Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A13

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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 2708888 characters in sequence are not A, C, G, or T


File 96 of 332

Found at i:30849750 original size:27 final size:27

Alignment explanation

Indices: 30849387--30849756 Score: 185 Period size: 27 Copynumber: 13.7 Consensus size: 27 30849377 TAGAAAGTCA * * 30849387 AGGGTATTTCT-GTAACTTTGTAAATC- 1 AGGGTATTT-TGGTAATTTTATAAATCG ** * 30849413 AGGGGTATTTTGGTAATTTTACGAATTG 1 A-GGGTATTTTGGTAATTTTATAAATCG * * * * 30849441 AGGGTATTTCGGTAATTTCACAAA-CC 1 AGGGTATTTTGGTAATTTTATAAATCG * * 30849467 AGTGGTATTTTGGTAATTTTACAAA-CT 1 AG-GGTATTTTGGTAATTTTATAAATCG * * * * * * 30849494 AGTGATATTTTAGCAATTTTACAGA-CT 1 AG-GGTATTTTGGTAATTTTATAAATCG 30849521 AGGGTATTTTGGTAATTTTACT-AATCG 1 AGGGTATTTTGGTAATTTTA-TAAATCG * * * * 30849548 AAGGTATTTTGGTAATTTTGTAAACCA 1 AGGGTATTTTGGTAATTTTATAAATCG * * 30849575 AGGGTATTTTAGTAATTTTGTAAATCG 1 AGGGTATTTTGGTAATTTTATAAATCG ***** * 30849602 AGGGTAAAACAGTAATTTTGTAAATCG 1 AGGGTATTTTGGTAATTTTATAAATCG ***** * 30849629 AGGGTAAAACAGTAATTCTATAAATCG 1 AGGGTATTTTGGTAATTTTATAAATCG **** * * 30849656 AGGGTAAAACGGTAATTCTGTAAATCG 1 AGGGTATTTTGGTAATTTTATAAATCG **** * * 30849683 AGGGTAAAACGGTAATTCTGTAAATCG 1 AGGGTATTTTGGTAATTTTATAAATCG **** 30849710 AGGGTAAAACGGTAATTTTATAAATCG 1 AGGGTATTTTGGTAATTTTATAAATCG * 30849737 AGGGTACTTTGGTAATTTTA 1 AGGGTATTTTGGTAATTTTA 30849757 CAATTTGAGG Statistics Matches: 292, Mismatches: 45, Indels: 13 0.83 0.13 0.04 Matches are distributed among these distances: 26 21 0.07 27 270 0.92 28 1 0.00 ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36 Consensus pattern (27 bp): AGGGTATTTTGGTAATTTTATAAATCG Found at i:30849753 original size:54 final size:54 Alignment explanation

Indices: 30849558--30849742 Score: 262 Period size: 54 Copynumber: 3.4 Consensus size: 54 30849548 AAGGTATTTT * * **** * 30849558 GGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAAC 1 GGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAAC * * 30849612 AGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAAC 1 GGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAAC * * 30849666 GGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC 1 GGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAAC * 30849720 GGTAATTTTATAAATCGAGGGTA 1 GGTAATTTTGTAAATCGAGGGTA 30849743 CTTTGGTAAT Statistics Matches: 116, Mismatches: 15, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 54 116 1.00 ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30 Consensus pattern (54 bp): GGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAAC Found at i:30852624 original size:27 final size:27 Alignment explanation

Indices: 30852586--30852639 Score: 83 Period size: 27 Copynumber: 2.0 Consensus size: 27 30852576 GCAAGTGAAG 30852586 ATAGTAACAGAAAAGATA-TCGGATCGT 1 ATAGTAACAGAAAAGATACT-GGATCGT * 30852613 ATAGTAATAGAAAAGATACTGGATCGT 1 ATAGTAACAGAAAAGATACTGGATCGT 30852640 GCGTTGAAGG Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 27 24 0.96 28 1 0.04 ACGTcount: A:0.44, C:0.09, G:0.22, T:0.24 Consensus pattern (27 bp): ATAGTAACAGAAAAGATACTGGATCGT Found at i:30860771 original size:67 final size:67 Alignment explanation

Indices: 30860658--30860803 Score: 231 Period size: 67 Copynumber: 2.2 Consensus size: 67 30860648 AAGCATTCTG * 30860658 GCAGCCTCGCTGCAAACTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAATATC 1 GCAGCCTCGCTGCAAACTGGTGGCCTAGCCACATATATCTGTTCTGGTGACTTCGTCACAATATC 30860723 TA 66 TA * * * 30860725 GTAGCCTCGCTGCAATCTGGTGGCCTAGCCACA-ATATCTGTATCTGGTTACTTCGTCACAATAT 1 GCAGCCTCGCTGCAAACTGGTGGCCTAGCCACATATATCTGT-TCTGGTGACTTCGTCACAATAT * 30860789 CTG 65 CTA 30860792 GCAGCCTCGCTG 1 GCAGCCTCGCTG 30860804 TAATTTTTGT Statistics Matches: 72, Mismatches: 6, Indels: 2 0.90 0.08 0.03 Matches are distributed among these distances: 66 8 0.11 67 64 0.89 ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29 Consensus pattern (67 bp): GCAGCCTCGCTGCAAACTGGTGGCCTAGCCACATATATCTGTTCTGGTGACTTCGTCACAATATC TA Found at i:30867142 original size:26 final size:27 Alignment explanation

Indices: 30867113--30867172 Score: 77 Period size: 27 Copynumber: 2.3 Consensus size: 27 30867103 CCACATATAT * 30867113 ATATCTGT-TCTGGTGGCCTAGCCACA 1 ATATCTGTATCTGGTGACCTAGCCACA * * * 30867139 ATATCTGTATCTGGTGACTTCGTCACA 1 ATATCTGTATCTGGTGACCTAGCCACA 30867166 ATATCTG 1 ATATCTG 30867173 GCAGCCTTGC Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 26 8 0.28 27 21 0.72 ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35 Consensus pattern (27 bp): ATATCTGTATCTGGTGACCTAGCCACA Found at i:30875436 original size:39 final size:40 Alignment explanation

Indices: 30875391--30875615 Score: 215 Period size: 40 Copynumber: 5.7 Consensus size: 40 30875381 GCTCCTCGTT * * * * 30875391 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * * 30875431 C-AATGCCTTTGGGACTTAACCCGGATTTAATGACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * 30875470 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * * * 30875510 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA 1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA ** * * * * 30875550 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA * 30875591 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAACCCGGA 30875616 CAGCATTCAA Statistics Matches: 153, Mismatches: 26, Indels: 12 0.80 0.14 0.06 Matches are distributed among these distances: 39 36 0.24 40 103 0.67 41 14 0.09 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA Found at i:30875485 original size:40 final size:38 Alignment explanation

Indices: 30875358--30875615 Score: 191 Period size: 40 Copynumber: 6.5 Consensus size: 38 30875348 AAATCACGTA * * * 30875358 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG 1 CCTTCGGGACTTAACCCGGATTTAG-TACTCG--CACAATG * * * * 30875397 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG 1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCACAATG * * 30875436 CCTTTGGGACTTAACCCGGATTTAATGACTCGCACGAATG 1 CCTTCGGGACTTAACCCGGATTTAGT-ACTCGCAC-AATG * 30875476 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG 1 CCTTCGGGACTTAACCCGGATTTAGTA-CTCGCAC-AATG * * 30875516 CCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCACAAATG 1 CCTTCGGGACTTAACCCGG-ATTTAGTA-CTCGCAC-AATG ** * * * * 30875556 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAG 1 CCTTCGGGA-CTTAACCCGGATTTAGT-AC-TCGCACAATG * 30875596 CCTTCGGGACTTAGCCCGGA 1 CCTTCGGGACTTAACCCGGA 30875616 CAGCATTCAA Statistics Matches: 178, Mismatches: 30, Indels: 21 0.78 0.13 0.09 Matches are distributed among these distances: 38 2 0.01 39 49 0.28 40 115 0.65 41 12 0.07 ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27 Consensus pattern (38 bp): CCTTCGGGACTTAACCCGGATTTAGTACTCGCACAATG Found at i:30875624 original size:41 final size:41 Alignment explanation

Indices: 30875547--30875624 Score: 97 Period size: 40 Copynumber: 1.9 Consensus size: 41 30875537 CTTGTATCTC * * * 30875547 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA 1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA 30875588 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA 1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA 30875625 ATTAATCATG Statistics Matches: 32, Mismatches: 3, Indels: 4 0.82 0.08 0.10 Matches are distributed among these distances: 40 17 0.53 41 15 0.47 ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24 Consensus pattern (41 bp): GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA Found at i:30881177 original size:49 final size:49 Alignment explanation

Indices: 30881109--30881215 Score: 180 Period size: 49 Copynumber: 2.2 Consensus size: 49 30881099 TATCACAGTT * 30881109 ATACACTTCCACTTCCATCACATTGGCCATTCGGCCTTATCACATATAC 1 ATACACTTTCACTTCCATCACATTGGCCATTCGGCCTTATCACATATAC * 30881158 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCAGATATAC 1 ATACACTTTCAC-TTCCATCACATTGGCCATTCGGCCTTATCACATATAC 30881207 ATACACTTT 1 ATACACTTT 30881216 GGCCATTCGG Statistics Matches: 55, Mismatches: 2, Indels: 2 0.93 0.03 0.03 Matches are distributed among these distances: 49 53 0.96 50 2 0.04 ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33 Consensus pattern (49 bp): ATACACTTTCACTTCCATCACATTGGCCATTCGGCCTTATCACATATAC Found at i:30881223 original size:34 final size:34 Alignment explanation

Indices: 30881180--30881249 Score: 131 Period size: 34 Copynumber: 2.1 Consensus size: 34 30881170 ATTCATCACA * 30881180 TTGGCCATTCGGCCTTATCAGATATACATACACT 1 TTGGCCATTCGGCCTTATCACATATACATACACT 30881214 TTGGCCATTCGGCCTTATCACATATACATACACT 1 TTGGCCATTCGGCCTTATCACATATACATACACT 30881248 TT 1 TT 30881250 CACATTCATC Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 34 35 1.00 ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34 Consensus pattern (34 bp): TTGGCCATTCGGCCTTATCACATATACATACACT Found at i:30881263 original size:49 final size:49 Alignment explanation

Indices: 30881214--30881504 Score: 527 Period size: 49 Copynumber: 6.0 Consensus size: 49 30881204 TACATACACT * 30881214 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACT 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA 30881263 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA * 30881312 TGGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA 30881361 TTGGCCATTCGGCCTTATCAC--ATACATACACTTTCACATTCATCACA 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA 30881408 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA * 30881457 TGGGCCATTCGGCCTTATCAC--ATACATACACTTTCACATTCATCACA 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA 30881504 T 1 T 30881505 AAAATCCTAA Statistics Matches: 236, Mismatches: 4, Indels: 6 0.96 0.02 0.02 Matches are distributed among these distances: 47 74 0.31 49 162 0.69 ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32 Consensus pattern (49 bp): TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACA Found at i:30881270 original size:83 final size:83 Alignment explanation

Indices: 30881131--30881298 Score: 318 Period size: 83 Copynumber: 2.0 Consensus size: 83 30881121 TTCCATCACA 30881131 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT * 30881196 ATCAGATATACATACACT 66 ATCACATATACATACACT * 30881214 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACTTTGGCCATTCGGCCTT 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT 30881279 ATCACATATACATACACT 66 ATCACATATACATACACT 30881297 TT 1 TT 30881299 CACATTCATC Statistics Matches: 83, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 83 83 1.00 ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34 Consensus pattern (83 bp): TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT ATCACATATACATACACT Found at i:30881435 original size:145 final size:144 Alignment explanation

Indices: 30881214--30881504 Score: 539 Period size: 145 Copynumber: 2.0 Consensus size: 144 30881204 TACATACACT * 30881214 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACTTTGGCCATTCGGCCTT 1 TTGGCCATTCGGCCTTATCACA-ATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT 30881279 ATCACATATACATACACTTTCACATTCATCACATGGGCCATTCGGCCTTATCACATATACATACA 65 ATCACATATACATACACTTTCACATTCATCACATGGGCCATTCGGCCTTATCAC--ATACATACA 30881344 CTTTCACATTCATCACA 128 CTTTCACATTCATCACA 30881361 TTGGCCATTCGGCCTTATCAC-ATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTA 1 TTGGCCATTCGGCCTTATCACAATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTA 30881425 TCACATATACATACACTTTCACATTCATCACATGGGCCATTCGGCCTTATCACATACATACACTT 66 TCACATATACATACACTTTCACATTCATCACATGGGCCATTCGGCCTTATCACATACATACACTT 30881490 TCACATTCATCACA 131 TCACATTCATCACA 30881504 T 1 T 30881505 AAAATCCTAA Statistics Matches: 143, Mismatches: 1, Indels: 4 0.97 0.01 0.03 Matches are distributed among these distances: 143 27 0.19 145 95 0.66 147 21 0.15 ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32 Consensus pattern (144 bp): TTGGCCATTCGGCCTTATCACAATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTA TCACATATACATACACTTTCACATTCATCACATGGGCCATTCGGCCTTATCACATACATACACTT TCACATTCATCACA Found at i:30881450 original size:96 final size:96 Alignment explanation

Indices: 30881214--30881504 Score: 537 Period size: 96 Copynumber: 3.0 Consensus size: 96 30881204 TACATACACT * 30881214 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACTTTGGCCATTCGGCCTT 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT 30881279 ATCACATATACATACACTTTCACATTCATCACA 66 ATCAC--ATACATACACTTTCACATTCATCACA * 30881312 TGGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT 30881377 ATCACATACATACACTTTCACATTCATCACA 66 ATCACATACATACACTTTCACATTCATCACA * 30881408 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATGGGCCATTCGGCCTT 1 TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT 30881473 ATCACATACATACACTTTCACATTCATCACA 66 ATCACATACATACACTTTCACATTCATCACA 30881504 T 1 T 30881505 AAAATCCTAA Statistics Matches: 189, Mismatches: 4, Indels: 2 0.97 0.02 0.01 Matches are distributed among these distances: 96 121 0.64 98 68 0.36 ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32 Consensus pattern (96 bp): TTGGCCATTCGGCCTTATCACATATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTT ATCACATACATACACTTTCACATTCATCACA Found at i:30893757 original size:22 final size:22 Alignment explanation

Indices: 30893714--30893758 Score: 56 Period size: 22 Copynumber: 2.0 Consensus size: 22 30893704 AATTTGTTAC * 30893714 ATTATATATGTAATTTGTTTTT 1 ATTATATATGTAATTTATTTTT * 30893736 ATTATATAT-TGATTTATGTTTT 1 ATTATATATGTAATTTAT-TTTT 30893758 A 1 A 30893759 AACATGTCAG Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 21 6 0.30 22 14 0.70 ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62 Consensus pattern (22 bp): ATTATATATGTAATTTATTTTT Found at i:30897817 original size:44 final size:40 Alignment explanation

Indices: 30897769--30897866 Score: 108 Period size: 40 Copynumber: 2.4 Consensus size: 40 30897759 AAACGATCTT 30897769 GCACACTTAGTGCCATCTCAAATAACCGAAGCTA-TCTCAGTATC 1 GCACACTTAGTGCC-T-T-AAATAACCGAAGCTATTC-CA-TATC * * * * 30897813 GCACACTTAGTGCCTTATATAGCTGAAGCTATTCCATTTC 1 GCACACTTAGTGCCTTAAATAACCGAAGCTATTCCATATC 30897853 GCACACTTAGTGCC 1 GCACACTTAGTGCC 30897867 GAACATAGTC Statistics Matches: 49, Mismatches: 4, Indels: 6 0.83 0.07 0.10 Matches are distributed among these distances: 40 17 0.35 41 14 0.29 42 3 0.06 43 1 0.02 44 14 0.29 ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29 Consensus pattern (40 bp): GCACACTTAGTGCCTTAAATAACCGAAGCTATTCCATATC Found at i:30905929 original size:15 final size:16 Alignment explanation

Indices: 30905909--30905938 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 30905899 AAGATCTTAA 30905909 AATCATAA-CTTACTC 1 AATCATAACCTTACTC 30905924 AATCATAACCTTACT 1 AATCATAACCTTACT 30905939 GATGGTTCAT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 8 0.57 16 6 0.43 ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33 Consensus pattern (16 bp): AATCATAACCTTACTC Found at i:30906221 original size:42 final size:42 Alignment explanation

Indices: 30906102--30906228 Score: 141 Period size: 42 Copynumber: 3.0 Consensus size: 42 30906092 AACACGGTAC * * * 30906102 CATACCAATGCCATATCCTAGATATGGTCTTACATGT-GATCT 1 CATATCAATGCCATATCCCAGATATGGTCTTACACGTAG-TCT ** * * 30906144 TGTATCAATGCCAATAGCCCA-ACTATGGTCTTACACATAGTCT 1 CATATCAATGCC-ATATCCCAGA-TATGGTCTTACACGTAGTCT * 30906187 CATATCGATGCCATATCCCAGATATGGTCTTACACGTAGTCT 1 CATATCAATGCCATATCCCAGATATGGTCTTACACGTAGTCT 30906229 TAATAACCCT Statistics Matches: 69, Mismatches: 12, Indels: 8 0.78 0.13 0.09 Matches are distributed among these distances: 42 36 0.52 43 32 0.46 44 1 0.01 ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31 Consensus pattern (42 bp): CATATCAATGCCATATCCCAGATATGGTCTTACACGTAGTCT Found at i:30913349 original size:17 final size:18 Alignment explanation

Indices: 30913327--30913366 Score: 57 Period size: 16 Copynumber: 2.3 Consensus size: 18 30913317 TATTGTAATG 30913327 CCCAAAAAATCCT-AAAA 1 CCCAAAAAATCCTGAAAA * 30913344 CCC-AAAAATCCTGAAAT 1 CCCAAAAAATCCTGAAAA 30913361 CCCAAA 1 CCCAAA 30913367 CTTTCTTTGT Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 16 9 0.45 17 9 0.45 18 2 0.10 ACGTcount: A:0.53, C:0.33, G:0.03, T:0.12 Consensus pattern (18 bp): CCCAAAAAATCCTGAAAA Found at i:30914743 original size:29 final size:28 Alignment explanation

Indices: 30914688--30914802 Score: 133 Period size: 29 Copynumber: 4.0 Consensus size: 28 30914678 GTGAGCATGA * * * 30914688 ATATGAATGTGACTGGGCCTAACGGGCC 1 ATATAAATGTGATTGGGCCTAATGGGCC 30914716 ATATAAATGTGATTTGGGCCTAATGGGCC 1 ATATAAATGTGA-TTGGGCCTAATGGGCC * 30914745 ATATACAA-GTGATTTGGGCCTAATAGGCC 1 ATATA-AATGTGA-TTGGGCCTAATGGGCC * * * 30914774 ATATGAATATGATTGGGCTTAATGGGCC 1 ATATAAATGTGATTGGGCCTAATGGGCC 30914802 A 1 A 30914803 AATACAGGTA Statistics Matches: 76, Mismatches: 8, Indels: 6 0.84 0.09 0.07 Matches are distributed among these distances: 28 28 0.37 29 46 0.61 30 2 0.03 ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28 Consensus pattern (28 bp): ATATAAATGTGATTGGGCCTAATGGGCC Found at i:30915116 original size:26 final size:25 Alignment explanation

Indices: 30915083--30915135 Score: 61 Period size: 26 Copynumber: 2.1 Consensus size: 25 30915073 ACCGTAATTA * * * * 30915083 AGGGAAAATTTACCGAAATGCCCCT 1 AGGGAAAAATGACCAAAATACCCCT 30915108 AGGGTAAAAATGACCAAAATACCCCT 1 AGGG-AAAAATGACCAAAATACCCCT 30915134 AG 1 AG 30915136 ATGTTAAATG Statistics Matches: 23, Mismatches: 4, Indels: 1 0.82 0.14 0.04 Matches are distributed among these distances: 25 4 0.17 26 19 0.83 ACGTcount: A:0.42, C:0.23, G:0.19, T:0.17 Consensus pattern (25 bp): AGGGAAAAATGACCAAAATACCCCT Found at i:30919225 original size:53 final size:54 Alignment explanation

Indices: 30919162--30919368 Score: 209 Period size: 53 Copynumber: 3.8 Consensus size: 54 30919152 TTCCTTTTTA * * * * 30919162 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G 1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG * * * * * 30919215 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAG 1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG ** * * * * * * * 30919269 TAGTTTATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCTTGCCTTGTAA 1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG * * * 30919324 AACTTACCAATTCCATGCCTTGGCATGGTCTTACTTGGTATCCTT 1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT 30919369 AAACCCTAAT Statistics Matches: 121, Mismatches: 31, Indels: 3 0.78 0.20 0.02 Matches are distributed among these distances: 53 45 0.37 54 36 0.30 55 40 0.33 ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38 Consensus pattern (54 bp): AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG Found at i:30919317 original size:55 final size:53 Alignment explanation

Indices: 30919174--30919368 Score: 183 Period size: 55 Copynumber: 3.6 Consensus size: 53 30919164 CTTACCATTT * * 30919174 CCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCATTG 1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG * * * * ** * * 30919227 CCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATAGTAGTTTATCAATG 1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-AACTCACCAATG * * * * * * * 30919282 CCATGTCTTGACATAGTCTTACATGATTTCCTTGCCTTGTAAAACTTACCAATT 1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATG * * * 30919336 CCATGCCTTGGCATGGTCTTACTTGGTATCCTT 1 CCATGTCTTGACATGGTCTTACATGGTATCCTT 30919369 AAACCCTAAT Statistics Matches: 111, Mismatches: 29, Indels: 3 0.78 0.20 0.02 Matches are distributed among these distances: 53 35 0.32 54 36 0.32 55 40 0.36 ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38 Consensus pattern (53 bp): CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG Found at i:30923676 original size:14 final size:14 Alignment explanation

Indices: 30923643--30923677 Score: 52 Period size: 14 Copynumber: 2.5 Consensus size: 14 30923633 TCACATTTCA * 30923643 ACTCATCCCTCATC 1 ACTCATCCCTCACC 30923657 ACTCATCCCTCACC 1 ACTCATCCCTCACC * 30923671 ATTCATC 1 ACTCATC 30923678 ATTCTCTACT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.23, C:0.49, G:0.00, T:0.29 Consensus pattern (14 bp): ACTCATCCCTCACC Found at i:30927699 original size:39 final size:39 Alignment explanation

Indices: 30927648--30927830 Score: 249 Period size: 39 Copynumber: 4.7 Consensus size: 39 30927638 TGTGTGAGAT * * 30927648 TTATATCTGGGCTAAGTCCCGAAGGCATTCGTACTAGTG 1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTG * * * * 30927687 TTATATCCGGGCTATGTCCTGAAGGCATTTGTGCTAGTC 1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTG * * * * 30927726 TTATATCCGGGCTAAATCTCAAAGGCATTCGTGCTGGTG 1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTG * * 30927765 TTATATCCGGGCTAAATCCCGAAGGCATTCGTGCTGGTG 1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTG * 30927804 TTATATCCGGGCTAAGTCTCGAAGGCA 1 TTATATCCGGGCTAAGTCCCGAAGGCA 30927831 AATGTGTTGG Statistics Matches: 126, Mismatches: 18, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 39 126 1.00 ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31 Consensus pattern (39 bp): TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTG Found at i:30932351 original size:46 final size:46 Alignment explanation

Indices: 30932204--30932372 Score: 159 Period size: 46 Copynumber: 3.6 Consensus size: 46 30932194 TTTGTGCACT * * 30932204 AGTGTAAGACATGTCTGGGACATGCATCGACC---ACACTATGAGAGCC 1 AGTGTAAGACATGTCTGGGACATGCATCG-CCTTGAGACGAT-A-AGCC * * * * 30932250 AGTGTAAGACCATGTCTAGGACATGGCATCCGCATTGAGACGA-GAGCA 1 AGTGTAAGA-CATGTCTGGGACAT-GCAT-CGCCTTGAGACGATAAGCC * 30932298 AGTGTAAGACATGTCTGGGACATGCATCAGCCTTGTGAC-ATAAGCC 1 AGTGTAAGACATGTCTGGGACATGCATC-GCCTTGAGACGATAAGCC * * 30932344 AGTGTAAGACATGTTTGAGACATGCATCG 1 AGTGTAAGACATGTCTGGGACATGCATCG 30932373 ACTACGAGAT Statistics Matches: 102, Mismatches: 13, Indels: 17 0.77 0.10 0.13 Matches are distributed among these distances: 45 3 0.03 46 50 0.49 47 26 0.25 48 17 0.17 49 2 0.02 51 4 0.04 ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22 Consensus pattern (46 bp): AGTGTAAGACATGTCTGGGACATGCATCGCCTTGAGACGATAAGCC Found at i:30932456 original size:50 final size:48 Alignment explanation

Indices: 30932387--30932563 Score: 148 Period size: 49 Copynumber: 3.6 Consensus size: 48 30932377 CGAGATGTGT * * * * 30932387 TAGTGGAAGGCCATATCTGGGACATGGCATTGGCAC-AGATATGT-GAGAG 1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTAGAT-T-TCGAGAG * * * 30932436 CTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGATAG 1 -TAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGATTTCGAGAG * * * * 30932485 TCAGTGTAAGACTATGTCTGGGACATGGCATC-GACTTGA--TGGATGAG 1 T-AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGATTTCGA-GAG * 30932532 TCAGTGTAAGACCATGTCTAGGACATGGCATC 1 T-AGTGTAAGACCATGTCTGGGACATGGCATC 30932564 AACATTATAC Statistics Matches: 108, Mismatches: 15, Indels: 11 0.81 0.11 0.08 Matches are distributed among these distances: 46 3 0.03 47 32 0.30 48 7 0.06 49 34 0.31 50 32 0.30 ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25 Consensus pattern (48 bp): TAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTAGATTTCGAGAG Found at i:30932502 original size:49 final size:47 Alignment explanation

Indices: 30932204--30932563 Score: 187 Period size: 47 Copynumber: 7.6 Consensus size: 47 30932194 TTTGTGCACT * * * 30932204 AGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-C-ACACTATGAGAGCC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGA-TCGAT--GAGTC * * * 30932250 AGTGTAAGACCATGTCTAGGACATGGCATCCG-CATTGAGACGA-GAG-C 1 AGTGTAAGACCATGTCTGGGACATGGCAT-CGAC-TCGA-TCGATGAGTC * * * * 30932297 AAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTTG-T-GACATAAGCC 1 -AGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGATCG--ATGAGTC * * * * 30932344 AGTGTAAGA-CATGTTTGAGACAT-GCATCGACTACGA--GATGTGTT 1 AGTGTAAGACCATGTCTGGGACATGGCATCGACT-CGATCGATGAGTC * * * * * * * * 30932388 AGTGGAAGGCCATATCTGGGACATGGCATTGGCACAGATATG-TGAGAGC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTC-GAT-CGATGAG-TC * * 30932437 TAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGAT-AGTC 1 -AGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGA--TCGATGAGTC * * * 30932487 AGTGTAAGACTATGTCTGGGACATGGCATCGACTTGATGGATGAGTC 1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATCGATGAGTC * 30932534 AGTGTAAGACCATGTCTAGGACATGGCATC 1 AGTGTAAGACCATGTCTGGGACATGGCATC 30932564 AACATTATAC Statistics Matches: 244, Mismatches: 42, Indels: 55 0.72 0.12 0.16 Matches are distributed among these distances: 43 1 0.00 44 10 0.04 45 17 0.07 46 59 0.24 47 61 0.25 48 25 0.10 49 31 0.13 50 28 0.11 51 10 0.04 52 2 0.01 ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24 Consensus pattern (47 bp): AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATCGATGAGTC Found at i:30932561 original size:140 final size:136 Alignment explanation

Indices: 30932204--30932570 Score: 330 Period size: 140 Copynumber: 2.6 Consensus size: 136 30932194 TTTGTGCACT * 30932204 AGTGTAAGACATGTCTGGGACATGCATCGACCACACTAT-GA-GAGCCAGTGTAAGACCATGTCT 1 AGTGTAAGACATGTCTGGGACATGCATCG-----ACTATGGATGAGTCAGTGTAAGACCATGTCT * * 30932267 AGGACATGGCATCCGCATTGAGACGAGAGCAAGTGTAAGACATGTCTGGGACATGCATCAGCCTT 61 AGGACATGGCATCAGCATT-AGACGAGAGCAAGTGTAAGACATGTCTGGGACATGCATCAGCCTC 30932332 GTGACATAAGCC 125 GTGACATAAGCC * * * * * * * * * 30932344 AGTGTAAGACATGTTTGAGACATGCATCGACTACGAGATGTGTTAGTGGAAGGCCATATCTGGGA 1 AGTGTAAGACATGTCTGGGACATGCATCGACTATG-GATGAGTCAGTGTAAGACCATGTCTAGGA * * * * * 30932409 CATGGCATTGGCA-CAGATATG-TGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCC 65 CATGGCA-T--CAGCA-TTA-GACGAGAGCAAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCC ** * 30932472 TCGATTTCGAT-AGTC 123 TCG-TGAC-ATAAGCC 30932487 AGTGTAAGACTATGTCTGGGACATGGCATCGACTTGATGGATGAGTCAGTGTAAGACCATGTCTA 1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGAC-T-ATGGATGAGTCAGTGTAAGACCATGTCTA * 30932552 GGACATGGCATCAACATTA 62 GGACATGGCATCAGCATTA 30932571 TACCCTATGT Statistics Matches: 180, Mismatches: 30, Indels: 31 0.75 0.12 0.13 Matches are distributed among these distances: 135 4 0.02 137 2 0.01 138 26 0.14 139 1 0.01 140 45 0.25 141 17 0.09 142 9 0.05 143 19 0.11 144 15 0.08 145 9 0.05 146 31 0.17 147 2 0.01 ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24 Consensus pattern (136 bp): AGTGTAAGACATGTCTGGGACATGCATCGACTATGGATGAGTCAGTGTAAGACCATGTCTAGGAC ATGGCATCAGCATTAGACGAGAGCAAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGTGACA TAAGCC Found at i:30933779 original size:20 final size:20 Alignment explanation

Indices: 30933743--30933781 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 30933733 GTTATAATGA * 30933743 CCACACGGCGTGTTGCCCTT 1 CCACACGGCGTGATGCCCTT 30933763 CCACACGAGCGT-ATGCCCT 1 CCACACG-GCGTGATGCCCT 30933782 ATTTCAAGAG Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 13 0.76 21 4 0.24 ACGTcount: A:0.15, C:0.41, G:0.23, T:0.21 Consensus pattern (20 bp): CCACACGGCGTGATGCCCTT Found at i:30934347 original size:9 final size:9 Alignment explanation

Indices: 30934333--30934358 Score: 52 Period size: 9 Copynumber: 2.9 Consensus size: 9 30934323 TCCGAACACT 30934333 CCACCTCCC 1 CCACCTCCC 30934342 CCACCTCCC 1 CCACCTCCC 30934351 CCACCTCC 1 CCACCTCC 30934359 TCTGATTCTT 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:0.12, C:0.77, G:0.00, T:0.12 Consensus pattern (9 bp): CCACCTCCC Found at i:30939232 original size:78 final size:81 Alignment explanation

Indices: 30939112--30939294 Score: 234 Period size: 78 Copynumber: 2.3 Consensus size: 81 30939102 TGAATGATGT * 30939112 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAG-TCCCGAAGGCATT * 30939175 TGTGCGAGTTACTA-ATT 65 TGTGCGAGTTACTATA-A * * * ** 30939192 CC-GGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATTT 30939254 GTGCGAGTTACTATAA 66 GTGCGAGTTACTATAA * 30939270 CCGGGCTATGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTG 30939295 AACGAGTAGC Statistics Matches: 90, Mismatches: 8, Indels: 10 0.83 0.07 0.09 Matches are distributed among these distances: 77 1 0.01 78 52 0.58 79 21 0.23 80 16 0.18 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (81 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGTCCCGAAGGCATTT GTGCGAGTTACTATAA Found at i:30939308 original size:40 final size:40 Alignment explanation

Indices: 30939112--30939294 Score: 216 Period size: 40 Copynumber: 4.6 Consensus size: 40 30939102 TGAATGATGT * * * * 30939112 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA * * 30939152 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT 1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A 30939192 CC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA * 30939229 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA * 30939270 CCGGGCTATGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTG 30939295 AACGAGTAGC Statistics Matches: 126, Mismatches: 9, Indels: 16 0.83 0.06 0.11 Matches are distributed among these distances: 38 28 0.22 39 13 0.10 40 75 0.60 41 10 0.08 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA Found at i:30939313 original size:80 final size:77 Alignment explanation

Indices: 30939164--30939327 Score: 206 Period size: 78 Copynumber: 2.1 Consensus size: 77 30939154 GGACTAAGAT * ** 30939164 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA 1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA * 30939229 TCCGGGTTAAGTC 66 TCC-GGTTAAATC * 30939242 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC 1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACC-GGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C * * 30939305 TATATCCGGTTAAATT 62 TAAATCCGGTTAAATC 30939321 CCGAAGG 1 CCGAAGG 30939328 TACGTGATTT Statistics Matches: 75, Mismatches: 7, Indels: 7 0.84 0.08 0.08 Matches are distributed among these distances: 77 2 0.03 78 26 0.35 79 22 0.29 80 25 0.33 ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26 Consensus pattern (77 bp): CCGAAGGCATTTGTGCGAGTTACTAATACCGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAA TCCGGTTAAATC Found at i:30947243 original size:40 final size:40 Alignment explanation

Indices: 30947048--30947229 Score: 185 Period size: 40 Copynumber: 4.6 Consensus size: 40 30947038 AATGATGTCT * * * * 30947048 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC * * * * 30947088 AGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCC 1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACC 30947128 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC * * * 30947167 GGGTTAAGTCCCGAAAGCATTTGTGCAAGTTACTATAACC 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC * 30947207 GGGCTATGTCCCGAAGGCATTTG 1 GGGCTAAGTCCCGAAGGCATTTG 30947230 AACGAGTAGC Statistics Matches: 119, Mismatches: 16, Indels: 14 0.80 0.11 0.09 Matches are distributed among these distances: 39 35 0.29 40 74 0.62 41 10 0.08 ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25 Consensus pattern (40 bp): GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC Found at i:30947251 original size:79 final size:79 Alignment explanation

Indices: 30947098--30947252 Score: 190 Period size: 79 Copynumber: 2.0 Consensus size: 79 30947088 AGACTAAGAT * * * ** 30947098 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA 1 CCGAAAGCATTTGTGCAAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA 30947163 ATCCGGGTTAAGTC 66 ATCCGGGTTAAGTC * * 30947177 CCGAAAGCATTTGTGCAAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC 1 CCGAAAGCATTTGTGCAAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C * 30947240 TATATCC-GGTTAA 63 TAAATCCGGGTTAA 30947253 ATTCCGAAGG Statistics Matches: 65, Mismatches: 8, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 78 2 0.03 79 38 0.58 80 25 0.38 ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26 Consensus pattern (79 bp): CCGAAAGCATTTGTGCAAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA ATCCGGGTTAAGTC Found at i:30949133 original size:40 final size:40 Alignment explanation

Indices: 30949063--30949240 Score: 218 Period size: 40 Copynumber: 4.5 Consensus size: 40 30949053 AAGCCAAGTA * * * * * * 30949063 CCTTCGGGATTTA-ACCAGATATAGGT-ACTCGCTCGAATA 1 CCTTCGGGACTTAGCCCGGATATA-GTAACTCGCACAAATG * 30949102 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * 30949142 CCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * * 30949182 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG 1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG 30949222 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 30949241 TTATCATCCA Statistics Matches: 123, Mismatches: 13, Indels: 5 0.87 0.09 0.04 Matches are distributed among these distances: 39 14 0.11 40 109 0.89 ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:30957412 original size:40 final size:40 Alignment explanation

Indices: 30957358--30957558 Score: 280 Period size: 40 Copynumber: 5.0 Consensus size: 40 30957348 GGATATAACT * * * ** 30957358 GGATATAGCT-ACTCGCTCGAATACCTTCGGGACAGAGCCC 1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCC 30957398 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC 1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC 30957438 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC 1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC ** 30957478 GGATATAGTAACTCGCACAAATGCCTTCAAGACTTAGCCC 1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC * * * 30957518 GGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCC 1 GGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC 30957558 G 1 G 30957559 ATTATCATCC Statistics Matches: 147, Mismatches: 12, Indels: 4 0.90 0.07 0.02 Matches are distributed among these distances: 39 2 0.01 40 145 0.99 ACGTcount: A:0.27, C:0.28, G:0.23, T:0.21 Consensus pattern (40 bp): GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC Found at i:30961456 original size:13 final size:13 Alignment explanation

Indices: 30961438--30961464 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 30961428 AAGTAAGTGA 30961438 TCTTGATGATTTT 1 TCTTGATGATTTT 30961451 TCTTGATGATTTT 1 TCTTGATGATTTT 30961464 T 1 T 30961465 GTATTTTTAG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63 Consensus pattern (13 bp): TCTTGATGATTTT Found at i:30964358 original size:65 final size:65 Alignment explanation

Indices: 30964254--30964384 Score: 235 Period size: 65 Copynumber: 2.0 Consensus size: 65 30964244 CCCCTAGGGT * * * 30964254 TAAGGTTGACCTGAATGCATGTTTGATTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA 1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATCTTATTATTATCTGA 30964319 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATCTTATTATTATCTGA 1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATCTTATTATTATCTGA 30964384 T 1 T 30964385 GCATGGGACT Statistics Matches: 63, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 65 63 1.00 ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43 Consensus pattern (65 bp): TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATCTTATTATTATCTGA Found at i:30965550 original size:49 final size:47 Alignment explanation

Indices: 30965488--30965618 Score: 138 Period size: 47 Copynumber: 2.7 Consensus size: 47 30965478 GGATATGTGA * * * * 30965488 GAGCTAGTGTAAGACCATGTCTAGGACATGGCGTCGGCCTCGATTTTGAT 1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GACTCGA--TGGAT * * * * 30965538 -AGTCAGTGTAAGACCATATCTAGAACATGGCATCGACTTGATGGAT 1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTCGATGGAT * * 30965584 GAGCCAATGTAAGACCATGTCTGGGACATGGCATC 1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC 30965619 AGCATTATAC Statistics Matches: 67, Mismatches: 13, Indels: 5 0.79 0.15 0.06 Matches are distributed among these distances: 46 4 0.06 47 29 0.43 48 5 0.07 49 29 0.43 ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25 Consensus pattern (47 bp): GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTCGATGGAT Found at i:30986515 original size:25 final size:25 Alignment explanation

Indices: 30986487--30986538 Score: 72 Period size: 25 Copynumber: 2.1 Consensus size: 25 30986477 TACCAATTTG 30986487 CAGCTCGTGA-GAGCTTATT-GATTCT 1 CAGCTCGT-ATGAGCTT-TTCGATTCT 30986512 CAGCTCGTATGAGCTTTTCGATTCT 1 CAGCTCGTATGAGCTTTTCGATTCT 30986537 CA 1 CA 30986539 ACTTGTTTGA Statistics Matches: 25, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 24 3 0.12 25 22 0.88 ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37 Consensus pattern (25 bp): CAGCTCGTATGAGCTTTTCGATTCT Found at i:31003541 original size:21 final size:21 Alignment explanation

Indices: 31003515--31003556 Score: 84 Period size: 21 Copynumber: 2.0 Consensus size: 21 31003505 AAAAAAAGAG 31003515 ATCATCATACATGTTTCTTCC 1 ATCATCATACATGTTTCTTCC 31003536 ATCATCATACATGTTTCTTCC 1 ATCATCATACATGTTTCTTCC 31003557 TAGCCGAATC Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43 Consensus pattern (21 bp): ATCATCATACATGTTTCTTCC Found at i:31005516 original size:47 final size:47 Alignment explanation

Indices: 31005450--31006002 Score: 953 Period size: 47 Copynumber: 11.6 Consensus size: 47 31005440 GAAATGATAG 31005450 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 31005497 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA * 31005544 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA * 31005593 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 31005640 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 31005687 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA * 31005734 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA * * 31005783 TAGGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATACGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 31005830 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA * 31005877 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA * * 31005926 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGA * 31005975 TAGGGCCTAATGGCCGATGTGATGAATG 1 TAAGGCCTAATGGCCGATGTGATGAATG 31006003 GGCCTAATGG Statistics Matches: 488, Mismatches: 12, Indels: 10 0.96 0.02 0.02 Matches are distributed among these distances: 47 313 0.64 49 175 0.36 ACGTcount: A:0.31, C:0.10, G:0.30, T:0.29 Consensus pattern (47 bp): TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA Found at i:31005711 original size:143 final size:142 Alignment explanation

Indices: 31005450--31006002 Score: 957 Period size: 143 Copynumber: 3.9 Consensus size: 142 31005440 GAAATGATAG 31005450 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATACGTGATAAGGCCTAATGGCCGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATACGTGATAAGGCCTAATGGCCGA 31005514 TGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT 66 TGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT * 31005579 GTATATATATGTGA 131 G--TATATACGTGA * 31005593 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATACGTGATAAGGCCTAATGGCCGA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATACGTGATAAGGCCTAATGGCCGA 31005657 TGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT 66 TGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT 31005722 GTATATACGTGA 131 GTATATACGTGA * * * 31005734 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCA 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATACGTGATAAGGCCTAATGGCCG 31005799 ATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG 65 ATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG 31005864 TGTATATACGTGA 130 TGTATATACGTGA * * 31005877 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATACGTGATAAGGCCTAATGGCCG * * 31005942 ATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATG 65 ATGTGATGAATGTGAAAGTG--TATATACGTGATAAGGCCTAATGGCCGATGTGATGAATG 31006003 GGCCTAATGG Statistics Matches: 397, Mismatches: 9, Indels: 6 0.96 0.02 0.01 Matches are distributed among these distances: 141 45 0.11 143 315 0.79 145 37 0.09 ACGTcount: A:0.31, C:0.10, G:0.30, T:0.29 Consensus pattern (142 bp): TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATACGTGATAAGGCCTAATGGCCGA TGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGT GTATATACGTGA Found at i:31005773 original size:190 final size:190 Alignment explanation

Indices: 31005450--31006002 Score: 1061 Period size: 190 Copynumber: 2.9 Consensus size: 190 31005440 GAAATGATAG 31005450 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT 31005515 GTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG 66 GTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG 31005580 TATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 131 TATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 31005640 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT 31005705 GTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG 66 GTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG * 31005770 TATATATATGTGATAGGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATACGTGA 131 TATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA 31005830 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT 1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT * * 31005895 GTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAG 66 GTGATGAATGTGAAAGTG--TATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG 31005960 TGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATG 129 TGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATG 31006003 GGCCTAATGG Statistics Matches: 357, Mismatches: 4, Indels: 2 0.98 0.01 0.01 Matches are distributed among these distances: 190 272 0.76 192 85 0.24 ACGTcount: A:0.31, C:0.10, G:0.30, T:0.29 Consensus pattern (190 bp): TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGAT GTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG TATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA Found at i:31005997 original size:22 final size:24 Alignment explanation

Indices: 31005969--31006027 Score: 86 Period size: 25 Copynumber: 2.5 Consensus size: 24 31005959 GTGTATATAT 31005969 ATGTGAT-A-GGGCCTAATGGCCG 1 ATGTGATAATGGGCCTAATGGCCG 31005991 ATGTGATGAATGGGCCTAATGGCCG 1 ATGTGAT-AATGGGCCTAATGGCCG 31006016 ATGTGATGAATG 1 ATGTGAT-AATG 31006028 TGAAAGTGTA Statistics Matches: 34, Mismatches: 0, Indels: 3 0.92 0.00 0.08 Matches are distributed among these distances: 22 7 0.21 24 1 0.03 25 26 0.76 ACGTcount: A:0.25, C:0.14, G:0.36, T:0.25 Consensus pattern (24 bp): ATGTGATAATGGGCCTAATGGCCG Found at i:31006008 original size:25 final size:25 Alignment explanation

Indices: 31005977--31006027 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 31005967 ATATGTGATA 31005977 GGGCCTAATGGCCGATGTGATGAAT 1 GGGCCTAATGGCCGATGTGATGAAT 31006002 GGGCCTAATGGCCGATGTGATGAAT 1 GGGCCTAATGGCCGATGTGATGAAT 31006027 G 1 G 31006028 TGAAAGTGTA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.24, C:0.16, G:0.37, T:0.24 Consensus pattern (25 bp): GGGCCTAATGGCCGATGTGATGAAT Found at i:31006053 original size:47 final size:47 Alignment explanation

Indices: 31006002--31006093 Score: 130 Period size: 47 Copynumber: 2.0 Consensus size: 47 31005992 TGTGATGAAT * * * * 31006002 GGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACA 1 GGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGACA * * 31006049 GGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA 1 GGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGA 31006094 TAAGTCCCGA Statistics Matches: 39, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 47 39 1.00 ACGTcount: A:0.29, C:0.11, G:0.35, T:0.25 Consensus pattern (47 bp): GGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGACA Found at i:31006271 original size:37 final size:37 Alignment explanation

Indices: 31006215--31006293 Score: 122 Period size: 37 Copynumber: 2.1 Consensus size: 37 31006205 CCGAGCTCTA * * * 31006215 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT 1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT * 31006252 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT 1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT 31006289 AAGAC 1 AAGAC 31006294 TTCGTAATAA Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25 Consensus pattern (37 bp): AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT Found at i:31008463 original size:58 final size:59 Alignment explanation

Indices: 31008401--31008513 Score: 138 Period size: 58 Copynumber: 1.9 Consensus size: 59 31008391 AGTGATTAAC * * * * * * * * 31008401 TTAATATTAAATTTAATTTAATGTTTATGTTAAT-AGTATTCTATTATTTTAATAAGAT 1 TTAATATCAAATTCAATCTAATATTTATCTTAATAAATATTATATTAATTTAATAAGAT * 31008459 TTAATATCAAATTCAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA 1 TTAATATCAAATTCAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA 31008514 TTAAAGTGAT Statistics Matches: 45, Mismatches: 9, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 58 28 0.62 59 17 0.38 ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50 Consensus pattern (59 bp): TTAATATCAAATTCAATCTAATATTTATCTTAATAAATATTATATTAATTTAATAAGAT Found at i:31021137 original size:28 final size:28 Alignment explanation

Indices: 31021101--31021154 Score: 74 Period size: 28 Copynumber: 1.9 Consensus size: 28 31021091 GGTAGGAAAG * 31021101 AATATCCTTTGT-GAAGAATAATGAAAAA 1 AATAACCTTTGTGGAA-AATAATGAAAAA * 31021129 AATAACCTTTTTGGAAAATAATGAAA 1 AATAACCTTTGTGGAAAATAATGAAA 31021155 TGATAGCCCT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 28 20 0.87 29 3 0.13 ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30 Consensus pattern (28 bp): AATAACCTTTGTGGAAAATAATGAAAAA Found at i:31032926 original size:55 final size:55 Alignment explanation

Indices: 31032790--31032928 Score: 143 Period size: 55 Copynumber: 2.5 Consensus size: 55 31032780 TGCGACATGG * * * * * * ** 31032790 CCGTGGGTGAACCTGCCAAAACAAAACAGGCGTGCGACACGCTCGTGCCTGGAAA 1 CCGTGGGTGAACCTGCCAAAACAACACGGGCGTACAACACACCCGTGCCAAGAAA * * ** ** * 31032845 TCGTGGCTGAACCTATCAAATTAACACGGGCGTACAACACACCCGTGCCAAGCAA 1 CCGTGGGTGAACCTGCCAAAACAACACGGGCGTACAACACACCCGTGCCAAGAAA 31032900 CCGTGGGTGAACCTGCCAAAACAACACGG 1 CCGTGGGTGAACCTGCCAAAACAACACGG 31032929 CCGTGGACCT Statistics Matches: 63, Mismatches: 21, Indels: 0 0.75 0.25 0.00 Matches are distributed among these distances: 55 63 1.00 ACGTcount: A:0.31, C:0.30, G:0.25, T:0.14 Consensus pattern (55 bp): CCGTGGGTGAACCTGCCAAAACAACACGGGCGTACAACACACCCGTGCCAAGAAA Found at i:31036257 original size:33 final size:33 Alignment explanation

Indices: 31036219--31036281 Score: 117 Period size: 33 Copynumber: 1.9 Consensus size: 33 31036209 TTTTTCTAGT 31036219 TAGGCAATTTTTCAATTCAATCTCAATTCTTGC 1 TAGGCAATTTTTCAATTCAATCTCAATTCTTGC * 31036252 TAGGCAATTTTTCAATTCAATCTCGATTCT 1 TAGGCAATTTTTCAATTCAATCTCAATTCT 31036282 AACCCTTTCT Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 33 29 1.00 ACGTcount: A:0.27, C:0.21, G:0.10, T:0.43 Consensus pattern (33 bp): TAGGCAATTTTTCAATTCAATCTCAATTCTTGC Found at i:31039366 original size:27 final size:27 Alignment explanation

Indices: 31039335--31039512 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 31039325 TAAATTGTAC * 31039335 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGAATTGACTATGT * * * 31039362 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGAATTGACTATGT * * 31039388 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGAATTGACTATGT * * 31039416 GGCACTAAGTGTGCGAGTTGACTATGT 1 AGCACTAAGTGTGCGAATTGACTATGT * * 31039443 AGCACTAAGTGTGCGAGTTTGATTATGT 1 AGCACTAAGTGTGCGA-ATTGACTATGT * * * 31039471 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGAATTGACTATGT * 31039498 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 31039513 GACTTAATAT Statistics Matches: 130, Mismatches: 18, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 105 0.81 28 25 0.19 ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGAATTGACTATGT Found at i:31039396 original size:54 final size:55 Alignment explanation

Indices: 31039335--31039512 Score: 227 Period size: 54 Copynumber: 3.3 Consensus size: 55 31039325 TAAATTGTAC * ** 31039335 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT 1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT * * ** * 31039390 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T 1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT * * 31039443 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTAT-AT 1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT * 31039498 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 31039513 GACTTAATAT Statistics Matches: 106, Mismatches: 14, Indels: 6 0.84 0.11 0.05 Matches are distributed among these distances: 53 1 0.01 54 60 0.57 55 45 0.42 ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30 Consensus pattern (55 bp): AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT Found at i:31047289 original size:27 final size:27 Alignment explanation

Indices: 31047258--31047435 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 31047248 TAAATTGTAC * 31047258 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGAATTGACTATGT * * * 31047285 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGAATTGACTATGT * * 31047311 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGAATTGACTATGT * * 31047339 GGCACTAAGTGTGCGAGTTGACTATGT 1 AGCACTAAGTGTGCGAATTGACTATGT * * 31047366 AGCACTAAGTGTGCGAGTTTGATTATGT 1 AGCACTAAGTGTGCGA-ATTGACTATGT * * * 31047394 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGAATTGACTATGT * 31047421 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 31047436 GACTTAATAT Statistics Matches: 130, Mismatches: 18, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 105 0.81 28 25 0.19 ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGAATTGACTATGT Found at i:31047319 original size:54 final size:55 Alignment explanation

Indices: 31047258--31047435 Score: 227 Period size: 54 Copynumber: 3.3 Consensus size: 55 31047248 TAAATTGTAC * ** 31047258 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT 1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT * * ** * 31047313 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTGACTATG-T 1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT * * 31047366 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTAT-AT 1 AGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT * 31047421 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 31047436 GACTTAATAT Statistics Matches: 106, Mismatches: 14, Indels: 6 0.84 0.11 0.05 Matches are distributed among these distances: 53 1 0.01 54 60 0.57 55 45 0.42 ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30 Consensus pattern (55 bp): AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGAT Found at i:31049586 original size:26 final size:25 Alignment explanation

Indices: 31049557--31049631 Score: 105 Period size: 26 Copynumber: 2.9 Consensus size: 25 31049547 CAACACACCA * 31049557 ATATCGCAGCAAAGCTGCCAGTAATC 1 ATATCGCAACAAAGCTGCCAGTAA-C * 31049583 ATATCGCAACAAAGCTACCAGTAAC 1 ATATCGCAACAAAGCTGCCAGTAAC * 31049608 AGTAACGCAACAAAGCTGCCAGTA 1 A-TATCGCAACAAAGCTGCCAGTA 31049632 TCAGTATATG Statistics Matches: 44, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 25 2 0.05 26 42 0.95 ACGTcount: A:0.40, C:0.27, G:0.17, T:0.16 Consensus pattern (25 bp): ATATCGCAACAAAGCTGCCAGTAAC Found at i:31049815 original size:27 final size:26 Alignment explanation

Indices: 31049768--31049818 Score: 75 Period size: 27 Copynumber: 1.9 Consensus size: 26 31049758 ATAGTACATG 31049768 TTAGTCATTTACCCTCAAGGGGTAAA 1 TTAGTCATTTACCCTCAAGGGGTAAA ** 31049794 TTAGTCATTTTACCCTTTAGGGGTA 1 TTAGTCA-TTTACCCTCAAGGGGTA 31049819 TTTTGGTTAT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 26 7 0.32 27 15 0.68 ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37 Consensus pattern (26 bp): TTAGTCATTTACCCTCAAGGGGTAAA Found at i:31056460 original size:42 final size:42 Alignment explanation

Indices: 31056394--31056489 Score: 174 Period size: 42 Copynumber: 2.3 Consensus size: 42 31056384 TACAGGGGAC 31056394 ACACGCCCGTGTGGCCCGGCCGTGTGTCTAACACGGCCAAAG 1 ACACGCCCGTGTGGCCCGGCCGTGTGTCTAACACGGCCAAAG * * 31056436 ACACGCCCGTGTGGCTCGGTCGTGTGTCTAACACGGCCAAAG 1 ACACGCCCGTGTGGCCCGGCCGTGTGTCTAACACGGCCAAAG 31056478 ACACGCCCGTGT 1 ACACGCCCGTGT 31056490 CACAGGCTGT Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 42 52 1.00 ACGTcount: A:0.19, C:0.34, G:0.30, T:0.17 Consensus pattern (42 bp): ACACGCCCGTGTGGCCCGGCCGTGTGTCTAACACGGCCAAAG Found at i:31057851 original size:48 final size:48 Alignment explanation

Indices: 31057789--31057884 Score: 147 Period size: 48 Copynumber: 2.0 Consensus size: 48 31057779 TGAAAGTCTT * * 31057789 GCACCCGAAGTGCCAATATCATGGCCCAAATACAACTCATTGAATCTC 1 GCACCCGAAGTGCCAATATCATGGCCCAAAGACAACTCAATGAATCTC * * * 31057837 GCACCTGAAGTGCCAATATCATGGCCCAAAGCCAACTTAATGAATCTC 1 GCACCCGAAGTGCCAATATCATGGCCCAAAGACAACTCAATGAATCTC 31057885 CTAATAACAT Statistics Matches: 43, Mismatches: 5, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 48 43 1.00 ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21 Consensus pattern (48 bp): GCACCCGAAGTGCCAATATCATGGCCCAAAGACAACTCAATGAATCTC Found at i:31060746 original size:19 final size:18 Alignment explanation

Indices: 31060722--31060783 Score: 54 Period size: 19 Copynumber: 3.2 Consensus size: 18 31060712 TTGCATATAG 31060722 TTTTATGTGTTTTTTTTA 1 TTTTATGTGTTTTTTTTA * 31060740 CTTTTAT-TGTTTTCATGTTA 1 -TTTTATGTGTTTT--TTTTA * 31060760 TTTTGTGTGTTTATTTTTAA 1 TTTTATGTGTTT-TTTTT-A 31060780 TTTT 1 TTTT 31060784 TCATATTTTT Statistics Matches: 35, Mismatches: 3, Indels: 9 0.74 0.06 0.19 Matches are distributed among these distances: 18 6 0.17 19 14 0.40 20 14 0.40 21 1 0.03 ACGTcount: A:0.13, C:0.03, G:0.11, T:0.73 Consensus pattern (18 bp): TTTTATGTGTTTTTTTTA Found at i:31065431 original size:33 final size:33 Alignment explanation

Indices: 31065389--31065498 Score: 159 Period size: 33 Copynumber: 3.3 Consensus size: 33 31065379 CAGTACAGTT 31065389 CAGTATCAGTTGGGCATTAGCCCATTACAGTAC 1 CAGTATCAGTTGGGCATTAGCCCATTACAGTAC 31065422 CAGTATCAGTTGGGCATTAGCCCATTACAGTAC 1 CAGTATCAGTTGGGCATTAGCCCATTACAGTAC * * * * 31065455 CAGTATCAATGTGAGCCTTAGCCCAATT-CAGTAA 1 CAGTATCAGT-TGGGCATTAGCCC-ATTACAGTAC 31065489 CAGTATCAGT 1 CAGTATCAGT 31065499 ATCAGTACAA Statistics Matches: 70, Mismatches: 5, Indels: 3 0.90 0.06 0.04 Matches are distributed among these distances: 33 42 0.60 34 25 0.36 35 3 0.04 ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27 Consensus pattern (33 bp): CAGTATCAGTTGGGCATTAGCCCATTACAGTAC Found at i:31072563 original size:46 final size:46 Alignment explanation

Indices: 31072510--31072685 Score: 200 Period size: 46 Copynumber: 3.8 Consensus size: 46 31072500 TGGTTGAGCA 31072510 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG * * 31072556 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G * * * 31072601 CATCCGAACTCGTTGAGTTGAGTCCGGGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG * * 31072649 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG 1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 31072686 GCAGGTTACA Statistics Matches: 110, Mismatches: 10, Indels: 20 0.79 0.07 0.14 Matches are distributed among these distances: 42 2 0.02 43 6 0.05 45 5 0.05 46 60 0.55 47 28 0.25 48 3 0.03 50 4 0.04 51 2 0.02 ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG Found at i:31072666 original size:93 final size:93 Alignment explanation

Indices: 31072507--31072678 Score: 292 Period size: 93 Copynumber: 1.8 Consensus size: 93 31072497 AGATGGTTGA * * 31072507 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT 31072572 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * * 31072600 GCATCCGAACTCGTTGAGTTGAGTCCGGGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG 31072664 TTGAGTCCGAGTTCG 65 TTGAGTCCGAGTTCG 31072679 CTTATGGGCA Statistics Matches: 74, Mismatches: 4, Indels: 2 0.93 0.05 0.03 Matches are distributed among these distances: 92 2 0.03 93 72 0.97 ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:31077992 original size:40 final size:40 Alignment explanation

Indices: 31077850--31077994 Score: 119 Period size: 40 Copynumber: 3.6 Consensus size: 40 31077840 TACTCGAATG * * * * * * 31077850 ATATCCAGGCTAAGTCCCGAAGGCTTTTGTGCTAAGAGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCT-AGCGACC * ** * * * * 31077891 ACATCTAGACTAAGATCCGAAGGCATTTGTGCTAGCGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACC * * * * 31077931 ATATCCGGGCTAGGTCTCGAAGGCATTTATGCTAGTGACC 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACC * 31077971 ATATCCGGGTTAAGACCCGAAGGC 1 ATATCCGGGCTAAGACCCGAAGGC 31077995 CTTGTGCGAG Statistics Matches: 82, Mismatches: 22, Indels: 1 0.78 0.21 0.01 Matches are distributed among these distances: 40 55 0.67 41 27 0.33 ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACC Found at i:31100265 original size:37 final size:35 Alignment explanation

Indices: 31100224--31100334 Score: 105 Period size: 37 Copynumber: 3.0 Consensus size: 35 31100214 TAATCACTCG * * 31100224 TAAGAGCTAATCCACTCAATAACATGCCAGATGCTCA 1 TAAGAGC-AATCCAC-CAATAACACGCCAAATGCTCA * * * 31100261 TAAGAGGCAATCCACCTGAGAACACGCCAAATGTTCA 1 TAAGA-GCAATCCACC-AATAACACGCCAAATGCTCA * 31100298 TAAGAGCCAATCCACCAGATAACACACCAAATTGCTC 1 TAAGAG-CAATCCACCA-ATAACACGCCAAA-TGCTC 31100335 CGAAGAGCTA Statistics Matches: 60, Mismatches: 9, Indels: 9 0.77 0.12 0.12 Matches are distributed among these distances: 36 2 0.03 37 52 0.87 38 6 0.10 ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18 Consensus pattern (35 bp): TAAGAGCAATCCACCAATAACACGCCAAATGCTCA Found at i:31107166 original size:8 final size:8 Alignment explanation

Indices: 31107153--31107192 Score: 80 Period size: 8 Copynumber: 5.0 Consensus size: 8 31107143 TTATCAACTC 31107153 TTATTATT 1 TTATTATT 31107161 TTATTATT 1 TTATTATT 31107169 TTATTATT 1 TTATTATT 31107177 TTATTATT 1 TTATTATT 31107185 TTATTATT 1 TTATTATT 31107193 CTGAATTTTT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 32 1.00 ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75 Consensus pattern (8 bp): TTATTATT Found at i:31107202 original size:24 final size:24 Alignment explanation

Indices: 31107153--31107203 Score: 68 Period size: 24 Copynumber: 2.1 Consensus size: 24 31107143 TTATCAACTC * * 31107153 TTATTATTTTATTATTTTATTATT 1 TTATTATTTTATTATTTGAATATT 31107177 TTATTATTTTATTATTCTGAAT-TT 1 TTATTATTTTATTATT-TGAATATT 31107201 TTA 1 TTA 31107204 ATAATTATTA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 24 21 0.88 25 3 0.12 ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71 Consensus pattern (24 bp): TTATTATTTTATTATTTGAATATT Found at i:31120472 original size:40 final size:40 Alignment explanation

Indices: 31120378--31120598 Score: 255 Period size: 40 Copynumber: 5.5 Consensus size: 40 31120368 TATTCGAATG * * * 31120378 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GCGACT * * * * * * 31120419 ATAACTGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-CGACT * * 31120459 ATATACGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT * * 31120499 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT * * * * 31120539 ATATCCGGGCTAAAACCCGAAGGCATTTATGCTAGTGACC 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT * 31120579 ACATCCGGGCTAAGACCCGA 1 ATATCCGGGCTAAGACCCGA 31120599 GGGCCTTGTG Statistics Matches: 155, Mismatches: 23, Indels: 5 0.85 0.13 0.03 Matches are distributed among these distances: 39 1 0.01 40 125 0.81 41 29 0.19 ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT Found at i:31120663 original size:19 final size:19 Alignment explanation

Indices: 31120639--31120676 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 31120629 AATCCCGAAG 31120639 ATTACTTGAGTTTGGGAAT 1 ATTACTTGAGTTTGGGAAT 31120658 ATTACTTGAGTTTGGGAAT 1 ATTACTTGAGTTTGGGAAT 31120677 GAGCGATCTG Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.26, C:0.05, G:0.26, T:0.42 Consensus pattern (19 bp): ATTACTTGAGTTTGGGAAT Found at i:31129662 original size:40 final size:40 Alignment explanation

Indices: 31129568--31129788 Score: 282 Period size: 40 Copynumber: 5.5 Consensus size: 40 31129558 TATTCGAATG * * 31129568 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT * * * * 31129609 ATAACCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT * * 31129649 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT * * * 31129689 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT * * * 31129729 ATATCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGACC 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT * 31129769 ACATCCGGGCTAAGACCCGA 1 ATATCCGGGCTAAGACCCGA 31129789 GGGCCTTGTG Statistics Matches: 157, Mismatches: 21, Indels: 5 0.86 0.11 0.03 Matches are distributed among these distances: 39 1 0.01 40 126 0.80 41 30 0.19 ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT Found at i:31129748 original size:80 final size:80 Alignment explanation

Indices: 31129568--31129828 Score: 287 Period size: 80 Copynumber: 3.3 Consensus size: 80 31129558 TATTCGAATG * * * * * 31129568 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC * 31129633 ATTTGTGCGAGTTGCT 65 ATTTGTGCGAGTCGCT * * * 31129649 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA * * 31129714 TTTGTGCTAG-CGATT 66 TTTGTGCGAGTCG-CT * * * * * 31129729 ATATCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAGGGC- 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA * * * * 31129793 CTTGTGCAAGTAGTT 66 TTTGTGCGAGTCGCT 31129808 ATATCC-GGCTAA-ATCCCGAAG 1 ATATCCGGGCTAAGA-CCCGAAG 31129829 ATTACTTGAG Statistics Matches: 154, Mismatches: 23, Indels: 9 0.83 0.12 0.05 Matches are distributed among these distances: 78 13 0.08 79 17 0.11 80 92 0.60 81 32 0.21 ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24 Consensus pattern (80 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA TTTGTGCGAGTCGCT Found at i:31129785 original size:120 final size:120 Alignment explanation

Indices: 31129568--31129828 Score: 314 Period size: 120 Copynumber: 2.2 Consensus size: 120 31129558 TATTCGAATG * * * * 31129568 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC 1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGACCCGAAGGC * * * * * 31129633 ATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGA-TT 66 ATTTATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGC-CTTGTGCAAG-GAGTT * * * * * 31129689 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGATTATATCCGGGCTAAGCCCCGAAGGC 1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGACCCGAAGGC * * * 31129753 ATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAGGGCCTTGTGCAAGTAGTT 66 ATTTATGCGAGTTG-CCACATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGGAGTT 31129808 ATATCC-GGCTAAATCCCGAAG 1 ATATCCGGGCTAAATCCCGAAG 31129829 ATTACTTGAG Statistics Matches: 120, Mismatches: 18, Indels: 7 0.83 0.12 0.05 Matches are distributed among these distances: 118 15 0.12 119 18 0.15 120 56 0.47 121 31 0.26 ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24 Consensus pattern (120 bp): ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGACCCGAAGGC ATTTATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGGAGTT Found at i:31131437 original size:47 final size:47 Alignment explanation

Indices: 31131368--31131582 Score: 175 Period size: 47 Copynumber: 4.5 Consensus size: 47 31131358 ATTGACGGAA * * * * 31131368 AAGACCATGGTTGGAGC-ATGGCAAC-ATGTGATATGTGATTTCCATAT 1 AAGACCATAGCTGG-GCTATGGCAACGATGTGATATGTG-CTTCCGTAT * 31131415 AAGACCATAGCTGGGCTATGGCATCGGAGAGATGTGATTATGTGCTTCCGTAT 1 AAGACCATAGCTGGGCTATGGCA----A-CGATGTGA-TATGTGCTTCCGTAT * * * * * * 31131468 AAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTACTGTAT 1 AAGACCATAGCTGGGCTATGGCAACGATGTGATATGTGCTTCCGTAT * * * * * * 31131515 AAGACCATATCTGGGATATGGCATCGGTGTGATATGTG-ATCCGTGT 1 AAGACCATAGCTGGGCTATGGCAACGATGTGATATGTGCTTCCGTAT * 31131561 AAGACCATGGCTGGGCTATGGC 1 AAGACCATAGCTGGGCTATGGC 31131583 TTCGGTGTGT Statistics Matches: 141, Mismatches: 19, Indels: 17 0.80 0.11 0.10 Matches are distributed among these distances: 46 25 0.18 47 69 0.49 48 6 0.04 51 1 0.01 53 34 0.24 54 6 0.04 ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29 Consensus pattern (47 bp): AAGACCATAGCTGGGCTATGGCAACGATGTGATATGTGCTTCCGTAT Found at i:31131473 original size:53 final size:47 Alignment explanation

Indices: 31131394--31131600 Score: 218 Period size: 47 Copynumber: 4.2 Consensus size: 47 31131384 CATGGCAACA * * * 31131394 TGTGATATGTGATTTCCATATAAGACCATAGCTGGGCTATGGCATCGGAGAG 1 TGTGATATGTG-CTTCCGTATAAGACCATAGCTGGGATATGGCATC---G-G * 31131446 ATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCGG 1 -TGTGA-TATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGG * * * 31131495 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCGG 1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGG * * * * * 31131542 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGCTTCGGTG 1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATC-G-G 31131590 TGTGATATGTG 1 TGTGATATGTG 31131601 ACTATTTGCA Statistics Matches: 137, Mismatches: 14, Indels: 11 0.85 0.09 0.07 Matches are distributed among these distances: 46 25 0.18 47 52 0.38 48 17 0.12 49 1 0.01 50 1 0.01 53 35 0.26 54 6 0.04 ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32 Consensus pattern (47 bp): TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGG Found at i:31131590 original size:93 final size:100 Alignment explanation

Indices: 31131412--31131600 Score: 239 Period size: 93 Copynumber: 1.9 Consensus size: 100 31131402 GTGATTTCCA * * 31131412 TATAAGACCATAGCTGGGCTATGGCATCGGAGAGATGTGATTATGTGCTTCCGTATAAGACCATA 1 TATAAGACCATAGCTGGGATATGGCATC-G-GAGATGTGATTATGTGCATCCGTATAAGACCATA * 31131477 TCTGGGATATGGCATC-G-GTGTGATATGTGCTACTG 64 GCTGGGATATGGCATCGGTGTGTGATATGTGCTACTG * * * 31131512 TATAAGACCATATCTGGGATATGGCATC-G-G-TGTGA-TATGTG-ATCCGTGTAAGACCATGGC 1 TATAAGACCATAGCTGGGATATGGCATCGGAGATGTGATTATGTGCATCCGTATAAGACCATAGC * * 31131572 TGGGCTATGGCTTCGGTGTGTGATATGTG 66 TGGGATATGGCATCGGTGTGTGATATGTG 31131601 ACTATTTGCA Statistics Matches: 79, Mismatches: 8, Indels: 9 0.82 0.08 0.09 Matches are distributed among these distances: 93 27 0.34 94 7 0.09 95 17 0.22 96 1 0.01 97 1 0.01 100 26 0.33 ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31 Consensus pattern (100 bp): TATAAGACCATAGCTGGGATATGGCATCGGAGATGTGATTATGTGCATCCGTATAAGACCATAGC TGGGATATGGCATCGGTGTGTGATATGTGCTACTG Found at i:31142897 original size:16 final size:16 Alignment explanation

Indices: 31142876--31142924 Score: 52 Period size: 16 Copynumber: 3.3 Consensus size: 16 31142866 TGTAATTTGT 31142876 AATGAATATGAAATTA 1 AATGAATATGAAATTA 31142892 AATGAA-ATG---TTA 1 AATGAATATGAAATTA * * 31142904 AATGAATATAAAATGA 1 AATGAATATGAAATTA 31142920 AATGA 1 AATGA 31142925 TGATTATGAA Statistics Matches: 27, Mismatches: 2, Indels: 8 0.73 0.05 0.22 Matches are distributed among these distances: 12 9 0.33 13 2 0.07 15 3 0.11 16 13 0.48 ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29 Consensus pattern (16 bp): AATGAATATGAAATTA Found at i:31143059 original size:22 final size:22 Alignment explanation

Indices: 31143053--31143128 Score: 77 Period size: 22 Copynumber: 3.4 Consensus size: 22 31143043 AATGTAAACG 31143053 AAATGAAATGAAATGAAAATAC 1 AAATGAAATGAAATGAAAATAC * 31143075 AAATGAAATGAACAAGAAGAA-AC 1 AAATGAAATGAA-ATGAA-AATAC 31143098 GAAATGCAAATGAAAT-ATAAATA- 1 -AAATG-AAATGAAATGA-AAATAC 31143121 AAATGAAA 1 AAATGAAA 31143129 AAACAATTGA Statistics Matches: 46, Mismatches: 2, Indels: 13 0.75 0.03 0.21 Matches are distributed among these distances: 21 3 0.07 22 17 0.37 23 9 0.20 24 10 0.22 25 7 0.15 ACGTcount: A:0.64, C:0.05, G:0.14, T:0.16 Consensus pattern (22 bp): AAATGAAATGAAATGAAAATAC Found at i:31143062 original size:5 final size:5 Alignment explanation

Indices: 31143033--31143128 Score: 61 Period size: 5 Copynumber: 18.2 Consensus size: 5 31143023 AATAATTTAG * * 31143033 ATGAA ATGTAA ATGTAA ACGAA ATGAA ATGAA ATGAAA ATACAA ATGAA 1 ATGAA ATG-AA ATG-AA ATGAA ATGAA ATGAA ATG-AA AT-GAA ATGAA * * * * 31143082 ATGAA CAAG-A A-GAA ACGAA ATGCAA ATGAA ATATAA ATAAA ATGAA 1 ATGAA -ATGAA ATGAA ATGAA ATG-AA ATGAA AT-GAA ATGAA ATGAA 31143128 A 1 A 31143129 AAACAATTGA Statistics Matches: 74, Mismatches: 9, Indels: 16 0.75 0.09 0.16 Matches are distributed among these distances: 3 1 0.01 4 3 0.04 5 41 0.55 6 29 0.39 ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18 Consensus pattern (5 bp): ATGAA Found at i:31143072 original size:11 final size:11 Alignment explanation

Indices: 31143036--31143129 Score: 50 Period size: 11 Copynumber: 8.3 Consensus size: 11 31143026 AATTTAGATG * 31143036 AAATGTAAATGT 1 AAATG-AAATGA * 31143048 AAACGAAATG- 1 AAATGAAATGA 31143058 AAATGAAATGA 1 AAATGAAATGA * 31143069 AAATACAAATG- 1 AAAT-GAAATGA * 31143080 AAATGAACAAGAA 1 AAATGAA-ATG-A * * 31143093 GAAACGAAATGC 1 -AAATGAAATGA 31143105 AAATGAAAT-A 1 AAATGAAATGA * 31143115 TAAATAAAATGA 1 -AAATGAAATGA 31143127 AAA 1 AAA 31143130 AACAATTGAA Statistics Matches: 63, Mismatches: 11, Indels: 17 0.69 0.12 0.19 Matches are distributed among these distances: 10 11 0.17 11 34 0.54 12 10 0.16 13 2 0.03 14 6 0.10 ACGTcount: A:0.63, C:0.05, G:0.15, T:0.17 Consensus pattern (11 bp): AAATGAAATGA Found at i:31143072 original size:27 final size:27 Alignment explanation

Indices: 31143033--31143086 Score: 72 Period size: 27 Copynumber: 2.0 Consensus size: 27 31143023 AATAATTTAG * ** 31143033 ATGAAATGTAAATGTAAACGAAATGAA 1 ATGAAATGAAAATACAAACGAAATGAA * 31143060 ATGAAATGAAAATACAAATGAAATGAA 1 ATGAAATGAAAATACAAACGAAATGAA 31143087 CAAGAAGAAA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 27 23 1.00 ACGTcount: A:0.59, C:0.04, G:0.17, T:0.20 Consensus pattern (27 bp): ATGAAATGAAAATACAAACGAAATGAA Found at i:31144534 original size:89 final size:90 Alignment explanation

Indices: 31144312--31144721 Score: 327 Period size: 91 Copynumber: 4.6 Consensus size: 90 31144302 AGTACACGAC * * * * * 31144312 AAATTAAATTTACAGACACAATAAAATACAAATATTCT-ACAATATTAATACA-AAAAATATAAA 1 AAATTAAATTTACAGATACAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAA * * 31144375 ATTCAAACAAAAAT-A-AAATGC-ACT 66 AATCAAACATAAATCATAAA--CAACT * * * ** * * * * * * * * 31144399 AAGTTAAATTTAAACACCCAACAAACTACAAACAGAT-GAGAAAAATTAATACACGAAAATTTTA 1 AAATTAAATTTACAGATACAAAAAAATACAAATA-TTCTAAAAAAATTAATACACGAAAATATAA * * * 31144463 AATTCAAAC-TACAT-ATAATACGAATT 65 AAATCAAACATAAATCATAA-AC-AACT * * 31144489 AAATTAAATTTACAGATACAAAAAAATACAAATATTCT-AAGAAATTAATACATGAAAATATAAA 1 AAATTAAATTTACAGATACAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAA * * 31144553 AATGAAACATTAAATCCTAAACAACT 66 AATCAAACA-TAAATCATAAACAACT * * * 31144579 ATATTAAATTTACATATATAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAA 1 AAATTAAATTTACAGATACAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAA * * * * * 31144644 AATGATACCTTAATTCCTAAACAACT 66 AATCA-AACATAAATCATAAACAACT * * * * * 31144670 ATATTAAATTTATAGATATAAAAAAATACAAACATTCTAAATAAA-TAATACA 1 AAATTAAATTTACAGATACAAAAAAATACAAATATTCTAAAAAAATTAATACA 31144722 ATTATTTTGA Statistics Matches: 260, Mismatches: 50, Indels: 23 0.78 0.15 0.07 Matches are distributed among these distances: 87 27 0.10 88 17 0.07 89 46 0.18 90 74 0.28 91 91 0.35 92 5 0.02 ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27 Consensus pattern (90 bp): AAATTAAATTTACAGATACAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAA AATCAAACATAAATCATAAACAACT Found at i:31144648 original size:91 final size:91 Alignment explanation

Indices: 31144491--31144721 Score: 358 Period size: 91 Copynumber: 2.6 Consensus size: 91 31144481 TACGAATTAA * * * 31144491 ATTAAATTTACAGATACAAAAAAATACAAATATTCT-AAGAAATTAATACATGAAAATATAAAAA 1 ATTAAATTTACAGATATAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAAAA 31144555 TGAAACATTAAATCCTAAACAACTAT 66 TGAAACATTAAATCCTAAACAACTAT * 31144581 ATTAAATTTACATATATAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAAAA 1 ATTAAATTTACAGATATAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAAAA * * * 31144646 TGATACCTTAATTCCTAAACAACTAT 66 TGAAACATTAAATCCTAAACAACTAT * * * 31144672 ATTAAATTTATAGATATAAAAAAATACAAACATTCTAAATAAA-TAATACA 1 ATTAAATTTACAGATATAAAAAAATACAAATATTCTAAAAAAATTAATACA 31144722 ATTATTTTGA Statistics Matches: 129, Mismatches: 11, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 90 41 0.32 91 88 0.68 ACGTcount: A:0.58, C:0.11, G:0.03, T:0.29 Consensus pattern (91 bp): ATTAAATTTACAGATATAAAAAAATACAAATATTCTAAAAAAATTAATACACGAAAATATAAAAA TGAAACATTAAATCCTAAACAACTAT Found at i:31150838 original size:40 final size:40 Alignment explanation

Indices: 31150794--31151025 Score: 297 Period size: 40 Copynumber: 5.8 Consensus size: 40 31150784 ATAACCACAA * 31150794 GCACAAATGCCCTCGGGTCTTAGCCCGGATATATCAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC 31150834 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC * * 31150874 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA 1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC * * * * 31150914 GCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC * * * * 31150954 GCACAAATGCCTTCGGGTCTTGGCCCAGATAAAATC-ACTA 1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC * * * * 31150994 GCACGATTGCCTTCGGGACTTAGCCCAGATAT 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT 31151026 CATTCAAATG Statistics Matches: 167, Mismatches: 22, Indels: 7 0.85 0.11 0.04 Matches are distributed among these distances: 39 4 0.02 40 156 0.93 41 7 0.04 ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24 Consensus pattern (40 bp): GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC Found at i:31150897 original size:80 final size:80 Alignment explanation

Indices: 31150794--31151025 Score: 340 Period size: 80 Copynumber: 2.9 Consensus size: 80 31150784 ATAACCACAA * * * * 31150794 GCACAAATGCCCTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTCTTAGC * 31150858 CCGGATATATCAACTC 65 CCGGATATAGCAACTC * 31150874 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC * 31150939 CGGGTATAGCAACTC 66 CGGATATAGCAACTC * * * * 31150954 GCACAAATGCCTTCGGGTCTTGGCCCAGATAAAATCACTAGCACGATTGCCTTCGGGACTTAGCC 1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC * 31151019 CAGATAT 66 CGGATAT 31151026 CATTCAAATG Statistics Matches: 137, Mismatches: 14, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 80 133 0.97 81 4 0.03 ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24 Consensus pattern (80 bp): GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCC CGGATATAGCAACTC Found at i:31151005 original size:120 final size:120 Alignment explanation

Indices: 31150765--31151024 Score: 335 Period size: 120 Copynumber: 2.2 Consensus size: 120 31150755 ACCCAAGTTT * * * * 31150765 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATATC 1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATAGC * * * 31150829 AACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGC 66 AACTCGCACAAATGCCTTCGGGTCTTAGCCCAGATAAATCAACTAGCACAAATGC * * * * * * * 31150884 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGC 1 CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATAGC * * * 31150949 AACTCGCACAAATGCCTTCGGGTCTTGGCCCAGATAAAATC-ACTAGCACGATTGC 66 AACTCGCACAAATGCCTTCGGGTCTTAGCCCAGAT-AAATCAACTAGCACAAATGC * 31151004 CTTCGGGACTTAGCCCAGATA 1 CTTCGGGACTTAGCCCGGATA 31151025 TCATTCAAAT Statistics Matches: 120, Mismatches: 19, Indels: 3 0.85 0.13 0.02 Matches are distributed among these distances: 119 10 0.08 120 106 0.88 121 4 0.03 ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24 Consensus pattern (120 bp): CTTCGGGACTTAGCCCGGATAAAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATAGC AACTCGCACAAATGCCTTCGGGTCTTAGCCCAGATAAATCAACTAGCACAAATGC Found at i:31164114 original size:42 final size:42 Alignment explanation

Indices: 31163999--31164114 Score: 119 Period size: 42 Copynumber: 2.8 Consensus size: 42 31163989 AGGTTATTAA * * 31163999 GATTCCATATAAGACCATATCCA-GGATATGGCCTCGGTATGT 1 GATTTCATATAAGACCATAT-CAGGGATATGGCCTCGATATGT * * * * * 31164041 GATTTCGTATAAGACCATGTCGGGGACATGGCGTCGATATGAT 1 GATTTCATATAAGACCATATCAGGGATATGGCCTCGATATG-T * * 31164084 -ATTTCATGTAAGACCATATAAGGGATATGGC 1 GATTTCATATAAGACCATATCAGGGATATGGC 31164115 ATTGAAACGA Statistics Matches: 59, Mismatches: 13, Indels: 4 0.78 0.17 0.05 Matches are distributed among these distances: 41 1 0.02 42 57 0.97 43 1 0.02 ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28 Consensus pattern (42 bp): GATTTCATATAAGACCATATCAGGGATATGGCCTCGATATGT Found at i:31165569 original size:23 final size:25 Alignment explanation

Indices: 31165543--31165589 Score: 62 Period size: 25 Copynumber: 2.0 Consensus size: 25 31165533 TATCATTCAT * 31165543 TTCATTATAT-CA-ATATTTTATGC 1 TTCATCATATCCATATATTTTATGC * 31165566 TTCATCATTTCCATATATTTTATG 1 TTCATCATATCCATATATTTTATG 31165590 TATATTTATT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 23 8 0.40 24 2 0.10 25 10 0.50 ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53 Consensus pattern (25 bp): TTCATCATATCCATATATTTTATGC Found at i:31165910 original size:46 final size:46 Alignment explanation

Indices: 31165850--31166115 Score: 352 Period size: 46 Copynumber: 6.0 Consensus size: 46 31165840 TTTGACGTGA * * * * * * 31165850 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT ** * * * 31165896 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT * 31165942 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 31165988 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 31166034 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT 31166072 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG 1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG 31166116 AGAGCACACT Statistics Matches: 198, Mismatches: 13, Indels: 18 0.86 0.06 0.08 Matches are distributed among these distances: 38 33 0.17 39 1 0.01 40 3 0.02 41 1 0.01 43 1 0.01 44 3 0.02 45 5 0.03 46 151 0.76 ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38 Consensus pattern (46 bp): TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT Found at i:31166080 original size:38 final size:38 Alignment explanation

Indices: 31166029--31166104 Score: 152 Period size: 38 Copynumber: 2.0 Consensus size: 38 31166019 CATTTCATAT 31166029 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA 1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA 31166067 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA 1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA 31166105 TTTCATATCA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 38 38 1.00 ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32 Consensus pattern (38 bp): CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA Found at i:31175499 original size:16 final size:16 Alignment explanation

Indices: 31175480--31175510 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 31175470 CTTCTTCACT 31175480 TACTCACTTACTTAAA 1 TACTCACTTACTTAAA * 31175496 TACTTACTTACTTAA 1 TACTCACTTACTTAA 31175511 TCAAATTTAT 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:0.35, C:0.23, G:0.00, T:0.42 Consensus pattern (16 bp): TACTCACTTACTTAAA Found at i:31175516 original size:20 final size:20 Alignment explanation

Indices: 31175477--31175516 Score: 53 Period size: 20 Copynumber: 2.0 Consensus size: 20 31175467 AAACTTCTTC * * 31175477 ACTTACTCACTTACTTAAAT 1 ACTTACTCACTTAATCAAAT * 31175497 ACTTACTTACTTAATCAAAT 1 ACTTACTCACTTAATCAAAT 31175517 TTATTAATAC Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40 Consensus pattern (20 bp): ACTTACTCACTTAATCAAAT Found at i:31175627 original size:23 final size:24 Alignment explanation

Indices: 31175589--31175633 Score: 74 Period size: 23 Copynumber: 1.9 Consensus size: 24 31175579 TTTGCTCTTC * 31175589 TAGCATGAACTTGTCTTACCTTTT 1 TAGCATGAACTCGTCTTACCTTTT 31175613 TAGCAT-AACTCGTCTTACCTT 1 TAGCATGAACTCGTCTTACCTT 31175634 ACCTTACCTT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 23 14 0.70 24 6 0.30 ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42 Consensus pattern (24 bp): TAGCATGAACTCGTCTTACCTTTT Found at i:31175831 original size:53 final size:53 Alignment explanation

Indices: 31175702--31175956 Score: 236 Period size: 55 Copynumber: 4.8 Consensus size: 53 31175692 ACACGGGTAC * * * 31175702 CTTACC-ATAGCCATGACTTGTCATGGTCTTACGTGGTATCCTT---TTA-AAA 1 CTTACCAAT-GCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA * 31175751 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA 1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA * * * * * * 31175804 CTCACTAATGCCATGTCTTGGCATGGTCTTACATGGGA-CCTTTGCTTTATAGTAA 1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGC-CT-TAGAAA * * * * 31175859 CTTATCAATGCCATGTCTTGACATGGTCTTAAATGATTTCCTTGCCTTAGAAA 1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA * * * * 31175912 CCTTACCAATTTCCATGCCTTGGCATCGTCTTACATGGTATCCTT 1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGTATCCTT 31175957 AAACCCTAAT Statistics Matches: 165, Mismatches: 28, Indels: 20 0.77 0.13 0.09 Matches are distributed among these distances: 49 37 0.22 50 1 0.01 52 5 0.03 53 44 0.27 54 10 0.06 55 66 0.40 56 2 0.01 ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37 Consensus pattern (53 bp): CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA Found at i:31175901 original size:108 final size:110 Alignment explanation

Indices: 31175749--31175949 Score: 282 Period size: 108 Copynumber: 1.8 Consensus size: 110 31175739 ATCCTTTTAA * * * * 31175749 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACTAA 1 AACTTACCAATGCCATGTCTTGACATGGTCTTAAATGATATCCTTGCCTTA-GAAACCTCACCAA * * 31175812 -TGCCATGTCTTGGCATGGTCTTACATGGGACCTTTGCTTTATAGT 65 TTGCCATGCCTTGGCATCGTCTTACATGGGACCTTTGCTTTATAGT * * * 31175857 AACTTATCAATGCCATGTCTTGACATGGTCTTAAATGATTTCCTTGCCTTAGAAACCTTACCAAT 1 AACTTACCAATGCCATGTCTTGACATGGTCTTAAATGATATCCTTGCCTTAGAAACCTCACCAAT * 31175922 TTCCATGCCTTGGCATCGTCTTACATGG 66 TGCCATGCCTTGGCATCGTCTTACATGG 31175950 TATCCTTAAA Statistics Matches: 80, Mismatches: 10, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 107 1 0.01 108 48 0.60 109 6 0.08 110 25 0.31 ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36 Consensus pattern (110 bp): AACTTACCAATGCCATGTCTTGACATGGTCTTAAATGATATCCTTGCCTTAGAAACCTCACCAAT TGCCATGCCTTGGCATCGTCTTACATGGGACCTTTGCTTTATAGT Found at i:31177481 original size:93 final size:93 Alignment explanation

Indices: 31177348--31177518 Score: 272 Period size: 93 Copynumber: 1.8 Consensus size: 93 31177338 GCCCCTAAGT * * * * 31177348 GAACTCGGACTCAACTCAATGAGCTTGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * * 31177413 TGAGTTTGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC 31177441 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 GAACTCGGACTCAACTCAACGAGCTT-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 31177505 ACGAGTTCGGATGC 65 ACGAGTTCGGATGC 31177519 TCAACCATCC Statistics Matches: 71, Mismatches: 6, Indels: 2 0.90 0.08 0.03 Matches are distributed among these distances: 92 2 0.03 93 69 0.97 ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:31177512 original size:46 final size:46 Alignment explanation

Indices: 31177343--31177515 Score: 176 Period size: 46 Copynumber: 3.7 Consensus size: 46 31177333 AACCCGCCCC * * * * 31177343 TAAGTGAACTCGGACTCAACTCAATGAGCTT-GGGCGTTCGTATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCA * * * 31177389 TAAGTGAACTCGGACTCAACTCAATGAGTTTGGATGCCTAGTT-ACAT-C- 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA * * 31177437 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 31177482 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 31177516 TGCTCAACCA Statistics Matches: 106, Mismatches: 11, Indels: 20 0.77 0.08 0.15 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 2 0.02 45 4 0.04 46 59 0.56 47 27 0.25 48 2 0.02 49 2 0.02 50 2 0.02 51 2 0.02 ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA Found at i:31177534 original size:46 final size:44 Alignment explanation

Indices: 31177391--31177534 Score: 123 Period size: 46 Copynumber: 3.1 Consensus size: 44 31177381 CGTATCCATA * * 31177391 AGTGAACTCGGACTCAACTCAATGAGTTTGGATGCCTAGTTA-CATCT 1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT * * * * 31177438 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A 1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT 31177484 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT 1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT 31177530 AGTGA 1 AGTGA 31177535 CATGTCACTT Statistics Matches: 78, Mismatches: 11, Indels: 16 0.74 0.10 0.15 Matches are distributed among these distances: 44 9 0.12 45 1 0.01 46 33 0.42 47 29 0.37 48 1 0.01 49 4 0.05 50 1 0.01 ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24 Consensus pattern (44 bp): AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT Found at i:31177972 original size:30 final size:30 Alignment explanation

Indices: 31177938--31177997 Score: 93 Period size: 30 Copynumber: 2.0 Consensus size: 30 31177928 ATTTAATACG 31177938 AACTTTGGAAAAATTACACTTTTGCCCCTA 1 AACTTTGGAAAAATTACACTTTTGCCCCTA * * * 31177968 AACTTTTGCATAATTACACTTTTGCCCCTA 1 AACTTTGGAAAAATTACACTTTTGCCCCTA 31177998 GGCTCGGGAA Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37 Consensus pattern (30 bp): AACTTTGGAAAAATTACACTTTTGCCCCTA Found at i:31180131 original size:44 final size:44 Alignment explanation

Indices: 31180082--31180168 Score: 156 Period size: 44 Copynumber: 2.0 Consensus size: 44 31180072 GGATGAACCG 31180082 CCAAACAAACATTATGTGCTTCATGCAAAATATTTTGAATCAAA 1 CCAAACAAACATTATGTGCTTCATGCAAAATATTTTGAATCAAA * * 31180126 CCAAACAACCATTATGTGCTTCATGCAAAATCTTTTGAATCAA 1 CCAAACAAACATTATGTGCTTCATGCAAAATATTTTGAATCAA 31180169 CTCATCATTT Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 44 41 1.00 ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30 Consensus pattern (44 bp): CCAAACAAACATTATGTGCTTCATGCAAAATATTTTGAATCAAA Found at i:31185079 original size:93 final size:93 Alignment explanation

Indices: 31184967--31185137 Score: 299 Period size: 93 Copynumber: 1.8 Consensus size: 93 31184957 GCCCCTAAAT * 31184967 GAACTCGGACTCAACTCAACGAGCTT-GGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 31185031 ACAAGTTCGGATGCCTAGTTACATCTCAC 65 ACAAGTTCGGATGCCTAGTTACATCTCAC * 31185060 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * 31185125 CGAGTTCGGATGC 66 CAAGTTCGGATGC 31185138 TCAACCATCC Statistics Matches: 74, Mismatches: 3, Indels: 2 0.94 0.04 0.03 Matches are distributed among these distances: 92 2 0.03 93 72 0.97 ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CAAGTTCGGATGCCTAGTTACATCTCAC Found at i:31185126 original size:46 final size:46 Alignment explanation

Indices: 31184966--31185134 Score: 202 Period size: 46 Copynumber: 3.7 Consensus size: 46 31184956 CGCCCCTAAA * * 31184966 TGAACTCGGACTCAACTCAACGAGCTT-GGGCATTCGCATCCATAAG 1 TGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCATCCATAAG * * * * 31185012 TGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTTACAT-C-TCA- 1 TGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCATAAG * 31185059 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG 1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG 31185105 TGAACTCGGACTCAACTCAACGAGTTCGGA 1 TGAACTCGGACTCAACTCAACGAGTTCGGA 31185135 TGCTCAACCA Statistics Matches: 103, Mismatches: 12, Indels: 16 0.79 0.09 0.12 Matches are distributed among these distances: 43 6 0.06 44 2 0.02 45 4 0.04 46 54 0.52 47 28 0.27 48 2 0.02 49 2 0.02 50 5 0.05 ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22 Consensus pattern (46 bp): TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG Found at i:31185591 original size:30 final size:30 Alignment explanation

Indices: 31185557--31185616 Score: 93 Period size: 30 Copynumber: 2.0 Consensus size: 30 31185547 ATTTAATACG 31185557 AACTTTGGAAAAATTACACTTTTGCCCCTA 1 AACTTTGGAAAAATTACACTTTTGCCCCTA * * * 31185587 AACTTTTGCATAATTACACTTTTGCCCCTA 1 AACTTTGGAAAAATTACACTTTTGCCCCTA 31185617 GGCTCGGGAA Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37 Consensus pattern (30 bp): AACTTTGGAAAAATTACACTTTTGCCCCTA Found at i:31189295 original size:48 final size:48 Alignment explanation

Indices: 31189228--31189341 Score: 124 Period size: 48 Copynumber: 2.3 Consensus size: 48 31189218 ACACGGGTAG * * * * 31189228 ACCACACGCCCGTGTCTATTTAACAGATTGT-AACATGACCTAAGCCAC 1 ACCACACG-GCGTGTCTATTTAACAGACTCTAAACACGACCTAAGCCAC * * 31189276 ACCACACGGTCGTGTCTATTTAGCAGACTCTAAACACGGCCTAAGCCAC 1 ACCACACGG-CGTGTCTATTTAACAGACTCTAAACACGACCTAAGCCAC 31189325 -CTCACACAGGCGTGTCT 1 AC-CACAC-GGCGTGTCT 31189342 CTGTCGAGCC Statistics Matches: 56, Mismatches: 6, Indels: 7 0.81 0.09 0.10 Matches are distributed among these distances: 48 27 0.48 49 27 0.48 50 2 0.04 ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22 Consensus pattern (48 bp): ACCACACGGCGTGTCTATTTAACAGACTCTAAACACGACCTAAGCCAC Found at i:31189331 original size:49 final size:48 Alignment explanation

Indices: 31189238--31189341 Score: 122 Period size: 49 Copynumber: 2.1 Consensus size: 48 31189228 ACCACACGCC * * * 31189238 CGTGTCTATTTAACAGATTGTAACATGACCTAAGCCACACCACAC-GG 1 CGTGTCTATTTAACAGACTCTAACACGACCTAAGCCACACCACACAGG * * 31189285 TCGTGTCTATTTAGCAGACTCTAAACACGGCCTAAGCCAC-CTCACACAGG 1 -CGTGTCTATTTAACAGACTCT-AACACGACCTAAGCCACAC-CACACAGG 31189335 CGTGTCT 1 CGTGTCT 31189342 CTGTCGAGCC Statistics Matches: 48, Mismatches: 5, Indels: 5 0.83 0.09 0.09 Matches are distributed among these distances: 48 19 0.40 49 27 0.56 50 2 0.04 ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24 Consensus pattern (48 bp): CGTGTCTATTTAACAGACTCTAACACGACCTAAGCCACACCACACAGG Found at i:31193390 original size:29 final size:29 Alignment explanation

Indices: 31193356--31193415 Score: 102 Period size: 29 Copynumber: 2.1 Consensus size: 29 31193346 GCTTATTTTA * 31193356 GCTCATACCACGGGCAGCGACATAGCCGT 1 GCTCATACCACGGGCAGCGACACAGCCGT * 31193385 GCTCATACCACGGGCGGCGACACAGCCGT 1 GCTCATACCACGGGCAGCGACACAGCCGT 31193414 GC 1 GC 31193416 GATATGGCCG Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.22, C:0.37, G:0.30, T:0.12 Consensus pattern (29 bp): GCTCATACCACGGGCAGCGACACAGCCGT Found at i:31199240 original size:22 final size:22 Alignment explanation

Indices: 31199214--31199258 Score: 56 Period size: 22 Copynumber: 2.0 Consensus size: 22 31199204 ATTTCAACAC 31199214 AAATAT-AATCGCATACATATCA 1 AAATATCAATCGCA-ACATATCA * * 31199236 AAATATCGATCTCAACATATCA 1 AAATATCAATCGCAACATATCA 31199258 A 1 A 31199259 TCATCATAAT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 22 15 0.75 23 5 0.25 ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27 Consensus pattern (22 bp): AAATATCAATCGCAACATATCA Found at i:31204216 original size:5 final size:5 Alignment explanation

Indices: 31204206--31204231 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 31204196 ATCATTTTTA 31204206 TTATT TTATT TTATT TTATT TTATT T 1 TTATT TTATT TTATT TTATT TTATT T 31204232 GTTAGTTGAG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81 Consensus pattern (5 bp): TTATT Found at i:31207586 original size:21 final size:21 Alignment explanation

Indices: 31207534--31207578 Score: 90 Period size: 21 Copynumber: 2.1 Consensus size: 21 31207524 ATAAGATTGA 31207534 CTAATTACAATAATTACTTGG 1 CTAATTACAATAATTACTTGG 31207555 CTAATTACAATAATTACTTGG 1 CTAATTACAATAATTACTTGG 31207576 CTA 1 CTA 31207579 GTTTCAATGA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38 Consensus pattern (21 bp): CTAATTACAATAATTACTTGG Found at i:31209631 original size:93 final size:93 Alignment explanation

Indices: 31209472--31209643 Score: 283 Period size: 93 Copynumber: 1.8 Consensus size: 93 31209462 CGCCCATAAG * * 31209472 CGAACTCAGACTCAACTCAACGAGCTCGAGCGTTCGCATCCATAGGTGAACTCAGACTCAACTCA 1 CGAACTCAGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA 31209537 ACGAGTTCGGATGCCTAGTTGCATTTCA 66 ACGAGTTCGGATGCCTAGTTGCATTTCA * * * 31209565 CGAACTCGGACTCAACTCAACGAGTTCG-GACATTCGCATCCATAAGTGAACTCGGACTCAACTC 1 CGAACTCAGACTCAACTCAACGAGCTCGAG-CATTCGCATCCATAAGTGAACTCAGACTCAACTC 31209629 AACGAGTTCGGATGC 65 AACGAGTTCGGATGC 31209644 TCAACCATCC Statistics Matches: 73, Mismatches: 5, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 92 1 0.01 93 72 0.99 ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22 Consensus pattern (93 bp): CGAACTCAGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAAGTGAACTCAGACTCAACTCA ACGAGTTCGGATGCCTAGTTGCATTTCA Found at i:31209639 original size:46 final size:47 Alignment explanation

Indices: 31209465--31209640 Score: 193 Period size: 46 Copynumber: 3.8 Consensus size: 47 31209455 TGTAACCCGC * * 31209465 CCATAAGCGAACTCAGACTCAACTCAACGAGCTC-GAGCGTTCGCAT 1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGAGCATTCGCAT * * 31209511 CCATAGGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-GCAT 1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCAT * * * 31209561 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCAT 1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGAGCATTCGCAT * * 31209604 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGA 31209641 TGCTCAACCA Statistics Matches: 109, Mismatches: 12, Indels: 18 0.78 0.09 0.13 Matches are distributed among these distances: 42 2 0.02 43 5 0.05 44 1 0.01 45 2 0.02 46 60 0.55 47 30 0.28 48 2 0.02 49 1 0.01 50 4 0.04 51 2 0.02 ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21 Consensus pattern (47 bp): CCATAAGCGAACTCAGACTCAACTCAACGAGTTCGGAGCATTCGCAT Found at i:31212030 original size:14 final size:14 Alignment explanation

Indices: 31212011--31212070 Score: 52 Period size: 14 Copynumber: 4.3 Consensus size: 14 31212001 CAAAGATAAC 31212011 AAGAAAACCGAATA 1 AAGAAAACCGAATA * * 31212025 AAGAAATCC-AAGA 1 AAGAAAACCGAATA * 31212038 TAGAGAAACCGAATA 1 AAGA-AAACCGAATA * 31212053 AA-AAATCCAGAATA 1 AAGAAAACC-GAATA 31212067 AAGA 1 AAGA 31212071 GATCCAGGAT Statistics Matches: 35, Mismatches: 7, Indels: 7 0.71 0.14 0.14 Matches are distributed among these distances: 13 10 0.29 14 20 0.57 15 5 0.14 ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10 Consensus pattern (14 bp): AAGAAAACCGAATA Found at i:31212077 original size:15 final size:15 Alignment explanation

Indices: 31212011--31212087 Score: 74 Period size: 15 Copynumber: 5.4 Consensus size: 15 31212001 CAAAGATAAC * 31212011 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 31212025 AAGAAATCCA-AGATA 1 AAGAAATCCAGA-ATA * 31212040 GAGAAA-CC-GAATA 1 AAGAAATCCAGAATA 31212053 AA-AAATCCAGAATA 1 AAGAAATCCAGAATA * * 31212067 AAGAGATCCAGGATA 1 AAGAAATCCAGAATA 31212082 AAGAAA 1 AAGAAA 31212088 CCCAAGATAC Statistics Matches: 51, Mismatches: 6, Indels: 11 0.75 0.09 0.16 Matches are distributed among these distances: 12 3 0.06 13 6 0.12 14 19 0.37 15 23 0.45 ACGTcount: A:0.60, C:0.13, G:0.17, T:0.10 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:31212096 original size:15 final size:15 Alignment explanation

Indices: 31212022--31212096 Score: 68 Period size: 15 Copynumber: 5.2 Consensus size: 15 31212012 AGAAAACCGA 31212022 ATAAAGAAATCCAAG 1 ATAAAGAAATCCAAG * * 31212037 ATAGAGAAA-CCGA- 1 ATAAAGAAATCCAAG 31212050 ATAAA-AAATCC-AG 1 ATAAAGAAATCCAAG * * 31212063 AATAAAGAGATCCAGG 1 -ATAAAGAAATCCAAG * 31212079 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 31212094 ATA 1 ATA 31212097 CGATACTATG Statistics Matches: 47, Mismatches: 8, Indels: 10 0.72 0.12 0.15 Matches are distributed among these distances: 12 4 0.09 13 6 0.13 14 8 0.17 15 28 0.60 16 1 0.02 ACGTcount: A:0.57, C:0.15, G:0.16, T:0.12 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:31215150 original size:93 final size:91 Alignment explanation

Indices: 31214992--31215161 Score: 304 Period size: 93 Copynumber: 1.8 Consensus size: 91 31214982 CGCCCATAAG * 31214992 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAGTGAACTCGGACTCAACTCAAC 1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAGTGAACTCGGACTCAACTCAAC 31215057 GAGTTCGGATGCCTAGTTACATTTCA 66 GAGTTCGGATGCCTAGTTACATTTCA * 31215083 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCAT-AGTGAACTCGGACTCAACTCA 31215148 ACGAGTTCGGATGC 64 ACGAGTTCGGATGC 31215162 TCAACCATCC Statistics Matches: 75, Mismatches: 2, Indels: 2 0.95 0.03 0.03 Matches are distributed among these distances: 91 28 0.37 92 12 0.16 93 35 0.47 ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22 Consensus pattern (91 bp): CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAGTGAACTCGGACTCAACTCAAC GAGTTCGGATGCCTAGTTACATTTCA Found at i:31215177 original size:46 final size:45 Alignment explanation

Indices: 31214993--31215177 Score: 148 Period size: 44 Copynumber: 4.0 Consensus size: 45 31214983 GCCCATAAGC * * * * * 31214993 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCA--TAGT 1 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCATCTAGT * * 31215037 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTTCA-C 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AGT * * * * 31215084 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT 1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCTAGT 31215130 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT 1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAGT 31215176 GA 1 GA 31215178 CATGTCACTT Statistics Matches: 114, Mismatches: 13, Indels: 26 0.75 0.08 0.17 Matches are distributed among these distances: 42 1 0.01 43 3 0.03 44 36 0.32 45 3 0.03 46 33 0.29 47 32 0.28 48 1 0.01 49 4 0.04 50 1 0.01 ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22 Consensus pattern (45 bp): GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAGT Found at i:31221661 original size:44 final size:42 Alignment explanation

Indices: 31221579--31221707 Score: 134 Period size: 42 Copynumber: 3.0 Consensus size: 42 31221569 AGGATTTCTG * * * * * 31221579 ATATGTGATATCGTGTAAGACCACGTCTGGGACGTTGGCATC 1 ATATCTGATTTCGTGTAAGACCATGTCTAGGACATTGGCATC * * 31221621 GACT-TTTGTTTTACGTGTAAGACCATGTCTAGGACATTGGCATC 1 -A-TATCTGATTT-CGTGTAAGACCATGTCTAGGACATTGGCATC * * * 31221665 ATATCTGATTTCGTATAAGACCCTGTCTAGGACAGTGGCATC 1 ATATCTGATTTCGTGTAAGACCATGTCTAGGACATTGGCATC 31221707 A 1 A 31221708 ATGTTTGATT Statistics Matches: 72, Mismatches: 11, Indels: 7 0.80 0.12 0.08 Matches are distributed among these distances: 42 30 0.42 43 13 0.18 44 29 0.40 ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32 Consensus pattern (42 bp): ATATCTGATTTCGTGTAAGACCATGTCTAGGACATTGGCATC Found at i:31225238 original size:15 final size:15 Alignment explanation

Indices: 31225218--31225270 Score: 54 Period size: 15 Copynumber: 3.5 Consensus size: 15 31225208 GTATCTTGGG 31225218 TTTCTTTATTCTGGA 1 TTTCTTTATTCTGGA * * 31225233 TTTCTTTATTATGGG 1 TTTCTTTATTCTGGA * * 31225248 TTTCTCTA-TCTTGAA 1 TTTCTTTATTC-TGGA 31225263 TTTCTTTA 1 TTTCTTTA 31225271 CTTGGTTTTC Statistics Matches: 30, Mismatches: 7, Indels: 2 0.77 0.18 0.05 Matches are distributed among these distances: 14 1 0.03 15 29 0.97 ACGTcount: A:0.15, C:0.13, G:0.11, T:0.60 Consensus pattern (15 bp): TTTCTTTATTCTGGA Done.