Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold25

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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34

Warning! 6276 characters in sequence are not A, C, G, or T


File 50 of 56

Found at i:8529204 original size:19 final size:20

Alignment explanation

Indices: 8529155--8529204 Score: 57 Period size: 19 Copynumber: 2.5 Consensus size: 20 8529145 CACACCCAGA * 8529155 TGTATCAAAACATATTGCTT 1 TGTATCAATACATATTGCTT * * * 8529175 AGTATCGATACATGTT-CTT 1 TGTATCAATACATATTGCTT 8529194 TGTATCAATAC 1 TGTATCAATAC 8529205 CCCATAAAAT Statistics Matches: 24, Mismatches: 6, Indels: 1 0.77 0.19 0.03 Matches are distributed among these distances: 19 12 0.50 20 12 0.50 ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40 Consensus pattern (20 bp): TGTATCAATACATATTGCTT Found at i:8529319 original size:52 final size:52 Alignment explanation

Indices: 8529257--8529355 Score: 155 Period size: 52 Copynumber: 1.9 Consensus size: 52 8529247 TAAGTGAATT * 8529257 GTATCGATACA-TAGTAAATTGTATCGATATATTGAGCCTAACGGCTATAATC 1 GTATCGATACATTA-TAAATTGTATCGATACATTGAGCCTAACGGCTATAATC * * 8529309 GTATCGATACATTATGAATTGTATCGATACATTGAGTCTAACGGCTA 1 GTATCGATACATTATAAATTGTATCGATACATTGAGCCTAACGGCTA 8529356 GAATTTTAAA Statistics Matches: 43, Mismatches: 3, Indels: 2 0.90 0.06 0.04 Matches are distributed among these distances: 52 41 0.95 53 2 0.05 ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33 Consensus pattern (52 bp): GTATCGATACATTATAAATTGTATCGATACATTGAGCCTAACGGCTATAATC Found at i:8529816 original size:35 final size:34 Alignment explanation

Indices: 8529770--8529835 Score: 114 Period size: 35 Copynumber: 1.9 Consensus size: 34 8529760 AAAATGATTG * 8529770 AGAGGTTTTATCTTAGCCTTTATAAAAGATAGGGA 1 AGAGGCTTTATCTTAGCCTTTA-AAAAGATAGGGA 8529805 AGAGGCTTTATCTTAGCCTTTAAAAAGATAG 1 AGAGGCTTTATCTTAGCCTTTAAAAAGATAG 8529836 TGTTGTAAGG Statistics Matches: 30, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 34 9 0.30 35 21 0.70 ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33 Consensus pattern (34 bp): AGAGGCTTTATCTTAGCCTTTAAAAAGATAGGGA Found at i:8531442 original size:21 final size:21 Alignment explanation

Indices: 8531417--8531472 Score: 67 Period size: 21 Copynumber: 2.6 Consensus size: 21 8531407 GATGTGCTTA * 8531417 AAAAGAAAGTAAATGAGTTAG 1 AAAAGAAAATAAATGAGTTAG * * 8531438 AAAAGAAAATATATGAGTTAT 1 AAAAGAAAATAAATGAGTTAG * 8531459 AAGAAGACAATAAA 1 AA-AAGAAAATAAA 8531473 AAAAATTAAC Statistics Matches: 29, Mismatches: 5, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 21 20 0.69 22 9 0.31 ACGTcount: A:0.61, C:0.02, G:0.18, T:0.20 Consensus pattern (21 bp): AAAAGAAAATAAATGAGTTAG Found at i:8532266 original size:73 final size:73 Alignment explanation

Indices: 8532179--8532316 Score: 258 Period size: 73 Copynumber: 1.9 Consensus size: 73 8532169 TATTGTCAAT 8532179 TATGTGACAAAGGAATGAAAGTCATATTTAAATCACAAAATTGTCACGTAGTTGATACGCTTAGC 1 TATGTGACAAAGGAATGAAAGTCATATTTAAATCACAAAATTGTCACGTAGTTGATACGCTTAGC 8532244 AACCAAAC 66 AACCAAAC * * 8532252 TATGTGACAAAGGAATGAAAGTCATATTTGAATCACAAAATTGTCACGTAGTTGATATGCTTAGC 1 TATGTGACAAAGGAATGAAAGTCATATTTAAATCACAAAATTGTCACGTAGTTGATACGCTTAGC 8532317 CCCCTTAGTA Statistics Matches: 63, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 73 63 1.00 ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28 Consensus pattern (73 bp): TATGTGACAAAGGAATGAAAGTCATATTTAAATCACAAAATTGTCACGTAGTTGATACGCTTAGC AACCAAAC Found at i:8532581 original size:21 final size:21 Alignment explanation

Indices: 8532548--8532588 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 8532538 CTAAGTAAAA 8532548 ATACGTATTGTATCAATACAT 1 ATACGTATTGTATCAATACAT * 8532569 ATAC-TATTGGTATTAATACA 1 ATACGTATT-GTATCAATACA 8532589 CAAGGTTGAC Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39 Consensus pattern (21 bp): ATACGTATTGTATCAATACAT Found at i:8532653 original size:20 final size:19 Alignment explanation

Indices: 8532628--8532698 Score: 70 Period size: 20 Copynumber: 3.6 Consensus size: 19 8532618 ACCCTGAAAA 8532628 GTATCGATACACATTTAAAT 1 GTATCGATACACA-TTAAAT * ** 8532648 GTATCGATACAAATTGCAT 1 GTATCGATACACATTAAAT ** 8532667 AGTATCGATACACACAAATAT 1 -GTATCGATACACATTAA-AT 8532688 GTATCGATACA 1 GTATCGATACA 8532699 GGACATTAGC Statistics Matches: 41, Mismatches: 8, Indels: 4 0.77 0.15 0.08 Matches are distributed among these distances: 19 4 0.10 20 35 0.85 21 2 0.05 ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30 Consensus pattern (19 bp): GTATCGATACACATTAAAT Found at i:8532751 original size:53 final size:53 Alignment explanation

Indices: 8532668--8532804 Score: 238 Period size: 53 Copynumber: 2.6 Consensus size: 53 8532658 AAATTGCATA 8532668 GTATCGATACACACAAATATGTATCGATACAGGACATTAGCAGTAGCCAAATTT 1 GTATCGATACACAC-AATATGTATCGATACAGGACATTAGCAGTAGCCAAATTT * * 8532722 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT 1 GTATCGATACACACAATATGTATCGATACAGGACATTAGCAGTAGCCAAATTT * 8532775 GTATCGATACACAAAATATGTATCGATACA 1 GTATCGATACACACAATATGTATCGATACA 8532805 TTGGTATTGG Statistics Matches: 80, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 53 66 0.82 54 14 0.17 ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27 Consensus pattern (53 bp): GTATCGATACACACAATATGTATCGATACAGGACATTAGCAGTAGCCAAATTT Found at i:8532847 original size:10 final size:10 Alignment explanation

Indices: 8532828--8532858 Score: 53 Period size: 10 Copynumber: 3.1 Consensus size: 10 8532818 AATCTCATTT 8532828 TCACTGTTCA 1 TCACTGTTCA * 8532838 TCACTATTCA 1 TCACTGTTCA 8532848 TCACTGTTCA 1 TCACTGTTCA 8532858 T 1 T 8532859 GTATCGTTAA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42 Consensus pattern (10 bp): TCACTGTTCA Found at i:8532910 original size:13 final size:13 Alignment explanation

Indices: 8532892--8532930 Score: 60 Period size: 13 Copynumber: 3.0 Consensus size: 13 8532882 TCACTATTCA 8532892 TGTATCGATACAT 1 TGTATCGATACAT * 8532905 TGTATCGATACAG 1 TGTATCGATACAT * 8532918 TGTATCAATACAT 1 TGTATCGATACAT 8532931 CATAAATAGT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 13 23 1.00 ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8537130 original size:20 final size:20 Alignment explanation

Indices: 8537107--8537147 Score: 82 Period size: 20 Copynumber: 2.0 Consensus size: 20 8537097 TATAAATTTG 8537107 GTTTTATCAACTTAGCTTAT 1 GTTTTATCAACTTAGCTTAT 8537127 GTTTTATCAACTTAGCTTAT 1 GTTTTATCAACTTAGCTTAT 8537147 G 1 G 8537148 AACCAAAAAG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49 Consensus pattern (20 bp): GTTTTATCAACTTAGCTTAT Found at i:8538030 original size:21 final size:21 Alignment explanation

Indices: 8538006--8538046 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 8537996 CTAAGTAATA 8538006 ATACGTATT-GTATCAATACAT 1 ATAC-TATTGGTATCAATACAT * 8538027 ATACTATTGGTATTAATACA 1 ATACTATTGGTATCAATACA 8538047 CAAGGTTGAC Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39 Consensus pattern (21 bp): ATACTATTGGTATCAATACAT Found at i:8538210 original size:53 final size:53 Alignment explanation

Indices: 8538126--8538262 Score: 222 Period size: 53 Copynumber: 2.6 Consensus size: 53 8538116 AAATTGCATA * 8538126 GTATCGATACACACAAATATGTATCAATACAGGAT-ATTGGCAGTAGCCAAATTT 1 GTATCGATACACAC-AATATGTATCGATACAGG-TCATTGGCAGTAGCCAAATTT * 8538180 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCTAAATTT 1 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT * 8538233 GTATCGATACACAAAATATGTATCGATACA 1 GTATCGATACACACAATATGTATCGATACA 8538263 TTGGTAGTGG Statistics Matches: 79, Mismatches: 3, Indels: 3 0.93 0.04 0.04 Matches are distributed among these distances: 52 1 0.01 53 64 0.81 54 14 0.18 ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28 Consensus pattern (53 bp): GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT Found at i:8538368 original size:13 final size:13 Alignment explanation

Indices: 8538350--8538388 Score: 69 Period size: 13 Copynumber: 3.0 Consensus size: 13 8538340 TCACTATTCA 8538350 TGTATCGATACAT 1 TGTATCGATACAT * 8538363 TGTATCGATACAG 1 TGTATCGATACAT 8538376 TGTATCGATACAT 1 TGTATCGATACAT 8538389 CATAAATAGT Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 13 24 1.00 ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8541703 original size:13 final size:13 Alignment explanation

Indices: 8541685--8541709 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 8541675 TAATTATTCA 8541685 TGTATCGATACAT 1 TGTATCGATACAT 8541698 TGTATCGATACA 1 TGTATCGATACA 8541710 ATGTGCCATG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8541797 original size:13 final size:13 Alignment explanation

Indices: 8541779--8541804 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 8541769 TACAGTGAAC 8541779 ATGTATCGATACA 1 ATGTATCGATACA 8541792 ATGTATCGATACA 1 ATGTATCGATACA 8541805 TCTGGATATG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:8548907 original size:15 final size:15 Alignment explanation

Indices: 8548887--8548918 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 8548877 GTCAACTTCC 8548887 TCATTATCATCATCA 1 TCATTATCATCATCA * 8548902 TCATTATCTTCATCA 1 TCATTATCATCATCA 8548917 TC 1 TC 8548919 TTTGATGGTT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44 Consensus pattern (15 bp): TCATTATCATCATCA Found at i:8553066 original size:78 final size:78 Alignment explanation

Indices: 8552937--8553155 Score: 255 Period size: 79 Copynumber: 2.8 Consensus size: 78 8552927 ACAATGGGGC * * * 8552937 TGGAGTATCCCTGATTATGGAAAATCTG-TGTTCTGAAAATAAAACCGGGGTTGGAGTATCCCTC 1 TGGAGTATCCCTGATTATGAAAAATC-GATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCTC * 8553001 -AGAAATAACAGGGA 65 GA-AAATAACAGAGA * * * 8553015 TGGAGTATCCCTGATTATAAAAAATCGATATTTTGAAAATAAAATCGGGGTTAGAGTATCCCCTC 1 TGGAGTATCCCTGATTATGAAAAATCGATATTTTGAAAATAAAACCGGGGTTGGAGTAT-CCCTC * 8553080 GAAAATAACAGAGT 65 GAAAATAACAGAGA * * * ** * 8553094 TGGAGAATCCCTGATTGTGAAAAATCGATGATTTAG-AAATAAGGCCGGGGTTGAAGTATCCC 1 TGGAGTATCCCTGATTATGAAAAATCGAT-ATTTTGAAAATAAAACCGGGGTTGGAGTATCCC 8553156 CGATTGTGAG Statistics Matches: 120, Mismatches: 17, Indels: 8 0.83 0.12 0.06 Matches are distributed among these distances: 77 1 0.01 78 54 0.45 79 59 0.49 80 6 0.05 ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26 Consensus pattern (78 bp): TGGAGTATCCCTGATTATGAAAAATCGATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCTCG AAAATAACAGAGA Found at i:8553161 original size:51 final size:51 Alignment explanation

Indices: 8553100--8553207 Score: 130 Period size: 51 Copynumber: 2.1 Consensus size: 51 8553090 GAGTTGGAGA * * * 8553100 ATCCCTGATTGTGAAAAATCGATGA-TTTAGAAATAAGGCCG-GGGTTGAAGT 1 ATCCCCGATTGTGAAAAATCAAT-ATTTTAGAAATAAAGCCGAGGG-TGAAGT * * * 8553151 ATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGAGGGTGGAGT 1 ATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCCGAGGGTGAAGT 8553202 ATCCCC 1 ATCCCC 8553208 TCGAAAATAA Statistics Matches: 49, Mismatches: 6, Indels: 4 0.83 0.10 0.07 Matches are distributed among these distances: 50 1 0.02 51 45 0.92 52 3 0.06 ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26 Consensus pattern (51 bp): ATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAGCCGAGGGTGAAGT Found at i:8553222 original size:79 final size:79 Alignment explanation

Indices: 8553139--8553286 Score: 217 Period size: 79 Copynumber: 1.9 Consensus size: 79 8553129 GAAATAAGGC * * 8553139 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGAGGG-TGGAGTA 1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAACC-AGGGTTGGAGTA 8553203 TCCCCTCGAAAATAA 65 TCCCCTCGAAAATAA * * * * * 8553218 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTATTGTTTTGGAAATAAAATCAGGGTTGGAGTAT 1 CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAACCAGGGTTGGAGTAT 8553283 CCCC 66 CCCC 8553287 GATTATGAAA Statistics Matches: 61, Mismatches: 7, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 78 4 0.07 79 57 0.93 ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27 Consensus pattern (79 bp): CGGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAACCAGGGTTGGAGTAT CCCCTCGAAAATAA Found at i:8553263 original size:130 final size:130 Alignment explanation

Indices: 8553009--8553415 Score: 428 Period size: 130 Copynumber: 3.1 Consensus size: 130 8552999 TCAGAAATAA * * * * * * * 8553009 CAGGGATGGAGTATCCCTGATTATAAAAAATCGATATTTTGAAAATAAAATCG-GGGTTAGAGTA 1 CAGGGTTGAAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAA-CGAGGGTTGGAGTA * * * * ** 8553073 TCCCCTCGAAAATAACAGAGTTGGAGAATCCCTGATTGTGAAAAATCGATGATTTAGAAATAAGG 65 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAAA 8553138 C 130 C * * * * 8553139 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGAGGG-TGGAGTA 1 CAGGGTTGAAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAA-ACGAGGGTTGGAGTA * * * 8553203 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAAT-TATTGTTTTGGAAATAAA 65 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGA-TGATTTAGAAATAAA * 8553267 AT 129 AC * * * * * * 8553269 CAGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTAGGGTTGGAGTAT 1 CAGGGTTGAAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAACGAGGGTTGGAGTAT * * * * * * * 8553334 CCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTGTGAAAACTAG-TGTTTTAGGAATAAAAT 66 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAAAC * 8553398 C-GAGGTTGGAGTATCCCC 1 CAG-GGTTGAAGTATCCCC 8553416 TCAGAAATAA Statistics Matches: 234, Mismatches: 37, Indels: 13 0.82 0.13 0.05 Matches are distributed among these distances: 128 1 0.00 129 37 0.16 130 193 0.82 131 3 0.01 ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27 Consensus pattern (130 bp): CAGGGTTGAAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAACGAGGGTTGGAGTAT CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAAAC Found at i:8553285 original size:51 final size:51 Alignment explanation

Indices: 8553220--8553337 Score: 193 Period size: 51 Copynumber: 2.3 Consensus size: 51 8553210 GAAAATAACG * * * 8553220 GGGTTGGAGTATCCCCGATTGTGAAAAATTATTGTTTTGGAAATAAAA-TCA 1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACT-A 8553271 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTA 1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTA 8553322 GGGTTGGAGTATCCCC 1 GGGTTGGAGTATCCCC 8553338 TCAAAAATAA Statistics Matches: 63, Mismatches: 3, Indels: 2 0.93 0.04 0.03 Matches are distributed among these distances: 51 62 0.98 52 1 0.02 ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31 Consensus pattern (51 bp): GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTA Found at i:8553354 original size:79 final size:79 Alignment explanation

Indices: 8553271--8553494 Score: 319 Period size: 78 Copynumber: 2.8 Consensus size: 79 8553261 AATAAAATCA 8553271 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTAGGGTTGGAGTATCC 1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTAGGGTTGGAGTATCC 8553336 CCTCAAAAATAACG 66 CCTCAAAAATAACG * * * * * 8553350 GGGTTGGAGTATCCCCAATTGTG-AAAACTAGTGTTTTAGGAATAAAA-TCGAGGTTGGAGTATC 1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTAG-GGTTGGAGTATC * 8553413 CCCTCAGAAATAACG 65 CCCTCAAAAATAACG * * ** 8553428 GGATTGGAGTATCCCCGATTATGAAAAATT-GATGTTTTGGAAATAAAACCGGGGTTGGAGTATC 1 GGGTTGGAGTATCCCCGATTATGAAAAATTAG-TGTTTTAGAAATAAAACTAGGGTTGGAGTATC 8553492 CCC 65 CCC 8553495 GAGATGAAAA Statistics Matches: 127, Mismatches: 14, Indels: 8 0.85 0.09 0.05 Matches are distributed among these distances: 77 2 0.02 78 69 0.54 79 55 0.43 80 1 0.01 ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28 Consensus pattern (79 bp): GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTAGGGTTGGAGTATCC CCTCAAAAATAACG Found at i:8555810 original size:20 final size:19 Alignment explanation

Indices: 8555785--8555858 Score: 94 Period size: 20 Copynumber: 3.7 Consensus size: 19 8555775 AAAATGCCTG * 8555785 AATGTATCGATACATTGTAA 1 AATGTATCGATACAATG-AA * 8555805 AATGTATCGATACAATGAGT 1 AATGTATCGATACAATGA-A * 8555825 AATGTATCGATATAATGCAA 1 AATGTATCGATACAATG-AA 8555845 AATGTATCGATACA 1 AATGTATCGATACA 8555859 TCTGGGTAAA Statistics Matches: 47, Mismatches: 5, Indels: 4 0.84 0.09 0.07 Matches are distributed among these distances: 19 1 0.02 20 45 0.96 21 1 0.02 ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31 Consensus pattern (19 bp): AATGTATCGATACAATGAA Found at i:8555921 original size:13 final size:13 Alignment explanation

Indices: 8555874--8555903 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 8555864 GTAAACCCAG * 8555874 AATGTATTGATAC 1 AATGTATCGATAC 8555887 AATGTATCGATAC 1 AATGTATCGATAC 8555900 AATG 1 AATG 8555904 AACAATGTAT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33 Consensus pattern (13 bp): AATGTATCGATAC Found at i:8556763 original size:31 final size:33 Alignment explanation

Indices: 8556728--8556806 Score: 101 Period size: 33 Copynumber: 2.5 Consensus size: 33 8556718 CCTTTTCAAG * * * * 8556728 TTTCATCAAATTC-TCATC-AAATCTCTTTGTT 1 TTTCATCAAATTCATCAACAAAAACACTTTCTT 8556759 TTTCATCAAATTCATCAACAAAAACACTTTCTT 1 TTTCATCAAATTCATCAACAAAAACACTTTCTT 8556792 TTTCATCAAA-TCATC 1 TTTCATCAAATTCATC 8556807 CATCCAAAAC Statistics Matches: 42, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 31 13 0.31 32 9 0.21 33 20 0.48 ACGTcount: A:0.33, C:0.24, G:0.01, T:0.42 Consensus pattern (33 bp): TTTCATCAAATTCATCAACAAAAACACTTTCTT Found at i:8559099 original size:13 final size:13 Alignment explanation

Indices: 8559081--8559105 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 8559071 ATATTGCTTA 8559081 GTATCGATACATT 1 GTATCGATACATT 8559094 GTATCGATACAT 1 GTATCGATACAT 8559106 GTTCTTTGTA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): GTATCGATACATT Found at i:8559122 original size:32 final size:33 Alignment explanation

Indices: 8559062--8559123 Score: 99 Period size: 32 Copynumber: 1.9 Consensus size: 33 8559052 CACCCAAATA 8559062 TATCGATACATATTGCTTAGTATCGATACATTG 1 TATCGATACATATTGCTTAGTATCGATACATTG * * 8559095 TATCGATACATGTT-CTTTGTATCGATACA 1 TATCGATACATATTGCTTAGTATCGATACA 8559124 CCATAAAATA Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 32 14 0.52 33 13 0.48 ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40 Consensus pattern (33 bp): TATCGATACATATTGCTTAGTATCGATACATTG Found at i:8559237 original size:52 final size:52 Alignment explanation

Indices: 8559171--8559273 Score: 163 Period size: 52 Copynumber: 2.0 Consensus size: 52 8559161 ACCCTAAGTG * 8559171 AATTGTATCGATACATGATAAATTGTATCGATACATTGAG-CCTAACGGCTAT 1 AATTGTATCGATACATGATAAATTATATCGATACATTGAGTCC-AACGGCTAT * * 8559223 AATTGTATCGATACATTATGAATTATATCGATACATTGAGTCCAACGGCTA 1 AATTGTATCGATACATGATAAATTATATCGATACATTGAGTCCAACGGCTA 8559274 GAATATCAAA Statistics Matches: 47, Mismatches: 3, Indels: 2 0.90 0.06 0.04 Matches are distributed among these distances: 52 45 0.96 53 2 0.04 ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33 Consensus pattern (52 bp): AATTGTATCGATACATGATAAATTATATCGATACATTGAGTCCAACGGCTAT Found at i:8559739 original size:35 final size:34 Alignment explanation

Indices: 8559688--8559753 Score: 105 Period size: 35 Copynumber: 1.9 Consensus size: 34 8559678 GAAGTGATTG * 8559688 AGAGTTTCTATCTTAGCCTTTACAAAAGATAGGGA 1 AGAGGTTCTATCTTAGCCTTT-CAAAAGATAGGGA * 8559723 AGAGGTTCTATCTTAGCCTTTGAAAAGATAG 1 AGAGGTTCTATCTTAGCCTTTCAAAAGATAG 8559754 TGTTGTAAGG Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 34 9 0.31 35 20 0.69 ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32 Consensus pattern (34 bp): AGAGGTTCTATCTTAGCCTTTCAAAAGATAGGGA Found at i:8561070 original size:40 final size:40 Alignment explanation

Indices: 8561015--8561096 Score: 146 Period size: 40 Copynumber: 2.0 Consensus size: 40 8561005 ATTTAATCTT 8561015 ATATCTCATTTAACTTTGGTATGTCCAACTAACTAAGAAA 1 ATATCTCATTTAACTTTGGTATGTCCAACTAACTAAGAAA * * 8561055 ATATCTCATTTAACTTTGGTATTTCTAACTAACTAAGAAA 1 ATATCTCATTTAACTTTGGTATGTCCAACTAACTAAGAAA 8561095 AT 1 AT 8561097 TGACTGATGC Statistics Matches: 40, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 40 40 1.00 ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38 Consensus pattern (40 bp): ATATCTCATTTAACTTTGGTATGTCCAACTAACTAAGAAA Found at i:8561762 original size:112 final size:112 Alignment explanation

Indices: 8561521--8561741 Score: 370 Period size: 112 Copynumber: 2.0 Consensus size: 112 8561511 ATTTAATTAA ** 8561521 TAATATATAAACATCTATCAAATAGCTCAATCTCTATTTTATCAGGAAAAATTTTGAAAAATTGT 1 TAATATATAAACATCTATCAAATAGCTCAATCTCTATTTTATCAGGAAAAATTTTGAAAAATAAT * * 8561586 AGTTTTACTTTTAAGTTTAAAAAGAAAAATAAAACAAATTAACACAT 66 AATTTTACTTTAAAGTTTAAAAAGAAAAATAAAACAAATTAACACAT * * * 8561633 TAATATATAAACATCTATCAAATAGCTCAATTTCTATTTTATCAGGCAAAATTTTGAAAAGTAAT 1 TAATATATAAACATCTATCAAATAGCTCAATCTCTATTTTATCAGGAAAAATTTTGAAAAATAAT * 8561698 AATTTTACTTTAAAGTTTAAAAAGAAAAATAAGACAAATTAACA 66 AATTTTACTTTAAAGTTTAAAAAGAAAAATAAAACAAATTAACA 8561742 TGTTAACTTA Statistics Matches: 101, Mismatches: 8, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 112 101 1.00 ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34 Consensus pattern (112 bp): TAATATATAAACATCTATCAAATAGCTCAATCTCTATTTTATCAGGAAAAATTTTGAAAAATAAT AATTTTACTTTAAAGTTTAAAAAGAAAAATAAAACAAATTAACACAT Found at i:8562005 original size:2 final size:2 Alignment explanation

Indices: 8561998--8562033 Score: 54 Period size: 2 Copynumber: 18.0 Consensus size: 2 8561988 CATAAAATAG * * 8561998 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AG AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 8562034 TTATGATCAT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44 Consensus pattern (2 bp): AT Found at i:8565584 original size:28 final size:28 Alignment explanation

Indices: 8565553--8565608 Score: 103 Period size: 28 Copynumber: 2.0 Consensus size: 28 8565543 ATTTATGCAG 8565553 AAAATTTAAATCAAACCCATGATACAGT 1 AAAATTTAAATCAAACCCATGATACAGT * 8565581 AAAATTTAAATCAAACCCATGTTACAGT 1 AAAATTTAAATCAAACCCATGATACAGT 8565609 TTTAGGAATG Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 28 27 1.00 ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27 Consensus pattern (28 bp): AAAATTTAAATCAAACCCATGATACAGT Found at i:8568428 original size:16 final size:15 Alignment explanation

Indices: 8568403--8568432 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 8568393 TTGGTCATGA 8568403 TAAAAAATAAATAAG 1 TAAAAAATAAATAAG 8568418 TAAATAAATAAATAA 1 TAAA-AAATAAATAA 8568433 AGGTGAATCA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 4 0.29 16 10 0.71 ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23 Consensus pattern (15 bp): TAAAAAATAAATAAG Found at i:8570272 original size:22 final size:22 Alignment explanation

Indices: 8570244--8570299 Score: 94 Period size: 22 Copynumber: 2.5 Consensus size: 22 8570234 AGCCACGATC * * 8570244 CCACATCTAAACCCTTAATAGT 1 CCACATCTAAACCCTCAACAGT 8570266 CCACATCTAAACCCTCAACAGT 1 CCACATCTAAACCCTCAACAGT 8570288 CCACATCTAAAC 1 CCACATCTAAAC 8570300 ACATAACCAA Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 22 32 1.00 ACGTcount: A:0.38, C:0.38, G:0.04, T:0.21 Consensus pattern (22 bp): CCACATCTAAACCCTCAACAGT Found at i:8571194 original size:33 final size:33 Alignment explanation

Indices: 8571156--8571221 Score: 114 Period size: 33 Copynumber: 2.0 Consensus size: 33 8571146 AATTAAAAAC * * 8571156 CTAAAGTAGCCCTACAAATACAATTGGAAATGG 1 CTAAAGTAGCCATACAAATACAACTGGAAATGG 8571189 CTAAAGTAGCCATACAAATACAACTGGAAATGG 1 CTAAAGTAGCCATACAAATACAACTGGAAATGG 8571222 TTAGATGTTA Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 33 31 1.00 ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20 Consensus pattern (33 bp): CTAAAGTAGCCATACAAATACAACTGGAAATGG Found at i:8572254 original size:13 final size:13 Alignment explanation

Indices: 8572217--8572254 Score: 58 Period size: 13 Copynumber: 2.9 Consensus size: 13 8572207 AACTCACTCA * 8572217 GTATCGATACAGT 1 GTATCGATACATT 8572230 GTATCGATACATT 1 GTATCGATACATT * 8572243 GTATCTATACAT 1 GTATCGATACAT 8572255 AGTGAAATGT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 13 23 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37 Consensus pattern (13 bp): GTATCGATACATT Found at i:8573837 original size:3 final size:3 Alignment explanation

Indices: 8573829--8573871 Score: 86 Period size: 3 Copynumber: 14.3 Consensus size: 3 8573819 TTAACCATCA 8573829 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A 1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A 8573872 AGTTGACTCG Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 40 1.00 ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33 Consensus pattern (3 bp): ATG Found at i:8577336 original size:32 final size:32 Alignment explanation

Indices: 8577295--8577375 Score: 126 Period size: 32 Copynumber: 2.5 Consensus size: 32 8577285 TTTCAACAAT * * 8577295 TTGTATCGATACAGTGTATCGATGCAGAAGTG 1 TTGTATCGATACAATGTATCGATACAGAAGTG * * 8577327 TTGTATCGATACAATGTATCGATACATAAGTT 1 TTGTATCGATACAATGTATCGATACAGAAGTG 8577359 TTGTATCGATACAATGT 1 TTGTATCGATACAATGT 8577376 GTCGCTACGA Statistics Matches: 45, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 32 45 1.00 ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36 Consensus pattern (32 bp): TTGTATCGATACAATGTATCGATACAGAAGTG Found at i:8577346 original size:13 final size:13 Alignment explanation

Indices: 8577328--8577352 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 8577318 GCAGAAGTGT 8577328 TGTATCGATACAA 1 TGTATCGATACAA 8577341 TGTATCGATACA 1 TGTATCGATACA 8577353 TAAGTTTTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:8577444 original size:13 final size:13 Alignment explanation

Indices: 8577426--8577450 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 8577416 TACTCAAATG 8577426 TATCGATACATTA 1 TATCGATACATTA 8577439 TATCGATACATT 1 TATCGATACATT 8577451 GATCTTTTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40 Consensus pattern (13 bp): TATCGATACATTA Found at i:8589494 original size:20 final size:21 Alignment explanation

Indices: 8589458--8589497 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 8589448 ATATAAATGT 8589458 TTTTCAAGTATAAAAATAATA 1 TTTTCAAGTATAAAAATAATA 8589479 TTTTCAAGTA-AAAAATAAT 1 TTTTCAAGTATAAAAATAAT 8589498 CCAAAATAGC Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 9 0.47 21 10 0.53 ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38 Consensus pattern (21 bp): TTTTCAAGTATAAAAATAATA Found at i:8589616 original size:20 final size:19 Alignment explanation

Indices: 8589593--8589647 Score: 83 Period size: 19 Copynumber: 2.8 Consensus size: 19 8589583 CACACCCAGA * 8589593 TGTATTGATACATATTACTT 1 TGTATCGATACATATT-CTT 8589613 TGTATCGATACATATTCTT 1 TGTATCGATACATATTCTT * 8589632 GGTATCGATACATATT 1 TGTATCGATACATATT 8589648 GAATTGTGTC Statistics Matches: 33, Mismatches: 2, Indels: 1 0.92 0.06 0.03 Matches are distributed among these distances: 19 18 0.55 20 15 0.45 ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45 Consensus pattern (19 bp): TGTATCGATACATATTCTT Found at i:8589638 original size:19 final size:20 Alignment explanation

Indices: 8589594--8589665 Score: 85 Period size: 20 Copynumber: 3.6 Consensus size: 20 8589584 ACACCCAGAT * * 8589594 GTATTGATACATATTACTTT 1 GTATCGATACATATTACTTG 8589614 GTATCGATACATATT-CTTG 1 GTATCGATACATATTACTTG * 8589633 GTATCGATACATATTGAATT- 1 GTATCGATACATATT-ACTTG * 8589653 GTGTCGATACATA 1 GTATCGATACATA 8589666 AAACTAGCAG Statistics Matches: 46, Mismatches: 4, Indels: 4 0.85 0.07 0.07 Matches are distributed among these distances: 19 18 0.39 20 26 0.57 21 2 0.04 ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42 Consensus pattern (20 bp): GTATCGATACATATTACTTG Found at i:8594692 original size:79 final size:78 Alignment explanation

Indices: 8594592--8594839 Score: 259 Period size: 80 Copynumber: 3.1 Consensus size: 78 8594582 AATAACGGGG * * * * * * 8594592 TTGGAGTATCCCCTT-GAAAATAACGGGTTTGGAGTATCCCCGATTGTGAAAAATCGATGATTTC 1 TTGGAGTAT-CCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAATGTAAAAAATTGATGTTTTA 8594656 GAAATAAAATCGAGA 65 GAAATAAAATCG-GA * * * * * * 8594671 TTGGAGTATCCCTTCGGAAATAACGGGGTTAGAGTATCTCTGACTATAAAAAAATTGATGTTTTA 1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAATGT-AAAAAATTGATGTTTTA * * 8594736 GAAATAAAACCGGGG 65 GAAATAAAATC-GGA * * * 8594751 TTGGAGTATCTCC-ACGAAAATAAGGGGGTTGGAGTATCCCC-AATGAAAAAAATTGATGTTTTA 1 TTGGAGTATC-CCTTCGAAAATAACGGGGTTGGAGTATCCCCGAATGTAAAAAATTGATGTTTTA 8594814 GAAATAAAATCGGA 65 GAAATAAAATCGGA * 8594828 GTTAGAGTATCC 1 -TTGGAGTATCC 8594840 TCGATTATGG Statistics Matches: 139, Mismatches: 25, Indels: 12 0.79 0.14 0.07 Matches are distributed among these distances: 77 3 0.02 78 41 0.29 79 36 0.26 80 56 0.40 81 3 0.02 ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28 Consensus pattern (78 bp): TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAATGTAAAAAATTGATGTTTTAG AAATAAAATCGGA Found at i:8594862 original size:51 final size:51 Alignment explanation

Indices: 8594782--8594942 Score: 182 Period size: 51 Copynumber: 3.2 Consensus size: 51 8594772 AAGGGGGTTG * * * 8594782 GAGTATCCCCAATGAA-AAAAATTGATGTTTTAGAAATAAAATCGGAGTTA 1 GAGTATCCCCGATTAAGAAAAATGGATGTTTTAGAAATAAAATCGGAGTTA * * * * * 8594832 GAGTATCCTCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGAGTTG 1 GAGTATCCCCGATTAAGAAAAATGGATGTTTTAGAAATAAAATCGGAGTTA * * * * * 8594883 GAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACCGG-GATTG 1 GAGTATCCCCGATTAAGAAAAATGGATGTTTTAGAAATAAAATCGGAG-TTA 8594934 GAGTATCCC 1 GAGTATCCC 8594943 TAAGATGAAA Statistics Matches: 93, Mismatches: 16, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 50 13 0.14 51 80 0.86 ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29 Consensus pattern (51 bp): GAGTATCCCCGATTAAGAAAAATGGATGTTTTAGAAATAAAATCGGAGTTA Found at i:8597248 original size:20 final size:19 Alignment explanation

Indices: 8597223--8597337 Score: 158 Period size: 20 Copynumber: 5.8 Consensus size: 19 8597213 AAAATGCCTG * 8597223 AATGTATCGATACATTGTAA 1 AATGTATCGATACAATG-AA * 8597243 AATGTATCGATACAATGAGC 1 AATGTATCGATACAATGA-A 8597263 AATGTATCGATACAATGCAA 1 AATGTATCGATACAATG-AA * 8597283 AATGTATCGATACAATGAGC 1 AATGTATCGATACAATGA-A 8597303 AATGTATCGATACAATGAA 1 AATGTATCGATACAATGAA 8597322 CAATGTATCGATACAA 1 -AATGTATCGATACAA 8597338 ATTATGAAAA Statistics Matches: 86, Mismatches: 5, Indels: 8 0.87 0.05 0.08 Matches are distributed among these distances: 19 2 0.02 20 83 0.97 21 1 0.01 ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27 Consensus pattern (19 bp): AATGTATCGATACAATGAA Found at i:8597285 original size:40 final size:39 Alignment explanation

Indices: 8597223--8597337 Score: 194 Period size: 40 Copynumber: 2.9 Consensus size: 39 8597213 AAAATGCCTG * 8597223 AATGTATCGATACATTGTAAAATGTATCGATACAATGAGC 1 AATGTATCGATACAATG-AAAATGTATCGATACAATGAGC 8597263 AATGTATCGATACAATGCAAAATGTATCGATACAATGAGC 1 AATGTATCGATACAATG-AAAATGTATCGATACAATGAGC 8597303 AATGTATCGATACAATGAACAATGTATCGATACAA 1 AATGTATCGATACAATGAA-AATGTATCGATACAA 8597338 ATTATGAAAA Statistics Matches: 72, Mismatches: 2, Indels: 2 0.95 0.03 0.03 Matches are distributed among these distances: 39 2 0.03 40 70 0.97 ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27 Consensus pattern (39 bp): AATGTATCGATACAATGAAAATGTATCGATACAATGAGC Found at i:8597316 original size:60 final size:60 Alignment explanation

Indices: 8597223--8597337 Score: 187 Period size: 60 Copynumber: 1.9 Consensus size: 60 8597213 AAAATGCCTG * * 8597223 AATGTATCGATACATTGTAAAATGTATCGATACAATGAGCAATGTATCGATACAATGCAA 1 AATGTATCGATACAATGTAAAATGTATCGATACAATGAACAATGTATCGATACAATGCAA * 8597283 AATGTATCGATACAATG-AGCAATGTATCGATACAATGAACAATGTATCGATACAA 1 AATGTATCGATACAATGTA-AAATGTATCGATACAATGAACAATGTATCGATACAA 8597338 ATTATGAAAA Statistics Matches: 51, Mismatches: 3, Indels: 2 0.91 0.05 0.04 Matches are distributed among these distances: 59 1 0.02 60 50 0.98 ACGTcount: A:0.43, C:0.14, G:0.17, T:0.27 Consensus pattern (60 bp): AATGTATCGATACAATGTAAAATGTATCGATACAATGAACAATGTATCGATACAATGCAA Found at i:8601178 original size:13 final size:13 Alignment explanation

Indices: 8601160--8601185 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 8601150 AATTTTTTTG 8601160 TGTATCGATACAT 1 TGTATCGATACAT 8601173 TGTATCGATACAT 1 TGTATCGATACAT 8601186 ACTTGGTGTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8603354 original size:32 final size:32 Alignment explanation

Indices: 8603318--8603384 Score: 134 Period size: 32 Copynumber: 2.1 Consensus size: 32 8603308 CTGCCTAGGG 8603318 GGTTGCTGGTTCAGGCTTTTTGCCGAACAGGT 1 GGTTGCTGGTTCAGGCTTTTTGCCGAACAGGT 8603350 GGTTGCTGGTTCAGGCTTTTTGCCGAACAGGT 1 GGTTGCTGGTTCAGGCTTTTTGCCGAACAGGT 8603382 GGT 1 GGT 8603385 GGTCACTACT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 35 1.00 ACGTcount: A:0.12, C:0.18, G:0.36, T:0.34 Consensus pattern (32 bp): GGTTGCTGGTTCAGGCTTTTTGCCGAACAGGT Found at i:8603793 original size:13 final size:13 Alignment explanation

Indices: 8603775--8603800 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 8603765 ATAATCCCCC 8603775 TGTATCGATACAA 1 TGTATCGATACAA 8603788 TGTATCGATACAA 1 TGTATCGATACAA 8603801 ACACAAATGT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): TGTATCGATACAA Found at i:8607685 original size:22 final size:20 Alignment explanation

Indices: 8607636--8607687 Score: 59 Period size: 21 Copynumber: 2.5 Consensus size: 20 8607626 ATCATGCAAG 8607636 TTTTTATTTTTCTTAGCTAAT 1 TTTTTA-TTTTCTTAGCTAAT ** 8607657 TCATTATTTTCATTAGCTAAAT 1 TTTTTATTTTC-TTAGCT-AAT 8607679 TTTTTATTT 1 TTTTTATTT 8607688 CAATTTGCAA Statistics Matches: 25, Mismatches: 4, Indels: 3 0.78 0.12 0.09 Matches are distributed among these distances: 20 5 0.20 21 10 0.40 22 10 0.40 ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63 Consensus pattern (20 bp): TTTTTATTTTCTTAGCTAAT Found at i:8613547 original size:25 final size:24 Alignment explanation

Indices: 8613500--8613547 Score: 60 Period size: 25 Copynumber: 2.0 Consensus size: 24 8613490 ATTCTTATAA * * 8613500 TTTTAAAAATATAATTTTATTATT 1 TTTTAAAAATAAAATTATATTATT * 8613524 TTTTAAAAGATAAAATTATCTTAT 1 TTTTAAAA-ATAAAATTATATTAT 8613548 CTTTAACCAA Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 24 8 0.40 25 12 0.60 ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52 Consensus pattern (24 bp): TTTTAAAAATAAAATTATATTATT Found at i:8614664 original size:20 final size:20 Alignment explanation

Indices: 8614618--8614674 Score: 73 Period size: 20 Copynumber: 3.0 Consensus size: 20 8614608 TTATATCGAT 8614618 ACAA-TGTATCGATACAT-G 1 ACAATTGTATCGATACATGG *** 8614636 TTTATTGTATCGATACATGG 1 ACAATTGTATCGATACATGG 8614656 ACAATTGTATCGATACATG 1 ACAATTGTATCGATACATG 8614675 AAACTAGCAG Statistics Matches: 31, Mismatches: 6, Indels: 2 0.79 0.15 0.05 Matches are distributed among these distances: 18 1 0.03 19 13 0.42 20 17 0.55 ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35 Consensus pattern (20 bp): ACAATTGTATCGATACATGG Found at i:8614728 original size:20 final size:20 Alignment explanation

Indices: 8614703--8614756 Score: 74 Period size: 20 Copynumber: 2.7 Consensus size: 20 8614693 CTATCACTAT * 8614703 TTGTATCGATACATGGT-ACA 1 TTGTATCGATACATGATGA-A * 8614723 TTGTATAGATACATGATGAA 1 TTGTATCGATACATGATGAA 8614743 TTGTATCGATACAT 1 TTGTATCGATACAT 8614757 TGCTTCTAAC Statistics Matches: 30, Mismatches: 3, Indels: 2 0.86 0.09 0.06 Matches are distributed among these distances: 20 29 0.97 21 1 0.03 ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37 Consensus pattern (20 bp): TTGTATCGATACATGATGAA Found at i:8616338 original size:3 final size:3 Alignment explanation

Indices: 8616330--8616365 Score: 54 Period size: 3 Copynumber: 12.0 Consensus size: 3 8616320 TCAACCATCA * * 8616330 ATG ATG ATG AAG ATG ATA ATG ATG ATG ATG ATG ATG 1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG 8616366 GTGACTCAGA Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 3 29 1.00 ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31 Consensus pattern (3 bp): ATG Found at i:8621089 original size:20 final size:21 Alignment explanation

Indices: 8621053--8621092 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 8621043 TTACAAATTT * 8621053 CTTCATTTTTACTTCAAAATA 1 CTTCATTTTTACATCAAAATA 8621074 CTTCATTTTT-CATCAAAAT 1 CTTCATTTTTACATCAAAAT 8621093 CACTAACAAA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 8 0.44 21 10 0.56 ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47 Consensus pattern (21 bp): CTTCATTTTTACATCAAAATA Found at i:8623462 original size:13 final size:13 Alignment explanation

Indices: 8623444--8623470 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 8623434 ACATTATGCT 8623444 TTGTATCGATACA 1 TTGTATCGATACA 8623457 TTGTATCGATACA 1 TTGTATCGATACA 8623470 T 1 T 8623471 GGACAATTGT 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:0.30, C:0.15, G:0.15, T:0.41 Consensus pattern (13 bp): TTGTATCGATACA Found at i:8623545 original size:20 final size:20 Alignment explanation

Indices: 8623520--8623573 Score: 74 Period size: 20 Copynumber: 2.7 Consensus size: 20 8623510 CTATCACTAT * 8623520 TTGTATCGATACATGGT-AGA 1 TTGTATCGATACATGATGA-A * 8623540 TTGTATAGATACATGATGAA 1 TTGTATCGATACATGATGAA 8623560 TTGTATCGATACAT 1 TTGTATCGATACAT 8623574 TGCTTCTAAT Statistics Matches: 30, Mismatches: 3, Indels: 2 0.86 0.09 0.06 Matches are distributed among these distances: 20 29 0.97 21 1 0.03 ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37 Consensus pattern (20 bp): TTGTATCGATACATGATGAA Found at i:8625264 original size:7 final size:6 Alignment explanation

Indices: 8625227--8625278 Score: 52 Period size: 6 Copynumber: 8.7 Consensus size: 6 8625217 TTTATGATTA * * * * 8625227 TTAATT TTTATT TTAATT TT-CTT TTAATT TTAAATT TTTATT TTATTT 1 TTAATT TTAATT TTAATT TTAATT TTAATT TT-AATT TTAATT TTAATT 8625275 TTAA 1 TTAA 8625279 ACTAGTTTCA Statistics Matches: 36, Mismatches: 8, Indels: 4 0.75 0.17 0.08 Matches are distributed among these distances: 5 4 0.11 6 26 0.72 7 6 0.17 ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71 Consensus pattern (6 bp): TTAATT Found at i:8625276 original size:25 final size:25 Alignment explanation

Indices: 8625191--8625278 Score: 63 Period size: 24 Copynumber: 3.5 Consensus size: 25 8625181 ATCAAGATTT * * * * 8625191 TTTTATTATTTTATTTCAAAATTTTG 1 TTTTATT-TTTAATTTTAAATTTTTA * * * 8625217 TTTATGATTATTAATTTT-TATTTTAA 1 TTT-T-ATTTTTAATTTTAAATTTTTA * 8625243 TTTT-CTTTTAATTTTAAATTTTTA 1 TTTTATTTTTAATTTTAAATTTTTA 8625267 TTTTATTTTTAA 1 TTTTATTTTTAA 8625279 ACTAGTTTCA Statistics Matches: 46, Mismatches: 12, Indels: 9 0.69 0.18 0.13 Matches are distributed among these distances: 23 9 0.20 24 10 0.22 25 7 0.15 26 10 0.22 27 7 0.15 28 3 0.07 ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68 Consensus pattern (25 bp): TTTTATTTTTAATTTTAAATTTTTA Found at i:8625277 original size:11 final size:11 Alignment explanation

Indices: 8625227--8625275 Score: 53 Period size: 11 Copynumber: 4.2 Consensus size: 11 8625217 TTTATGATTA 8625227 TTAATTTTTATT 1 TTAA-TTTTATT * 8625239 TTAATTTTCTT 1 TTAATTTTATT 8625250 TTAATTTTAAATT 1 TTAATTTT--ATT * 8625263 TTTATTTTATT 1 TTAATTTTATT 8625274 TT 1 TT 8625276 TAAACTAGTT Statistics Matches: 32, Mismatches: 3, Indels: 5 0.80 0.08 0.12 Matches are distributed among these distances: 11 19 0.59 12 4 0.12 13 9 0.28 ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73 Consensus pattern (11 bp): TTAATTTTATT Found at i:8627385 original size:152 final size:151 Alignment explanation

Indices: 8627017--8627386 Score: 372 Period size: 153 Copynumber: 2.4 Consensus size: 151 8627007 TATTATTTTT * * 8627017 CATGTCCTTTAGGTTAGTAGGATA-TTTCATGTTGAAGGTATACCTTAGAGGCATTTTAGTAATT 1 CATGTCCTTAAGGTTACTAGGATATTTTCATGTTGAAGGTATACCTTAGAGGCATTTT-GTAATT * * * * 8627081 TTCCCTAGAACCGAGTCTTATGTAGTCATTGGGATGCATATATGTCAAAGGTGTACATTTAGGAT 65 TTCCCTAGAACCGAGTCTTATGTAATCATCGAGATGCATATATGTCAAAGGTGCACATTTAGGAT * * * 8627146 AGGTTTATCCTTTTATCATTTT 130 AGGTTCATCCTTTTATCACTTC * * * * * * * * * * 8627168 CATGTCATTGAGGGT-CATCAAGATATTTTGATGTTGAAGGAATATCATAGTGGCATATTGATAA 1 CATGTCCTTAAGGTTAC-T-AGGATATTTTCATGTTGAAGGTATACCTTAGAGGCATTTTG-TAA * ** * * * * 8627232 TTTT-TCTAGAATTGAGT-TTGATGTAATCGTCGAGATGCTTTTATGTCAAAGGTGCGCATTTAG 63 TTTTCCCTAGAACCGAGTCTT-ATGTAATCATCGAGATGCATATATGTCAAAGGTGCACATTTAG 8627295 GATAGGTTCATCCTTTCATATC-CTTC 127 GATAGGTTCATCCTTT--TATCACTTC * * * 8627321 CATGTCCGTTAAGGTTACTAGGATATTTTCATGTAGAAGGTATACCTTAGGGGTATTTTGTAATT 1 CATGTCC-TTAAGGTTACTAGGATATTTTCATGTTGAAGGTATACCTTAGAGGCATTTTGTAATT 8627386 T 65 T 8627387 CTTTATAATC Statistics Matches: 173, Mismatches: 37, Indels: 17 0.76 0.16 0.07 Matches are distributed among these distances: 151 15 0.09 152 72 0.42 153 74 0.43 154 11 0.06 155 1 0.01 ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40 Consensus pattern (151 bp): CATGTCCTTAAGGTTACTAGGATATTTTCATGTTGAAGGTATACCTTAGAGGCATTTTGTAATTT TCCCTAGAACCGAGTCTTATGTAATCATCGAGATGCATATATGTCAAAGGTGCACATTTAGGATA GGTTCATCCTTTTATCACTTC Found at i:8628908 original size:2 final size:2 Alignment explanation

Indices: 8628901--8628937 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 8628891 TTTTTAAATG 8628901 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 8628938 AAAGAGTTAG Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:8629818 original size:74 final size:74 Alignment explanation

Indices: 8629660--8629818 Score: 187 Period size: 74 Copynumber: 2.1 Consensus size: 74 8629650 TATTTTCTCT * * 8629660 AAATTAAATTAATATAACAAATCATACAAAATATATGATGAATTGAAATATAACACGAATATATA 1 AAATTAAAATAATATAACAAATCATACAAAATAAATGATGAATTGAAATATAACACGAATATATA ***** 8629725 AATTTTTCG 66 AATTAAAAA * * * * 8629734 AAATTGAAATACTATAACAAATTATGCAAAATAAATGATGAATTGAAATATAACAC-AA-ATATA 1 AAATTAAAATAATATAACAAATCATACAAAATAAATGATGAATTGAAATATAACACGAATATATA 8629797 ATATTAAAAA 66 A-ATTAAAAA 8629807 ATAATTAAAATA 1 A-AATTAAAATA 8629819 TGACATGAAA Statistics Matches: 71, Mismatches: 12, Indels: 4 0.82 0.14 0.05 Matches are distributed among these distances: 72 6 0.08 73 6 0.08 74 59 0.83 ACGTcount: A:0.57, C:0.07, G:0.06, T:0.30 Consensus pattern (74 bp): AAATTAAAATAATATAACAAATCATACAAAATAAATGATGAATTGAAATATAACACGAATATATA AATTAAAAA Found at i:8631726 original size:18 final size:18 Alignment explanation

Indices: 8631703--8631741 Score: 78 Period size: 18 Copynumber: 2.2 Consensus size: 18 8631693 CGCCAAACTC 8631703 ACACCTCTTTTTTCACAA 1 ACACCTCTTTTTTCACAA 8631721 ACACCTCTTTTTTCACAA 1 ACACCTCTTTTTTCACAA 8631739 ACA 1 ACA 8631742 AAACAGACTT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36 Consensus pattern (18 bp): ACACCTCTTTTTTCACAA Found at i:8633725 original size:12 final size:12 Alignment explanation

Indices: 8633702--8633938 Score: 92 Period size: 12 Copynumber: 21.2 Consensus size: 12 8633692 TTCCCTTACT 8633702 ATAATAATATTTA 1 ATAAT-ATATTTA 8633715 ATAATATATTTCA 1 ATAATATATTT-A * * * 8633728 AT-ATTTAATCTG 1 ATAATAT-ATTTA 8633740 AT-A-ATATTTA 1 ATAATATATTTA * 8633750 ATGATATATTTA 1 ATAATATATTTA * 8633762 ATAGTATA-TTA 1 ATAATATATTTA 8633773 A-ACATAT-TTTA 1 ATA-ATATATTTA * 8633784 ATATTATATTTA 1 ATAATATATTTA * 8633796 ATAATGTA-TTA 1 ATAATATATTTA 8633807 A-AAT-TATTTTA 1 ATAATATA-TTTA * 8633818 AAAATATTATTTA 1 ATAATA-TATTTA * 8633831 AT--TATATTAA 1 ATAATATATTTA * 8633841 AT-A-ATA-CTA 1 ATAATATATTTA * * 8633850 ATAACATATTAA 1 ATAATATATTTA 8633862 AT-A-ATATTTA 1 ATAATATATTTA 8633872 ATAATATA-TT- 1 ATAATATATTTA * 8633882 A-AATGT-TTTA 1 ATAATATATTTA * * 8633892 AAAATTTTATTTA 1 ATAA-TATATTTA 8633905 ATAATATA--T- 1 ATAATATATTTA 8633914 -TAA-ATATTTA 1 ATAATATATTTA * 8633924 ATAATATATTAA 1 ATAATATATTTA 8633936 ATA 1 ATA 8633939 TTTAATATAT Statistics Matches: 171, Mismatches: 24, Indels: 59 0.67 0.09 0.23 Matches are distributed among these distances: 7 3 0.02 8 3 0.02 9 12 0.07 10 31 0.18 11 38 0.22 12 59 0.35 13 23 0.13 14 2 0.01 ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47 Consensus pattern (12 bp): ATAATATATTTA Found at i:8633747 original size:15 final size:14 Alignment explanation

Indices: 8633727--8633763 Score: 51 Period size: 15 Copynumber: 2.7 Consensus size: 14 8633717 AATATATTTC 8633727 AATATTTAATCTGAT 1 AATATTTAAT-TGAT 8633742 AATATTTAA-TGAT 1 AATATTTAATTGAT 8633755 -ATATTTAAT 1 AATATTTAAT 8633764 AGTATATTAA Statistics Matches: 21, Mismatches: 0, Indels: 4 0.84 0.00 0.16 Matches are distributed among these distances: 12 8 0.38 13 4 0.19 15 9 0.43 ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49 Consensus pattern (14 bp): AATATTTAATTGAT Found at i:8633792 original size:34 final size:32 Alignment explanation

Indices: 8633746--8633841 Score: 97 Period size: 34 Copynumber: 2.8 Consensus size: 32 8633736 TCTGATAATA 8633746 TTTAATGATATATTTAATAGTATATTAAACA-TAT 1 TTTAAT-ATATATTTAATA-TATATTAAA-ATTAT * 8633780 TTTAATATTATATTTAATAATGTATTAAAATTAT 1 TTTAATA-TATATTTAAT-ATATATTAAAATTAT * 8633814 TTTAAAAATATTATTTAAT-TATATTAAA 1 TTT-AATATA-TATTTAATATATATTAAA 8633842 TAATACTAAT Statistics Matches: 54, Mismatches: 3, Indels: 11 0.79 0.04 0.16 Matches are distributed among these distances: 33 10 0.19 34 32 0.59 35 12 0.22 ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50 Consensus pattern (32 bp): TTTAATATATATTTAATATATATTAAAATTAT Found at i:8633880 original size:22 final size:22 Alignment explanation

Indices: 8633704--8633885 Score: 110 Period size: 22 Copynumber: 8.1 Consensus size: 22 8633694 CCCTTACTAT 8633704 AATAATATTTAATAATATATT- 1 AATAATATTTAATAATATATTA * * 8633725 --TCAATATTTAATCTGATAATATTT 1 AAT-AATATTTAA--TAAT-ATATTA * 8633749 AATGATATATTTAATAGTATATTA 1 AAT-A-ATATTTAATAATATATTA * * * 8633773 AA-CATATTTTAATATTATATTT 1 AATAATA-TTTAATAATATATTA * * 8633795 AATAATGTATTAA-AATTATTTTA 1 AATAATAT-TTAATAA-TATATTA * 8633818 AA-AATA-TTATTTAATTATATTA 1 AATAATATTTA-ATAA-TATATTA * * 8633840 AATAATA-CTAATAACATATTA 1 AATAATATTTAATAATATATTA 8633861 AATAATATTTAATAATATATTA 1 AATAATATTTAATAATATATTA 8633883 AAT 1 AAT 8633886 GTTTTAAAAA Statistics Matches: 124, Mismatches: 21, Indels: 31 0.70 0.12 0.18 Matches are distributed among these distances: 19 1 0.01 20 12 0.10 21 16 0.13 22 52 0.42 23 24 0.19 24 7 0.06 25 2 0.02 26 2 0.02 27 8 0.06 ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47 Consensus pattern (22 bp): AATAATATTTAATAATATATTA Found at i:8633906 original size:74 final size:75 Alignment explanation

Indices: 8633704--8633938 Score: 210 Period size: 74 Copynumber: 3.1 Consensus size: 75 8633694 CCCTTACTAT ** ** * * 8633704 AATAATATTTAATAATATATTTCAA-TA-TTTAATCTGATAATATTTAATGATATATTTAATAGT 1 AATAATATTTAATAATATATTAAAATTATTTTAA--AAATATTATTTAAT-ATATATTAAATA-T * * 8633767 ATATTAAACATATTTTA 62 CTAAT-AACATA--TTA * * 8633784 ATATTATATTTAATAATGTATTAAAATTATTTTAAAAATATTATTTAAT-TATATTAAATAATAC 1 A-ATAATATTTAATAATATATTAAAATTATTTTAAAAATATTATTTAATATATATTAAAT-AT-C 8633848 TAATAACATATTA 63 TAATAACATATTA * * * 8633861 AATAATATTTAATAATATATT-AAA-TGTTTTAAAAATTTTATTTAATAATATATTAAATATTTA 1 AATAATATTTAATAATATATTAAAATTATTTTAAAAATATTATTTAAT-ATATATTAAATATCTA * 8633924 ATAATATATTA 65 ATAACATATTA 8633935 AATA 1 AATA 8633939 TTTAATATAT Statistics Matches: 132, Mismatches: 16, Indels: 20 0.79 0.10 0.12 Matches are distributed among these distances: 74 36 0.27 75 5 0.04 76 28 0.21 77 4 0.03 79 16 0.12 80 5 0.04 81 31 0.23 82 2 0.02 83 5 0.04 ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47 Consensus pattern (75 bp): AATAATATTTAATAATATATTAAAATTATTTTAAAAATATTATTTAATATATATTAAATATCTAA TAACATATTA Found at i:8633953 original size:19 final size:19 Alignment explanation

Indices: 8633825--8633945 Score: 105 Period size: 19 Copynumber: 6.5 Consensus size: 19 8633815 TTAAAAATAT 8633825 TATTTAAT--TATATTAAA 1 TATTTAATAATATATTAAA * * 8633842 TAATACTAATAACATATTAAATAA 1 T-AT-TTAATAATATATT--A-AA 8633866 TATTTAATAATATATTAAA 1 TATTTAATAATATATTAAA * 8633885 TGTTTTAA-AA-AT-TT--- 1 T-ATTTAATAATATATTAAA 8633899 TATTTAATAATATATTAAA 1 TATTTAATAATATATTAAA 8633918 TATTTAATAATATATTAAA 1 TATTTAATAATATATTAAA 8633937 TATTTAATA 1 TATTTAATA 8633946 TATTATTAGA Statistics Matches: 84, Mismatches: 6, Indels: 26 0.72 0.05 0.22 Matches are distributed among these distances: 13 5 0.06 14 3 0.04 15 2 0.02 16 2 0.02 17 3 0.04 18 4 0.05 19 37 0.44 20 6 0.07 21 5 0.06 22 11 0.13 23 3 0.04 24 3 0.04 ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47 Consensus pattern (19 bp): TATTTAATAATATATTAAA Found at i:8641079 original size:15 final size:17 Alignment explanation

Indices: 8641048--8641080 Score: 52 Period size: 15 Copynumber: 2.1 Consensus size: 17 8641038 TCCTTTTATA 8641048 TAAATATATATATATGT 1 TAAATATATATATATGT 8641065 TAAATA-ATA-ATATGT 1 TAAATATATATATATGT 8641080 T 1 T 8641081 GGATAATATT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 15 7 0.44 16 3 0.19 17 6 0.38 ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45 Consensus pattern (17 bp): TAAATATATATATATGT Found at i:8641317 original size:2 final size:2 Alignment explanation

Indices: 8641310--8641348 Score: 71 Period size: 2 Copynumber: 20.0 Consensus size: 2 8641300 TACCTTCGAA 8641310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 8641349 TAAGCAAAGG Statistics Matches: 36, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 35 0.97 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:8641743 original size:2 final size:2 Alignment explanation

Indices: 8641736--8641762 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 8641726 CCTCAATTTC 8641736 CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT C 8641763 CCTTTCTCTT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:8643701 original size:16 final size:16 Alignment explanation

Indices: 8643678--8643738 Score: 68 Period size: 16 Copynumber: 3.8 Consensus size: 16 8643668 TTTATATTAG 8643678 TTTAGGTTCGAGCCTA 1 TTTAGGTTCGAGCCTA * * * 8643694 TTTGGGTTTGAGCTTA 1 TTTAGGTTCGAGCCTA ** 8643710 TTTAGGTTCGAGTTTA 1 TTTAGGTTCGAGCCTA * 8643726 TTCAGGTTCGAGC 1 TTTAGGTTCGAGC 8643739 ATTTTCAAGT Statistics Matches: 37, Mismatches: 8, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 16 37 1.00 ACGTcount: A:0.16, C:0.13, G:0.28, T:0.43 Consensus pattern (16 bp): TTTAGGTTCGAGCCTA Found at i:8643745 original size:16 final size:16 Alignment explanation

Indices: 8643698--8643768 Score: 58 Period size: 16 Copynumber: 4.4 Consensus size: 16 8643688 AGCCTATTTG * 8643698 GGTTTGAGCTTATTT-A 1 GGTTCGAGCTT-TTTCA 8643714 GGTTCGAG-TTTATTCA 1 GGTTCGAGCTTT-TTCA * 8643730 GGTTCGAGCATTTTCA 1 GGTTCGAGCTTTTTCA * 8643746 AGTTC-ATGCTTTTTCAA 1 GGTTCGA-GCTTTTTC-A 8643763 GGTTCG 1 GGTTCG 8643769 CTCCTTTTTA Statistics Matches: 44, Mismatches: 5, Indels: 10 0.75 0.08 0.17 Matches are distributed among these distances: 14 1 0.02 15 5 0.11 16 31 0.70 17 7 0.16 ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44 Consensus pattern (16 bp): GGTTCGAGCTTTTTCA Found at i:8643934 original size:14 final size:14 Alignment explanation

Indices: 8643912--8643959 Score: 51 Period size: 14 Copynumber: 3.3 Consensus size: 14 8643902 AAGTAAATTA 8643912 TTAAATTATTATTT 1 TTAAATTATTATTT * * 8643926 TTAAGTTATTTTTT 1 TTAAATTATTATTT * 8643940 TTATAATATGTTATTT 1 TTA-AAT-TATTATTT 8643956 TTAA 1 TTAA 8643960 TATATTCATT Statistics Matches: 27, Mismatches: 5, Indels: 3 0.77 0.14 0.09 Matches are distributed among these distances: 14 15 0.56 15 3 0.11 16 9 0.33 ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65 Consensus pattern (14 bp): TTAAATTATTATTT Found at i:8645141 original size:527 final size:532 Alignment explanation

Indices: 8644142--8645205 Score: 1471 Period size: 527 Copynumber: 2.0 Consensus size: 532 8644132 ATTTGTATTG * * * * 8644142 TATAATCTTTTTGCATTTGAAATTTTTAATTTTGTGCCACATTATATTTATATTCGTAACACTCG 1 TATAATCTTGTTGCATTTGAAATTTTTAATTTTGTACCACATTATATTTATATTCATAACACTCA * * * * * 8644207 ATTCAAATAGCTTAATCAAGTTTTTTTTATTTTTTATATATATTTTTAATATTTTAATATGAAAT 66 ACTCAAATAACTCAATCAAG-TCTTTTTATTTTATATATATATTTTTAATATTTTAATATGAAAT * 8644272 TATCTTTTTATCCTTAATATATATACACACTTAAAACCCAAAATTTAATTTTTTTCCTTTCGATA 130 TATCTTTTTATCCTTAATATATATACACACTTAAAACCCAAAATCTAATTTTTTTCCTTTCGATA * ** * * * 8644337 GTAGCAACTCTTATTTTCCTTAATATTAGTAAAAACCCAAAACCTAATTTTTCCTTTTGGTAGTG 195 GTAGCAACTCTTATTTTCCTTAACACCAGTAAAAACCCAAAACCTAATTTCTCCCTTTGGTAGCG * * * * * * * 8644402 TAATTCTTATTTTAGTGAAAATCTGAATTTACTTTGACATTTTCAGGCGATTATAACCTAAATTA 260 CAACTCTTAGTTTAGTGAAAATCTAAATTTACTTTGACATTTTAAGGCGATTACAACCAAAATTA * * * * * 8644467 TCTTTCAAATTTTCTTCCTCAATTATGACTATAGATGAAGGAAAACAAAAAGAGTTAAGTCACAT 325 TCTCTCAAATCTTCTTCCTCAATTACGACCATAGATGAAGGAAAACAAAAAGAGCTAAGTCACAT * * * * 8644532 CACAACTTTTAAGTTTGTCTCTAAAATTAAGCTGATAGCTATCATGTAATTTTTAAAGTGTAAAG 390 CACAACTTTTAAGTTTGTCTCCAAAATTAAACTGATAGCTATCATGCAACTTTTAAAGTGTAAAG 8644597 TATATTTGTGTGCTTCTTATACTTAAAGAAACTATAAAAAAATTTAACAGTCCCCACAGTTTTGT 455 TATATTTGTGTGCTTCTTATACTTAAAGAAACTATAAAAAAATTTAACAGTCCCCACAGTTTTGT * * 8644662 ATTTAGAATATGA 520 ATTTAAAATATAA * * 8644675 TATAATCTTGTTGCATTTGAAATTTTTAATTTTGTATCACATTATATTTATATTCATAATACTCA 1 TATAATCTTGTTGCATTTGAAATTTTTAATTTTGTACCACATTATATTTATATTCATAACACTCA * * * 8644740 ACTCAAGTAACTCAATCGAG-CTTTTTA-TTTAT-TATATA-TTTTAATATTTTAATATTAAATT 66 ACTCAAATAACTCAATCAAGTCTTTTTATTTTATATATATATTTTTAATATTTTAATATGAAATT * 8644801 AT-TATTTTATTCTTAATATATATACACACTTAAAACCCAAAATCTAATTTTTTTCCCTTT-GAT 131 ATCT-TTTTATCCTTAATATATATACACACTTAAAACCCAAAATCTAATTTTTTT-CCTTTCGAT * * * 8644864 AGTCGCAACTCTTATTTTCCTTAGCACCAGTAAAAACCC-AAATCTAATTTCTCCCTTTGGTAGC 194 AGTAGCAACTCTTATTTTCCTTAACACCAGTAAAAACCCAAAACCTAATTTCTCCCTTTGGTAGC * 8644928 GCAACTCTTAGTTTAGT-AAAATCTCAAATTTACTTTGACATTTTAAGGCGATTACAATCAAAAT 259 GCAACTCTTAGTTTAGTGAAAATCT-AAATTTACTTTGACATTTTAAGGCGATTACAACCAAAAT * * * * * 8644992 TATCTCTCAAGTCTTCTTCCTTAATTACGGCCATAG-TCGAAGGAAAAGAAAATGAGCTAAGTCA 323 TATCTCTCAAATCTTCTTCCTCAATTACGACCATAGAT-GAAGGAAAACAAAAAGAGCTAAGTCA * * * * * * 8645056 CATCACGATTTTTAGGTTTGTTTCCAAAATTAAACTGATAGGTATCATGCAACTTTTGAAGTGTA 387 CATCACAACTTTTAAGTTTGTCTCCAAAATTAAACTGATAGCTATCATGCAACTTTTAAAGTGTA * * * ** 8645121 AAGTATATTTGTGTGCTTCTTGTACTTAAAGAAACTGTAAAAAATTTTAACAGTCCTTACAGTTT 452 AAGTATATTTGTGTGCTTCTTATACTTAAAGAAACTATAAAAAAATTTAACAGTCCCCACAGTTT * 8645186 TGTGTTTAAAATATAA 517 TGTATTTAAAATATAA 8645202 TATA 1 TATA 8645206 GCTTTTTGAT Statistics Matches: 466, Mismatches: 61, Indels: 14 0.86 0.11 0.03 Matches are distributed among these distances: 526 8 0.02 527 254 0.55 528 109 0.23 529 11 0.02 530 4 0.01 531 6 0.01 533 74 0.16 ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42 Consensus pattern (532 bp): TATAATCTTGTTGCATTTGAAATTTTTAATTTTGTACCACATTATATTTATATTCATAACACTCA ACTCAAATAACTCAATCAAGTCTTTTTATTTTATATATATATTTTTAATATTTTAATATGAAATT ATCTTTTTATCCTTAATATATATACACACTTAAAACCCAAAATCTAATTTTTTTCCTTTCGATAG TAGCAACTCTTATTTTCCTTAACACCAGTAAAAACCCAAAACCTAATTTCTCCCTTTGGTAGCGC AACTCTTAGTTTAGTGAAAATCTAAATTTACTTTGACATTTTAAGGCGATTACAACCAAAATTAT CTCTCAAATCTTCTTCCTCAATTACGACCATAGATGAAGGAAAACAAAAAGAGCTAAGTCACATC ACAACTTTTAAGTTTGTCTCCAAAATTAAACTGATAGCTATCATGCAACTTTTAAAGTGTAAAGT ATATTTGTGTGCTTCTTATACTTAAAGAAACTATAAAAAAATTTAACAGTCCCCACAGTTTTGTA TTTAAAATATAA Found at i:8645620 original size:16 final size:17 Alignment explanation

Indices: 8645598--8645642 Score: 67 Period size: 16 Copynumber: 2.8 Consensus size: 17 8645588 ATTAATTAAA 8645598 ATTTTAATATTTAGTTT 1 ATTTTAATATTTAGTTT * 8645615 -TTTTAATTTTTAGTTT 1 ATTTTAATATTTAGTTT 8645631 ATTTT-ATATTTA 1 ATTTTAATATTTA 8645643 TTATCACAAT Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 16 21 0.84 17 4 0.16 ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69 Consensus pattern (17 bp): ATTTTAATATTTAGTTT Found at i:8646052 original size:15 final size:15 Alignment explanation

Indices: 8646032--8646065 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 8646022 TATTTTTATG 8646032 ATTTAA-TATATATAT 1 ATTTAATTATATAT-T 8646047 ATTTAATTATATATT 1 ATTTAATTATATATT 8646062 ATTT 1 ATTT 8646066 TGTATTTTAG Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 15 11 0.61 16 7 0.39 ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59 Consensus pattern (15 bp): ATTTAATTATATATT Found at i:8646608 original size:22 final size:22 Alignment explanation

Indices: 8646556--8646599 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 8646546 AAAGCTCATG * 8646556 ATATAATTTACCTTTTGATAAA 1 ATATAATTTACCTTTTCATAAA * 8646578 ATATAATTTACTTTTTCATAAA 1 ATATAATTTACCTTTTCATAAA 8646600 TTACTATTTC Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48 Consensus pattern (22 bp): ATATAATTTACCTTTTCATAAA Found at i:8646844 original size:16 final size:16 Alignment explanation

Indices: 8646815--8646859 Score: 54 Period size: 16 Copynumber: 2.8 Consensus size: 16 8646805 CGGGTTTAGG * * * 8646815 TTCTTTCGACTTTGAT 1 TTCTTTTGAGTTTGAA 8646831 TTCTTTTGAGTTTGAA 1 TTCTTTTGAGTTTGAA * 8646847 TTATTTTGAGTTT 1 TTCTTTTGAGTTT 8646860 AAACCATTTG Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 16 25 1.00 ACGTcount: A:0.16, C:0.09, G:0.16, T:0.60 Consensus pattern (16 bp): TTCTTTTGAGTTTGAA Found at i:8647884 original size:31 final size:32 Alignment explanation

Indices: 8647846--8647915 Score: 124 Period size: 31 Copynumber: 2.2 Consensus size: 32 8647836 AAACTATAAC 8647846 TGTATCGATACATAAGTGTTG-ATCGATACAA 1 TGTATCGATACATAAGTGTTGTATCGATACAA * 8647877 TGTATCGATACATAAGTTTTGTATCGATACAA 1 TGTATCGATACATAAGTGTTGTATCGATACAA 8647909 TGTATCG 1 TGTATCG 8647916 CTACGAAGCT Statistics Matches: 37, Mismatches: 1, Indels: 1 0.95 0.03 0.03 Matches are distributed among these distances: 31 20 0.54 32 17 0.46 ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36 Consensus pattern (32 bp): TGTATCGATACATAAGTGTTGTATCGATACAA Found at i:8647901 original size:19 final size:18 Alignment explanation

Indices: 8647846--8647907 Score: 64 Period size: 19 Copynumber: 3.7 Consensus size: 18 8647836 AAACTATAAC 8647846 TGTATCGATACATAAGTGT 1 TGTATCGATACATAAGT-T 8647865 TG-ATCGATAC--AA--- 1 TGTATCGATACATAAGTT 8647877 TGTATCGATACATAAGTTT 1 TGTATCGATACATAAG-TT 8647896 TGTATCGATACA 1 TGTATCGATACA 8647908 ATGTATCGCT Statistics Matches: 36, Mismatches: 0, Indels: 14 0.72 0.00 0.28 Matches are distributed among these distances: 12 2 0.06 13 8 0.22 15 2 0.06 16 2 0.06 18 8 0.22 19 14 0.39 ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35 Consensus pattern (18 bp): TGTATCGATACATAAGTT Found at i:8653756 original size:13 final size:13 Alignment explanation

Indices: 8653738--8653763 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 8653728 CAATTTTTTG 8653738 TGTATCGATACAT 1 TGTATCGATACAT 8653751 TGTATCGATACAT 1 TGTATCGATACAT 8653764 ACTTGCTGTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8656327 original size:13 final size:13 Alignment explanation

Indices: 8656309--8656347 Score: 69 Period size: 13 Copynumber: 3.0 Consensus size: 13 8656299 ATAATCACCC * 8656309 TGTATCGATACAG 1 TGTATCGATACAA 8656322 TGTATCGATACAA 1 TGTATCGATACAA 8656335 TGTATCGATACAA 1 TGTATCGATACAA 8656348 AGAAAAATGT Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 13 25 1.00 ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31 Consensus pattern (13 bp): TGTATCGATACAA Found at i:8660281 original size:21 final size:21 Alignment explanation

Indices: 8660252--8660296 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 8660242 AAGTTTTCAT * 8660252 TTTTCTTAGCTAAC-TCATTA 1 TTTTCTTAGCCAACTTCATTA * 8660272 TTTTCATTAGCCAACTTCTTTA 1 TTTTC-TTAGCCAACTTCATTA 8660294 TTT 1 TTT 8660297 CAACTTGCAA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 5 0.24 21 8 0.38 22 8 0.38 ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53 Consensus pattern (21 bp): TTTTCTTAGCCAACTTCATTA Found at i:8662519 original size:13 final size:13 Alignment explanation

Indices: 8662501--8662526 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 8662491 CAATTTTTTG 8662501 TGTATCGATACAT 1 TGTATCGATACAT 8662514 TGTATCGATACAT 1 TGTATCGATACAT 8662527 ACTTGCTGTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8663491 original size:158 final size:158 Alignment explanation

Indices: 8663203--8663512 Score: 584 Period size: 158 Copynumber: 2.0 Consensus size: 158 8663193 ATATGCTACG * 8663203 AGTGTAAGAAGCCAGGGCATATTAAATTTGATTGTCCAAATTTAAAGAAGAAAAGTATAAGCAAA 1 AGTGTAAGAAGCCAGGGCATATTAAATTTGATTGTCCAAATTTAAAAAAGAAAAGTATAAGCAAA * 8663268 CTAAAGAAGAAAGCCATGATAGCCACATGGAGTGATAGCAACTCATCCGATGATGATGAAGAAGT 66 CTAAAGAAGAAAGCCATGATAGCCACATGGAGTGATAGCAACACATCCGATGATGATGAAGAAGT 8663333 CGCAAATCTATGTCTTATGGCTCCAAGT 131 CGCAAATCTATGTCTTATGGCTCCAAGT * 8663361 AGTGTAAGAAGCCAGGGCATATTAAATTTGATTGTCCAAATTTAAAAAAGAAAAGTATGAGCAAA 1 AGTGTAAGAAGCCAGGGCATATTAAATTTGATTGTCCAAATTTAAAAAAGAAAAGTATAAGCAAA * 8663426 CTAAAGAAGAAAGCCATGGTAGCCACATGGAGTGATAGCAACACATCCGATGATGATGAAGAAGT 66 CTAAAGAAGAAAGCCATGATAGCCACATGGAGTGATAGCAACACATCCGATGATGATGAAGAAGT 8663491 CGCAAATCTATGTCTTATGGCT 131 CGCAAATCTATGTCTTATGGCT 8663513 TACGAAGACT Statistics Matches: 148, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 158 148 1.00 ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23 Consensus pattern (158 bp): AGTGTAAGAAGCCAGGGCATATTAAATTTGATTGTCCAAATTTAAAAAAGAAAAGTATAAGCAAA CTAAAGAAGAAAGCCATGATAGCCACATGGAGTGATAGCAACACATCCGATGATGATGAAGAAGT CGCAAATCTATGTCTTATGGCTCCAAGT Found at i:8669839 original size:13 final size:13 Alignment explanation

Indices: 8669821--8669847 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 8669811 ACATTATGCT 8669821 TTGTATCGATACA 1 TTGTATCGATACA 8669834 TTGTATCGATACA 1 TTGTATCGATACA 8669847 T 1 T 8669848 GATACATGAA 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:0.30, C:0.15, G:0.15, T:0.41 Consensus pattern (13 bp): TTGTATCGATACA Found at i:8669919 original size:63 final size:62 Alignment explanation

Indices: 8669848--8669978 Score: 235 Period size: 63 Copynumber: 2.1 Consensus size: 62 8669838 ATCGATACAT * 8669848 GATACATGAAACTGGCAGTAGCTACCCTACCACTGTTTGTATCGATACATGGACAATTGTATC 1 GATACATGAAACTGGCAGTAGCTACCCTACCACTGTTTGTATCGATACATGGAC-ATCGTATC * 8669911 GATACATGAAACTGGCAGTAGCTACCCTACCATTGTTTGTATCGATACATGGACATCGTATC 1 GATACATGAAACTGGCAGTAGCTACCCTACCACTGTTTGTATCGATACATGGACATCGTATC 8669973 GATACA 1 GATACA 8669979 ATGTATCGAT Statistics Matches: 66, Mismatches: 2, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 62 13 0.20 63 53 0.80 ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28 Consensus pattern (62 bp): GATACATGAAACTGGCAGTAGCTACCCTACCACTGTTTGTATCGATACATGGACATCGTATC Found at i:8669973 original size:19 final size:19 Alignment explanation

Indices: 8669949--8670044 Score: 90 Period size: 19 Copynumber: 5.7 Consensus size: 19 8669939 ACCATTGTTT 8669949 GTATCGATACATGGACATC 1 GTATCGATACATGGACATC 8669968 GTATCGATAC----A-AT- 1 GTATCGATACATGGACATC 8669981 GTATCGATACATGGACATC 1 GTATCGATACATGGACATC 8670000 GTATCGATAC----A-AT- 1 GTATCGATACATGGACATC * 8670013 GTATCGATATATGGACATC 1 GTATCGATACATGGACATC * 8670032 ATATCGATACATG 1 GTATCGATACATG 8670045 ATGAATTGTA Statistics Matches: 62, Mismatches: 3, Indels: 24 0.70 0.03 0.27 Matches are distributed among these distances: 13 19 0.31 14 4 0.06 15 2 0.03 17 2 0.03 18 4 0.06 19 31 0.50 ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29 Consensus pattern (19 bp): GTATCGATACATGGACATC Found at i:8669986 original size:13 final size:13 Alignment explanation

Indices: 8669968--8670021 Score: 54 Period size: 13 Copynumber: 3.7 Consensus size: 13 8669958 CATGGACATC 8669968 GTATCGATACAAT 1 GTATCGATACAAT 8669981 GTATCGATACATGGACAT 1 GTATCGATAC----A-AT 8669999 CGTATCGATACAAT 1 -GTATCGATACAAT 8670013 GTATCGATA 1 GTATCGATA 8670022 TATGGACATC Statistics Matches: 35, Mismatches: 0, Indels: 12 0.74 0.00 0.26 Matches are distributed among these distances: 13 19 0.54 14 2 0.06 15 1 0.03 17 1 0.03 18 2 0.06 19 10 0.29 ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30 Consensus pattern (13 bp): GTATCGATACAAT Found at i:8669989 original size:32 final size:32 Alignment explanation

Indices: 8669948--8670042 Score: 172 Period size: 32 Copynumber: 3.0 Consensus size: 32 8669938 TACCATTGTT 8669948 TGTATCGATACATGGACATCGTATCGATACAA 1 TGTATCGATACATGGACATCGTATCGATACAA 8669980 TGTATCGATACATGGACATCGTATCGATACAA 1 TGTATCGATACATGGACATCGTATCGATACAA * * 8670012 TGTATCGATATATGGACATCATATCGATACA 1 TGTATCGATACATGGACATCGTATCGATACA 8670043 TGATGAATTG Statistics Matches: 61, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 61 1.00 ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29 Consensus pattern (32 bp): TGTATCGATACATGGACATCGTATCGATACAA Found at i:8675227 original size:20 final size:20 Alignment explanation

Indices: 8675202--8675255 Score: 67 Period size: 20 Copynumber: 2.7 Consensus size: 20 8675192 GTTATAAGCA 8675202 ATGTATCAATACAAT-T-CATC 1 ATGTATCAATACAATGTGC--C * 8675222 ATGTATCGATACAATGTGCC 1 ATGTATCAATACAATGTGCC 8675242 ATGTATCAATACAA 1 ATGTATCAATACAA 8675256 ACAGTGGTAG Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 20 28 0.93 21 1 0.03 22 1 0.03 ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31 Consensus pattern (20 bp): ATGTATCAATACAATGTGCC Found at i:8676374 original size:20 final size:20 Alignment explanation

Indices: 8676330--8676387 Score: 64 Period size: 20 Copynumber: 3.0 Consensus size: 20 8676320 ATTTCAACGA *** 8676330 TTTGTATCGATACATAAAGT 1 TTTGTATCGATACATATTTT * 8676350 GTTGTATCGATACATATTTT 1 TTTGTATCGATACATATTTT * 8676370 TTTGTATTGATACA-ATTT 1 TTTGTATCGATACATATTT 8676388 AAGCTACTGC Statistics Matches: 32, Mismatches: 6, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 19 4 0.12 20 28 0.88 ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48 Consensus pattern (20 bp): TTTGTATCGATACATATTTT Found at i:8676423 original size:13 final size:13 Alignment explanation

Indices: 8676405--8676429 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 8676395 TGCCAAAAAA 8676405 TGTATCGATACAT 1 TGTATCGATACAT 8676418 TGTATCGATACA 1 TGTATCGATACA 8676430 CTGATCTTTG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8676496 original size:52 final size:52 Alignment explanation

Indices: 8676438--8676566 Score: 213 Period size: 52 Copynumber: 2.5 Consensus size: 52 8676428 CACTGATCTT * 8676438 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA 1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA * * 8676490 TGTATCGATACGTGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA 1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA * * 8676542 TGTATCGATTCATGCAGGTAAATTT 1 TGTATCGATACATGCAGGCAAATTT 8676567 TCATATTTCG Statistics Matches: 71, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 52 71 1.00 ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31 Consensus pattern (52 bp): TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA Found at i:8687219 original size:13 final size:13 Alignment explanation

Indices: 8687201--8687225 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 8687191 CAATTCATCA 8687201 TGTATCGATACAT 1 TGTATCGATACAT 8687214 TGTATCGATACA 1 TGTATCGATACA 8687226 ATATGCCATG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:8687223 original size:33 final size:32 Alignment explanation

Indices: 8687181--8687245 Score: 96 Period size: 33 Copynumber: 2.0 Consensus size: 32 8687171 TTATAAGCAA 8687181 TGTATCGATACAAT-TCATCATGTATCGATACAT 1 TGTATCGATACAATATC--CATGTATCGATACAT 8687214 TGTATCGATACAATATGCCATGTATCGATACA 1 TGTATCGATACAATAT-CCATGTATCGATACA 8687246 AACAGTGGTA Statistics Matches: 30, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 33 28 0.93 34 1 0.03 35 1 0.03 ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34 Consensus pattern (32 bp): TGTATCGATACAATATCCATGTATCGATACAT Found at i:8687300 original size:20 final size:20 Alignment explanation

Indices: 8687275--8687328 Score: 83 Period size: 19 Copynumber: 2.8 Consensus size: 20 8687265 TTGCCAGTTT * * 8687275 CATGTATCGATACAATTGTA 1 CATGTATCGATACAAGTGAA 8687295 CATGTATCGATAC-AGTGAA 1 CATGTATCGATACAAGTGAA 8687314 CATGTATCGATACAA 1 CATGTATCGATACAA 8687329 AGCATAATGT Statistics Matches: 31, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 19 17 0.55 20 14 0.45 ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30 Consensus pattern (20 bp): CATGTATCGATACAAGTGAA Found at i:8687866 original size:20 final size:20 Alignment explanation

Indices: 8687841--8687878 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 8687831 CTCTCTCATC 8687841 CCACCTCCTTAAAGATTACG 1 CCACCTCCTTAAAGATTACG ** 8687861 CCACCTTTTTAAAGATTA 1 CCACCTCCTTAAAGATTA 8687879 TTGGCTTTAG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.32, C:0.29, G:0.08, T:0.32 Consensus pattern (20 bp): CCACCTCCTTAAAGATTACG Found at i:8688967 original size:204 final size:201 Alignment explanation

Indices: 8688614--8689003 Score: 663 Period size: 204 Copynumber: 1.9 Consensus size: 201 8688604 TGGTGGAATG 8688614 ATAAAATGGGTGGCAGAAGAATACATTAGCTTAGTTGGGACAAGCTATGCATGCTAAAATCAATA 1 ATAAAATGGGTGGCAGAAGAATACATTAGCTTAGTTGGGACAAGCTATGCATGCTAAAATCAATA * * 8688679 GGACTTGGGTTTGGGACCTACACCTTTTTAATTGAACATTTTTAGGCAAGCAAAAATGATGCTAT 66 GGACTTGGGTTTGGGACCTACACCATTTTAATTGAACATTTTTAGGCAAGCAAAAATAATGCTAT * * 8688744 TCATCCCACTGACTCTTTGTGCTCTAAGGTCCTTAAAGCTAAATAGTTTGCTTAAAATTATTGGT 131 TCATCACACTGACTCTTTGTGCTCTAAGGTCCTTAAAGCTAAATACTTTGCTTAAAATTATTGGT 8688809 GAAACA 196 GAAACA * * 8688815 ATAAAATGGGTGGTAGAAGAATACATTAGCTTAGTTGGGACAAGCTATGCATGCTAAAATTAATA 1 ATAAAATGGGTGGCAGAAGAATACATTAGCTTAGTTGGGACAAGCTATGCATGCTAAAATCAATA * * 8688880 GAAGAACTTGGGTTTGGGACCTGCACCATTTTAATTGAGCATTTTTAGGCAAGCAAAAATAATGC 66 G--G-ACTTGGGTTTGGGACCTACACCATTTTAATTGAACATTTTTAGGCAAGCAAAAATAATGC * * 8688945 TATTCATCATACTGATTCTTTGTGCTCTAAGGTCCTTAAAGCTAAATACTTTGCTTAAA 128 TATTCATCACACTGACTCTTTGTGCTCTAAGGTCCTTAAAGCTAAATACTTTGCTTAAA 8689004 TTTTTTTTAG Statistics Matches: 176, Mismatches: 10, Indels: 3 0.93 0.05 0.02 Matches are distributed among these distances: 201 64 0.36 203 1 0.01 204 111 0.63 ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32 Consensus pattern (201 bp): ATAAAATGGGTGGCAGAAGAATACATTAGCTTAGTTGGGACAAGCTATGCATGCTAAAATCAATA GGACTTGGGTTTGGGACCTACACCATTTTAATTGAACATTTTTAGGCAAGCAAAAATAATGCTAT TCATCACACTGACTCTTTGTGCTCTAAGGTCCTTAAAGCTAAATACTTTGCTTAAAATTATTGGT GAAACA Found at i:8696563 original size:19 final size:20 Alignment explanation

Indices: 8696516--8696569 Score: 65 Period size: 19 Copynumber: 2.8 Consensus size: 20 8696506 CTGCCAGTTT * ** 8696516 CATGTATCAATACAATTGTC 1 CATGTATCGATACAATTGAA * 8696536 CATGCATCGATACAA-TGAA 1 CATGTATCGATACAATTGAA 8696555 CATGTATCGATACAA 1 CATGTATCGATACAA 8696570 AGCGTAATGT Statistics Matches: 29, Mismatches: 5, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 19 16 0.55 20 13 0.45 ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28 Consensus pattern (20 bp): CATGTATCGATACAATTGAA Found at i:8703671 original size:19 final size:20 Alignment explanation

Indices: 8703620--8703672 Score: 63 Period size: 19 Copynumber: 2.7 Consensus size: 20 8703610 TTTCCAGTTT ** 8703620 CATGTATCAATACAATTGTC 1 CATGTATCAATACAATTGAA * * 8703640 CATGCATCGATACAA-TGAA 1 CATGTATCAATACAATTGAA 8703659 CATGTATCAATACA 1 CATGTATCAATACA 8703673 TTGTATCGAT Statistics Matches: 27, Mismatches: 6, Indels: 1 0.79 0.18 0.03 Matches are distributed among these distances: 19 14 0.52 20 13 0.48 ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28 Consensus pattern (20 bp): CATGTATCAATACAATTGAA Found at i:8709284 original size:33 final size:34 Alignment explanation

Indices: 8709246--8709312 Score: 127 Period size: 34 Copynumber: 2.0 Consensus size: 34 8709236 AGAGAATAGA 8709246 GAAGAA-TTTTTATTATCTTTTCATTCAAATTCT 1 GAAGAATTTTTTATTATCTTTTCATTCAAATTCT 8709279 GAAGAATTTTTTATTATCTTTTCATTCAAATTCT 1 GAAGAATTTTTTATTATCTTTTCATTCAAATTCT 8709313 TCTTTACACA Statistics Matches: 33, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 33 6 0.18 34 27 0.82 ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52 Consensus pattern (34 bp): GAAGAATTTTTTATTATCTTTTCATTCAAATTCT Found at i:8727543 original size:2 final size:2 Alignment explanation

Indices: 8727536--8727567 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 8727526 AAAACATTCT 8727536 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 8727568 GAAAGGGACA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:8732087 original size:22 final size:24 Alignment explanation

Indices: 8732062--8732117 Score: 71 Period size: 22 Copynumber: 2.4 Consensus size: 24 8732052 TATTGAAATA 8732062 TAAAAATAAATA-ATAAAATAT-T 1 TAAAAATAAATATATAAAATATAT * * * 8732084 TAAAATTAAATATATAAATTTTAT 1 TAAAAATAAATATATAAAATATAT 8732108 TAAAAATAAA 1 TAAAAATAAA 8732118 GATTTATCAA Statistics Matches: 28, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 22 11 0.39 23 7 0.25 24 10 0.36 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (24 bp): TAAAAATAAATATATAAAATATAT Found at i:8734503 original size:16 final size:16 Alignment explanation

Indices: 8734464--8734503 Score: 62 Period size: 16 Copynumber: 2.5 Consensus size: 16 8734454 TTATACTTAA 8734464 TTTAAGTTTGAATCAT 1 TTTAAGTTTGAATCAT ** 8734480 TTCGAGTTTGAATCAT 1 TTTAAGTTTGAATCAT 8734496 TTTAAGTT 1 TTTAAGTT 8734504 AAGATTATTT Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50 Consensus pattern (16 bp): TTTAAGTTTGAATCAT Found at i:8737890 original size:22 final size:24 Alignment explanation

Indices: 8737831--8737878 Score: 59 Period size: 21 Copynumber: 2.2 Consensus size: 24 8737821 TTTTTAGGTC * 8737831 AAAAATAT-ATT-TAT-TTTTTAG 1 AAAAATATAATTGTATAATTTTAG 8737852 AAAAATATAATTGTATAATTTTA- 1 AAAAATATAATTGTATAATTTTAG 8737875 AAAA 1 AAAA 8737879 TTAAATTTTA Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 21 8 0.35 22 3 0.13 23 7 0.30 24 5 0.22 ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44 Consensus pattern (24 bp): AAAAATATAATTGTATAATTTTAG Found at i:8743859 original size:42 final size:42 Alignment explanation

Indices: 8743790--8743882 Score: 150 Period size: 42 Copynumber: 2.2 Consensus size: 42 8743780 TGAACAAATA * * * 8743790 TATATATTTAGAATGATGGTAAGGAATGTTAACATAATTTAT 1 TATATATTTAGAATCATAGTAAAGAATGTTAACATAATTTAT 8743832 TATATATTTAGAATCATAGTAAAGAATGTTAACATAATTTAT 1 TATATATTTAGAATCATAGTAAAGAATGTTAACATAATTTAT * 8743874 TATTTATTT 1 TATATATTT 8743883 TTATAATAAA Statistics Matches: 47, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 42 47 1.00 ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44 Consensus pattern (42 bp): TATATATTTAGAATCATAGTAAAGAATGTTAACATAATTTAT Found at i:8745147 original size:2 final size:2 Alignment explanation

Indices: 8745140--8745169 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 8745130 ACGTAAGATT 8745140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 8745170 ATAAGTTATA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:8745417 original size:21 final size:22 Alignment explanation

Indices: 8745375--8745418 Score: 56 Period size: 21 Copynumber: 2.0 Consensus size: 22 8745365 ATATTGTTAA * 8745375 ATATATTTTTATGTTAATATTT 1 ATATATTTTTATATTAATATTT 8745397 ATATA-TTTTATAATTAA-ATTT 1 ATATATTTTTAT-ATTAATATTT 8745418 A 1 A 8745419 AATAAAATTT Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 21 11 0.55 22 9 0.45 ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59 Consensus pattern (22 bp): ATATATTTTTATATTAATATTT Found at i:8747064 original size:18 final size:17 Alignment explanation

Indices: 8747015--8747069 Score: 64 Period size: 17 Copynumber: 3.4 Consensus size: 17 8747005 ATATATATTT 8747015 TAAAATTTATA-AAATA 1 TAAAATTTATATAAATA 8747031 T-AAA-TTAT-TAATATA 1 TAAAATTTATATAA-ATA 8747046 TCAAAATTTATATAAATA 1 T-AAAATTTATATAAATA 8747064 TAAAAT 1 TAAAAT 8747070 ATCTTAAACA Statistics Matches: 33, Mismatches: 0, Indels: 11 0.75 0.00 0.25 Matches are distributed among these distances: 14 6 0.18 15 7 0.21 16 1 0.03 17 8 0.24 18 8 0.24 19 3 0.09 ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40 Consensus pattern (17 bp): TAAAATTTATATAAATA Found at i:8750443 original size:49 final size:49 Alignment explanation

Indices: 8750367--8750464 Score: 124 Period size: 49 Copynumber: 2.0 Consensus size: 49 8750357 TTTTTCATGC * * * * 8750367 ACATTTTTTAAATATGGATGCACTATTAACATGTTAGGTATCAACAAAT 1 ACATTTTTTAAATATAGATACACTATTAACATATTAGATATCAACAAAT * * * * 8750416 ACATTTTTTAAATGTAGATATATTATTAACATATTAGATATCAATAAAT 1 ACATTTTTTAAATATAGATACACTATTAACATATTAGATATCAACAAAT 8750465 TTCCAGTGTA Statistics Matches: 41, Mismatches: 8, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 49 41 1.00 ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40 Consensus pattern (49 bp): ACATTTTTTAAATATAGATACACTATTAACATATTAGATATCAACAAAT Found at i:8750718 original size:35 final size:35 Alignment explanation

Indices: 8750679--8750745 Score: 98 Period size: 35 Copynumber: 1.9 Consensus size: 35 8750669 AAATTTTAAA * * * 8750679 ATTTTTAACTTATTCAAAAAGTTTATTTGAAAGCT 1 ATTTTTAACTAATGCAAAAAGTTCATTTGAAAGCT * 8750714 ATTTTTAACTAATGCAAAGAGTTCATTTGAAA 1 ATTTTTAACTAATGCAAAAAGTTCATTTGAAA 8750746 AGCTCTATGT Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 35 28 1.00 ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42 Consensus pattern (35 bp): ATTTTTAACTAATGCAAAAAGTTCATTTGAAAGCT Found at i:8752333 original size:19 final size:19 Alignment explanation

Indices: 8752301--8752348 Score: 73 Period size: 18 Copynumber: 2.6 Consensus size: 19 8752291 CTTGACTAGC 8752301 AAAATCAAAT-AATAATAAT 1 AAAAT-AAATAAATAATAAT 8752320 AAAATAAATAAATAATAAT 1 AAAATAAATAAATAATAAT 8752339 -AAATAAATAA 1 AAAATAAATAA 8752349 GGAAATAATT Statistics Matches: 28, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 18 14 0.50 19 14 0.50 ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25 Consensus pattern (19 bp): AAAATAAATAAATAATAAT Done.