTCTGTATTTTTAGC 66 AATGGTCTGTATTTGTAGC * * 49874875 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGTCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT 49874940 AATGGTCTGTATTTGTAGC 66 AATGGTCTGTATTTGTAGC 49874959 GGCGTTTTCA Statistics Matches: 80, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 84 80 1.00 ACGTcount: A:0.17, C:0.20, G:0.29, T:0.35 Consensus pattern (84 bp): AAAATACAACGGCGTCGTTTAGTGGCCTTCGGTGGCCTTAGTGGCATTTTTGGTCTAGCGCCGCT AATGGTCTGTATTTGTAGC Found at i:49875208 original size:113 final size:113 Alignment explanation

Indices: 49874875--49875231 Score: 443 Period size: 104 Copynumber: 3.2 Consensus size: 113 49874865 TATTTTTAGC * * ** 49874875 AAAATACAACGGCGTCGTTTAGTGGCCT-TCGGTGGCCTTAGTGGCGTTTTTGGTCTAGCGTCGC 1 AAAATACAACGGCGTCGTTTAGTGG-CTAT-GGTGGCATTAGTGGCATTTTTGGTCTAGCACCGC * * * * * 49874939 TAATGGTCTGTATTTGTAGCGGCGTTTTCAGAAAAAACGCCGCAAAAAAT 64 TAATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAATAATGCCGCAAAAAAT * * 49874989 AAAATATAACGTCGTCGTTTAGTGGC--------C-TTAGTGGCATTTTTGGTCTAGCACCGCTA 1 AAAATACAACGGCGTCGTTTAGTGGCTATGGTGGCATTAGTGGCATTTTTGGTCTAGCACCGCTA * 49875045 ATGGTCTGTGTTTTTAGCGGCGTTTTTAGGAATAATGCCGCAAAAAAT 66 ATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAATAATGCCGCAAAAAAT * * 49875093 AAAATACAACGTCGTCGTTTAGTGGCTATGGTGGCATTAGTGGCATTTTTGGTCT-GCCGCCGCT 1 AAAATACAACGGCGTCGTTTAGTGGCTATGGTGGCATTAGTGGCATTTTTGGTCTAG-CACCGCT * 49875157 AATTGTCTGTGTTTTTAGCGGCGTTTTCAGG-ATAAATGCCG-AGAAAAAT 65 AATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAAT-AATGCCGCA-AAAAAT 49875206 AAAATACAACGGCGTCGTTTAGTGGC 1 AAAATACAACGGCGTCGTTTAGTGGC 49875232 CTTCGGTGGC Statistics Matches: 215, Mismatches: 16, Indels: 25 0.84 0.06 0.10 Matches are distributed among these distances: 104 93 0.43 105 1 0.00 112 5 0.02 113 93 0.43 114 23 0.11 ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32 Consensus pattern (113 bp): AAAATACAACGGCGTCGTTTAGTGGCTATGGTGGCATTAGTGGCATTTTTGGTCTAGCACCGCTA ATGGTCTGTGTTTTTAGCGGCGTTTTCAGGAATAATGCCGCAAAAAAT Found at i:49876545 original size:391 final size:385 Alignment explanation

Indices: 49875824--49876744 Score: 1453 Period size: 391 Copynumber: 2.4 Consensus size: 385 49875814 GTTCATATAA * * * * * * * 49875824 TTTTAAGGTTTAGGGAGTACTATATATATAT-T-TATATATGGATTATAGATTAGGGGTTTTGCT 1 TTTTAATGTTTAGGGAGTACTATATATATATATGGATTTAGGGATTATAGATTATGGATTATGCT * 49875887 TAATTAAGGGTTAGTCGAGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTTAGTGGTTAAGACTT 66 TAATTAAGGGTTGGTCGAGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTTAGTGGTTAAGACTT * * * 49875952 AGGGATTT-TGTGTTTAGGGTTTCAGGGGTCGGGTTACAGTTTTGGTTTAGATTATTTTTTTATT 131 AGGGATTTAAG-GTTTAGGGTTTCAGAGGTCGGGTTACAATTTTGGTTTAGATTATTTTTTTATT * * 49876016 TATATTTTAAATATGTTCTTATGTAATTGTAAAATATGTATAATTTAGGGTTTAATTAATTATGC 195 TATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAA-TAATTATGC * * 49876081 CTTGAGAGATATATATATAATAGATAGAGTACTTAAATATTTATATCCCTTCAATGGTTAATTTA 259 CTTGAGAGAGATATATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTTAATTTA 49876146 GGCGGGTTTAATAAGATTAAGGTTTAACTAAGATTTTGAATTTTATACAATTAATTAATGCT 324 GGCGGGTTTAATAAGATTAAGGTTTAACTAAGATTTTGAATTTTATACAATTAATTAATGCT 49876208 TTTTAATGTTTAGGGAGTACTATATATATATATGGATTTAGGGATTATAGATTATGGATTATGCT 1 TTTTAATGTTTAGGGAGTACTATATATATATATGGATTTAGGGATTATAGATTATGGATTATGCT * * * 49876273 TAACTAAGGGTTGGTCGGGATTTAAGGTTTAGGGGAGGGGTTTAGGGGTTAGATGTTAGTTGTTA 66 TAATTAAGGGTTGGTCGAGATTTAAGGTTT-----AGGGG-TTAGGGGTTAGATGTTAGTGGTTA * * 49876338 AAACTTAGGGATTTAAGGTTTAGGGTTTCAGAGGTCTGGTTACAATTTTGGATTTAGATTAATTT 125 AGACTTAGGGATTTAAGGTTTAGGGTTTCAGAGGTCGGGTTACAATTTTGG-TTTAGATT-ATTT 49876403 TTTTATTTATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTT-A-AA 188 TTTTATTTATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAATAA 49876466 TTATGCCTTGAGAGAGATATATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTT 253 TTATGCCTTGAGAGAGATATATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTT * 49876531 AATTTAGGCGGGTTTAATAAGATTAAGGTTTAACTGAGATTTTGAATTTTATACAATTAATTAAT 318 AATTTAGGCGGGTTTAATAAGATTAAGGTTTAACTAAGATTTTGAATTTTATACAATTAATTAAT 49876596 GCT 383 GCT * 49876599 TTTTAATGTTTAGGGAGTGC--TATATATATATGGATTTAGGGATTATAGATTATGGATTATGCT 1 TTTTAATGTTTAGGGAGTACTATATATATATATGGATTTAGGGATTATAGATTATGGATTATGCT * * 49876662 TAATTAAGGGTTGG-CTGAGATTTAAGATTTAGGGGTTAGGGGTTAGATGCTAGTGGTTAAGACT 66 TAATTAAGGGTTGGTC-GAGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTTAGTGGTTAAGACT * * 49876726 TAGGAATTTAGGGTTTAGG 130 TAGGGATTTAAGGTTTAGG 49876745 AGAGGACCAA Statistics Matches: 495, Mismatches: 30, Indels: 25 0.90 0.05 0.05 Matches are distributed among these distances: 383 43 0.09 384 35 0.07 385 1 0.00 386 52 0.11 388 1 0.00 389 68 0.14 391 156 0.32 392 67 0.14 393 10 0.02 394 62 0.13 ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42 Consensus pattern (385 bp): TTTTAATGTTTAGGGAGTACTATATATATATATGGATTTAGGGATTATAGATTATGGATTATGCT TAATTAAGGGTTGGTCGAGATTTAAGGTTTAGGGGTTAGGGGTTAGATGTTAGTGGTTAAGACTT AGGGATTTAAGGTTTAGGGTTTCAGAGGTCGGGTTACAATTTTGGTTTAGATTATTTTTTTATTT ATATTTTAAATATGTTCTTATGTAATTGTAAAAGATGTATAAATTAGGGTTTAATAATTATGCCT TGAGAGAGATATATATAATAGATAGAATACTTAAATATTTATATCCCTTCAATGGTTAATTTAGG CGGGTTTAATAAGATTAAGGTTTAACTAAGATTTTGAATTTTATACAATTAATTAATGCT Found at i:49880866 original size:21 final size:21 Alignment explanation

Indices: 49880826--49880896 Score: 90 Period size: 21 Copynumber: 3.4 Consensus size: 21 49880816 CCACAACTTA * * 49880826 AAGCAGAGGCGGCAGAGAGGG 1 AAGCAGAGGCTGCAGCGAGGG * 49880847 AAG-ATGCGGCTGCAGCGAGGG 1 AAGCA-GAGGCTGCAGCGAGGG * 49880868 AAGCAGAGGCTGCAGCGAGAG 1 AAGCAGAGGCTGCAGCGAGGG 49880889 AAGCAGAG 1 AAGCAGAG 49880897 CAGAGCAAAA Statistics Matches: 43, Mismatches: 5, Indels: 4 0.83 0.10 0.08 Matches are distributed among these distances: 20 1 0.02 21 41 0.95 22 1 0.02 ACGTcount: A:0.32, C:0.17, G:0.46, T:0.04 Consensus pattern (21 bp): AAGCAGAGGCTGCAGCGAGGG Found at i:49882355 original size:2 final size:2 Alignment explanation

Indices: 49882348--49882381 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 49882338 GAGAAATCAA 49882348 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 49882382 CTAGTTAGGG Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:49885334 original size:17 final size:17 Alignment explanation

Indices: 49885287--49885336 Score: 57 Period size: 17 Copynumber: 2.9 Consensus size: 17 49885277 AAAAAAATTA * 49885287 AATTATAATATTCAAAG 1 AATTATAATATTTAAAG * 49885304 AATACATAA-ATTTAAAG 1 AAT-TATAATATTTAAAG * 49885321 AATTATAATCTTTAAA 1 AATTATAATATTTAAA 49885337 TTTTTACTCT Statistics Matches: 27, Mismatches: 4, Indels: 4 0.77 0.11 0.11 Matches are distributed among these distances: 16 4 0.15 17 19 0.70 18 4 0.15 ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36 Consensus pattern (17 bp): AATTATAATATTTAAAG Found at i:49885585 original size:22 final size:22 Alignment explanation

Indices: 49885560--49885606 Score: 78 Period size: 22 Copynumber: 2.1 Consensus size: 22 49885550 AATTTTAATA 49885560 TTCAATTTAGTACTTGAA-TTTT 1 TTCAATTTAGTACTT-AAGTTTT 49885582 TTCAATTTAGTACTTAAGTTTT 1 TTCAATTTAGTACTTAAGTTTT 49885604 TTC 1 TTC 49885607 TTTGTCTCAT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 21 2 0.08 22 22 0.92 ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55 Consensus pattern (22 bp): TTCAATTTAGTACTTAAGTTTT Found at i:49889365 original size:27 final size:27 Alignment explanation

Indices: 49889322--49889373 Score: 70 Period size: 27 Copynumber: 1.9 Consensus size: 27 49889312 TCCGCAGGGA 49889322 CAATAAACATAGAGTAGTCCGTCAGGT 1 CAATAAACATAGAGTAGTCCGTCAGGT * * 49889349 CAATAAATA-AGATGTAGTCTGTCAG 1 CAATAAACATAGA-GTAGTCCGTCAG 49889374 AACATCAAGC Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 26 3 0.14 27 19 0.86 ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25 Consensus pattern (27 bp): CAATAAACATAGAGTAGTCCGTCAGGT Found at i:49893858 original size:68 final size:68 Alignment explanation

Indices: 49893728--49893862 Score: 193 Period size: 68 Copynumber: 2.0 Consensus size: 68 49893718 TGATTAAACT * 49893728 TAATCACTTTAATATTAAATTAATGTAATATTTATCAAGATAAACATTAAATTTAATTTAATATT 1 TAATCACTTTAATATTAAATTAA-GTAATATTTATCAAGATAAACATTAAATTAAATTTAATATT 49893793 AAGA 65 AAGA * ** 49893797 TAATCACTTTAATATTAAATTAA-TAA-ATTACTATTAAGATAAGTATTAAATTAAATTTAATAT 1 TAATCACTTTAATATTAAATTAAGTAATATT--TATCAAGATAAACATTAAATTAAATTTAATAT 49893860 TAA 64 TAA 49893863 ATTATTAAAA Statistics Matches: 60, Mismatches: 4, Indels: 5 0.87 0.06 0.07 Matches are distributed among these distances: 66 3 0.05 67 3 0.05 68 31 0.52 69 23 0.38 ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42 Consensus pattern (68 bp): TAATCACTTTAATATTAAATTAAGTAATATTTATCAAGATAAACATTAAATTAAATTTAATATTA AGA Found at i:49895504 original size:16 final size:16 Alignment explanation

Indices: 49895483--49895513 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 49895473 CTATGCATGC * 49895483 AAAATATAAAAGACAG 1 AAAATACAAAAGACAG 49895499 AAAATACAAAAGACA 1 AAAATACAAAAGACA 49895514 TAATAGTGAA 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:0.71, C:0.10, G:0.10, T:0.10 Consensus pattern (16 bp): AAAATACAAAAGACAG Found at i:49906510 original size:48 final size:48 Alignment explanation

Indices: 49906454--49906549 Score: 192 Period size: 48 Copynumber: 2.0 Consensus size: 48 49906444 CGCTTCAGGT 49906454 GTAACTTGGATTCGAGTCGCACTAATTGCGTTACTGTTAGGGTTTTAC 1 GTAACTTGGATTCGAGTCGCACTAATTGCGTTACTGTTAGGGTTTTAC 49906502 GTAACTTGGATTCGAGTCGCACTAATTGCGTTACTGTTAGGGTTTTAC 1 GTAACTTGGATTCGAGTCGCACTAATTGCGTTACTGTTAGGGTTTTAC 49906550 TCTCCTTTTA Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 48 48 1.00 ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38 Consensus pattern (48 bp): GTAACTTGGATTCGAGTCGCACTAATTGCGTTACTGTTAGGGTTTTAC Found at i:49907534 original size:19 final size:18 Alignment explanation

Indices: 49907512--49907554 Score: 68 Period size: 18 Copynumber: 2.3 Consensus size: 18 49907502 AATACAAAAA 49907512 AAAAATCAAAATAATTTTT 1 AAAAATCAAAAT-ATTTTT * 49907531 AAAATTCAAAATATTTTT 1 AAAAATCAAAATATTTTT 49907549 AAAAAT 1 AAAAAT 49907555 TCTAAAACTT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 18 11 0.50 19 11 0.50 ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37 Consensus pattern (18 bp): AAAAATCAAAATATTTTT Found at i:49907555 original size:19 final size:19 Alignment explanation

Indices: 49907511--49907576 Score: 71 Period size: 19 Copynumber: 3.3 Consensus size: 19 49907501 AAATACAAAA * 49907511 AAAAAATCAAAATAATTTTT 1 AAAAATTCAAAAT-ATTTTT 49907531 -AAAATTCAAAATATTTTT 1 AAAAATTCAAAATATTTTT 49907549 AAAAATTCTAAAACTTATCTTTT 1 AAAAATTC-AAAA--TAT-TTTT 49907572 AAAAA 1 AAAAA 49907577 AATTATAATT Statistics Matches: 40, Mismatches: 1, Indels: 7 0.83 0.02 0.15 Matches are distributed among these distances: 18 6 0.15 19 18 0.45 20 4 0.10 22 3 0.08 23 9 0.22 ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38 Consensus pattern (19 bp): AAAAATTCAAAATATTTTT Found at i:49907694 original size:35 final size:35 Alignment explanation

Indices: 49907658--49907734 Score: 136 Period size: 35 Copynumber: 2.2 Consensus size: 35 49907648 TTTGGGAACT 49907658 AAATAATTTAATTAATGATTTAAGTTTATCATACTA 1 AAAT-ATTTAATTAATGATTTAAGTTTATCATACTA * 49907694 AAATATTTAATTAATGATTTAAGTTTATCATACCA 1 AAATATTTAATTAATGATTTAAGTTTATCATACTA 49907729 AAATAT 1 AAATAT 49907735 CTTCTTCTTT Statistics Matches: 40, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 35 36 0.90 36 4 0.10 ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43 Consensus pattern (35 bp): AAATATTTAATTAATGATTTAAGTTTATCATACTA Found at i:49908179 original size:125 final size:123 Alignment explanation

Indices: 49907957--49908208 Score: 371 Period size: 125 Copynumber: 2.0 Consensus size: 123 49907947 AATGCTCACC * * 49907957 CCTAATTATACCTATTCTTTTAACCGCCACTTTATCTTGTTGTTTGTGATTTTAACAAGAGTGAC 1 CCTAATTATACCAATTCTTTTAACCGCCACTTTATCTTGTTGTTTGTAATTTTAACAAGAGTGAC * 49908022 CAAAATGACCGAACTATGTAACGTGGGTGCTTAAATTACAAACTTTTTTTATTTTAAGTG 66 CAAAATGACCGAACTATATAACGTGGGTGCTTAAATTACAAA--TTTTTTATTTTAAGTG * * * * 49908082 CCTAATTATATCAATTCTTTTAACTGTCACTTTATCTTGTTGTTTGTAATTTTAACGAGAGTGA- 1 CCTAATTATACCAATTCTTTTAACCGCCACTTTATCTTGTTGTTTGTAATTTTAACAAGAGTGAC * * * * 49908146 CAACAATTATCGAACTATATAACGTTGGTGCTTAAATTGCAAATTTTTTATTTTAAGTG 66 CAA-AATGACCGAACTATATAACGTGGGTGCTTAAATTACAAATTTTTTATTTTAAGTG 49908205 CCTA 1 CCTA 49908209 TAATAAAAAA Statistics Matches: 115, Mismatches: 11, Indels: 4 0.88 0.08 0.03 Matches are distributed among these distances: 123 20 0.17 124 3 0.03 125 92 0.80 ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42 Consensus pattern (123 bp): CCTAATTATACCAATTCTTTTAACCGCCACTTTATCTTGTTGTTTGTAATTTTAACAAGAGTGAC CAAAATGACCGAACTATATAACGTGGGTGCTTAAATTACAAATTTTTTATTTTAAGTG Found at i:49912201 original size:24 final size:24 Alignment explanation

Indices: 49912151--49912201 Score: 77 Period size: 24 Copynumber: 2.2 Consensus size: 24 49912141 TATAACATTT ** 49912151 AAAAATTCCTAAAATTTATGGATA 1 AAAAATTCCTAAAATTTATAAATA 49912175 AAAAATTCCTAAAATTTA-AAATA 1 AAAAATTCCTAAAATTTATAAATA 49912198 AAAA 1 AAAA 49912202 TAAAAATTAT Statistics Matches: 25, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 23 7 0.28 24 18 0.72 ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29 Consensus pattern (24 bp): AAAAATTCCTAAAATTTATAAATA Found at i:49913476 original size:23 final size:23 Alignment explanation

Indices: 49913449--49913504 Score: 112 Period size: 23 Copynumber: 2.4 Consensus size: 23 49913439 ATCCCTTTAG 49913449 AATCTCAATTATAGATTGGCTTT 1 AATCTCAATTATAGATTGGCTTT 49913472 AATCTCAATTATAGATTGGCTTT 1 AATCTCAATTATAGATTGGCTTT 49913495 AATCTCAATT 1 AATCTCAATT 49913505 GTTGATGGAA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 33 1.00 ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43 Consensus pattern (23 bp): AATCTCAATTATAGATTGGCTTT Found at i:49917818 original size:3 final size:3 Alignment explanation

Indices: 49917797--49917835 Score: 51 Period size: 3 Copynumber: 13.0 Consensus size: 3 49917787 AAGCATAAAC * * * 49917797 TAA TAA AAA TAA AAA TAA TAA TAA TAA TAA TAA TGA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 49917836 CATTGGAATA Statistics Matches: 30, Mismatches: 6, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 3 30 1.00 ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28 Consensus pattern (3 bp): TAA Found at i:49917949 original size:22 final size:23 Alignment explanation

Indices: 49917932--49917994 Score: 85 Period size: 24 Copynumber: 2.7 Consensus size: 23 49917922 TGTATACACG 49917932 TACATAATAA-AATATATACTAA 1 TACATAATAATAATATATACTAA 49917954 TACATAATAATAATAGTAATACTAA 1 TACATAATAATAATA-T-ATACTAA * 49917979 TA-ATACTAATAATATA 1 TACATAATAATAATATA 49917995 AAATAACAAG Statistics Matches: 37, Mismatches: 1, Indels: 6 0.84 0.02 0.14 Matches are distributed among these distances: 22 11 0.30 23 5 0.14 24 12 0.32 25 9 0.24 ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33 Consensus pattern (23 bp): TACATAATAATAATATATACTAA Found at i:49917965 original size:3 final size:3 Alignment explanation

Indices: 49917935--49918000 Score: 57 Period size: 3 Copynumber: 22.3 Consensus size: 3 49917925 ATACACGTAC * * * 49917935 ATA ATA A-A ATA TATA CTA ATA CATA ATA ATA ATA GTA ATA CTA ATA 1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA * 49917981 ATA CTA ATA AT- ATA A-A ATA A 1 ATA ATA ATA ATA ATA ATA ATA A 49918001 CAAGGATATT Statistics Matches: 50, Mismatches: 8, Indels: 10 0.74 0.12 0.15 Matches are distributed among these distances: 2 6 0.12 3 38 0.76 4 6 0.12 ACGTcount: A:0.61, C:0.06, G:0.02, T:0.32 Consensus pattern (3 bp): ATA Found at i:49918600 original size:15 final size:16 Alignment explanation

Indices: 49918580--49918618 Score: 53 Period size: 16 Copynumber: 2.4 Consensus size: 16 49918570 AGGTAAAAAA * 49918580 TTTTATTT-TTTTATT 1 TTTTATTTCTTGTATT 49918595 TTTTATTTCTTGTATT 1 TTTTATTTCTTGTATT 49918611 TTTATATT 1 TTT-TATT 49918619 ATACTTTCAT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 8 0.38 16 9 0.43 17 4 0.19 ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79 Consensus pattern (16 bp): TTTTATTTCTTGTATT Found at i:49919942 original size:72 final size:73 Alignment explanation

Indices: 49919834--49919985 Score: 211 Period size: 72 Copynumber: 2.1 Consensus size: 73 49919824 CAAACAGATT * * 49919834 TTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATT-AA 1 TTGAAAATACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAAATTGAA 49919898 AACACAAAAA 65 AA-ACAAAAA * * ** 49919908 TTGAAAATACCTCAGC-GTGCCCCGAGGCTCAACTCACCTCTAGCGATATGAGTTGATTTTGAAA 1 TTGAAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAAATTGAAA 49919972 AACAAAAA 66 AACAAAAA 49919980 TT-AAAA 1 TTGAAAA 49919986 GGCTTAACTC Statistics Matches: 71, Mismatches: 6, Indels: 5 0.87 0.07 0.06 Matches are distributed among these distances: 71 4 0.06 72 48 0.68 73 4 0.06 74 15 0.21 ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23 Consensus pattern (73 bp): TTGAAAATACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGAAATTGAAA AACAAAAA Found at i:49920078 original size:120 final size:123 Alignment explanation

Indices: 49919860--49920087 Score: 363 Period size: 120 Copynumber: 1.9 Consensus size: 123 49919850 ATGTGACCCG * 49919860 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG 1 AGGCTCAACTCACCTCTCGCAATATGAGTTG-AATT-AAACACAAAAATCGAAAATACCTCAGCG * 49919925 TGCCCCGAGGCTCAACTCACCTCTAGCGATATGAGTTGATTTTGAAAAACAAAAATTAAA 64 TGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA * * * 49919985 AGGCTTAACTCACCTCTCGCAATATGAGTTG-A-T-AACACAAAAGTCGAAAATACCTCAGTGTG 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTAAACACAAAAATCGAAAATACCTCAGCGTG * 49920047 CCCCGAGGCTCAACTCACTTCTAGCAATATGAGTTGATTTT 66 CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT 49920088 TTTGAAAAAC Statistics Matches: 97, Mismatches: 6, Indels: 5 0.90 0.06 0.05 Matches are distributed among these distances: 120 65 0.67 122 1 0.01 123 1 0.01 125 30 0.31 ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25 Consensus pattern (123 bp): AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTAAACACAAAAATCGAAAATACCTCAGCGTG CCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA Found at i:49920312 original size:144 final size:144 Alignment explanation

Indices: 49920052--49920330 Score: 321 Period size: 144 Copynumber: 1.9 Consensus size: 144 49920042 GTGTGCCCCG * * *** 49920052 AGGCTCAACTCACTTCTAGCAATATGAGTTGATTTTTTTGAAAAACAGATTTTGAAGAGCAGAAA 1 AGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTTTTGAAAAACAGAAACTGAAGAGCAGAAA * ** * * * * * * 49920117 TTGTAAATACCTCGGCGTGTCCCGAGGTTCAACTCACTTCTTGCAATATGAGTCGATTTTTTGAA 66 TTGAAAATACCTCAACCTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTCTTTCAA 49920182 AAACAGAAATTAAA 131 AAACAGAAATTAAA * ** * * 49920196 AGGCTCAACTCACCTCTCGCAATATGAGCTGATCTTTTTTTTAAAACATAAACTGACGA-CAGAA 1 AGGCTCAACTCACCTCTAGCAATATGAGCTGAT-TTTTTTGAAAAACAGAAACTGAAGAGCAGAA * * 49920260 ATCT-AAAATACCTCAACCTG-CCCTGAGGCTCGACTCACCTCTCGCAATATGAGTTGATTCTTT 65 AT-TGAAAATACCTCAACCTGTCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTCGATTCTTT 49920323 CAAAAACA 128 CAAAAACA 49920331 TAATAATGAA Statistics Matches: 111, Mismatches: 21, Indels: 6 0.80 0.15 0.04 Matches are distributed among these distances: 143 3 0.03 144 89 0.80 145 19 0.17 ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29 Consensus pattern (144 bp): AGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTTTTGAAAAACAGAAACTGAAGAGCAGAAA TTGAAAATACCTCAACCTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTCTTTCAA AAACAGAAATTAAA Found at i:49920377 original size:88 final size:87 Alignment explanation

Indices: 49920196--49920429 Score: 261 Period size: 88 Copynumber: 2.6 Consensus size: 87 49920186 AGAAATTAAA * * ** * ** 49920196 AGGCTCAACTCACCTCTCGCAATATGAGCTGATCTTTTTTTTAAAACATAAACTGACGACAGAAA 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTCTTTCAAAAACATAAAATGAAAACAGAAA * * 49920261 TCTAAAATACCTCAACCTGCCCTG 64 TCGAAAATACCTCAACCTGACCTG * 49920285 AGGCTCGACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACATAATAATGAAAACAGAAAT 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACATAA-AATGAAAACAGAAAT * **** 49920350 GGAAAATACCTCGGTGTGACCTG 65 CGAAAATACCTCAACCTGACCTG * * * * 49920373 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAA 1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTCTTTCAAAAACATAAAATGAAA 49920430 TTACCTCAGC Statistics Matches: 123, Mismatches: 20, Indels: 5 0.83 0.14 0.03 Matches are distributed among these distances: 87 14 0.11 88 65 0.53 89 44 0.36 ACGTcount: A:0.35, C:0.22, G:0.15, T:0.27 Consensus pattern (87 bp): AGGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTCAAAAACATAAAATGAAAACAGAAATC GAAAATACCTCAACCTGACCTG Found at i:49920462 original size:75 final size:75 Alignment explanation

Indices: 49920339--49920483 Score: 236 Period size: 75 Copynumber: 1.9 Consensus size: 75 49920329 CATAATAATG * * * 49920339 AAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 1 AAAACAGAAATGGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG 49920404 ATTTTTTTGA 66 ATTTTTTTGA * * * 49920414 AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG 1 AAAACAGAAATGGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG 49920479 ATTTT 66 ATTTT 49920484 GAAAAACAAA Statistics Matches: 64, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 75 64 1.00 ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28 Consensus pattern (75 bp): AAAACAGAAATGGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG ATTTTTTTGA Found at i:49920645 original size:68 final size:70 Alignment explanation

Indices: 49920501--49920673 Score: 210 Period size: 68 Copynumber: 2.5 Consensus size: 70 49920491 AAAAATTAAA * * * * ** 49920501 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG 1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG 49920565 CCCTG 66 CCCTG * * 49920570 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAA-A-AAATTAAAAATACCTCAACGTG 1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG * * 49920633 TCTTG 66 CCCTG * 49920638 AGGCTCAACTCA-TCTCTTGCAATATGAGTTGATTTT 1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT 49920674 CCTTGGAAAA Statistics Matches: 91, Mismatches: 11, Indels: 5 0.85 0.10 0.05 Matches are distributed among these distances: 67 1 0.01 68 55 0.60 69 27 0.30 70 8 0.09 ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31 Consensus pattern (70 bp): AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG CCCTG Found at i:49933344 original size:23 final size:22 Alignment explanation

Indices: 49933318--49933371 Score: 74 Period size: 23 Copynumber: 2.5 Consensus size: 22 49933308 TGTATACACG 49933318 TACATAATAAAAATATATACTAA 1 TACATAATAAAAATA-ATACTAA * * 49933341 TACATAATAATAATAATAGTAA 1 TACATAATAAAAATAATACTAA 49933363 TAC-TAATAA 1 TACATAATAA 49933372 TACTAATAAT Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 21 6 0.21 22 9 0.31 23 14 0.48 ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31 Consensus pattern (22 bp): TACATAATAAAAATAATACTAA Found at i:49933352 original size:3 final size:3 Alignment explanation

Indices: 49933321--49933391 Score: 63 Period size: 3 Copynumber: 23.3 Consensus size: 3 49933311 ATACACGTAC * * * * 49933321 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA 1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA * * 49933368 ATA ATA CTA ATA AT- ATA AAA ATA A 1 ATA ATA ATA ATA ATA ATA ATA ATA A 49933392 CAAGGATATT Statistics Matches: 53, Mismatches: 12, Indels: 6 0.75 0.17 0.08 Matches are distributed among these distances: 2 2 0.04 3 45 0.85 4 6 0.11 ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31 Consensus pattern (3 bp): ATA Found at i:49933882 original size:18 final size:18 Alignment explanation

Indices: 49933855--49933892 Score: 58 Period size: 18 Copynumber: 2.1 Consensus size: 18 49933845 AGAAAAAAAA * 49933855 AGAAGAGAGAGGGAAGAG 1 AGAAGAGAGAGAGAAGAG * 49933873 AGAAGGGAGAGAGAAGAG 1 AGAAGAGAGAGAGAAGAG 49933891 AG 1 AG 49933893 GGGAATCCGG Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (18 bp): AGAAGAGAGAGAGAAGAG Found at i:49933887 original size:11 final size:12 Alignment explanation

Indices: 49933856--49933888 Score: 52 Period size: 11 Copynumber: 2.9 Consensus size: 12 49933846 GAAAAAAAAA 49933856 GAAGAGAG-AGG 1 GAAGAGAGAAGG 49933867 GAAGAGAGAAGG 1 GAAGAGAGAAGG 49933879 G-AGAGAGAAG 1 GAAGAGAGAAG 49933889 AGAGGGGAAT Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 11 17 0.81 12 4 0.19 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (12 bp): GAAGAGAGAAGG Found at i:49934008 original size:15 final size:16 Alignment explanation

Indices: 49933988--49934024 Score: 58 Period size: 16 Copynumber: 2.4 Consensus size: 16 49933978 AGGTAAAAAA * 49933988 TTTTATTT-TTTTATT 1 TTTTATTTCTTGTATT 49934003 TTTTATTTCTTGTATT 1 TTTTATTTCTTGTATT 49934019 TTTTAT 1 TTTTAT 49934025 ATTATACTTT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 15 8 0.40 16 12 0.60 ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81 Consensus pattern (16 bp): TTTTATTTCTTGTATT Found at i:49940815 original size:16 final size:16 Alignment explanation

Indices: 49940794--49940824 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 49940784 TTAACTATTA * 49940794 TGTCTTTTGTATTTTC 1 TGTCTTTTATATTTTC 49940810 TGTCTTTTATATTTT 1 TGTCTTTTATATTTT 49940825 GCATGCATAG 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:0.10, C:0.10, G:0.10, T:0.71 Consensus pattern (16 bp): TGTCTTTTATATTTTC Found at i:49942963 original size:19 final size:21 Alignment explanation

Indices: 49942939--49942978 Score: 66 Period size: 21 Copynumber: 2.0 Consensus size: 21 49942929 ATTTTTCTGC 49942939 AACAAACT-GG-TTTCCAGAA 1 AACAAACTCGGTTTTCCAGAA 49942958 AACAAACTCGGTTTTCCAGAA 1 AACAAACTCGGTTTTCCAGAA 49942979 TATAATGATC Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 19 8 0.42 20 2 0.11 21 9 0.47 ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23 Consensus pattern (21 bp): AACAAACTCGGTTTTCCAGAA Found at i:49953173 original size:39 final size:40 Alignment explanation

Indices: 49953130--49953218 Score: 99 Period size: 44 Copynumber: 2.1 Consensus size: 40 49953120 TTATTTTCTT * * 49953130 CTTCTTCTAC-CCTACTTTAGGTTTTATTTTCTGCATTTA 1 CTTCTTCTACTACTACTTTAGGTTTCATTTTCTGCATTTA * * 49953169 CTTCTTGAATTTACTATTACTTTAGGTTTCATTTTCTGCATTTA 1 CTTC-T---TCTACTACTACTTTAGGTTTCATTTTCTGCATTTA 49953213 CTTCTT 1 CTTCTT 49953219 GCATTTACTG Statistics Matches: 41, Mismatches: 4, Indels: 9 0.76 0.07 0.17 Matches are distributed among these distances: 39 4 0.10 40 2 0.05 43 5 0.12 44 30 0.73 ACGTcount: A:0.17, C:0.20, G:0.08, T:0.55 Consensus pattern (40 bp): CTTCTTCTACTACTACTTTAGGTTTCATTTTCTGCATTTA Found at i:49953191 original size:44 final size:44 Alignment explanation

Indices: 49953142--49953233 Score: 157 Period size: 44 Copynumber: 2.1 Consensus size: 44 49953132 TCTTCTACCC * 49953142 TACTTTAGGTTTTATTTTCTGCATTTACTTCTTGAATTTACTAT 1 TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGAATTTACTAT * * 49953186 TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGCATTTACTGT 1 TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGAATTTACTAT 49953230 TACT 1 TACT 49953234 AAGGTTTATT Statistics Matches: 45, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 44 45 1.00 ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55 Consensus pattern (44 bp): TACTTTAGGTTTCATTTTCTGCATTTACTTCTTGAATTTACTAT Found at i:49953223 original size:22 final size:22 Alignment explanation

Indices: 49953155--49953224 Score: 56 Period size: 22 Copynumber: 3.2 Consensus size: 22 49953145 TTTAGGTTTT * 49953155 ATTTTCTGCATTTACTTCTTGA 1 ATTTTCTGCATTTACTTCTTGC * * * 49953177 ATTTACT--A-TTACTTTAGGTTTC 1 ATTTTCTGCATTTAC-TT--CTTGC 49953199 ATTTTCTGCATTTACTTCTTGC 1 ATTTTCTGCATTTACTTCTTGC 49953221 ATTT 1 ATTT 49953225 ACTGTTACTA Statistics Matches: 35, Mismatches: 7, Indels: 12 0.65 0.13 0.22 Matches are distributed among these distances: 19 4 0.11 20 3 0.09 22 21 0.60 24 3 0.09 25 4 0.11 ACGTcount: A:0.19, C:0.17, G:0.09, T:0.56 Consensus pattern (22 bp): ATTTTCTGCATTTACTTCTTGC Found at i:49953603 original size:40 final size:40 Alignment explanation

Indices: 49953558--49953651 Score: 152 Period size: 40 Copynumber: 2.4 Consensus size: 40 49953548 TGACTAAATC ** * 49953558 GTAATAAATTGGACTAAATTGAATAGAACTAAGAACTTAA 1 GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAA * 49953598 GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAG 1 GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAA 49953638 GTAATAAATTGGAC 1 GTAATAAATTGGAC 49953652 CAAGGACTAA Statistics Matches: 50, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 40 50 1.00 ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27 Consensus pattern (40 bp): GTAATAAATTGGACTAAATCAAATACAACTAAGAACTTAA Found at i:49963005 original size:14 final size:14 Alignment explanation

Indices: 49962986--49963013 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 49962976 ATAACAAGAA 49962986 GTCATGCCATAAAT 1 GTCATGCCATAAAT 49963000 GTCATGCCATAAAT 1 GTCATGCCATAAAT 49963014 TATTGTACCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29 Consensus pattern (14 bp): GTCATGCCATAAAT Found at i:49965548 original size:19 final size:18 Alignment explanation

Indices: 49965524--49965564 Score: 64 Period size: 19 Copynumber: 2.2 Consensus size: 18 49965514 AAAATATAAA * 49965524 AAAAATCATTAAAATGATT 1 AAAAATCATAAAAAT-ATT 49965543 AAAAATCATAAAAATATT 1 AAAAATCATAAAAATATT 49965561 AAAA 1 AAAA 49965565 TTTATATAAT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 18 7 0.33 19 14 0.67 ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27 Consensus pattern (18 bp): AAAAATCATAAAAATATT Found at i:49965581 original size:28 final size:28 Alignment explanation

Indices: 49965550--49965649 Score: 89 Period size: 28 Copynumber: 3.5 Consensus size: 28 49965540 ATTAAAAATC * * * 49965550 ATAAAAA-TATTAAAATTTATATAATATT 1 ATAAAAATTATAAAAACTTAT-CAATATT 49965578 ATAAAAATTATAAAAACTTATCAATATT 1 ATAAAAATTATAAAAACTTATCAATATT * * 49965606 ATAAAAGTTATAACAAA-TTAT-AATTTT 1 ATAAAAATTATAA-AAACTTATCAATATT * 49965633 TTATAAAATTAATAAAA 1 ATA-AAAATT-ATAAAA 49965650 CATATTTAAA Statistics Matches: 61, Mismatches: 7, Indels: 8 0.80 0.09 0.11 Matches are distributed among these distances: 27 7 0.11 28 36 0.59 29 18 0.30 ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39 Consensus pattern (28 bp): ATAAAAATTATAAAAACTTATCAATATT Found at i:49965588 original size:19 final size:18 Alignment explanation

Indices: 49965576--49965628 Score: 61 Period size: 19 Copynumber: 2.8 Consensus size: 18 49965566 TTATATAATA 49965576 TTATAAAAATTATAAAAAC 1 TTATAAAAATTAT-AAAAC * * * 49965595 TTATCAATATTATAAAAG 1 TTATAAAAATTATAAAAC 49965613 TTATAACAAATTATAA 1 TTATAA-AAATTATAA 49965629 TTTTTTATAA Statistics Matches: 28, Mismatches: 5, Indels: 2 0.80 0.14 0.06 Matches are distributed among these distances: 18 9 0.32 19 19 0.68 ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36 Consensus pattern (18 bp): TTATAAAAATTATAAAAC Found at i:49965607 original size:9 final size:9 Alignment explanation

Indices: 49965542--49965628 Score: 77 Period size: 9 Copynumber: 9.3 Consensus size: 9 49965532 TTAAAATGAT * 49965542 TAAAAATCA 1 TAAAAATTA 49965551 TAAAAA-TA 1 TAAAAATTA * 49965559 TTAAAATTTA 1 -TAAAAATTA * 49965569 TATAATATTA 1 TA-AAAATTA 49965579 TAAAAATTA 1 TAAAAATTA 49965588 TAAAAACTTA 1 TAAAAA-TTA * * 49965598 TCAATATTA 1 TAAAAATTA * 49965607 TAAAAGTTA 1 TAAAAATTA 49965616 TAACAAATTA 1 TAA-AAATTA 49965626 TAA 1 TAA 49965629 TTTTTTATAA Statistics Matches: 62, Mismatches: 11, Indels: 9 0.76 0.13 0.11 Matches are distributed among these distances: 8 1 0.02 9 37 0.60 10 24 0.39 ACGTcount: A:0.59, C:0.05, G:0.01, T:0.36 Consensus pattern (9 bp): TAAAAATTA Found at i:49966561 original size:9 final size:9 Alignment explanation

Indices: 49966495--49966795 Score: 132 Period size: 9 Copynumber: 31.3 Consensus size: 9 49966485 TATATTTTTA 49966495 TTTATAATT 1 TTTATAATT * 49966504 TATTAGAACTT 1 T-TTATAA-TT * * 49966515 ATTATGATTT 1 TTTAT-AATT * 49966525 TTTATAAGT 1 TTTATAATT * 49966534 TTTACAATT 1 TTTATAATT * * 49966543 AATGATAATT 1 -TTTATAATT 49966553 TTTATAATT 1 TTTATAATT 49966562 TGTATGATAATT 1 T-T-T-ATAATT 49966574 TATTATAACTT 1 T-TTATAA-TT 49966585 TTT-TGAATT 1 TTTAT-AATT * 49966594 TTTATAAGCT 1 TTTATAA-TT * 49966604 TTTATAATA 1 TTTATAATT 49966613 TTTATAAGTT 1 TTTATAA-TT * 49966623 TTGATGAATT 1 TTTAT-AATT * 49966633 CTTTATAAGT 1 -TTTATAATT 49966643 TTTA-AATAT 1 TTTATAAT-T 49966652 TTTA-AATAT 1 TTTATAAT-T 49966661 GTTT-TAA-T 1 -TTTATAATT * 49966669 TTTATTATT 1 TTTATAATT * 49966678 GTTATAATTATT 1 -TT-T-ATAATT 49966690 TTTATAATT 1 TTTATAATT * 49966699 TATTAGAA-T 1 T-TTATAATT * 49966708 TTTATAATG 1 TTTATAATT * 49966717 TTTATAAGT 1 TTTATAATT 49966726 TTTATGAATTTT 1 TTTAT-AA--TT 49966738 TTTATAATT 1 TTTATAATT 49966747 TTTATAAGTT 1 TTTATAA-TT * * 49966757 TATATAAAT 1 TTTATAATT 49966766 TTT-TAATAT 1 TTTATAAT-T * 49966775 TTTAT-GTAT 1 TTTATAAT-T 49966784 TTTATAATT 1 TTTATAATT 49966793 TTT 1 TTT 49966796 TATGAAAAAT Statistics Matches: 224, Mismatches: 37, Indels: 62 0.69 0.11 0.19 Matches are distributed among these distances: 7 3 0.01 8 13 0.06 9 96 0.43 10 73 0.33 11 19 0.08 12 20 0.09 ACGTcount: A:0.34, C:0.02, G:0.07, T:0.58 Consensus pattern (9 bp): TTTATAATT Found at i:49966639 original size:21 final size:19 Alignment explanation

Indices: 49966549--49966646 Score: 92 Period size: 19 Copynumber: 4.9 Consensus size: 19 49966539 AATTAATGAT 49966549 AATTTTTATAA-TTTGTATG 1 AATTTTTATAAGTTT-TATG * * 49966568 ATAATTTATTATAACTTTTTTG 1 --AATTT-TTATAAGTTTTATG 49966590 AATTTTTATAAGCTTTTAT- 1 AATTTTTATAAG-TTTTATG * 49966609 AATATTTATAAGTTTTGATG 1 AATTTTTATAAGTTTT-ATG 49966629 AATTCTTTATAAGTTTTA 1 AATT-TTTATAAGTTTTA 49966647 AATATTTTAA Statistics Matches: 66, Mismatches: 5, Indels: 13 0.79 0.06 0.15 Matches are distributed among these distances: 18 4 0.06 19 19 0.29 20 14 0.21 21 17 0.26 22 9 0.14 23 3 0.05 ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56 Consensus pattern (19 bp): AATTTTTATAAGTTTTATG Found at i:49966770 original size:104 final size:105 Alignment explanation

Indices: 49966603--49966796 Score: 249 Period size: 104 Copynumber: 1.9 Consensus size: 105 49966593 TTTTATAAGC * 49966603 TTTTATAATATTTATAAGTTTTGATGAATTCTTTATAAGTTTTAAATATTTTAAATATGTTTT-A 1 TTTTATAATATTTATAAGTTTTGATGAATTCTTTATAAGTTTTAAATATTATAAATATGTTTTAA 49966667 -ATTTTAT-TATTGTTATAATTATTTTTATAATTTATTAGAA 66 TATTTTATGTATT-TTATAATT-TTTTTATAATTTATTAGAA * * * 49966707 TTTTATAATGTTTATAAGTTTT-ATGAATTTTTTTATAATTTTTATAAGT-TTATATAA-AT-TT 1 TTTTATAATATTTATAAGTTTTGATGAA-TTCTTTATAAGTTTTA-AA-TATTATA-AATATGTT 49966768 TTAATATTTTATGTATTTTATAATTTTTT 62 TTAATATTTTATGTATTTTATAATTTTTT 49966797 ATGAAAAATA Statistics Matches: 79, Mismatches: 4, Indels: 13 0.82 0.04 0.14 Matches are distributed among these distances: 103 5 0.06 104 39 0.49 105 13 0.16 106 18 0.23 107 4 0.05 ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60 Consensus pattern (105 bp): TTTTATAATATTTATAAGTTTTGATGAATTCTTTATAAGTTTTAAATATTATAAATATGTTTTAA TATTTTATGTATTTTATAATTTTTTTATAATTTATTAGAA Found at i:49977171 original size:26 final size:26 Alignment explanation

Indices: 49977141--49977194 Score: 108 Period size: 26 Copynumber: 2.1 Consensus size: 26 49977131 TTCTAATATA 49977141 AGATAATTGTAATTATTGTTTAATAC 1 AGATAATTGTAATTATTGTTTAATAC 49977167 AGATAATTGTAATTATTGTTTAATAC 1 AGATAATTGTAATTATTGTTTAATAC 49977193 AG 1 AG 49977195 CATAGTTTTT 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:0.39, C:0.04, G:0.13, T:0.44 Consensus pattern (26 bp): AGATAATTGTAATTATTGTTTAATAC Found at i:49977239 original size:17 final size:17 Alignment explanation

Indices: 49977201--49977242 Score: 50 Period size: 17 Copynumber: 2.5 Consensus size: 17 49977191 ACAGCATAGT * 49977201 TTTTAATATATATTATA 1 TTTTAATATATAATATA * 49977218 ATTTAATATA-AATATCA 1 TTTTAATATATAATAT-A 49977235 TTTTAATA 1 TTTTAATA 49977243 ATTTTTAATT Statistics Matches: 21, Mismatches: 3, Indels: 2 0.81 0.12 0.08 Matches are distributed among these distances: 16 4 0.19 17 17 0.81 ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52 Consensus pattern (17 bp): TTTTAATATATAATATA Found at i:49977887 original size:43 final size:43 Alignment explanation

Indices: 49977839--49977924 Score: 172 Period size: 43 Copynumber: 2.0 Consensus size: 43 49977829 CAAAGAAAAA 49977839 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT 1 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT 49977882 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT 1 ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT 49977925 CGGTCCATGT Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 43 43 1.00 ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28 Consensus pattern (43 bp): ATGAGTGTGTAAAACATACTAGTACATAGTGCTATACCACAGT Found at i:49978349 original size:12 final size:12 Alignment explanation

Indices: 49978332--49978405 Score: 55 Period size: 12 Copynumber: 6.2 Consensus size: 12 49978322 CTCTTCGTCT 49978332 TTCTTCTTCTCC 1 TTCTTCTTCTCC * 49978344 TTCTTC-TCTTC 1 TTCTTCTTCTCC * 49978355 TT-TCTCTTCACC 1 TTCT-TCTTCTCC * * 49978367 TTCTACCTCATCC 1 TTCTTCTTC-TCC * 49978380 TTCTTCATT-TCT 1 TTCTTC-TTCTCC 49978392 TTCTTCTTCTCC 1 TTCTTCTTCTCC 49978404 TT 1 TT 49978406 TGCCTCTTTG Statistics Matches: 46, Mismatches: 10, Indels: 12 0.68 0.15 0.18 Matches are distributed among these distances: 10 1 0.02 11 10 0.22 12 26 0.57 13 8 0.17 14 1 0.02 ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57 Consensus pattern (12 bp): TTCTTCTTCTCC Found at i:49978459 original size:96 final size:96 Alignment explanation

Indices: 49978365--49979383 Score: 1404 Period size: 96 Copynumber: 10.7 Consensus size: 96 49978355 TTTCTCTTCA * * 49978365 CCTTCTACCTCAT-C-CTTCTTCATTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTCTCTTCTTT 1 CCTTCTACCTCATCCTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT 49978428 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT 66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT * 49978459 -CTTCTACCTCAT-C-CTTCTTTTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT 1 CCTTCTACCTCATCCTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT * 49978521 TCTTTCTTTCCCTCTTCTAATTCTTCAGCTT 66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT * 49978552 -CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTT 1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT * 49978616 TTCTTTCTTTCCCTCTTCTAATTCTTCAGCTT 65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT * 49978648 -CTTCTACCTTATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT 1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT 49978712 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT 65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT * 49978744 -CATCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT 1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT 49978808 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT 65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT * * * 49978840 -CTTCTACCTCATCCTTCTTCTTCTTTTCTTTTTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTT 1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT * 49978904 TTCTTTCTTTCCCTCTTCTAATTCTTCAGCTT 65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT * * 49978936 -CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTT 1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT 49979000 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCAT 65 TTCTTTCTTTCCCTCTTCTAATTCTTCATC-T--T * * 49979035 CTTCTTCTACCTCATCCTTCTTCTTCTTTCCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTC 1 C--CTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTC * 49979100 TTTTCTTTCTTTCCTTCTTCTAATTCTTCTTCATCTT 63 TTTTCTTTCTTTCCCTCTTCTAA---TTCTTCATCTT * * * 49979137 -CTTCTACCTCATCCTTCTTCTTCTTCTCTTT-TGC--CT-CTTTG--TC-CT-TC-TTCTT-TT 1 CCTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT * 49979191 CT-TT-CTTTCCCTCTTCTAATTCTTCATCTT 65 TTCTTTCTTTCCCTCTTCTAATTCTTCATCTT * ** 49979221 CATCTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCCCCTTTGTTTCTTTGTCTTTCTTC 1 C--CTTCTACCTCATCC-TCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTC * 49979286 TTTTCTTTCTTTCCCTCTTCTATTTCTTCATCTT 63 TTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTT * * * * * * 49979320 -CATCTTCTTC-TACTTTATCCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCCTTGTCTTTCTTCT 1 CCTTCTACCTCATCCTCT-T-CTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCT 49979383 T 64 T 49979384 CTCTGTCTCT Statistics Matches: 853, Mismatches: 43, Indels: 56 0.90 0.05 0.06 Matches are distributed among these distances: 84 11 0.01 87 44 0.05 88 4 0.00 89 3 0.00 90 6 0.01 91 7 0.01 92 1 0.00 93 105 0.12 94 4 0.00 95 9 0.01 96 503 0.59 97 4 0.00 98 4 0.00 99 55 0.06 102 83 0.10 104 1 0.00 105 9 0.01 ACGTcount: A:0.06, C:0.33, G:0.02, T:0.58 Consensus pattern (96 bp): CCTTCTACCTCATCCTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT TCTTTCTTTCCCTCTTCTAATTCTTCATCTT Found at i:49978586 original size:12 final size:12 Alignment explanation

Indices: 49978569--49978624 Score: 58 Period size: 12 Copynumber: 4.4 Consensus size: 12 49978559 CTCATCCTTC 49978569 TTCTTCTTTTCT 1 TTCTTCTTTTCT * 49978581 TTCTTCTTCTCCT 1 TTCTTCTT-TTCT * * 49978594 TCGCCTCTTTGTCT 1 T-TCTTCTTT-TCT 49978608 TTCTTCTTTTCT 1 TTCTTCTTTTCT 49978620 TTCTT 1 TTCTT 49978625 TCCCTCTTCT Statistics Matches: 35, Mismatches: 6, Indels: 6 0.74 0.13 0.13 Matches are distributed among these distances: 12 16 0.46 13 11 0.31 14 8 0.23 ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66 Consensus pattern (12 bp): TTCTTCTTTTCT Found at i:49978682 original size:12 final size:12 Alignment explanation

Indices: 49978665--49978816 Score: 72 Period size: 12 Copynumber: 11.4 Consensus size: 12 49978655 CTTATCCTTC 49978665 TTCTTCTTTTCT 1 TTCTTCTTTTCT * 49978677 TTCTTCTTCTCCT 1 TTCTTCTT-TTCT * 49978690 TTGCCTCTTTGTCT 1 TT-CTTCTTT-TCT 49978704 TTCTTCTTTTCT 1 TTCTTCTTTTCT * 49978716 TTCTTTCCCTCTTCT 1 TTC-TT--CTTTTCT * 49978731 AATTCTTCATCTTCAT 1 --TTCTTC-TTTTC-T * * * 49978747 CTACCTCATCCTTC- 1 -TTCTTC-T-TTTCT 49978761 TTCTTCTTTTCT 1 TTCTTCTTTTCT * 49978773 TTCTTCTTCTCCT 1 TTCTTCTT-TTCT * 49978786 TTGCCTCTTTGTCT 1 TT-CTTCTTT-TCT 49978800 TTCTTCTTTTCT 1 TTCTTCTTTTCT 49978812 TTCTT 1 TTCTT 49978817 TCCCTCTTCT Statistics Matches: 110, Mismatches: 15, Indels: 30 0.71 0.10 0.19 Matches are distributed among these distances: 11 3 0.03 12 31 0.28 13 30 0.27 14 19 0.17 15 17 0.15 16 7 0.06 17 3 0.03 ACGTcount: A:0.04, C:0.32, G:0.03, T:0.62 Consensus pattern (12 bp): TTCTTCTTTTCT Found at i:49978845 original size:288 final size:288 Alignment explanation

Indices: 49978366--49979383 Score: 1572 Period size: 288 Copynumber: 3.6 Consensus size: 288 49978356 TTCTCTTCAC * * 49978366 CTTCTACCTCAT-C--CTTCTTCATTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTCTCTTCTTT 1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT * 49978428 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTTCTACCTCATCCTTC-T-TT-TTTTCTTTCTT 66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT * 49978490 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCAGCTTCTT 131 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT 49978555 CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT 196 CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT 49978620 TTCTTTCCCTCTTCTAATTCTTCAGCTT 261 TTCTTTCCCTCTTCTAATTCTTCAGCTT * 49978648 CTTCTACCTTATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT 1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT 49978713 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT 66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT 49978778 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT 131 CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT * * 49978843 CTACCTCATCCTTCTTCTTCTTTTCTTTTTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT 196 CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT 49978908 TTCTTTCCCTCTTCTAATTCTTCAGCTT 261 TTCTTTCCCTCTTCTAATTCTTCAGCTT * * 49978936 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTTT 1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT * 49979001 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTTCTTCTACCTCATCCTTCTTCTTCTTTCC 66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCA------TCTACCTCATCCTTCTTCTTCTTTTC * * 49979066 TTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCTTCTTCTAATTCTTCTT 125 TTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAA---TTCTT * 49979131 CATCTTCTTCTACCTCAT-C--CTTCTTC--TTC-TTC-TC-T-T--TT-GCCTCTTTGTCCTTC 187 CATCTTCTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTC * 49979184 TTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCAT 252 TTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCAGC-T--T * ** 49979224 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCCCCTTTGTTTCTTTGTCTTTCTTCTTT 1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT * * * * 49979289 TCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCTTCTTC-TACTT-TATCCTTCTTTTCTTTC 66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCT-T-CTTCTTTTCTTTC * 49979352 TTCTTCTCCTTTGCCTCCTTGTCTTTCTTCTT 129 TTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT 49979384 CTCTGTCTCT Statistics Matches: 687, Mismatches: 29, Indels: 40 0.91 0.04 0.05 Matches are distributed among these distances: 280 1 0.00 281 5 0.01 282 59 0.09 283 1 0.00 285 142 0.21 286 4 0.01 287 2 0.00 288 355 0.52 289 1 0.00 290 1 0.00 291 2 0.00 292 3 0.00 294 87 0.13 296 1 0.00 297 23 0.03 ACGTcount: A:0.06, C:0.33, G:0.02, T:0.59 Consensus pattern (288 bp): CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTACCTCATCCTTCTTCTTCTTTTCTTTCTT CTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCTT CTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTTTCT TTCTTTCCCTCTTCTAATTCTTCAGCTT Found at i:49979384 original size:27 final size:28 Alignment explanation

Indices: 49979322--49979386 Score: 87 Period size: 27 Copynumber: 2.4 Consensus size: 28 49979312 TTCATCTTCA * * * * 49979322 TCTTCTTCTACTTTATCCTTCTTTTCTT 1 TCTTCTTCTCCTTTAGCCTCCTTGTCTT 49979350 TCTTCTTCTCCTTT-GCCTCCTTGTCTT 1 TCTTCTTCTCCTTTAGCCTCCTTGTCTT 49979377 TCTTCTTCTC 1 TCTTCTTCTC 49979387 TGTCTCTGTC Statistics Matches: 33, Mismatches: 4, Indels: 1 0.87 0.11 0.03 Matches are distributed among these distances: 27 20 0.61 28 13 0.39 ACGTcount: A:0.03, C:0.34, G:0.03, T:0.60 Consensus pattern (28 bp): TCTTCTTCTCCTTTAGCCTCCTTGTCTT Found at i:49979582 original size:12 final size:13 Alignment explanation

Indices: 49979553--49979597 Score: 53 Period size: 12 Copynumber: 3.8 Consensus size: 13 49979543 CTTCTCCTTG 49979553 TCTTTCTTCTTC- 1 TCTTTCTTCTTCA * 49979565 TGTTTCTTC-TCA 1 TCTTTCTTCTTCA 49979577 TCTTTC-TCTTCA 1 TCTTTCTTCTTCA 49979589 TC-TTCTTCT 1 TCTTTCTTCT 49979598 CCCTCCACCT Statistics Matches: 28, Mismatches: 2, Indels: 6 0.78 0.06 0.17 Matches are distributed among these distances: 11 7 0.25 12 21 0.75 ACGTcount: A:0.04, C:0.31, G:0.02, T:0.62 Consensus pattern (13 bp): TCTTTCTTCTTCA Found at i:49979792 original size:25 final size:22 Alignment explanation

Indices: 49979755--49979811 Score: 55 Period size: 25 Copynumber: 2.5 Consensus size: 22 49979745 TTCTCATCAT 49979755 CTTCTTCAT-CTTTGTGCATCTTCTC 1 CTTCTTC-TCCTTT-TGC-TCTT-TC * 49979780 CTTCTTCTCCTTTTTCTCTTTC 1 CTTCTTCTCCTTTTGCTCTTTC 49979802 CTT-TTCTCCT 1 CTTCTTCTCCT 49979812 CTTTATTCTT Statistics Matches: 30, Mismatches: 1, Indels: 6 0.81 0.03 0.16 Matches are distributed among these distances: 21 7 0.23 22 5 0.17 23 4 0.13 24 3 0.10 25 11 0.37 ACGTcount: A:0.04, C:0.35, G:0.04, T:0.58 Consensus pattern (22 bp): CTTCTTCTCCTTTTGCTCTTTC Found at i:49981954 original size:2 final size:2 Alignment explanation

Indices: 49981947--49981977 Score: 55 Period size: 2 Copynumber: 16.0 Consensus size: 2 49981937 TCTACCTTCT 49981947 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 49981978 ATTTTAATTA Statistics Matches: 28, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 1 1 0.04 2 27 0.96 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:49982621 original size:19 final size:18 Alignment explanation

Indices: 49982599--49982635 Score: 56 Period size: 19 Copynumber: 2.0 Consensus size: 18 49982589 AACATGAAAA 49982599 TTAAAATAAATATCGATAC 1 TTAAAATAAATAT-GATAC * 49982618 TTAAAATATATATGATAC 1 TTAAAATAAATATGATAC 49982636 CAATTATTAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 5 0.29 19 12 0.71 ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35 Consensus pattern (18 bp): TTAAAATAAATATGATAC Found at i:49983612 original size:15 final size:16 Alignment explanation

Indices: 49983592--49983622 Score: 55 Period size: 15 Copynumber: 2.0 Consensus size: 16 49983582 TAATTTGCTT 49983592 TATATAAAAA-TAATA 1 TATATAAAAATTAATA 49983607 TATATAAAAATTAATA 1 TATATAAAAATTAATA 49983623 CGGACAGGCC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 10 0.67 16 5 0.33 ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (16 bp): TATATAAAAATTAATA Found at i:49986548 original size:6 final size:6 Alignment explanation

Indices: 49986537--49986565 Score: 58 Period size: 6 Copynumber: 4.8 Consensus size: 6 49986527 TAAATTATTT 49986537 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA 1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTA 49986566 TCAAATTTTA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 23 1.00 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (6 bp): TTTTAA Found at i:49991781 original size:4 final size:4 Alignment explanation

Indices: 49991774--49991823 Score: 59 Period size: 4 Copynumber: 13.0 Consensus size: 4 49991764 TTAATTTGTT * * * 49991774 TGTA TGTA TGTA TGTA TGTA TG-- TGTG TGTG TGTG TGTA TGTA TGTA 1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA 49991820 TGTA 1 TGTA 49991824 AATATATGTG Statistics Matches: 43, Mismatches: 1, Indels: 4 0.90 0.02 0.08 Matches are distributed among these distances: 2 2 0.05 4 41 0.95 ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50 Consensus pattern (4 bp): TGTA Found at i:49998546 original size:20 final size:20 Alignment explanation

Indices: 49998521--49998568 Score: 71 Period size: 20 Copynumber: 2.4 Consensus size: 20 49998511 CTTAAAAGGG * 49998521 ACTTCTA-CCAATACAAGTCC 1 ACTTCTATCC-ATACAAATCC 49998541 ACTTCTATCCATACAAATCC 1 ACTTCTATCCATACAAATCC 49998561 ACTTCTAT 1 ACTTCTAT 49998569 TTGTAACACC Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 20 24 0.92 21 2 0.08 ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31 Consensus pattern (20 bp): ACTTCTATCCATACAAATCC Found at i:49999942 original size:20 final size:20 Alignment explanation

Indices: 49999917--49999956 Score: 71 Period size: 20 Copynumber: 2.0 Consensus size: 20 49999907 ACTTTAAAAT * 49999917 CAAGTTAAAATTATTTTAAC 1 CAAGTTAAAATGATTTTAAC 49999937 CAAGTTAAAATGATTTTAAC 1 CAAGTTAAAATGATTTTAAC 49999957 AAATCAAACT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38 Consensus pattern (20 bp): CAAGTTAAAATGATTTTAAC Found at i:50003181 original size:23 final size:23 Alignment explanation

Indices: 50003150--50003202 Score: 97 Period size: 23 Copynumber: 2.3 Consensus size: 23 50003140 AGAGTTAGGA * 50003150 TGATAAAATAGGATTTGTCAACT 1 TGATTAAATAGGATTTGTCAACT 50003173 TGATTAAATAGGATTTGTCAACT 1 TGATTAAATAGGATTTGTCAACT 50003196 TGATTAA 1 TGATTAA 50003203 CTCAAAATTT Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 23 29 1.00 ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38 Consensus pattern (23 bp): TGATTAAATAGGATTTGTCAACT Found at i:50006373 original size:24 final size:25 Alignment explanation

Indices: 50006346--50006402 Score: 71 Period size: 25 Copynumber: 2.3 Consensus size: 25 50006336 TAGCTCAGAG * * 50006346 GAGCTTACCG-TTTACAGCTCGTAA 1 GAGCATACCGATTCACAGCTCGTAA * * 50006370 GAGCATACCGATTCAGAGCTCGTAT 1 GAGCATACCGATTCACAGCTCGTAA 50006395 GAGCATAC 1 GAGCATAC 50006403 ATGTTTAGAA Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 24 9 0.32 25 19 0.68 ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25 Consensus pattern (25 bp): GAGCATACCGATTCACAGCTCGTAA Found at i:50008036 original size:16 final size:16 Alignment explanation

Indices: 50008011--50008044 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 50008001 ATGAATATAT * * 50008011 ATGTGTAAATGTGATA 1 ATGTGCAAATATGATA 50008027 ATGTGCAAATATGATA 1 ATGTGCAAATATGATA 50008043 AT 1 AT 50008045 TGAATATTGG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35 Consensus pattern (16 bp): ATGTGCAAATATGATA Found at i:50011426 original size:40 final size:39 Alignment explanation

Indices: 50011363--50011476 Score: 122 Period size: 40 Copynumber: 2.9 Consensus size: 39 50011353 CGTCAGATAG * * 50011363 ACCG-AACACACCACACAAAAGCTCATAAGAGTTGATCCA 1 ACCGAAACACACCA-ATAGAAGCTCATAAGAGTTGATCCA * ** * * * 50011402 ACCGAAATATGCCAAATAGAAGCTCGTAAGAGCTGGTCCA 1 ACCGAAACACACC-AATAGAAGCTCATAAGAGTTGATCCA * 50011442 CCCGAAACACACCAATAGAAGCTCATAAGAGTTGA 1 ACCGAAACACACCAATAGAAGCTCATAAGAGTTGA 50011477 ACAGAAGCTC Statistics Matches: 58, Mismatches: 15, Indels: 4 0.75 0.19 0.05 Matches are distributed among these distances: 39 23 0.40 40 34 0.59 41 1 0.02 ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15 Consensus pattern (39 bp): ACCGAAACACACCAATAGAAGCTCATAAGAGTTGATCCA Found at i:50013123 original size:17 final size:15 Alignment explanation

Indices: 50013098--50013141 Score: 52 Period size: 15 Copynumber: 2.8 Consensus size: 15 50013088 TATTTTTTTT * 50013098 AAATCTATAAAATATAA 1 AAATATATAAAAT-T-A * 50013115 AAATATATACAATTA 1 AAATATATAAAATTA 50013130 AAATATATAAAA 1 AAATATATAAAA 50013142 AGCTTATAAT Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 15 12 0.50 16 1 0.04 17 11 0.46 ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30 Consensus pattern (15 bp): AAATATATAAAATTA Found at i:50013309 original size:7 final size:9 Alignment explanation

Indices: 50013275--50013304 Score: 53 Period size: 9 Copynumber: 3.4 Consensus size: 9 50013265 TTCTTGAACT 50013275 TTTTAT-TA 1 TTTTATATA 50013283 TTTTATATA 1 TTTTATATA 50013292 TTTTATATA 1 TTTTATATA 50013301 TTTT 1 TTTT 50013305 TTATTAATAA Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 8 6 0.29 9 15 0.71 ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73 Consensus pattern (9 bp): TTTTATATA Found at i:50016199 original size:29 final size:29 Alignment explanation

Indices: 50016136--50016203 Score: 93 Period size: 29 Copynumber: 2.3 Consensus size: 29 50016126 TAATCAACCA 50016136 CGCACACTTAGTGCCATGCACTTTAAACT 1 CGCACACTTAGTGCCATGCACTTTAAACT * ** 50016165 CACACACTTAGTGCCATGCA-TTTCAAGTT 1 CGCACACTTAGTGCCATGCACTTT-AAACT 50016194 CGCACACTTA 1 CGCACACTTA 50016204 CCTTTTCCGC Statistics Matches: 34, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 28 3 0.09 29 31 0.91 ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28 Consensus pattern (29 bp): CGCACACTTAGTGCCATGCACTTTAAACT Found at i:50016322 original size:174 final size:175 Alignment explanation

Indices: 50016024--50016352 Score: 545 Period size: 174 Copynumber: 1.9 Consensus size: 175 50016014 AACTCAAGGT * * 50016024 ACTTACCTTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTTA 1 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTTA * * * 50016089 TAGAAAATATATATTGGGTTGCACGCATAACGTTTAGTAATCAACCACGCACACTTAGTGCCATG 66 TAGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATG 50016154 CACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC 131 CACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC 50016199 ACTTACC-TTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAA-TTTA 1 ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTTA ** * 50016262 TAGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCAT 66 TAGAAAATATATATTGGGTT-GCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCAT * * 50016327 GTACTTTAAACTCGCACACTTAGTGC 130 GCACTTTAAACTCACACACTTAGTGC 50016353 TGTACAATTT Statistics Matches: 143, Mismatches: 10, Indels: 3 0.92 0.06 0.02 Matches are distributed among these distances: 173 24 0.17 174 112 0.78 175 7 0.05 ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30 Consensus pattern (175 bp): ACTTACCTTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTTA TAGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATG CACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC Found at i:50016344 original size:29 final size:30 Alignment explanation

Indices: 50016305--50016383 Score: 110 Period size: 29 Copynumber: 2.7 Consensus size: 30 50016295 CTTAATAATC 50016305 AACCGCGCACACTTAGTGCCATGTAC-TTTA 1 AACC-CGCACACTTAGTGCCATGTACATTTA * 50016335 AACTCGCACACTTAGTG-C-TGTACAATTTA 1 AACCCGCACACTTAGTGCCATGTAC-ATTTA 50016364 AACCCGCACACTTAGTGCCA 1 AACCCGCACACTTAGTGCCA 50016384 ATCTCATGAC Statistics Matches: 43, Mismatches: 2, Indels: 7 0.83 0.04 0.13 Matches are distributed among these distances: 27 5 0.12 28 1 0.02 29 33 0.77 30 4 0.09 ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25 Consensus pattern (30 bp): AACCCGCACACTTAGTGCCATGTACATTTA Found at i:50024340 original size:29 final size:29 Alignment explanation

Indices: 50024277--50024344 Score: 93 Period size: 29 Copynumber: 2.3 Consensus size: 29 50024267 TAATCAACCA 50024277 CGCACACTTAGTGCCATGCACTTTAAACT 1 CGCACACTTAGTGCCATGCACTTTAAACT * ** 50024306 CACACACTTAGTGCCATGCA-TTTCAAGTT 1 CGCACACTTAGTGCCATGCACTTT-AAACT 50024335 CGCACACTTA 1 CGCACACTTA 50024345 CCTTTTCCGC Statistics Matches: 34, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 28 3 0.09 29 31 0.91 ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28 Consensus pattern (29 bp): CGCACACTTAGTGCCATGCACTTTAAACT Found at i:50024485 original size:29 final size:30 Alignment explanation

Indices: 50024446--50024524 Score: 110 Period size: 29 Copynumber: 2.7 Consensus size: 30 50024436 CTTAATAATC 50024446 AACCGCGCACACTTAGTGCCATGTAC-TTTA 1 AACC-CGCACACTTAGTGCCATGTACATTTA * 50024476 AACTCGCACACTTAGTG-C-TGTACAATTTA 1 AACCCGCACACTTAGTGCCATGTAC-ATTTA 50024505 AACCCGCACACTTAGTGCCA 1 AACCCGCACACTTAGTGCCA 50024525 ATCTCATGAC Statistics Matches: 43, Mismatches: 2, Indels: 7 0.83 0.04 0.13 Matches are distributed among these distances: 27 5 0.12 28 1 0.02 29 33 0.77 30 4 0.09 ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25 Consensus pattern (30 bp): AACCCGCACACTTAGTGCCATGTACATTTA Found at i:50030397 original size:14 final size:15 Alignment explanation

Indices: 50030372--50030400 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 50030362 ATAATAGAGA 50030372 GAGAGAAAGAAAAAT 1 GAGAGAAAGAAAAAT 50030387 GAGAG-AAGAAAAAT 1 GAGAGAAAGAAAAAT 50030401 AAAGAAAAGA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 9 0.64 15 5 0.36 ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07 Consensus pattern (15 bp): GAGAGAAAGAAAAAT Found at i:50033522 original size:23 final size:24 Alignment explanation

Indices: 50033490--50033537 Score: 62 Period size: 25 Copynumber: 2.0 Consensus size: 24 50033480 TTGAACATCA * 50033490 ATAATTTTAG-TTTAAAATATGTC 1 ATAATCTTAGATTTAAAATATGTC * 50033513 ATAATCTTAGCATTTTAAATATGTC 1 ATAATCTTAG-ATTTAAAATATGTC 50033538 TTAAGTTTAT Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 23 9 0.43 25 12 0.57 ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46 Consensus pattern (24 bp): ATAATCTTAGATTTAAAATATGTC Found at i:50035096 original size:39 final size:39 Alignment explanation

Indices: 50035045--50035254 Score: 210 Period size: 39 Copynumber: 5.4 Consensus size: 39 50035035 TTTTCAATCA * * * 50035045 CACCAGCACACAGCCTGCTAGGCATATAGTCCGAATAAT 1 CACCGGCACACAGCCTGCTAGGCACATAGACCGAATAAT ** * 50035084 CACCGGCACACAGTTTGCTAGGCACATAGCCCGAATAAT 1 CACCGGCACACAGCCTGCTAGGCACATAGACCGAATAAT * * ** * * 50035123 TACTGGCACACAGTTTGCTAAGTACATA-ACCTGAATAAT 1 CACCGGCACACAGCCTGCTAGGCACATAGACC-GAATAAT * * 50035162 TACTGGCACACAGCCTGCTAGGCACATA-ACACGAATAAT 1 CACCGGCACACAGCCTGCTAGGCACATAGAC-CGAATAAT * * * 50035201 CACTGGTACACAG-CTCGCTAGGCACATAGCCCGAATAAT 1 CACCGGCACACAGCCT-GCTAGGCACATAGACCGAATAAT * 50035240 CACCGGTACACAGCC 1 CACCGGCACACAGCC 50035255 CAAATAATCA Statistics Matches: 148, Mismatches: 18, Indels: 9 0.85 0.10 0.05 Matches are distributed among these distances: 38 4 0.03 39 141 0.95 40 3 0.02 ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19 Consensus pattern (39 bp): CACCGGCACACAGCCTGCTAGGCACATAGACCGAATAAT Found at i:50035277 original size:23 final size:23 Alignment explanation

Indices: 50035222--50035277 Score: 76 Period size: 23 Copynumber: 2.4 Consensus size: 23 50035212 AGCTCGCTAG * * 50035222 GCACATAGCCCGAATAATCACCG 1 GCACATAGCCCAAATAATCACCA * * 50035245 GTACACAGCCCAAATAATCACCA 1 GCACATAGCCCAAATAATCACCA 50035268 GCACATAGCC 1 GCACATAGCC 50035278 TGCTAGGCAC Statistics Matches: 27, Mismatches: 6, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.38, C:0.36, G:0.14, T:0.12 Consensus pattern (23 bp): GCACATAGCCCAAATAATCACCA Found at i:50041157 original size:24 final size:24 Alignment explanation

Indices: 50041130--50041181 Score: 77 Period size: 24 Copynumber: 2.2 Consensus size: 24 50041120 TTAGTAAGTC * 50041130 AAATAAACTATACTAATAAATGCT 1 AAATAAACTATACTAATAAATACT * * 50041154 AAATATATTATACTAATAAATACT 1 AAATAAACTATACTAATAAATACT 50041178 AAAT 1 AAAT 50041182 CTTCTAGAAA Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33 Consensus pattern (24 bp): AAATAAACTATACTAATAAATACT Found at i:50043124 original size:24 final size:24 Alignment explanation

Indices: 50043097--50043148 Score: 77 Period size: 24 Copynumber: 2.2 Consensus size: 24 50043087 TTAGTAAGTC * 50043097 AAATAAACTATACTAATAAATGCT 1 AAATAAACTATACTAATAAATACT * * 50043121 AAATATATTATACTAATAAATACT 1 AAATAAACTATACTAATAAATACT 50043145 AAAT 1 AAAT 50043149 CTTCTAGAAA Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33 Consensus pattern (24 bp): AAATAAACTATACTAATAAATACT Found at i:50044593 original size:12 final size:12 Alignment explanation

Indices: 50044576--50044603 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 50044566 CATCAAAAAC 50044576 ATTAAAATAAAT 1 ATTAAAATAAAT 50044588 ATTAAAATAAAT 1 ATTAAAATAAAT 50044600 ATTA 1 ATTA 50044604 CCCAATAAAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (12 bp): ATTAAAATAAAT Found at i:50046184 original size:26 final size:26 Alignment explanation

Indices: 50046155--50046206 Score: 86 Period size: 26 Copynumber: 2.0 Consensus size: 26 50046145 TTATCGGTCA * * 50046155 ATTTATTTTTATTTCAATAGATCTTT 1 ATTTATTTTTATTCCAATACATCTTT 50046181 ATTTATTTTTATTCCAATACATCTTT 1 ATTTATTTTTATTCCAATACATCTTT 50046207 TTCTTACTTT Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 24 1.00 ACGTcount: A:0.27, C:0.12, G:0.02, T:0.60 Consensus pattern (26 bp): ATTTATTTTTATTCCAATACATCTTT Found at i:50049716 original size:21 final size:21 Alignment explanation

Indices: 50049673--50049845 Score: 188 Period size: 21 Copynumber: 8.3 Consensus size: 21 50049663 GTACATTGTT * * 50049673 AACAGAAACTCGT-A-AGCTG 1 AACAGAAGCTCGTAAGAGCTA * 50049692 AACAGAAGCTTGTAAGAGCTA 1 AACAGAAGCTCGTAAGAGCTA * 50049713 AACAGAAGCTCATAAGAGCTA 1 AACAGAAGCTCGTAAGAGCTA * * * 50049734 AATAGAAGCTTGAAAGAGCTA 1 AACAGAAGCTCGTAAGAGCTA * * * 50049755 AACAGAAACTCATAAGAGTTA 1 AACAGAAGCTCGTAAGAGCTA * 50049776 AACAGAAGCTCGTAAGAGCTG 1 AACAGAAGCTCGTAAGAGCTA * * * 50049797 AACAGAAACTCGTAAAAGTTA 1 AACAGAAGCTCGTAAGAGCTA * 50049818 AATAGAAGCTCGTAAGAGCTA 1 AACAGAAGCTCGTAAGAGCTA * 50049839 AATAGAA 1 AACAGAA 50049846 AGTAAAACAC Statistics Matches: 125, Mismatches: 27, Indels: 2 0.81 0.18 0.01 Matches are distributed among these distances: 19 11 0.09 20 1 0.01 21 113 0.90 ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17 Consensus pattern (21 bp): AACAGAAGCTCGTAAGAGCTA Found at i:50049743 original size:42 final size:42 Alignment explanation

Indices: 50049695--50049846 Score: 214 Period size: 42 Copynumber: 3.6 Consensus size: 42 50049685 TAAGCTGAAC * * * 50049695 AGAAGCTTGTAAGAGCTAAACAGAAGCTCATAAGAGCTAAAT 1 AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT * * * 50049737 AGAAGCTTGAAAGAGCTAAACAGAAACTCATAAGAGTTAAAC 1 AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT * * * 50049779 AGAAGCTCGTAAGAGCTGAACAGAAACTCGTAAAAGTTAAAT 1 AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT * 50049821 AGAAGCTCGTAAGAGCTAAATAGAAA 1 AGAAGCTCGTAAGAGCTAAACAGAAA 50049847 GTAAAACACG Statistics Matches: 98, Mismatches: 12, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 42 98 1.00 ACGTcount: A:0.47, C:0.14, G:0.21, T:0.18 Consensus pattern (42 bp): AGAAGCTCGTAAGAGCTAAACAGAAACTCATAAGAGTTAAAT Found at i:50057743 original size:25 final size:25 Alignment explanation

Indices: 50057723--50057830 Score: 101 Period size: 25 Copynumber: 4.3 Consensus size: 25 50057713 AAGCTCCTCT 50057723 AAGCTGAATAACAGTAAGCTCATGC 1 AAGCTGAATAACAGTAAGCTCATGC * * 50057748 GAGCTGAATAACGGTAAGCTCATGC 1 AAGCTGAATAACAGTAAGCTCATGC * * * * * 50057773 GAGATGAGTATCAGTAAGCTCATAC 1 AAGCTGAATAACAGTAAGCTCATGC * * * * 50057798 GAGCTGAGTATC-GATAAGCTCATAC 1 AAGCTGAATAACAG-TAAGCTCATGC 50057823 AAGCTGAA 1 AAGCTGAA 50057831 ATCACTAACC Statistics Matches: 72, Mismatches: 10, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 24 1 0.01 25 71 0.99 ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21 Consensus pattern (25 bp): AAGCTGAATAACAGTAAGCTCATGC Found at i:50057767 original size:50 final size:50 Alignment explanation

Indices: 50057691--50057830 Score: 133 Period size: 50 Copynumber: 2.8 Consensus size: 50 50057681 ATACATGTAT * * * 50057691 GCTCATAAGAGCT--ATAAACGGTAAGCTCCT-CTAAGCTGAATAACAGTAA 1 GCTCATACGAGCTGAAT-AACGGTAAGCTCATGC-AAGATGAATAACAGTAA * * * * 50057740 GCTCATGCGAGCTGAATAACGGTAAGCTCATGCGAGATGAGTATCAGTAA 1 GCTCATACGAGCTGAATAACGGTAAGCTCATGCAAGATGAATAACAGTAA * * * * * 50057790 GCTCATACGAGCTGAGTATCGATAAGCTCATACAAGCTGAA 1 GCTCATACGAGCTGAATAACGGTAAGCTCATGCAAGATGAA 50057831 ATCACTAACC Statistics Matches: 73, Mismatches: 15, Indels: 5 0.78 0.16 0.05 Matches are distributed among these distances: 49 11 0.15 50 59 0.81 51 3 0.04 ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22 Consensus pattern (50 bp): GCTCATACGAGCTGAATAACGGTAAGCTCATGCAAGATGAATAACAGTAA Found at i:50061826 original size:32 final size:32 Alignment explanation

Indices: 50061790--50061854 Score: 112 Period size: 32 Copynumber: 2.0 Consensus size: 32 50061780 ACTAATTTCT * 50061790 TTCCCAATCTGCAGAAAACCTTGCTATTCAAC 1 TTCCCAATCTGCAGAAAACCCTGCTATTCAAC * 50061822 TTCCCAATCTGCAGAAAACCCTGCTCTTCAAC 1 TTCCCAATCTGCAGAAAACCCTGCTATTCAAC 50061854 T 1 T 50061855 CATGTTCTTC Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 32 31 1.00 ACGTcount: A:0.29, C:0.34, G:0.09, T:0.28 Consensus pattern (32 bp): TTCCCAATCTGCAGAAAACCCTGCTATTCAAC Found at i:50063919 original size:24 final size:24 Alignment explanation

Indices: 50063891--50063938 Score: 87 Period size: 24 Copynumber: 2.0 Consensus size: 24 50063881 CGGTTCTTGG * 50063891 CATTAAATAAGTAATGGAATAAAA 1 CATTAAATAAATAATGGAATAAAA 50063915 CATTAAATAAATAATGGAATAAAA 1 CATTAAATAAATAATGGAATAAAA 50063939 TATACCTTAC Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.60, C:0.04, G:0.10, T:0.25 Consensus pattern (24 bp): CATTAAATAAATAATGGAATAAAA Found at i:50068610 original size:21 final size:21 Alignment explanation

Indices: 50068577--50068629 Score: 61 Period size: 21 Copynumber: 2.5 Consensus size: 21 50068567 CATTATTTCT * * * 50068577 AATCTTACTGCTACAGTATCC 1 AATCTCACCGCTACAGTAACC * * 50068598 AATCTCACCGCTATAGTAACT 1 AATCTCACCGCTACAGTAACC 50068619 AATCTCACCGC 1 AATCTCACCGC 50068630 CACCGCTGTT Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 27 1.00 ACGTcount: A:0.30, C:0.32, G:0.09, T:0.28 Consensus pattern (21 bp): AATCTCACCGCTACAGTAACC Found at i:50072588 original size:21 final size:21 Alignment explanation

Indices: 50072564--50072603 Score: 71 Period size: 21 Copynumber: 1.9 Consensus size: 21 50072554 ATTGTCAATA 50072564 ACTTTTTAATATTTTTTTTTT 1 ACTTTTTAATATTTTTTTTTT * 50072585 ACTTTTTTATATTTTTTTT 1 ACTTTTTAATATTTTTTTT 50072604 GTAAATTTCA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78 Consensus pattern (21 bp): ACTTTTTAATATTTTTTTTTT Found at i:50076897 original size:26 final size:27 Alignment explanation

Indices: 50076868--50076925 Score: 82 Period size: 27 Copynumber: 2.2 Consensus size: 27 50076858 ATTATATTCA * 50076868 TATTTAATAT-ATTTTCTTATCCAATT 1 TATTTAATATGATTTTCTAATCCAATT * * 50076894 TATTTAATATGTTTTTCTAATTCAATT 1 TATTTAATATGATTTTCTAATCCAATT 50076921 TATTT 1 TATTT 50076926 TTCAAGTAAC Statistics Matches: 28, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 26 10 0.36 27 18 0.64 ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60 Consensus pattern (27 bp): TATTTAATATGATTTTCTAATCCAATT Found at i:50078400 original size:22 final size:22 Alignment explanation

Indices: 50078372--50078419 Score: 60 Period size: 22 Copynumber: 2.2 Consensus size: 22 50078362 TTTTACTTTT * 50078372 TCAATTCACTCTAAATTCTCTC 1 TCAATTCACTCTAAATACTCTC * * * 50078394 TCAATTCATTTTCAATACTCTC 1 TCAATTCACTCTAAATACTCTC 50078416 TCAA 1 TCAA 50078420 CTCTCAATTT Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42 Consensus pattern (22 bp): TCAATTCACTCTAAATACTCTC Found at i:50084600 original size:26 final size:26 Alignment explanation

Indices: 50084556--50084606 Score: 75 Period size: 26 Copynumber: 2.0 Consensus size: 26 50084546 TAAGTGTTCT 50084556 GAAACTGATACATGCTATGATATTCA 1 GAAACTGATACATGCTATGATATTCA * * * 50084582 GAAATTGATATATGTTATGATATTC 1 GAAACTGATACATGCTATGATATTC 50084607 TGAAGCTACT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 26 22 1.00 ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37 Consensus pattern (26 bp): GAAACTGATACATGCTATGATATTCA Found at i:50087977 original size:18 final size:18 Alignment explanation

Indices: 50087954--50087989 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 50087944 TAAAAGATGA 50087954 AATCAAATTTTATTGAGT 1 AATCAAATTTTATTGAGT 50087972 AATCAAATTTTATTGAGT 1 AATCAAATTTTATTGAGT 50087990 CTAGTTTTTC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44 Consensus pattern (18 bp): AATCAAATTTTATTGAGT Found at i:50092939 original size:68 final size:69 Alignment explanation

Indices: 50092798--50092941 Score: 184 Period size: 68 Copynumber: 2.1 Consensus size: 69 50092788 TTGATCACTT * * * * 50092798 TAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAGATAATT 1 TAATATTAAATTAATAAAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAAATAATT *** 50092863 ACTT 66 AAAA * * 50092867 TAATATTAAATTAATAAAATAC-TATAAAGATAATTATTAAATTTAATTTAATATTAAAACT-AT 1 TAATATTAAATTAATAAAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAAA-TAAT 50092930 TAAAA 65 TAAAA 50092935 TAATATT 1 TAATATT 50092942 GTTTTTGAAA Statistics Matches: 65, Mismatches: 9, Indels: 3 0.84 0.12 0.04 Matches are distributed among these distances: 68 43 0.66 69 22 0.34 ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42 Consensus pattern (69 bp): TAATATTAAATTAATAAAATACTTATAAAGATAAATATTAAATTAAATTTAATATTAAAATAATT AAAA Found at i:50097856 original size:37 final size:37 Alignment explanation

Indices: 50097793--50097871 Score: 108 Period size: 37 Copynumber: 2.1 Consensus size: 37 50097783 TTATTACGAA * 50097793 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG 1 GTCTTACCCGGACATAATCTCCACACGAAGTCATCGG * 50097830 GTCTTACCCGGACGA-AATC-CCTACACGTAGTCATCGG 1 GTCTTACCCGGAC-ATAATCTCC-ACACGAAGTCATCGG 50097867 GTCTT 1 GTCTT 50097872 TAGAGCTCAG Statistics Matches: 38, Mismatches: 2, Indels: 4 0.86 0.05 0.09 Matches are distributed among these distances: 36 2 0.05 37 35 0.92 38 1 0.03 ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25 Consensus pattern (37 bp): GTCTTACCCGGACATAATCTCCACACGAAGTCATCGG Done.