Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr04 98600468 

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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 273 characters in sequence are not A, C, G, or T


File 304 of 325

Found at i:92907864 original size:24 final size:26

Alignment explanation

Indices: 92907804--92907866 Score: 85 Period size: 26 Copynumber: 2.5 Consensus size: 26 92907794 GTAAAATAAA * 92907804 TTAAAACAAATAATATACGAAGCAAT 1 TTAAAACAAATAATATAAGAAGCAAT * 92907830 TTAAAATAAATAATATAAG-A-CAAT 1 TTAAAACAAATAATATAAGAAGCAAT * 92907854 TTAAAGCAAATAA 1 TTAAAACAAATAA 92907867 GAAGACAATT Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 24 15 0.45 25 1 0.03 26 17 0.52 ACGTcount: A:0.60, C:0.08, G:0.06, T:0.25 Consensus pattern (26 bp): TTAAAACAAATAATATAAGAAGCAAT Found at i:92908493 original size:14 final size:14 Alignment explanation

Indices: 92908476--92908567 Score: 73 Period size: 14 Copynumber: 6.7 Consensus size: 14 92908466 ATATTTGAGT * 92908476 ATTGAGGATTGAAA 1 ATTGAGAATTGAAA * 92908490 ATTGAAAATTGAAA 1 ATTGAGAATTGAAA * 92908504 ATTGAAAATTGAAA 1 ATTGAGAATTGAAA * * 92908518 ATAT-AAAATTGGAA 1 AT-TGAGAATTGAAA * * 92908532 ATTG-GGATTGAAG 1 ATTGAGAATTGAAA * * 92908545 ATTG-GGATTGAAG 1 ATTGAGAATTGAAA 92908558 ATTGAGAATT 1 ATTGAGAATT 92908568 TAGAAAGAAA Statistics Matches: 67, Mismatches: 8, Indels: 6 0.83 0.10 0.07 Matches are distributed among these distances: 13 23 0.34 14 43 0.64 15 1 0.01 ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30 Consensus pattern (14 bp): ATTGAGAATTGAAA Found at i:92908536 original size:7 final size:7 Alignment explanation

Indices: 92908483--92908535 Score: 81 Period size: 7 Copynumber: 7.6 Consensus size: 7 92908473 AGTATTGAGG 92908483 ATTGAAA 1 ATTGAAA 92908490 ATTGAAA 1 ATTGAAA 92908497 ATTGAAA 1 ATTGAAA 92908504 ATTGAAA 1 ATTGAAA 92908511 ATTGAAA 1 ATTGAAA 92908518 ATAT-AAA 1 AT-TGAAA * 92908525 ATTGGAA 1 ATTGAAA 92908532 ATTG 1 ATTG 92908536 GGATTGAAGA Statistics Matches: 43, Mismatches: 1, Indels: 4 0.90 0.02 0.08 Matches are distributed among these distances: 6 1 0.02 7 41 0.95 8 1 0.02 ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30 Consensus pattern (7 bp): ATTGAAA Found at i:92908548 original size:13 final size:13 Alignment explanation

Indices: 92908532--92908561 Score: 60 Period size: 13 Copynumber: 2.3 Consensus size: 13 92908522 AAAATTGGAA 92908532 ATTGGGATTGAAG 1 ATTGGGATTGAAG 92908545 ATTGGGATTGAAG 1 ATTGGGATTGAAG 92908558 ATTG 1 ATTG 92908562 AGAATTTAGA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33 Consensus pattern (13 bp): ATTGGGATTGAAG Found at i:92909031 original size:30 final size:31 Alignment explanation

Indices: 92908997--92909063 Score: 84 Period size: 30 Copynumber: 2.2 Consensus size: 31 92908987 TTCTATTTCT 92908997 GTCATTCATT-TTAAAAAAATTGTT-ATTTTA 1 GTCATTC-TTGTTAAAAAAATTGTTAATTTTA * * * 92909027 GTCATTCTTGTTAGATAAGTTGTTAATTTTA 1 GTCATTCTTGTTAAAAAAATTGTTAATTTTA 92909058 GTCATT 1 GTCATT 92909064 TCCGTTCGAC Statistics Matches: 32, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 29 2 0.06 30 18 0.56 31 12 0.38 ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51 Consensus pattern (31 bp): GTCATTCTTGTTAAAAAAATTGTTAATTTTA Found at i:92909078 original size:31 final size:31 Alignment explanation

Indices: 92909016--92909090 Score: 82 Period size: 31 Copynumber: 2.5 Consensus size: 31 92909006 TTTAAAAAAA * * 92909016 TTGTT-ATTTTAGTCATTCTTGTTAGATAAG 1 TTGTTAATTTTAGTCATTCTCGTTAGACAAG * 92909046 TTGTTAATTTTAGTCATT-TCCGTTCGACAAG 1 TTGTTAATTTTAGTCATTCT-CGTTAGACAAG * * 92909077 TTGTCAAATTTAGT 1 TTGTTAATTTTAGT 92909091 TACTCTACCA Statistics Matches: 38, Mismatches: 5, Indels: 3 0.83 0.11 0.07 Matches are distributed among these distances: 30 6 0.16 31 32 0.84 ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49 Consensus pattern (31 bp): TTGTTAATTTTAGTCATTCTCGTTAGACAAG Found at i:92910470 original size:20 final size:21 Alignment explanation

Indices: 92910445--92910491 Score: 60 Period size: 21 Copynumber: 2.2 Consensus size: 21 92910435 TGATGAAATA * * 92910445 TTATTT-TTTTAATTAATTGT 1 TTATTTATTTAAATCAATTGT 92910465 TTATTTATTTAAATCAATTGT 1 TTATTTATTTAAATCAATTGT 92910486 TATATT 1 T-TATT 92910492 AAAATATTAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 20 6 0.26 21 13 0.57 22 4 0.17 ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64 Consensus pattern (21 bp): TTATTTATTTAAATCAATTGT Found at i:92910503 original size:53 final size:53 Alignment explanation

Indices: 92910440--92910540 Score: 166 Period size: 53 Copynumber: 1.9 Consensus size: 53 92910430 TATTATGATG * * 92910440 AAATATTATTTTTTTAATTAATTGTTTATTTATTTAAATCAATTGTTATATTA 1 AAATATTATTTTTTTAATTAATTATTTATATATTTAAATCAATTGTTATATTA ** 92910493 AAATATTATTTTTTTAATTTTTTATTTATATATTTAAATCAATTGTTA 1 AAATATTATTTTTTTAATTAATTATTTATATATTTAAATCAATTGTTA 92910541 CGATGAAATA Statistics Matches: 44, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 53 44 1.00 ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59 Consensus pattern (53 bp): AAATATTATTTTTTTAATTAATTATTTATATATTTAAATCAATTGTTATATTA Found at i:92910550 original size:53 final size:52 Alignment explanation

Indices: 92910427--92910551 Score: 160 Period size: 53 Copynumber: 2.3 Consensus size: 52 92910417 GTTTTGAATA * * * 92910427 AATTATTATGATGAAATATTATTTTTTTAATTAATTGTTTATTTATTTAAATC 1 AATTGTTA-GATGAAATATTATTTTTTTAATTAATTATTTATATATTTAAATC * * ** 92910480 AATTGTTATATTAAAATATTATTTTTTTAATTTTTTATTTATATATTTAAATC 1 AATTGTTAGA-TGAAATATTATTTTTTTAATTAATTATTTATATATTTAAATC 92910533 AATTGTTACGATGAAATAT 1 AATTGTTA-GATGAAATAT 92910552 ATATATATAT Statistics Matches: 61, Mismatches: 9, Indels: 4 0.82 0.12 0.05 Matches are distributed among these distances: 52 1 0.02 53 59 0.97 54 1 0.02 ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55 Consensus pattern (52 bp): AATTGTTAGATGAAATATTATTTTTTTAATTAATTATTTATATATTTAAATC Found at i:92910566 original size:53 final size:53 Alignment explanation

Indices: 92910464--92910567 Score: 122 Period size: 53 Copynumber: 2.0 Consensus size: 53 92910454 TAATTAATTG * * * * * * 92910464 TTTATTTATTTAAATCAATTGTTATATTAAAATATTATTTTTTTAATTTTTTA 1 TTTATATATTTAAATCAATTGTTAGATGAAAATATTATATATATAATTTTTTA 92910517 TTTATATATTTAAATCAATTGTTACGATG-AAATA-TATATATATATATTTTT 1 TTTATATATTTAAATCAATTGTTA-GATGAAAATATTATATATATA-ATTTTT 92910568 AATCCATTGT Statistics Matches: 43, Mismatches: 6, Indels: 4 0.81 0.11 0.08 Matches are distributed among these distances: 52 7 0.16 53 34 0.79 54 2 0.05 ACGTcount: A:0.37, C:0.03, G:0.04, T:0.57 Consensus pattern (53 bp): TTTATATATTTAAATCAATTGTTAGATGAAAATATTATATATATAATTTTTTA Found at i:92911702 original size:28 final size:28 Alignment explanation

Indices: 92911662--92911718 Score: 114 Period size: 28 Copynumber: 2.0 Consensus size: 28 92911652 AGCTCTCTAC 92911662 TAAGAAAGAGGTCCTCGGTTCAGAATTG 1 TAAGAAAGAGGTCCTCGGTTCAGAATTG 92911690 TAAGAAAGAGGTCCTCGGTTCAGAATTG 1 TAAGAAAGAGGTCCTCGGTTCAGAATTG 92911718 T 1 T 92911719 GCCATGTTCA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 29 1.00 ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26 Consensus pattern (28 bp): TAAGAAAGAGGTCCTCGGTTCAGAATTG Found at i:92912470 original size:15 final size:16 Alignment explanation

Indices: 92912444--92912473 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 92912434 TCTTAAGCAT 92912444 CTCAGTGAAGATGACA 1 CTCAGTGAAGATGACA 92912460 CTCAG-GAAGATGAC 1 CTCAGTGAAGATGAC 92912474 GATACCTCGT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 9 0.64 16 5 0.36 ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17 Consensus pattern (16 bp): CTCAGTGAAGATGACA Found at i:92922853 original size:45 final size:45 Alignment explanation

Indices: 92922804--92922918 Score: 203 Period size: 45 Copynumber: 2.6 Consensus size: 45 92922794 ACAGTCCAAT * * 92922804 TGGCGAACAACATAAATAGCGAACAATTCAATTGGCAAACACACG 1 TGGCGAACAACATAAATAGCAAACAATTCAATTGGCAAACACACA 92922849 TGGCGAACAACATAAATAGCAAACAATTCAATTGGCAAACACACA 1 TGGCGAACAACATAAATAGCAAACAATTCAATTGGCAAACACACA * 92922894 TGGCGAACAACATAAATGGCAAACA 1 TGGCGAACAACATAAATAGCAAACA 92922919 CACGTGACGG Statistics Matches: 67, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 45 67 1.00 ACGTcount: A:0.47, C:0.22, G:0.17, T:0.15 Consensus pattern (45 bp): TGGCGAACAACATAAATAGCAAACAATTCAATTGGCAAACACACA Found at i:92932138 original size:16 final size:16 Alignment explanation

Indices: 92932119--92932220 Score: 59 Period size: 16 Copynumber: 6.5 Consensus size: 16 92932109 ACACATGATA 92932119 AACAACATAAATGGCG 1 AACAACATAAATGGCG * * 92932135 AACAGTC-TAATTGGCG 1 AACA-ACATAAATGGCG * * * 92932151 AAAAACATAAATGTCA 1 AACAACATAAATGGCG *** * 92932167 AACAGTTTAATTGGCG 1 AACAACATAAATGGCG * 92932183 AAC-AC--ACATGGCG 1 AACAACATAAATGGCG * 92932196 AACAACATAAATTGCG 1 AACAACATAAATGGCG 92932212 AACACACAT 1 AACA-ACAT 92932221 GGTGGACAAT Statistics Matches: 60, Mismatches: 20, Indels: 11 0.66 0.22 0.12 Matches are distributed among these distances: 13 9 0.15 14 2 0.03 15 1 0.02 16 43 0.72 17 5 0.08 ACGTcount: A:0.45, C:0.20, G:0.17, T:0.19 Consensus pattern (16 bp): AACAACATAAATGGCG Found at i:92932159 original size:32 final size:32 Alignment explanation

Indices: 92932122--92932184 Score: 99 Period size: 32 Copynumber: 2.0 Consensus size: 32 92932112 CATGATAAAC * 92932122 AACATAAATGGCGAACAGTCTAATTGGCGAAA 1 AACATAAATGGCAAACAGTCTAATTGGCGAAA * * 92932154 AACATAAATGTCAAACAGTTTAATTGGCGAA 1 AACATAAATGGCAAACAGTCTAATTGGCGAA 92932185 CACACATGGC Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 32 28 1.00 ACGTcount: A:0.44, C:0.14, G:0.19, T:0.22 Consensus pattern (32 bp): AACATAAATGGCAAACAGTCTAATTGGCGAAA Found at i:92943567 original size:29 final size:31 Alignment explanation

Indices: 92943536--92943593 Score: 84 Period size: 31 Copynumber: 1.9 Consensus size: 31 92943526 ATAAATTAAT * 92943536 AAAA-ATAA-AATTATATTTTAATTTTTTTTA 1 AAAATATAATAATT-TAATTTAATTTTTTTTA 92943566 AAAATATAATAATTTAATTTAATTTTTT 1 AAAATATAATAATTTAATTTAATTTTTT 92943594 AAAAATTATA Statistics Matches: 25, Mismatches: 1, Indels: 3 0.86 0.03 0.10 Matches are distributed among these distances: 30 4 0.16 31 17 0.68 32 4 0.16 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (31 bp): AAAATATAATAATTTAATTTAATTTTTTTTA Found at i:92952271 original size:35 final size:35 Alignment explanation

Indices: 92952205--92952371 Score: 185 Period size: 35 Copynumber: 4.6 Consensus size: 35 92952195 CATGGCAAAG 92952205 TGTGAAATGTAGGTATGGTA-TATCCATACTGAGT 1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT * 92952239 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC 1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT 92952274 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT 1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT ** * * 92952314 TAAGAAATGTAGGTATGGCATT-TCCCATACCGAGT 1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT *** 92952349 TAAAAAAATGTAGGTATGGTATT 1 T-GTGAAATGTAGGTATGGTATT 92952372 TCAATGAGGA Statistics Matches: 117, Mismatches: 8, Indels: 14 0.84 0.06 0.10 Matches are distributed among these distances: 34 21 0.18 35 44 0.38 36 20 0.17 37 1 0.01 38 1 0.01 39 1 0.01 40 29 0.25 ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34 Consensus pattern (35 bp): TGTGAAATGTAGGTATGGTATTATCCATACTGAGT Found at i:92952294 original size:40 final size:40 Alignment explanation

Indices: 92952216--92952331 Score: 122 Period size: 40 Copynumber: 3.0 Consensus size: 40 92952206 GTGAAATGTA 92952216 GGTATGGTA-TATCCATACTGAGTTGTGAAA--T--GTA- 1 GGTATGGTATTATCCATACTGAGTTGTGAAATGTAGGTAT * 92952250 GGTATGGTATTATCCATACTGAGCTGTGAAATGTAGGTAT 1 GGTATGGTATTATCCATACTGAGTTGTGAAATGTAGGTAT * ** 92952290 GGTAT--TATCAAATCCATACTGAGTTAAGAAATGTAGGTAT 1 GGTATGGTAT--TATCCATACTGAGTTGTGAAATGTAGGTAT 92952330 GG 1 GG 92952332 CATTTCCCAT Statistics Matches: 69, Mismatches: 5, Indels: 10 0.82 0.06 0.12 Matches are distributed among these distances: 34 9 0.13 35 20 0.29 37 1 0.01 38 3 0.04 39 3 0.04 40 33 0.48 ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34 Consensus pattern (40 bp): GGTATGGTATTATCCATACTGAGTTGTGAAATGTAGGTAT Found at i:92952328 original size:75 final size:75 Alignment explanation

Indices: 92952205--92952375 Score: 196 Period size: 75 Copynumber: 2.4 Consensus size: 75 92952195 CATGGCAAAG ** * 92952205 TGTGAAATGTAGGTATGG---TAT---ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT- 1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC * 92952263 CCATACTGAGC 65 CCATACCGAGC 92952274 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC 1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC * 92952339 CATACCGAGT 66 CATACCGAGC *** 92952349 TAAAAAAATGTAGGTATGGTATT-TCAA 1 T-GTGAAATGTAGGTATGGTATTATCAA 92952376 TGAGGAAAAC Statistics Matches: 86, Mismatches: 8, Indels: 10 0.83 0.08 0.10 Matches are distributed among these distances: 69 18 0.21 72 3 0.03 74 1 0.01 75 46 0.53 76 18 0.21 ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33 Consensus pattern (75 bp): TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC CATACCGAGC Found at i:92959338 original size:75 final size:75 Alignment explanation

Indices: 92959219--92959390 Score: 205 Period size: 75 Copynumber: 2.4 Consensus size: 75 92959209 CATGGCAAAG ** * 92959219 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT- 1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC * 92959278 CCATACTGAGC 65 CCATACCGAGC 92959289 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC 1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC * 92959354 CATACCGAGT 66 CATACCGAGC *** 92959364 TAAAAAAATGTAGGTATGGTATT-TCAA 1 T-GTGAAATGTAGGTATGGTATTATCAA 92959391 TGAGGAAAAC Statistics Matches: 87, Mismatches: 8, Indels: 9 0.84 0.08 0.09 Matches are distributed among these distances: 70 18 0.21 73 4 0.05 74 1 0.01 75 46 0.53 76 18 0.21 ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33 Consensus pattern (75 bp): TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC CATACCGAGC Found at i:92959357 original size:35 final size:35 Alignment explanation

Indices: 92959222--92959388 Score: 167 Period size: 35 Copynumber: 4.6 Consensus size: 35 92959212 GGCAAAGTGT * ** 92959222 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT 1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA * ** 92959257 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT 1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA 92959292 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA 1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA * * 92959332 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAAA 1 GAAATGTAGGTATGGTATTTCCCATACTGAGTT-AA * 92959368 AAAATGTAGGTATGGTATTTC 1 GAAATGTAGGTATGGTATTTC 92959389 AATGAGGAAA Statistics Matches: 116, Mismatches: 9, Indels: 13 0.84 0.07 0.09 Matches are distributed among these distances: 35 64 0.55 36 21 0.18 39 2 0.02 40 29 0.25 ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33 Consensus pattern (35 bp): GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA Found at i:92959380 original size:36 final size:35 Alignment explanation

Indices: 92959318--92959388 Score: 106 Period size: 36 Copynumber: 2.0 Consensus size: 35 92959308 ATTATCAAAT * * 92959318 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC 1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC * 92959353 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC 1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC 92959389 AATGAGGAAA Statistics Matches: 32, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 35 11 0.34 36 21 0.66 ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31 Consensus pattern (35 bp): CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC Found at i:92962411 original size:101 final size:102 Alignment explanation

Indices: 92962262--92962694 Score: 549 Period size: 105 Copynumber: 4.2 Consensus size: 102 92962252 ATTGGTATAC * * * * * 92962262 AAAATACAAG-TTTAAAAAAAAAATTGGTGTTGGCTTGTCAATGGCCGGCACCAAGTACAAAAAA 1 AAAATACGAGTTTTAAAAAAAAATTTGGTGCTAGCCTGTCAATGGCCGGCACCAAGTACAAAAAA * 92962326 AAA-TCAA-TTTTTTTAAAAAAAAATTTTGCTCTCCG 66 AAATTCAATTTTTTTTAAAAAAAAATTTTGCTCTCCA * * 92962361 AAAATACGAG-TTTAAAAAAAAATTTTGAGTGCTGGCCTGTCAATGACCGGCACCAAGTAC-AAA 1 AAAATACGAGTTTTAAAAAAAAA-TTTG-GTGCTAGCCTGTCAATGGCCGGCACCAAGTACAAAA * * 92962424 AAAAA-TCAA-TTTTTTTAAAAGAAAATTTCGCTCTCCA 64 AAAAATTCAATTTTTTTTAAAAAAAAATTTTGCTCTCCA * * 92962461 AAAATACGAGTTTTAAAAAAAAATTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACCAAAAA 1 AAAATACGAGTTTTAAAAAAAAATTTGGTGCTAGCCTGTCAATGGCCGGCACCAAGTA-CAAAAA 92962526 AAAATTCAAAATTTTTTTTAAAAAAAAATTTTGCTCTCCA 65 AAAATTC--AATTTTTTTTAAAAAAAAATTTTGCTCTCCA * * 92962566 AAAATATGAGTTTTAAAAAAAAATTAGGTGCTAGCCTGTCAATGGCCGGCACCAAGTA-AAAAAA 1 AAAATACGAGTTTTAAAAAAAAATTTGGTGCTAGCCTGTCAATGGCCGGCACCAAGTACAAAAAA * *** * * * 92962630 AAATTTAAGTTTTGTTTTAAAAAAGTTTTTTTGCTGTTCG 66 AAATTCAA-TTTT-TTTTAAAAAA-AAATTTTGCTCTCCA 92962670 AAAATACGAGTTTTAAAAAAAAATT 1 AAAATACGAGTTTTAAAAAAAAATT 92962695 GAATTTTTTG Statistics Matches: 297, Mismatches: 25, Indels: 19 0.87 0.07 0.06 Matches are distributed among these distances: 99 49 0.16 100 54 0.18 101 51 0.17 102 6 0.02 103 21 0.07 104 35 0.12 105 81 0.27 ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29 Consensus pattern (102 bp): AAAATACGAGTTTTAAAAAAAAATTTGGTGCTAGCCTGTCAATGGCCGGCACCAAGTACAAAAAA AAATTCAATTTTTTTTAAAAAAAAATTTTGCTCTCCA Found at i:92979545 original size:29 final size:29 Alignment explanation

Indices: 92979503--92979560 Score: 116 Period size: 29 Copynumber: 2.0 Consensus size: 29 92979493 ATATAACCAA 92979503 ACTTGTACCGCAAGTAACAATTCTCAAGT 1 ACTTGTACCGCAAGTAACAATTCTCAAGT 92979532 ACTTGTACCGCAAGTAACAATTCTCAAGT 1 ACTTGTACCGCAAGTAACAATTCTCAAGT 92979561 CTTCAATTTC Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28 Consensus pattern (29 bp): ACTTGTACCGCAAGTAACAATTCTCAAGT Found at i:92983198 original size:18 final size:18 Alignment explanation

Indices: 92983175--92983210 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 92983165 AACTTTCCTA * 92983175 AATAAAGCAGTAGAATCC 1 AATAAAGCAGCAGAATCC 92983193 AATAAAGCAGCAGAATCC 1 AATAAAGCAGCAGAATCC 92983211 CATTATGAAG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14 Consensus pattern (18 bp): AATAAAGCAGCAGAATCC Found at i:92994633 original size:38 final size:38 Alignment explanation

Indices: 92994471--92994631 Score: 209 Period size: 38 Copynumber: 4.2 Consensus size: 38 92994461 GACCAATCGA * * * * 92994471 AACATGCCAGTTTGCTCATAAGAGCTATTACACCCAAT 1 AACACGCCAGTTTGCTCATAAGAGCTATTCCATCCGAT * 92994509 AACACACCAGTTTGCTCATAAGAGCTA-TCTCATCCGAT 1 AACACGCCAGTTTGCTCATAAGAGCTATTC-CATCCGAT * 92994547 AACACGCCAGTTTGCTTATAAGAGCTATTCCA-CCTGAT 1 AACACGCCAGTTTGCTCATAAGAGCTATTCCATCC-GAT * * * 92994585 AACACGCCAATTTTCTCATAAGAGTTATTCCATCCGAT 1 AACACGCCAGTTTGCTCATAAGAGCTATTCCATCCGAT 92994623 AACACGCCA 1 AACACGCCA 92994632 ATATATTTGT Statistics Matches: 108, Mismatches: 11, Indels: 8 0.85 0.09 0.06 Matches are distributed among these distances: 37 3 0.03 38 101 0.94 39 4 0.04 ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27 Consensus pattern (38 bp): AACACGCCAGTTTGCTCATAAGAGCTATTCCATCCGAT Found at i:92996029 original size:21 final size:20 Alignment explanation

Indices: 92995986--92996030 Score: 54 Period size: 21 Copynumber: 2.2 Consensus size: 20 92995976 GATTTACATG * 92995986 ATGAATGTAGAATCATAGGT 1 ATGAATGTAGAATCATAGAT * * 92996006 ATGATATGTAGAATTATATAT 1 ATGA-ATGTAGAATCATAGAT 92996027 ATGA 1 ATGA 92996031 CATAAATGTG Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 20 4 0.19 21 17 0.81 ACGTcount: A:0.42, C:0.02, G:0.20, T:0.36 Consensus pattern (20 bp): ATGAATGTAGAATCATAGAT Found at i:92998368 original size:6 final size:6 Alignment explanation

Indices: 92998359--92998452 Score: 59 Period size: 6 Copynumber: 15.7 Consensus size: 6 92998349 TTTCTCTTTC * * * * * * 92998359 TCTTCT TCTTCT CCTTCA CCTTCC TCTTCT TCCTCT AT-TTCT TCTGCT 1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT -TCTTCT TCTTCT * * * 92998407 TCTTCT TCATCT GCTTCT TCTTCT GCTT-T GTC-TCT CTCTTCT TCTT 1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT -TCTTCT -TCTTCT TCTT 92998453 TCTCCATGCC Statistics Matches: 67, Mismatches: 16, Indels: 10 0.72 0.17 0.11 Matches are distributed among these distances: 5 3 0.04 6 60 0.90 7 4 0.06 ACGTcount: A:0.03, C:0.36, G:0.04, T:0.56 Consensus pattern (6 bp): TCTTCT Found at i:92998419 original size:15 final size:15 Alignment explanation

Indices: 92998401--92998429 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 92998391 CTCTATTTCT 92998401 TCTGCTTCTTCTTCA 1 TCTGCTTCTTCTTCA 92998416 TCTGCTTCTTCTTC 1 TCTGCTTCTTCTTC 92998430 TGCTTTGTCT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.03, C:0.34, G:0.07, T:0.55 Consensus pattern (15 bp): TCTGCTTCTTCTTCA Found at i:93004284 original size:2 final size:2 Alignment explanation

Indices: 93004277--93004307 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 93004267 ATCATGGGTA 93004277 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 93004308 TTCTTTACAC Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:93006594 original size:11 final size:11 Alignment explanation

Indices: 93006578--93006603 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 93006568 TCTCAATTTA 93006578 AAAAAAAAAAG 1 AAAAAAAAAAG 93006589 AAAAAAAAAAG 1 AAAAAAAAAAG 93006600 AAAA 1 AAAA 93006604 CCCAGTGCAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00 Consensus pattern (11 bp): AAAAAAAAAAG Found at i:93008425 original size:15 final size:16 Alignment explanation

Indices: 93008405--93008438 Score: 52 Period size: 16 Copynumber: 2.2 Consensus size: 16 93008395 AAATTAAAAC 93008405 TTTATATAT-AATTAT 1 TTTATATATAAATTAT * 93008420 TTTATATTTAAATTAT 1 TTTATATATAAATTAT 93008436 TTT 1 TTT 93008439 TTCCATTAAC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 8 0.47 16 9 0.53 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (16 bp): TTTATATATAAATTAT Found at i:93009274 original size:5 final size:5 Alignment explanation

Indices: 93009264--93009322 Score: 109 Period size: 5 Copynumber: 11.8 Consensus size: 5 93009254 AGTATAAATA * 93009264 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAC TATAT 1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT 93009314 TATAT TATA 1 TATAT TATA 93009323 ATAGTTTAAT Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 5 52 1.00 ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58 Consensus pattern (5 bp): TATAT Found at i:93009395 original size:17 final size:16 Alignment explanation

Indices: 93009369--93009404 Score: 54 Period size: 17 Copynumber: 2.2 Consensus size: 16 93009359 AAGAAAAAAA 93009369 AGAATGAAAAAGAAAC 1 AGAATGAAAAAGAAAC * 93009385 AGAATTGAAAACGAAAC 1 AGAA-TGAAAAAGAAAC 93009402 AGA 1 AGA 93009405 GAAGGAGAAA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 16 4 0.22 17 14 0.78 ACGTcount: A:0.64, C:0.08, G:0.19, T:0.08 Consensus pattern (16 bp): AGAATGAAAAAGAAAC Found at i:93014921 original size:17 final size:20 Alignment explanation

Indices: 93014878--93014918 Score: 59 Period size: 18 Copynumber: 2.1 Consensus size: 20 93014868 ATTGTTACTG 93014878 TTTTGTTGTTATTATATAAC 1 TTTTGTTGTTATTATATAAC * 93014898 TTTTGTT-TTATTGT-TAAC 1 TTTTGTTGTTATTATATAAC 93014916 TTT 1 TTT 93014919 GTTACTATTT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 18 7 0.35 19 6 0.30 20 7 0.35 ACGTcount: A:0.20, C:0.05, G:0.10, T:0.66 Consensus pattern (20 bp): TTTTGTTGTTATTATATAAC Found at i:93019934 original size:3 final size:3 Alignment explanation

Indices: 93019926--93019983 Score: 50 Period size: 3 Copynumber: 19.7 Consensus size: 3 93019916 CTTTATTAAA * * * 93019926 TAT TAT TAT TAT TAT T-T CTAA TAT TAT TAT CAA TAT TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT 93019971 T-T T-T TAT ATAT TA 1 TAT TAT TAT -TAT TA 93019984 GTGTATGTTT Statistics Matches: 45, Mismatches: 6, Indels: 8 0.76 0.10 0.14 Matches are distributed among these distances: 2 5 0.11 3 37 0.82 4 3 0.07 ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62 Consensus pattern (3 bp): TAT Found at i:93020585 original size:3 final size:3 Alignment explanation

Indices: 93020579--93020608 Score: 51 Period size: 3 Copynumber: 10.0 Consensus size: 3 93020569 TGTGCTTTAA * 93020579 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 93020609 CATTGTTAAT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 25 1.00 ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63 Consensus pattern (3 bp): TAT Found at i:93020945 original size:17 final size:17 Alignment explanation

Indices: 93020925--93020971 Score: 67 Period size: 17 Copynumber: 2.7 Consensus size: 17 93020915 ATGTTCATTT 93020925 TATATATATTATGTATA 1 TATATATATTATGTATA * 93020942 TATATATATTATGTATG 1 TATATATATTATGTATA * 93020959 TATTTAGTATTAT 1 TATATA-TATTAT 93020972 CATGTGTACG Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 17 21 0.78 18 6 0.22 ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55 Consensus pattern (17 bp): TATATATATTATGTATA Found at i:93020976 original size:21 final size:21 Alignment explanation

Indices: 93020925--93020976 Score: 56 Period size: 21 Copynumber: 2.6 Consensus size: 21 93020915 ATGTTCATTT 93020925 TATATAT-AT-TATGTATATA 1 TATATATCATGTATGTATATA * * 93020944 TATATATTATGTATGTATTTA 1 TATATATCATGTATGTATATA 93020965 GTAT-TATCATGT 1 -TATATATCATGT 93020977 GTACGTTTTT Statistics Matches: 28, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 19 7 0.25 20 2 0.07 21 16 0.57 22 3 0.11 ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54 Consensus pattern (21 bp): TATATATCATGTATGTATATA Found at i:93021021 original size:2 final size:2 Alignment explanation

Indices: 93021014--93021084 Score: 133 Period size: 2 Copynumber: 35.5 Consensus size: 2 93021004 ACATATTTTA * 93021014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 93021056 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 A 93021085 GCACTATTAG Statistics Matches: 67, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 67 1.00 ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48 Consensus pattern (2 bp): AT Found at i:93024560 original size:11 final size:11 Alignment explanation

Indices: 93024530--93024564 Score: 52 Period size: 11 Copynumber: 3.2 Consensus size: 11 93024520 ATCTTCTTTA * * 93024530 TTATTTTACTC 1 TTATTTTATTT 93024541 TTATTTTATTT 1 TTATTTTATTT 93024552 TTATTTTATTT 1 TTATTTTATTT 93024563 TT 1 TT 93024565 TTCCCCTTTT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 11 22 1.00 ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77 Consensus pattern (11 bp): TTATTTTATTT Found at i:93024622 original size:13 final size:13 Alignment explanation

Indices: 93024604--93024658 Score: 56 Period size: 13 Copynumber: 4.0 Consensus size: 13 93024594 TACATACATC 93024604 ATAATAAAAAAAT 1 ATAATAAAAAAAT * 93024617 ATAATAAAAATAT 1 ATAATAAAAAAAT * 93024630 ATATACAAAACAAAT 1 ATA-ATAAAA-AAAT * 93024645 ATTAAAAAAAAAAT 1 A-TAATAAAAAAAT 93024659 TTACCTTTTC Statistics Matches: 35, Mismatches: 4, Indels: 5 0.80 0.09 0.11 Matches are distributed among these distances: 13 15 0.43 14 9 0.26 15 9 0.26 16 2 0.06 ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24 Consensus pattern (13 bp): ATAATAAAAAAAT Found at i:93025275 original size:3 final size:3 Alignment explanation

Indices: 93025267--93025306 Score: 71 Period size: 3 Copynumber: 13.3 Consensus size: 3 93025257 TGTATTTCAA * 93025267 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT T 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T 93025307 GTACGTTAGT Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65 Consensus pattern (3 bp): TAT Found at i:93025415 original size:3 final size:3 Alignment explanation

Indices: 93025407--93025465 Score: 109 Period size: 3 Copynumber: 19.7 Consensus size: 3 93025397 TGTATTTCAA 93025407 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT * 93025455 TAT TAT CAT TA 1 TAT TAT TAT TA 93025466 ACATTACTAT Statistics Matches: 54, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 3 54 1.00 ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64 Consensus pattern (3 bp): TAT Found at i:93025879 original size:22 final size:21 Alignment explanation

Indices: 93025846--93025888 Score: 59 Period size: 22 Copynumber: 2.0 Consensus size: 21 93025836 GTATACGTTC * 93025846 TATATATGTTATATATATATT 1 TATATATCTTATATATATATT * 93025867 TATATTATCTTATGTATATATT 1 TATA-TATCTTATATATATATT 93025889 ACCTTATATT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 21 4 0.21 22 15 0.79 ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58 Consensus pattern (21 bp): TATATATCTTATATATATATT Found at i:93027819 original size:2 final size:2 Alignment explanation

Indices: 93027812--93027841 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 93027802 TACAAATAAT 93027812 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 93027842 AAAGCACATA 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:93028082 original size:23 final size:23 Alignment explanation

Indices: 93028054--93028108 Score: 67 Period size: 23 Copynumber: 2.3 Consensus size: 23 93028044 TGGGTAACTA 93028054 ATTTTTACAAGT-TTTTTTTAATG 1 ATTTTT-CAAGTGTTTTTTTAATG * 93028077 ATTTTTCATGTGTTTTTTTAATG 1 ATTTTTCAAGTGTTTTTTTAATG 93028100 CAATTTTTC 1 --ATTTTTC 93028109 GAAAGAGAAC Statistics Matches: 28, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 22 4 0.14 23 17 0.61 25 7 0.25 ACGTcount: A:0.22, C:0.07, G:0.09, T:0.62 Consensus pattern (23 bp): ATTTTTCAAGTGTTTTTTTAATG Found at i:93028358 original size:2 final size:2 Alignment explanation

Indices: 93028351--93028383 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 93028341 AAATGTTCAC 93028351 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 A 93028384 AAATATTCCG Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:93029873 original size:31 final size:31 Alignment explanation

Indices: 93029838--93029901 Score: 83 Period size: 31 Copynumber: 2.1 Consensus size: 31 93029828 CTTAACAGCC * * * 93029838 TAGTGATTTAAATAAAAATTTTTGAATAGTT 1 TAGTGACTTAAATAAAAATTTTCGAATAATT * * 93029869 TAGTGGCTTAAATGAAAATTTTCGAATAATT 1 TAGTGACTTAAATAAAAATTTTCGAATAATT 93029900 TA 1 TA 93029902 TTATTTATTA Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 31 28 1.00 ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42 Consensus pattern (31 bp): TAGTGACTTAAATAAAAATTTTCGAATAATT Found at i:93039757 original size:3 final size:3 Alignment explanation

Indices: 93039749--93039819 Score: 142 Period size: 3 Copynumber: 23.7 Consensus size: 3 93039739 AGATTTAAAA 93039749 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG 1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG 93039797 AAG AAG AAG AAG AAG AAG AAG AA 1 AAG AAG AAG AAG AAG AAG AAG AA 93039820 AGGTTTACTG Statistics Matches: 68, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 68 1.00 ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00 Consensus pattern (3 bp): AAG Found at i:93043143 original size:24 final size:26 Alignment explanation

Indices: 93043102--93043150 Score: 66 Period size: 25 Copynumber: 2.0 Consensus size: 26 93043092 TGCTGCAAAT ** 93043102 TTTTTTTGACAAGTGCAAC-ATCACC 1 TTTTTTTGACAACAGCAACAATCACC 93043127 TTTTTTT-ACAACAGCAACAATCAC 1 TTTTTTTGACAACAGCAACAATCAC 93043151 TTTCCATTTG Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 24 9 0.43 25 12 0.57 ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35 Consensus pattern (26 bp): TTTTTTTGACAACAGCAACAATCACC Found at i:93044438 original size:3 final size:3 Alignment explanation

Indices: 93044425--93044507 Score: 59 Period size: 3 Copynumber: 27.3 Consensus size: 3 93044415 GAGGGCATAT 93044425 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA 1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA * * 93044469 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA A 1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A 93044508 AAAAATAAAA Statistics Matches: 65, Mismatches: 6, Indels: 18 0.73 0.07 0.20 Matches are distributed among these distances: 2 9 0.14 3 45 0.69 4 9 0.14 5 2 0.03 ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30 Consensus pattern (3 bp): ATA Found at i:93044449 original size:12 final size:12 Alignment explanation

Indices: 93044425--93044508 Score: 75 Period size: 12 Copynumber: 6.8 Consensus size: 12 93044415 GAGGGCATAT 93044425 ATAATAT-AATA 1 ATAATATAAATA 93044436 ATAATATAAATA 1 ATAATATAAATA 93044448 ATAATATATACATGA 1 ATAATATA-A-AT-A 93044463 GA-AATA-ATAATA 1 -ATAATATA-AATA 93044475 ATAATATAAATA 1 ATAATATAAATA * * 93044487 ATAGTAAAAATA 1 ATAATATAAATA * 93044499 ATAAAATAAA 1 ATAATATAAA 93044509 AAAATAAAAC Statistics Matches: 61, Mismatches: 5, Indels: 13 0.77 0.06 0.16 Matches are distributed among these distances: 11 8 0.13 12 38 0.62 13 4 0.07 14 5 0.08 15 5 0.08 16 1 0.02 ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30 Consensus pattern (12 bp): ATAATATAAATA Found at i:93044469 original size:21 final size:18 Alignment explanation

Indices: 93044430--93044489 Score: 75 Period size: 18 Copynumber: 3.2 Consensus size: 18 93044420 CATATATAAT * 93044430 ATAATAATAATATAAATA 1 ATAATAATAATAGAAATA 93044448 ATAATATATACATGAGAAATA 1 ATAATA-ATA-AT-AGAAATA * 93044469 ATAATAATAATATAAATA 1 ATAATAATAATAGAAATA 93044487 ATA 1 ATA 93044490 GTAAAAATAA Statistics Matches: 37, Mismatches: 2, Indels: 6 0.82 0.04 0.13 Matches are distributed among these distances: 18 15 0.41 19 5 0.14 20 5 0.14 21 12 0.32 ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32 Consensus pattern (18 bp): ATAATAATAATAGAAATA Found at i:93045387 original size:41 final size:42 Alignment explanation

Indices: 93045324--93045409 Score: 111 Period size: 41 Copynumber: 2.1 Consensus size: 42 93045314 AGACACGTGA * * 93045324 CTTCAATTAATTCCACTAAAACTTTAAGGAGATCTGCTGTAG 1 CTTCAATTAATTCCACTAAAACTTCAAGGAAATCTGCTGTAG * * * * 93045366 CTTCGATTAA-TCCACTGAAACTTCAAGGAAATCTGTTGTGG 1 CTTCAATTAATTCCACTAAAACTTCAAGGAAATCTGCTGTAG 93045407 CTT 1 CTT 93045410 TTAGCTGCTC Statistics Matches: 38, Mismatches: 6, Indels: 1 0.84 0.13 0.02 Matches are distributed among these distances: 41 29 0.76 42 9 0.24 ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34 Consensus pattern (42 bp): CTTCAATTAATTCCACTAAAACTTCAAGGAAATCTGCTGTAG Found at i:93045488 original size:68 final size:68 Alignment explanation

Indices: 93045375--93045645 Score: 461 Period size: 68 Copynumber: 4.0 Consensus size: 68 93045365 GCTTCGATTA * * * 93045375 ATCCACTGAAACTTCAAGGAAATCTGTTGTGGCTTTTAGCTGCTCCAACGCCATTTCAGGGAGAA 1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAA 93045440 GAG 66 GAG * * * 93045443 ATTCACTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCCAACGCCATATCAGGGAGAA 1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAA 93045508 GAG 66 GAG * * 93045511 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCTATTTCAGGGAAAA 1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAA 93045576 GAG 66 GAG * 93045579 ATCCACTGAAACTTCAAGGAGATCTACTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAA 1 ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAA 93045644 GA 66 GA 93045646 TATTTGATTT Statistics Matches: 191, Mismatches: 12, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 68 191 1.00 ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25 Consensus pattern (68 bp): ATCCACTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAA GAG Found at i:93045732 original size:44 final size:43 Alignment explanation

Indices: 93045656--93045779 Score: 133 Period size: 44 Copynumber: 2.8 Consensus size: 43 93045646 TATTTGATTT * ** 93045656 TCAACCTGTTACCCTACTGCTTA-AGGGGTTAAGGCTTGTTATCA 1 TCAACCTGTTACCCTACTGCTTAGA-GGTTTAAGGCTTG-TAAAA ** * * * 93045700 TTGATCTGTTTCCCTACTGCTTAGAGGTTTAAGATCTTGTAAAA 1 TCAACCTGTTACCCTACTGCTTAGAGGTTTAAG-GCTTGTAAAA * 93045744 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCT 1 TCAACCTGTTACCCTACTGCTTAGAGGTTTAAGGCT 93045780 CATCGCCTTC Statistics Matches: 64, Mismatches: 14, Indels: 5 0.77 0.17 0.06 Matches are distributed among these distances: 43 2 0.03 44 57 0.89 45 5 0.08 ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36 Consensus pattern (43 bp): TCAACCTGTTACCCTACTGCTTAGAGGTTTAAGGCTTGTAAAA Found at i:93045795 original size:88 final size:86 Alignment explanation

Indices: 93045656--93045916 Score: 281 Period size: 87 Copynumber: 3.0 Consensus size: 86 93045646 TATTTGATTT ** * * * 93045656 TCAACCTGTTACCCTACTGCTTAAGGGG-TTAAGGCTTGTTATCATTGATCTGTTTCCCTACTGC 1 TCAACCTGTTACCCTACTGCTT-AGGGGTTTAAGGCTCATCA-CCTTAATCTGTTTCCCTACTGC * 93045720 TTAGAGGTTTAAGATCTTGTAAAA 64 TTAGAGGGTTAAGATC-TGTAAAA * 93045744 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCGCCTTCAATCTGTTTCCCTACTGCT 1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCACCTT-AATCTGTTTCCCTACTGCT * * 93045809 TAGGGGGTTAAGATCTGTAAAT 65 TAGAGGGTTAAGATCTGTAAAA * ** * * ** * * 93045831 TTAGTCTGTTACCCTACTGTTTAGGGTTTTAAAACTCATCATCTTTAATCTGCTTCCCTACTGCT 1 TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCA-CCTTAATCTGTTTCCCTACTGCT * ** 93045896 TAGGGGGTTGCGATCTGTAAA 65 TAGAGGGTTAAGATCTGTAAA 93045917 TCTTCAATCT Statistics Matches: 149, Mismatches: 21, Indels: 7 0.84 0.12 0.04 Matches are distributed among these distances: 87 84 0.56 88 65 0.44 ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37 Consensus pattern (86 bp): TCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCACCTTAATCTGTTTCCCTACTGCTT AGAGGGTTAAGATCTGTAAAA Found at i:93046068 original size:43 final size:43 Alignment explanation

Indices: 93046018--93046172 Score: 168 Period size: 44 Copynumber: 3.6 Consensus size: 43 93046008 TTTAAGCCTA * * * 93046018 TTACCCTACTACTTAGGGGGTTAAGGTCTATAAATTTGGCTTG 1 TTACCCTACTGCTTAGGGGGTTAAGATCTATAAATTTAGCTTG * * * * 93046061 TTACCCTACTGCTTAGGGGGTTAAAGAT-TATTATTTTCGATCTG 1 TTACCCTACTGCTTAGGGGGTT-AAGATCTATAAATTTAGCT-TG * * * * * 93046105 TTTCCCTACTGCTTAGGGTGATAAGATCTATGAACTTCAGCTTG 1 TTACCCTACTGCTTAGGGGGTTAAGATCTAT-AAATTTAGCTTG 93046149 TTACCCTACTGCTTAGGGGGTTAA 1 TTACCCTACTGCTTAGGGGGTTAA 93046173 AGCTCGTTGC Statistics Matches: 91, Mismatches: 17, Indels: 7 0.79 0.15 0.06 Matches are distributed among these distances: 43 35 0.38 44 51 0.56 45 5 0.05 ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37 Consensus pattern (43 bp): TTACCCTACTGCTTAGGGGGTTAAGATCTATAAATTTAGCTTG Found at i:93046188 original size:88 final size:85 Alignment explanation

Indices: 93046015--93046229 Score: 232 Period size: 88 Copynumber: 2.5 Consensus size: 85 93046005 AATTTTAAGC * * * * ** 93046015 CTATTACCCTACTACTTAGGGGGTTAAGGTCTATAAATTTGGCTTGTTACCCTACTGCTTAGGGG 1 CTATTCCCCTACTGCTTA-GGGG-TAAGATCTATGAATTCAGCTTGTTACCCTACTGCTTAGGGG * ** 93046080 GTTAAAGATTATTATTTTCGAT 64 GTTAAAGATCATTACCTTCGAT * * 93046102 CTGTTTCCCTACTGCTTAGGGTGATAAGATCTATGAACTTCAGCTTGTTACCCTACTGCTTAGGG 1 CTATTCCCCTACTGCTTAGGG-G-TAAGATCTATGAA-TTCAGCTTGTTACCCTACTGCTTAGGG * * * 93046167 GGTTAAAGCTCGTTGCCTTCGAT 63 GGTTAAAGATCATTACCTTCGAT * * 93046190 CTATTCCCCTATTGCTTATGGGGTAAGATCTGTGAATTCA 1 CTATTCCCCTACTGCTTA-GGGGTAAGATCTATGAATTCA 93046230 CTGATTCTAG Statistics Matches: 107, Mismatches: 18, Indels: 7 0.81 0.14 0.05 Matches are distributed among these distances: 86 7 0.07 87 39 0.36 88 58 0.54 89 3 0.03 ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37 Consensus pattern (85 bp): CTATTCCCCTACTGCTTAGGGGTAAGATCTATGAATTCAGCTTGTTACCCTACTGCTTAGGGGGT TAAAGATCATTACCTTCGAT Found at i:93056739 original size:19 final size:19 Alignment explanation

Indices: 93056701--93056738 Score: 53 Period size: 17 Copynumber: 2.1 Consensus size: 19 93056691 TAAAGTAAAG * 93056701 TAAATAATAATACTATATA 1 TAAAAAATAATACTATATA 93056720 TAAAAAAT-ATA-TATATA 1 TAAAAAATAATACTATATA 93056737 TA 1 TA 93056739 TGTATATAAT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 17 8 0.44 18 3 0.17 19 7 0.39 ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37 Consensus pattern (19 bp): TAAAAAATAATACTATATA Found at i:93056994 original size:3 final size:3 Alignment explanation

Indices: 93056986--93057178 Score: 68 Period size: 3 Copynumber: 63.3 Consensus size: 3 93056976 AATAGGGGTG * * 93056986 ATA ATA ATA ATA ATA CTA ATA CA-A ACA ATA AT- ATA TATA TATA TATA 1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA -ATA -ATA * * * * * 93057033 ATA ATA GTA GTCA GA-A ATA A-A A-A ATA ATA GA-A GTA ACA ATA ATG 1 ATA ATA ATA AT-A -ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA * * 93057077 ATA ATA ATA AT- ATAA ATA A-A TATG GTA ATA ATA AT- ATAA ATA ATA 1 ATA ATA ATA ATA AT-A ATA ATA -ATA ATA ATA ATA ATA AT-A ATA ATA * * 93057122 ATA TATA CATGA GA-A ATA ATA ATA ATA AT- ATAA ATA ATA GTA AAA 1 ATA -ATA -AT-A -ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA 93057167 ATA ATA A-A ATA A 1 ATA ATA ATA ATA A 93057179 AAAAAATAAA Statistics Matches: 147, Mismatches: 21, Indels: 44 0.69 0.10 0.21 Matches are distributed among these distances: 2 18 0.12 3 102 0.69 4 25 0.17 5 2 0.01 ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30 Consensus pattern (3 bp): ATA Found at i:93057095 original size:36 final size:36 Alignment explanation

Indices: 93057065--93057170 Score: 99 Period size: 39 Copynumber: 2.9 Consensus size: 36 93057055 AATAATAGAA 93057065 GTAACAATAATGAT-AATAATAATATAAATAAATATG 1 GTAACAATAAT-ATAAATAATAATATAAATAAATATG * * 93057101 GTAATAATAATATAAATAATAATATATACATGAGAA-ATA 1 GTAACAATAATATAAATAATAATATA-A-AT-A-AATATG * * * * 93057140 ATAATAATAATATAAATAATAGTAAAAATAA 1 GTAACAATAATATAAATAATAATATAAATAA 93057171 TAAAATAAAA Statistics Matches: 60, Mismatches: 5, Indels: 11 0.79 0.07 0.14 Matches are distributed among these distances: 35 3 0.05 36 23 0.38 37 3 0.05 38 3 0.05 39 26 0.43 40 2 0.03 ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30 Consensus pattern (36 bp): GTAACAATAATATAAATAATAATATAAATAAATATG Found at i:93057120 original size:39 final size:39 Alignment explanation

Indices: 93057077--93057160 Score: 109 Period size: 39 Copynumber: 2.2 Consensus size: 39 93057067 AACAATAATG ** 93057077 ATAATAATAATATAAAT-A-AATATGGTAATAATAATATAA 1 ATAATAAT-ATATAAATGAGAA-ATAATAATAATAATATAA * 93057116 ATAATAATATATACATGAGAAATAATAATAATAATATAA 1 ATAATAATATATAAATGAGAAATAATAATAATAATATAA 93057155 ATAATA 1 ATAATA 93057161 GTAAAAATAA Statistics Matches: 40, Mismatches: 3, Indels: 4 0.85 0.06 0.09 Matches are distributed among these distances: 38 7 0.17 39 31 0.77 40 2 0.05 ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32 Consensus pattern (39 bp): ATAATAATATATAAATGAGAAATAATAATAATAATATAA Found at i:93057157 original size:12 final size:12 Alignment explanation

Indices: 93057070--93057179 Score: 77 Period size: 12 Copynumber: 8.9 Consensus size: 12 93057060 TAGAAGTAAC 93057070 AATAATGAT-AAT 1 AATAAT-ATAAAT 93057082 AATAATATAAAT 1 AATAATATAAAT * 93057094 -A-AATATGGTAAT 1 AATAATAT--AAAT 93057106 AATAATATAAAT 1 AATAATATAAAT 93057118 AATAATATATACAT 1 AATAATATA-A-AT 93057132 GAGA-AATA-ATAAT 1 -A-ATAATATA-AAT 93057145 AATAATATAAAT 1 AATAATATAAAT * * 93057157 AATAGTAAAAAT 1 AATAATATAAAT * 93057169 AATAAAATAAA 1 AATAATATAAA 93057180 AAAAATAAAA Statistics Matches: 80, Mismatches: 7, Indels: 22 0.73 0.06 0.20 Matches are distributed among these distances: 10 5 0.06 11 4 0.05 12 50 0.62 13 5 0.06 14 10 0.12 15 5 0.06 16 1 0.01 ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30 Consensus pattern (12 bp): AATAATATAAAT Found at i:93061129 original size:6 final size:6 Alignment explanation

Indices: 93061120--93061150 Score: 53 Period size: 6 Copynumber: 5.2 Consensus size: 6 93061110 AAAGAGTCCA * 93061120 ACCATC ACCACC ACCATC ACCATC ACCATC A 1 ACCATC ACCATC ACCATC ACCATC ACCATC A 93061151 TCTTCCTCTT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 6 23 1.00 ACGTcount: A:0.35, C:0.52, G:0.00, T:0.13 Consensus pattern (6 bp): ACCATC Found at i:93063474 original size:16 final size:16 Alignment explanation

Indices: 93063453--93063483 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 93063443 AAAATATTTT * 93063453 TTATAAAGTTTATATA 1 TTATAAAATTTATATA 93063469 TTATAAAATTTATAT 1 TTATAAAATTTATAT 93063484 TAATTTCAAG 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:0.45, C:0.00, G:0.03, T:0.52 Consensus pattern (16 bp): TTATAAAATTTATATA Found at i:93069360 original size:87 final size:87 Alignment explanation

Indices: 93069214--93069373 Score: 259 Period size: 87 Copynumber: 1.8 Consensus size: 87 93069204 AATAGCATGT * * 93069214 TTATAAATCATTTGGATAACTAATTTTGACACTTGATTTGTATATGCATTGCTTTCAAATCATGT 1 TTATAAATCATTTGGATAACTAATTATGACACTTGATTCGTATATGCATTGCTTTCAAATCATGT 93069279 TAGAACCATTGAGCTCTTTTGC 66 TAGAACCATTGAGCTCTTTTGC * * 93069301 TTATAAATTATTTGGATAACTAAATTATG-TACTTGATTCGTATATGCATTGCTTTCAAATCATG 1 TTATAAATCATTTGGATAACT-AATTATGACACTTGATTCGTATATGCATTGCTTTCAAATCATG * 93069365 TTAGCACCA 65 TTAGAACCA 93069374 CCAACTCTTT Statistics Matches: 67, Mismatches: 5, Indels: 2 0.91 0.07 0.03 Matches are distributed among these distances: 87 61 0.91 88 6 0.09 ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42 Consensus pattern (87 bp): TTATAAATCATTTGGATAACTAATTATGACACTTGATTCGTATATGCATTGCTTTCAAATCATGT TAGAACCATTGAGCTCTTTTGC Found at i:93074034 original size:6 final size:6 Alignment explanation

Indices: 93074023--93074056 Score: 50 Period size: 6 Copynumber: 5.7 Consensus size: 6 93074013 CTCCATTCAG * * 93074023 AGAAGT AGAAGT AGAAGT AGAACT AGAACT AGAA 1 AGAAGT AGAAGT AGAAGT AGAAGT AGAAGT AGAA 93074057 CGGTCAAGGC Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 6 27 1.00 ACGTcount: A:0.53, C:0.06, G:0.26, T:0.15 Consensus pattern (6 bp): AGAAGT Found at i:93076008 original size:18 final size:18 Alignment explanation

Indices: 93075967--93076008 Score: 50 Period size: 18 Copynumber: 2.3 Consensus size: 18 93075957 AAGGGTTAAG 93075967 TATTAATTTACAATAATTA 1 TATT-ATTTACAATAATTA * 93075986 CATTATTTA-AATAAATTA 1 TATTATTTACAAT-AATTA 93076004 TATTA 1 TATTA 93076009 AAATTTCATC Statistics Matches: 20, Mismatches: 2, Indels: 3 0.80 0.08 0.12 Matches are distributed among these distances: 17 3 0.15 18 14 0.70 19 3 0.15 ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48 Consensus pattern (18 bp): TATTATTTACAATAATTA Found at i:93087018 original size:33 final size:33 Alignment explanation

Indices: 93086976--93087042 Score: 134 Period size: 33 Copynumber: 2.0 Consensus size: 33 93086966 TTGAATATGT 93086976 TTGTGAATCAATTCACTTGTGACGTTCATAGTG 1 TTGTGAATCAATTCACTTGTGACGTTCATAGTG 93087009 TTGTGAATCAATTCACTTGTGACGTTCATAGTG 1 TTGTGAATCAATTCACTTGTGACGTTCATAGTG 93087042 T 1 T 93087043 GATTTACCTA Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 34 1.00 ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40 Consensus pattern (33 bp): TTGTGAATCAATTCACTTGTGACGTTCATAGTG Found at i:93093910 original size:47 final size:47 Alignment explanation

Indices: 93093847--93093976 Score: 181 Period size: 47 Copynumber: 2.8 Consensus size: 47 93093837 GTGCAAATAA * *** * 93093847 TACCTTGATTTGGCTACGGGCCATGATATAGGTA-TTTTGAGAGGAGT 1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGGA-AGAAGT * 93093894 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGGAATAAGT 1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGGAAGAAGT * 93093941 TACCTTGATTTGGCTACGGGTCATGGTATAGGTACT 1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT 93093977 TATCGATTGT Statistics Matches: 75, Mismatches: 7, Indels: 2 0.89 0.08 0.02 Matches are distributed among these distances: 47 72 0.96 48 3 0.04 ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33 Consensus pattern (47 bp): TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGGAAGAAGT Found at i:93095862 original size:46 final size:44 Alignment explanation

Indices: 93095808--93095917 Score: 139 Period size: 44 Copynumber: 2.5 Consensus size: 44 93095798 GACAGAACGA * * 93095808 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGATAGG 1 AATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGG * * 93095854 ATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACAGG 1 AATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGG * ** 93095898 AATAATTCATGTAAGTCCAT 1 AATGAGCCATGTAAGTCCAT 93095918 GTCAAAAACA Statistics Matches: 56, Mismatches: 8, Indels: 2 0.85 0.12 0.03 Matches are distributed among these distances: 44 34 0.61 46 22 0.39 ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30 Consensus pattern (44 bp): AATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGG Found at i:93095909 original size:44 final size:45 Alignment explanation

Indices: 93095812--93095936 Score: 135 Period size: 44 Copynumber: 2.8 Consensus size: 45 93095802 GAACGAAATG * * * * 93095812 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGATAGGATTG 1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAATA * 93095858 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATA 1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATA ** * * * 93095902 ATTCATGTAAGTCCATGTCAAAAACATGGCATTGG 1 AGCCATGTAAGTCCATAT-TAAAATATGGCATTGG 93095937 CAGGATATTG Statistics Matches: 66, Mismatches: 11, Indels: 4 0.81 0.14 0.05 Matches are distributed among these distances: 44 35 0.53 46 31 0.47 ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29 Consensus pattern (45 bp): AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATA Found at i:93099033 original size:24 final size:24 Alignment explanation

Indices: 93098982--93099037 Score: 67 Period size: 24 Copynumber: 2.3 Consensus size: 24 93098972 TCTTAATTAA * * 93098982 AAGTCCCTTGGTTAAATAATCATT 1 AAGTCCCTTGGTTAAATAATAATC * ** 93099006 AAGTCCCTTGGTTAATTGCTAATC 1 AAGTCCCTTGGTTAAATAATAATC 93099030 AAGTCCCT 1 AAGTCCCT 93099038 GTATATTTTC Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 24 27 1.00 ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36 Consensus pattern (24 bp): AAGTCCCTTGGTTAAATAATAATC Found at i:93109435 original size:2 final size:2 Alignment explanation

Indices: 93109428--93109458 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 93109418 TTTAACGCAA 93109428 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 93109459 AAATAAGATC Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:93109552 original size:2 final size:2 Alignment explanation

Indices: 93109547--93109575 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 93109537 TCACACACAC 93109547 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 A 93109576 ACAGGATGAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:93117174 original size:18 final size:17 Alignment explanation

Indices: 93117147--93117180 Score: 50 Period size: 18 Copynumber: 1.9 Consensus size: 17 93117137 TTGTACCCAC * 93117147 AAATTTTGAGTCGAAAGA 1 AAATTCTGAGTC-AAAGA 93117165 AAATTCTGAGTCAAAG 1 AAATTCTGAGTCAAAG 93117181 TTATTGATGA Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 4 0.27 18 11 0.73 ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26 Consensus pattern (17 bp): AAATTCTGAGTCAAAGA Found at i:93124058 original size:25 final size:25 Alignment explanation

Indices: 93124006--93124056 Score: 95 Period size: 25 Copynumber: 2.1 Consensus size: 25 93123996 CCTAAATAAC 93124006 TTAGTTTGTTTTTCCTTTTTTTTGT 1 TTAGTTTGTTTTTCCTTTTTTTTGT 93124031 TTAGTTTGTTTTTCC-TTTTTTTGT 1 TTAGTTTGTTTTTCCTTTTTTTTGT 93124055 TT 1 TT 93124057 TATAATCTGA Statistics Matches: 26, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 24 11 0.42 25 15 0.58 ACGTcount: A:0.04, C:0.08, G:0.12, T:0.76 Consensus pattern (25 bp): TTAGTTTGTTTTTCCTTTTTTTTGT Found at i:93130563 original size:46 final size:46 Alignment explanation

Indices: 93130496--93130588 Score: 150 Period size: 46 Copynumber: 2.0 Consensus size: 46 93130486 GGAAATAGGG * * 93130496 CATACATACTGACTTGGGTTACACGGCCAACCATACACCAGTGTGT 1 CATACATACTGACTTGGGTTACACAGCCAACCACACACCAGTGTGT * * 93130542 CATACATACTGACTTGGGTTACACAGCCAACCACACGCCCGTGTGT 1 CATACATACTGACTTGGGTTACACAGCCAACCACACACCAGTGTGT 93130588 C 1 C 93130589 TAACCCGTGT Statistics Matches: 43, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 46 43 1.00 ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23 Consensus pattern (46 bp): CATACATACTGACTTGGGTTACACAGCCAACCACACACCAGTGTGT Found at i:93139132 original size:30 final size:30 Alignment explanation

Indices: 93139092--93139149 Score: 89 Period size: 30 Copynumber: 1.9 Consensus size: 30 93139082 CTGGGCATTT * * 93139092 CCACATGGGCTGGCCATACGCCCATGTGAG 1 CCACACGGGCTGGCCACACGCCCATGTGAG * 93139122 CCACACGGGCTGGCCACACGCCTATGTG 1 CCACACGGGCTGGCCACACGCCCATGTG 93139150 CTAGTCCGTG Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 25 1.00 ACGTcount: A:0.19, C:0.36, G:0.29, T:0.16 Consensus pattern (30 bp): CCACACGGGCTGGCCACACGCCCATGTGAG Found at i:93139406 original size:17 final size:18 Alignment explanation

Indices: 93139386--93139422 Score: 58 Period size: 19 Copynumber: 2.1 Consensus size: 18 93139376 TTTCTTTATG 93139386 TTTTGT-TGTTTTCCTAT 1 TTTTGTATGTTTTCCTAT 93139403 TTTTGTGATGTTTTCCTAT 1 TTTTGT-ATGTTTTCCTAT 93139422 T 1 T 93139423 ACATTATGAA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 17 6 0.33 19 12 0.67 ACGTcount: A:0.08, C:0.11, G:0.14, T:0.68 Consensus pattern (18 bp): TTTTGTATGTTTTCCTAT Found at i:93142420 original size:44 final size:44 Alignment explanation

Indices: 93142328--93142436 Score: 130 Period size: 44 Copynumber: 2.5 Consensus size: 44 93142318 TCAATTTCGA * * 93142328 TTTTTCAACATCGACGTGGTACAATAGAGAATTAATCCTTATTT 1 TTTTTCAACATCGACATGGTACAATAGAGAATCAATCCTTATTT * * * * 93142372 TTTTTCAACATCAACATGGTACAATGGAG-ATCAATTCTTGTTTT 1 TTTTTCAACATCGACATGGTACAATAGAGAATCAATCCTT-ATTT * * 93142416 TTTTTTAACATTGACATGGTA 1 TTTTTCAACATCGACATGGTA 93142437 AGGTAGAGAC Statistics Matches: 55, Mismatches: 9, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 43 8 0.15 44 47 0.85 ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41 Consensus pattern (44 bp): TTTTTCAACATCGACATGGTACAATAGAGAATCAATCCTTATTT Found at i:93142727 original size:70 final size:70 Alignment explanation

Indices: 93142537--93142735 Score: 224 Period size: 70 Copynumber: 2.8 Consensus size: 70 93142527 AAAATGGCGA * * * 93142537 GAAGAGCTTTTGCAACTTCAACATGGCTAGAGGAGGGCCCATTCCGAACTTTGCAACATCAACAT 1 GAAGAACTTTTGCAACTTCAACATGACTAGAGGAGGGCCCATTCTGAACTTTGCAACATCAACAT 93142602 GGAAG 66 GGAAG * ** * * 93142607 AAAGAACTTTTGCAACTTCAACATGA-TGAGAGGAGAACCCA-TCTCGAACTTTGTAACTTCAAC 1 GAAGAACTTTTGCAACTTCAACATGACT-AGAGGAGGGCCCATTCT-GAACTTTGCAACATCAAC 93142670 AT-GAAGG 64 ATGGAA-G ** * * * * 93142677 GAAGAACTTTTGCAACTTCAATGTGACTAGAGGAGGGTCGATTCTAAACTTCGCAACAT 1 GAAGAACTTTTGCAACTTCAACATGACTAGAGGAGGGCCCATTCTGAACTTTGCAACAT 93142736 TAAAACAGTT Statistics Matches: 105, Mismatches: 19, Indels: 10 0.78 0.14 0.07 Matches are distributed among these distances: 69 6 0.06 70 95 0.90 71 4 0.04 ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24 Consensus pattern (70 bp): GAAGAACTTTTGCAACTTCAACATGACTAGAGGAGGGCCCATTCTGAACTTTGCAACATCAACAT GGAAG Found at i:93149808 original size:2 final size:2 Alignment explanation

Indices: 93149803--93149844 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 93149793 CTTTTTTACC 93149803 TA TA TA TA TA TA 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 TA TA TA TA TA TA 93149845 GAACATATTA Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:93150493 original size:3 final size:3 Alignment explanation

Indices: 93150434--93150474 Score: 75 Period size: 3 Copynumber: 14.0 Consensus size: 3 93150424 TTACTTTATG 93150434 TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA 93150475 CTAGTATATG Statistics Matches: 37, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 2 2 0.05 3 35 0.95 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (3 bp): TTA Found at i:93155696 original size:46 final size:44 Alignment explanation

Indices: 93155637--93155751 Score: 149 Period size: 44 Copynumber: 2.6 Consensus size: 44 93155627 ACAGGACAGA * * 93155637 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG * * 93155683 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG * ** 93155727 ACAGGAATAATTCATGTAAGTCCAT 1 ACAGGAATGAGCCATGTAAGTCCAT 93155752 GTCAAAGACA Statistics Matches: 61, Mismatches: 8, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 44 35 0.57 46 26 0.43 ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28 Consensus pattern (44 bp): ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG Found at i:93155732 original size:44 final size:45 Alignment explanation

Indices: 93155637--93155770 Score: 153 Period size: 46 Copynumber: 3.0 Consensus size: 45 93155627 ACAGGACAGA * * 93155637 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG * * 93155683 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG * ** * * * 93155727 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG 93155771 CAGGATATTG Statistics Matches: 74, Mismatches: 12, Indels: 4 0.82 0.13 0.04 Matches are distributed among these distances: 44 36 0.49 45 1 0.01 46 37 0.50 ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27 Consensus pattern (45 bp): ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG Found at i:93161837 original size:46 final size:44 Alignment explanation

Indices: 93161778--93161892 Score: 149 Period size: 44 Copynumber: 2.6 Consensus size: 44 93161768 ACAGGACAGA * * 93161778 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG * * 93161824 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG * ** 93161868 ACAGGAATAATTCATGTAAGTCCAT 1 ACAGGAATGAGCCATGTAAGTCCAT 93161893 GTCAAAGACA Statistics Matches: 61, Mismatches: 8, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 44 35 0.57 46 26 0.43 ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28 Consensus pattern (44 bp): ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG Found at i:93161873 original size:44 final size:45 Alignment explanation

Indices: 93161778--93161911 Score: 153 Period size: 46 Copynumber: 3.0 Consensus size: 45 93161768 ACAGGACAGA * * 93161778 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG * * 93161824 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG * ** * * * 93161868 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG 1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG 93161912 CAGGATATTG Statistics Matches: 74, Mismatches: 12, Indels: 4 0.82 0.13 0.04 Matches are distributed among these distances: 44 36 0.49 45 1 0.01 46 37 0.50 ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27 Consensus pattern (45 bp): ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG Found at i:93167040 original size:25 final size:25 Alignment explanation

Indices: 93166992--93167040 Score: 64 Period size: 25 Copynumber: 2.0 Consensus size: 25 93166982 CATATCACAG * 93166992 CTCTTTATGAGCATTCTGACATAGA 1 CTCTTTATGAGCATTCTGAAATAGA * 93167017 CTCTTTGTGAGC-TTCTTGAAATAG 1 CTCTTTATGAGCATTC-TGAAATAG 93167041 CTCGCTTGAA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 24 3 0.14 25 18 0.86 ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39 Consensus pattern (25 bp): CTCTTTATGAGCATTCTGAAATAGA Found at i:93167404 original size:17 final size:17 Alignment explanation

Indices: 93167377--93167418 Score: 56 Period size: 16 Copynumber: 2.7 Consensus size: 17 93167367 TTATATGGAA 93167377 ATATG-ATATGAAAAGT 1 ATATGTATATGAAAAGT 93167393 ATATGTATATG-AAAGT 1 ATATGTATATGAAAAGT 93167409 -TAT-TATATGA 1 ATATGTATATGA 93167419 TGAGCTCATC Statistics Matches: 24, Mismatches: 0, Indels: 5 0.83 0.00 0.17 Matches are distributed among these distances: 14 6 0.25 15 3 0.12 16 10 0.42 17 5 0.21 ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38 Consensus pattern (17 bp): ATATGTATATGAAAAGT Found at i:93168776 original size:37 final size:38 Alignment explanation

Indices: 93168725--93168796 Score: 94 Period size: 37 Copynumber: 1.9 Consensus size: 38 93168715 ACAACTTTAA * 93168725 CACCCAATGTCTCATC-AATTAAA-TCGAAGCAAATTGG 1 CACCCAATGCCTCATCGAATTAAAGTCGAAG-AAATTGG * * 93168762 CACCCAGTGCCTCATCGACTTAAAGTCGAAGAAAT 1 CACCCAATGCCTCATCGAATTAAAGTCGAAGAAAT 93168797 CCCTGAACTC Statistics Matches: 30, Mismatches: 3, Indels: 3 0.83 0.08 0.08 Matches are distributed among these distances: 37 14 0.47 38 10 0.33 39 6 0.20 ACGTcount: A:0.36, C:0.26, G:0.15, T:0.22 Consensus pattern (38 bp): CACCCAATGCCTCATCGAATTAAAGTCGAAGAAATTGG Found at i:93169692 original size:10 final size:9 Alignment explanation

Indices: 93169669--93169702 Score: 50 Period size: 9 Copynumber: 3.7 Consensus size: 9 93169659 TTCGTTATCC * 93169669 TTCTTTTCT 1 TTCTTTTTT 93169678 TTCTTTATTT 1 TTCTTT-TTT 93169688 TTCTTTTTT 1 TTCTTTTTT 93169697 TTCTTT 1 TTCTTT 93169703 CTTCTTTTTC Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 9 15 0.65 10 8 0.35 ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82 Consensus pattern (9 bp): TTCTTTTTT Found at i:93169703 original size:13 final size:13 Alignment explanation

Indices: 93169673--93169715 Score: 52 Period size: 13 Copynumber: 3.2 Consensus size: 13 93169663 TTATCCTTCT 93169673 TTTCTTTCTTTATT- 1 TTTCTTT-TTT-TTC 93169687 TTTCTTTTTTTTC 1 TTTCTTTTTTTTC * 93169700 TTTCTTCTTTTTC 1 TTTCTTTTTTTTC 93169713 TTT 1 TTT 93169716 TAATTTGCAT Statistics Matches: 27, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 12 2 0.07 13 18 0.67 14 7 0.26 ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81 Consensus pattern (13 bp): TTTCTTTTTTTTC Found at i:93169710 original size:22 final size:23 Alignment explanation

Indices: 93169672--93169716 Score: 74 Period size: 22 Copynumber: 2.0 Consensus size: 23 93169662 GTTATCCTTC 93169672 TTTTCTTTCTTTATTTTTCTTTT 1 TTTTCTTTCTTTATTTTTCTTTT * 93169695 TTTTCTTTC-TTCTTTTTCTTTT 1 TTTTCTTTCTTTATTTTTCTTTT 93169717 AATTTGCATG Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 22 12 0.57 23 9 0.43 ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82 Consensus pattern (23 bp): TTTTCTTTCTTTATTTTTCTTTT Found at i:93179984 original size:9 final size:9 Alignment explanation

Indices: 93179970--93180073 Score: 120 Period size: 9 Copynumber: 11.6 Consensus size: 9 93179960 ATAAGTATAA 93179970 AATTAACCG 1 AATTAACCG * 93179979 AATTAACCT 1 AATTAACCG * 93179988 AATTAATCG 1 AATTAACCG ** 93179997 AATTAAAAG 1 AATTAACCG 93180006 AATT-ACCTG 1 AATTAACC-G * 93180015 AATTACCCG 1 AATTAACCG * * 93180024 AATTACCCA 1 AATTAACCG 93180033 AATTAACCG 1 AATTAACCG 93180042 AATTAACCG 1 AATTAACCG 93180051 AATTAACCG 1 AATTAACCG * 93180060 AATTAACCA 1 AATTAACCG 93180069 AATTA 1 AATTA 93180074 TTTGTATAAA Statistics Matches: 81, Mismatches: 12, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 8 1 0.01 9 78 0.96 10 2 0.02 ACGTcount: A:0.46, C:0.20, G:0.08, T:0.26 Consensus pattern (9 bp): AATTAACCG Found at i:93180104 original size:6 final size:6 Alignment explanation

Indices: 93180093--93180180 Score: 124 Period size: 6 Copynumber: 14.2 Consensus size: 6 93180083 AATTATAAGT * 93180093 TTTTTA TTTTTA TTTTTA GTTTTAAA TTTTTA TTTTTA TTTTTA TTTTTA 1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA 93180143 TTTTTA TTTTTA TTTATTA TTTTT- TTTTTAA TTTTTA T 1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTTT-A TTTTTA T 93180181 GATTGGGTTG Statistics Matches: 75, Mismatches: 2, Indels: 10 0.86 0.02 0.11 Matches are distributed among these distances: 5 5 0.07 6 50 0.67 7 19 0.25 8 1 0.01 ACGTcount: A:0.19, C:0.00, G:0.01, T:0.80 Consensus pattern (6 bp): TTTTTA Found at i:93180881 original size:17 final size:17 Alignment explanation

Indices: 93180859--93180893 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 93180849 AGTACCGAGT 93180859 CAGTTTGGATTGCGCAA 1 CAGTTTGGATTGCGCAA 93180876 CAGTTTGGATTGCGCAA 1 CAGTTTGGATTGCGCAA 93180893 C 1 C 93180894 TAAGAGGGTC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29 Consensus pattern (17 bp): CAGTTTGGATTGCGCAA Found at i:93188759 original size:14 final size:14 Alignment explanation

Indices: 93188740--93188769 Score: 60 Period size: 14 Copynumber: 2.1 Consensus size: 14 93188730 TTTCGCTTTA 93188740 TTACTTTATTTGCG 1 TTACTTTATTTGCG 93188754 TTACTTTATTTGCG 1 TTACTTTATTTGCG 93188768 TT 1 TT 93188770 TGATGTCTAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60 Consensus pattern (14 bp): TTACTTTATTTGCG Found at i:93190463 original size:22 final size:22 Alignment explanation

Indices: 93190438--93190480 Score: 86 Period size: 22 Copynumber: 2.0 Consensus size: 22 93190428 TCTGCAAGCT 93190438 TTAACAAAATTTAATGTACATA 1 TTAACAAAATTTAATGTACATA 93190460 TTAACAAAATTTAATGTACAT 1 TTAACAAAATTTAATGTACAT 93190481 GTATAAATTA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 21 1.00 ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37 Consensus pattern (22 bp): TTAACAAAATTTAATGTACATA Found at i:93197008 original size:25 final size:25 Alignment explanation

Indices: 93196974--93197024 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 93196964 TTTGAAACAA 93196974 ACAAAACCTTAGTGCATTTAAGGCT 1 ACAAAACCTTAGTGCATTTAAGGCT 93196999 ACAAAACCTTAGTGCATTTAAGGCT 1 ACAAAACCTTAGTGCATTTAAGGCT 93197024 A 1 A 93197025 TGTTAAATTA 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:0.37, C:0.20, G:0.16, T:0.27 Consensus pattern (25 bp): ACAAAACCTTAGTGCATTTAAGGCT Found at i:93210354 original size:60 final size:60 Alignment explanation

Indices: 93210264--93210478 Score: 304 Period size: 60 Copynumber: 3.6 Consensus size: 60 93210254 AAAATCCAAG * * * 93210264 ATAGTTGGGTGACAAAAAAACAAAATTGACTAATAGTTCAGTGACCATTTTGTAACTATTC 1 ATAGTTGGGTGACCAAAAAA-GAAATTGACTAATAGTTGAGTGACCATTTTGTAACTATTC * * * * 93210325 ATAGCTGGGTGACCAAAAAAGAAATTGACTAATAGTTGGGTGACTATTTTGTAAATATTC 1 ATAGTTGGGTGACCAAAAAAGAAATTGACTAATAGTTGAGTGACCATTTTGTAACTATTC * * * 93210385 ATAATTGGGTGATCAAAAAAGAAATTGACTAATAGTTGAGTGATCATTTTGTAACTATTC 1 ATAGTTGGGTGACCAAAAAAGAAATTGACTAATAGTTGAGTGACCATTTTGTAACTATTC * * * 93210445 ATAGTTGAGTGATCAAAAAAGAAATTTACTAATA 1 ATAGTTGGGTGACCAAAAAAGAAATTGACTAATA 93210479 TTTAAGCGAC Statistics Matches: 137, Mismatches: 17, Indels: 1 0.88 0.11 0.01 Matches are distributed among these distances: 60 119 0.87 61 18 0.13 ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32 Consensus pattern (60 bp): ATAGTTGGGTGACCAAAAAAGAAATTGACTAATAGTTGAGTGACCATTTTGTAACTATTC Found at i:93216608 original size:22 final size:21 Alignment explanation

Indices: 93216581--93216625 Score: 56 Period size: 22 Copynumber: 2.1 Consensus size: 21 93216571 TGGATATTTA 93216581 TATTTTGT-TTTAAATTTAAATT 1 TATTTT-TATTTAAA-TTAAATT * 93216603 TATTTTTATTTATATTAAATT 1 TATTTTTATTTAAATTAAATT 93216624 TA 1 TA 93216626 AATATTATTA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 21 10 0.48 22 11 0.52 ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64 Consensus pattern (21 bp): TATTTTTATTTAAATTAAATT Found at i:93220800 original size:19 final size:19 Alignment explanation

Indices: 93220776--93220813 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 93220766 TAATTTAGTG 93220776 TTTAATAAAATTAATTAAC 1 TTTAATAAAATTAATTAAC 93220795 TTTAATAAAATTAATTAAC 1 TTTAATAAAATTAATTAAC 93220814 ATGTTGAGAG 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:0.53, C:0.05, G:0.00, T:0.42 Consensus pattern (19 bp): TTTAATAAAATTAATTAAC Found at i:93228268 original size:33 final size:33 Alignment explanation

Indices: 93228226--93228298 Score: 121 Period size: 33 Copynumber: 2.2 Consensus size: 33 93228216 CAATCCCTCT * 93228226 AACACACCAATGCTCATAAGAGTTAAT-CAGACC 1 AACACACCAATGCTCATAAGAGCTAATCCA-ACC 93228259 AACACACCAATGCTCATAAGAGCTAATCCAACC 1 AACACACCAATGCTCATAAGAGCTAATCCAACC 93228292 AACACAC 1 AACACAC 93228299 TAAACAGAGT Statistics Matches: 38, Mismatches: 1, Indels: 2 0.93 0.02 0.05 Matches are distributed among these distances: 33 36 0.95 34 2 0.05 ACGTcount: A:0.44, C:0.32, G:0.10, T:0.15 Consensus pattern (33 bp): AACACACCAATGCTCATAAGAGCTAATCCAACC Found at i:93235667 original size:2 final size:2 Alignment explanation

Indices: 93235660--93235684 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 93235650 AATTTACTCT 93235660 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 93235685 TACAATATTA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:93237606 original size:30 final size:26 Alignment explanation

Indices: 93237549--93237601 Score: 88 Period size: 26 Copynumber: 2.0 Consensus size: 26 93237539 AGAACAAGAA * 93237549 TTAAAGGATGATTGAAAAAAATTCTT 1 TTAAAGGATGATCGAAAAAAATTCTT * 93237575 TTAAAGGATGATCGAAAAAAACTCTT 1 TTAAAGGATGATCGAAAAAAATTCTT 93237601 T 1 T 93237602 CTTTTGGGAG Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32 Consensus pattern (26 bp): TTAAAGGATGATCGAAAAAAATTCTT Found at i:93241238 original size:44 final size:45 Alignment explanation

Indices: 93241148--93241276 Score: 152 Period size: 44 Copynumber: 2.8 Consensus size: 45 93241138 ACAGAACAAA * 93241148 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG 1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG * * 93241194 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG 1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG * ** * * * 93241238 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG 1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG 93241277 CAGGATATTG Statistics Matches: 70, Mismatches: 11, Indels: 4 0.82 0.13 0.05 Matches are distributed among these distances: 44 36 0.51 45 1 0.01 46 33 0.47 ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28 Consensus pattern (45 bp): AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG Found at i:93242725 original size:13 final size:13 Alignment explanation

Indices: 93242709--93242746 Score: 60 Period size: 12 Copynumber: 2.9 Consensus size: 13 93242699 TAACCCAACC 93242709 CAAAAAAAAAAAT 1 CAAAAAAAAAAAT 93242722 C-AAAAAAAAAAT 1 CAAAAAAAAAAAT 93242734 CAAAAAAAGAAAA 1 CAAAAAAA-AAAA 93242747 AACCTAATCT Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 12 12 0.52 13 7 0.30 14 4 0.17 ACGTcount: A:0.84, C:0.08, G:0.03, T:0.05 Consensus pattern (13 bp): CAAAAAAAAAAAT Found at i:93242728 original size:12 final size:12 Alignment explanation

Indices: 93242711--93242741 Score: 62 Period size: 12 Copynumber: 2.6 Consensus size: 12 93242701 ACCCAACCCA 93242711 AAAAAAAAAATC 1 AAAAAAAAAATC 93242723 AAAAAAAAAATC 1 AAAAAAAAAATC 93242735 AAAAAAA 1 AAAAAAA 93242742 GAAAAAACCT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06 Consensus pattern (12 bp): AAAAAAAAAATC Found at i:93243028 original size:27 final size:26 Alignment explanation

Indices: 93242988--93243045 Score: 80 Period size: 27 Copynumber: 2.2 Consensus size: 26 93242978 AGAAGAAAAA * 93242988 TTTTTTTGAGATTCAAGAAGAGATTTT 1 TTTTTTTGAAATTCAAG-AGAGATTTT * * 93243015 TTTTTTTGAAATTCAAGAGGGGTTTT 1 TTTTTTTGAAATTCAAGAGAGATTTT 93243041 TTTTT 1 TTTTT 93243046 CTTGGGAACA Statistics Matches: 28, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 26 12 0.43 27 16 0.57 ACGTcount: A:0.24, C:0.03, G:0.19, T:0.53 Consensus pattern (26 bp): TTTTTTTGAAATTCAAGAGAGATTTT Found at i:93243161 original size:9 final size:10 Alignment explanation

Indices: 93243142--93243171 Score: 51 Period size: 10 Copynumber: 2.9 Consensus size: 10 93243132 TAATTTTTGA 93243142 TTTCTTTTTT 1 TTTCTTTTTT 93243152 TTTCTTTTTT 1 TTTCTTTTTT 93243162 TTTCATTTTT 1 TTTC-TTTTT 93243172 GATTTTGCTT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 14 0.74 11 5 0.26 ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87 Consensus pattern (10 bp): TTTCTTTTTT Found at i:93243748 original size:3 final size:3 Alignment explanation

Indices: 93243546--93243733 Score: 82 Period size: 3 Copynumber: 61.7 Consensus size: 3 93243536 TTTTCTTGCA * * * 93243546 TAT TATT TAC TAT TAT TAT TAT TACCT TCAT T-T CAT TAT TAT TAT TAC 1 TAT TA-T TAT TAT TAT TAT TAT TA--T T-AT TAT TAT TAT TAT TAT TAT ** * * * * 93243594 TAT TGC TAT T-T TTT TGT TGT T-T ATAT TTT TATT TAT TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT * * * 93243639 TAT TAT TAT TAT TAT TAT TAT TAT CTCCGT GAC TAT TAT TAT TAT T-T 1 TAT TAT TAT TAT TAT TAT TAT TAT -T--AT TAT TAT TAT TAT TAT TAT * * * * * * * 93243686 TGT TA- TAT TAT TGT TA- TAT TAT CAC TAT TTT TCT TAC TAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 93243732 TA 1 TA 93243734 CTACAACTAT Statistics Matches: 139, Mismatches: 31, Indels: 30 0.69 0.16 0.15 Matches are distributed among these distances: 2 10 0.07 3 115 0.83 4 10 0.07 5 2 0.01 6 2 0.01 ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62 Consensus pattern (3 bp): TAT Found at i:93243919 original size:21 final size:21 Alignment explanation

Indices: 93243870--93243954 Score: 79 Period size: 21 Copynumber: 4.2 Consensus size: 21 93243860 TTCTTTTCTC ** 93243870 TATT-TTATTACTATTATTAA 1 TATTATTATTACTATTATTTT * 93243890 TATCATTATTACTATTATTTT 1 TATTATTATTACTATTATTTT * 93243911 TATTTTTATT--T-TTATTTT 1 TATTATTATTACTATTATTTT * * * 93243929 TATTACTACTACTGTTATTTT 1 TATTATTATTACTATTATTTT 93243950 TATTA 1 TATTA 93243955 ACATATTTTT Statistics Matches: 53, Mismatches: 8, Indels: 7 0.78 0.12 0.10 Matches are distributed among these distances: 18 14 0.26 19 1 0.02 20 4 0.08 21 34 0.64 ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65 Consensus pattern (21 bp): TATTATTATTACTATTATTTT Found at i:93243952 original size:6 final size:6 Alignment explanation

Indices: 93243904--93243932 Score: 58 Period size: 6 Copynumber: 4.8 Consensus size: 6 93243894 ATTATTACTA 93243904 TTATTT TTATTT TTATTT TTATTT TTATT 1 TTATTT TTATTT TTATTT TTATTT TTATT 93243933 ACTACTACTG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 23 1.00 ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83 Consensus pattern (6 bp): TTATTT Found at i:93244073 original size:20 final size:20 Alignment explanation

Indices: 93244021--93244073 Score: 54 Period size: 20 Copynumber: 2.6 Consensus size: 20 93244011 CAACATATAC * 93244021 TATTAT-TATTAATGTACTAT 1 TATTATATATTTAT-TACTAT * * 93244041 TATTTTCTATTTATTACTAT 1 TATTATATATTTATTACTAT * 93244061 TATTATATTTTTA 1 TATTATATATTTA 93244074 CCCATTACTC Statistics Matches: 27, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 20 21 0.78 21 6 0.22 ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62 Consensus pattern (20 bp): TATTATATATTTATTACTAT Found at i:93252613 original size:205 final size:205 Alignment explanation

Indices: 93252254--93254870 Score: 4702 Period size: 205 Copynumber: 12.9 Consensus size: 205 93252244 GTAATAGGCC * * 93252254 ACACATAGCAGATCTCGCCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGTATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT * * * 93252319 GTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGTCTTTCACGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA * * 93252384 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAAAGAATCAAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA * 93252449 TGAAGAGCAG 196 TGGAGAGCAG * 93252459 ACACATGGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93252524 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA * 93252589 TCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93252654 TGGAGAGCAG 196 TGGAGAGCAG * 93252664 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTAGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93252729 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 93252794 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93252859 TGGAGAGCAG 196 TGGAGAGCAG 93252869 ACACATAGCAGATCTCACCTTCAGATGATTT-TGCTGAAGCGGATCCAAGATGGTTTGGCATCCT 1 ACACATAGCAGATCTCACCTTCAGATG-TTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCT * 93252933 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTCGCTTTCATGTGATTACGATGAAGCAA 65 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAA * 93252998 ATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG 130 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG 93253063 ATGGAGAGCAG 195 ATGGAGAGCAG 93253074 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93253139 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 93253204 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93253269 TGGAGAGCAG 196 TGGAGAGCAG 93253279 ACACATAGCAGATCTCACCTTCAGATGATTT-TGCTGAAGCGGATCCAAGATGGTTTGGCATCCT 1 ACACATAGCAGATCTCACCTTCAGATG-TTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCT 93253343 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAA 65 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAA * * 93253408 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCTAAGCTTGGCATCTTCACTTTG 130 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG 93253473 ATGGAGAGCAG 195 ATGGAGAGCAG 93253484 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93253549 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC------G---A 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 93253605 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93253670 TGGAGAGCAG 196 TGGAGAGCAG 93253680 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93253745 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA * 93253810 TCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93253875 TGGAGAGCAG 196 TGGAGAGCAG 93253885 ACACATAGCAGATCTCACCTTCAGATGATTT-TGCTGAAGCGGATCCAAGATGGTTTGGCATCCT 1 ACACATAGCAGATCTCACCTTCAGATG-TTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCT 93253949 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAA 65 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAA * 93254014 ATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG 130 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG 93254079 ATGGAGAGCAG 195 ATGGAGAGCAG * 93254090 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAAATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93254155 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC------G---A 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 93254211 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93254276 TGGAGAGCAG 196 TGGAGAGCAG 93254286 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93254351 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA * 93254416 TCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93254481 TGGAGAGCAG 196 TGGAGAGCAG 93254491 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93254556 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA * 93254621 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCAAAGTTTGGCATCTTCACTTTGA 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA 93254686 TGGAGAGCAG 196 TGGAGAGCAG * * * 93254696 ACACATAGCAGATCTCACCTTCGGATGTTTATGCTGAAACGGATCCAAGATGGATTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT * ** * * ** * * * 93254761 ATACTTACAAGGAACAAATCGAA-TCATAGTTGATTTGGCTTTCGCGTGCTTACGTTAAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA * * * * * * 93254825 TCTAAGATAATTTGGCATCTCTGTATTGTCAGAGATCAAATCGAAG 131 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAG 93254871 AAATAAATCT Statistics Matches: 2337, Mismatches: 51, Indels: 49 0.96 0.02 0.02 Matches are distributed among these distances: 196 386 0.17 199 2 0.00 202 2 0.00 204 82 0.04 205 1856 0.79 206 9 0.00 ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30 Consensus pattern (205 bp): ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGCAAA TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA TGGAGAGCAG Found at i:93253920 original size:606 final size:608 Alignment explanation

Indices: 93252254--93254803 Score: 4657 Period size: 606 Copynumber: 4.2 Consensus size: 608 93252244 GTAATAGGCC * * 93252254 ACACATAGCAGATCTCGCCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGTATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT * * * 93252319 GTGTTTACAAGGAGCAAATCGAAGACATAGCTGATTTGTCTTTCACGTGATTACGATGAAGCAAA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC-----AG--AA * * 93252384 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAAAGAATCAAAGTTTGGCATCTTCACTTTGA 124 TCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGA * * 93252449 TGAAGAGCAGACACATGGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTT 189 TGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTT 93252514 TGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACG 254 TGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACG 93252579 ATGAAGCAAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATC 319 ATGAAGCAAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATC 93252644 TTCACTTTGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATC 384 TTCACTTTGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATC * 93252709 CAAGATGGTTTAGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCA 449 CAAGATGGTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCA 93252774 TGTGATTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAA 514 TGTGATTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAA 93252839 GTTTGGCATCTTCACTTTGATGGAGAGCAG 579 GTTTGGCATCTTCACTTTGATGGAGAGCAG 93252869 ACACATAGCAGATCTCACCTTCAGATGATTT-TGCTGAAGCGGATCCAAGATGGTTTGGCATCCT 1 ACACATAGCAGATCTCACCTTCAGATG-TTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCT * 93252933 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTCGCTTTCATGTGATTACGATGAAGCAA 65 TGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC-----AG--A * 93252998 ATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG 123 ATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTG 93253063 ATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGT 188 ATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGT 93253128 TTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC 253 TTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC * 93253193 GATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCAT 318 GATGAAGCAAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCAT 93253258 CTTCACTTTGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGATTT-TGCTGAAGCGGA 383 CTTCACTTTGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATG-TTTATGCTGAAGCGGA 93253322 TCCAAGATGGTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTT 447 TCCAAGATGGTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTT * 93253387 CATGTGATTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCT 512 CATGTGATTACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCG * 93253452 AAGCTTGGCATCTTCACTTTGATGGAGAGCAG 577 AAGTTTGGCATCTTCACTTTGATGGAGAGCAG 93253484 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93253549 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC-G-ATCTAAGA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACAGAATCTAAGA 93253612 TGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAG 131 TGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAG 93253677 CAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATC 196 CAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATC 93253742 CTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGC 261 CTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGC 93253807 AAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTT 326 AAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTT 93253872 TGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGATTT-TGCTGAAGCGGATCCAAGAT 391 TGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATG-TTTATGCTGAAGCGGATCCAAGAT 93253936 GGTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGAT 455 GGTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGAT * 93254001 TACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGG 520 TACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGG 93254066 CATCTTCACTTTGATGGAGAGCAG 585 CATCTTCACTTTGATGGAGAGCAG * 93254090 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAAATGGTTTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT 93254155 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTAC-G-ATCTAAGA 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACAGAATCTAAGA 93254218 TGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAG 131 TGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAG 93254283 CAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATC 196 CAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATC 93254348 CTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGC 261 CTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGC 93254413 AAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTT 326 AAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTT 93254478 TGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATG 391 TGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATG 93254543 GTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATT 456 GTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATT * 93254608 ACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCAAAGTTTGGC 521 ACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGC 93254673 ATCTTCACTTTGATGGAGAGCAG 586 ATCTTCACTTTGATGGAGAGCAG * * * 93254696 ACACATAGCAGATCTCACCTTCGGATGTTTATGCTGAAACGGATCCAAGATGGATTGGCATCCTT 1 ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT * ** * * 93254761 ATACTTACAAGGAACAAATCGAA-TCATAGTTGATTTGGCTTTC 66 GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTC 93254804 GCGTGCTTAC Statistics Matches: 1898, Mismatches: 33, Indels: 18 0.97 0.02 0.01 Matches are distributed among these distances: 605 21 0.01 606 1161 0.61 609 1 0.00 614 3 0.00 615 706 0.37 616 6 0.00 ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30 Consensus pattern (608 bp): ACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTT GTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACAGAATCTAAGA TGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAG CAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATC CTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATTACGATGAAGC AAATCTAAGATGATTTCTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTT TGATGGAGAGCAGACACATAGCAGATCTCACCTTCAGATGTTTATGCTGAAGCGGATCCAAGATG GTTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCATGTGATT ACGATGAAGCAAATCTAAGATGATTTGTCGTCTCTGTATCGTCAGAGAACGAATCGAAGTTTGGC ATCTTCACTTTGATGGAGAGCAG Found at i:93255002 original size:44 final size:43 Alignment explanation

Indices: 93254924--93255009 Score: 111 Period size: 44 Copynumber: 2.0 Consensus size: 43 93254914 GATTTCAGCA * * 93254924 TGGCATCCCTGTGTTTATAAGGAGCAAGTTGAAGACAGCAGATT 1 TGGCATCCCTGTGTTTATAAGGAACAAGTCGAAGA-AGCAGATT ** 93254968 TGGCATCCCTGTGTTTATGGGGAAC-AGATCGAAGAAGCAGAT 1 TGGCATCCCTGTGTTTATAAGGAACAAG-TCGAAGAAGCAGAT 93255010 CAAGAACTCA Statistics Matches: 37, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 43 9 0.24 44 28 0.76 ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26 Consensus pattern (43 bp): TGGCATCCCTGTGTTTATAAGGAACAAGTCGAAGAAGCAGATT Done.