Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold145

Parameters: 2 7 7 80 10 50 500

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

Length: 1177157
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31

Warning! 98840 characters in sequence are not A, C, G, or T


File 4 of 3

Found at i:749872 original size:32 final size:32

Alignment explanation

Indices: 749827--749902 Score: 134 Period size: 32 Copynumber: 2.4 Consensus size: 32 749817 GATCAGCTGA 749827 CTCTCTCTCTCTGTCTCTGTCTGTCTGTCTCT 1 CTCTCTCTCTCTGTCTCTGTCTGTCTGTCTCT * * 749859 CTCTCTCTTTCTGTCTCTGTCTGTCTGTCTGT 1 CTCTCTCTCTCTGTCTCTGTCTGTCTGTCTCT 749891 CTCTCTCTCTCT 1 CTCTCTCTCTCT 749903 CTAAAAAAAA Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 32 41 1.00 ACGTcount: A:0.00, C:0.37, G:0.12, T:0.51 Consensus pattern (32 bp): CTCTCTCTCTCTGTCTCTGTCTGTCTGTCTCT Found at i:749932 original size:16 final size:14 Alignment explanation

Indices: 749905--749957 Score: 65 Period size: 15 Copynumber: 3.9 Consensus size: 14 749895 CTCTCTCTCT 749905 AAAAAAAAACAAAC 1 AAAAAAAAACAAAC * 749919 --AAACAAACAAAC 1 AAAAAAAAACAAAC * 749931 AAAAAAAACAAAAAC 1 AAAAAAAA-ACAAAC 749946 AAAAAAAAACAA 1 AAAAAAAAACAA 749958 GGCGGCTCAG Statistics Matches: 32, Mismatches: 4, Indels: 6 0.76 0.10 0.14 Matches are distributed among these distances: 12 11 0.34 14 8 0.25 15 13 0.41 ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00 Consensus pattern (14 bp): AAAAAAAAACAAAC Found at i:756534 original size:2 final size:2 Alignment explanation

Indices: 756527--756570 Score: 70 Period size: 2 Copynumber: 22.0 Consensus size: 2 756517 GAAAGAGTAT * * 756527 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TT TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 756569 TC 1 TC 756571 ACACACAGAA Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55 Consensus pattern (2 bp): TC Found at i:756548 original size:14 final size:14 Alignment explanation

Indices: 756529--756569 Score: 82 Period size: 14 Copynumber: 2.9 Consensus size: 14 756519 AAGAGTATTC 756529 TCTCTCTCTCTCTT 1 TCTCTCTCTCTCTT 756543 TCTCTCTCTCTCTT 1 TCTCTCTCTCTCTT 756557 TCTCTCTCTCTCT 1 TCTCTCTCTCTCT 756570 CACACACAGA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 27 1.00 ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56 Consensus pattern (14 bp): TCTCTCTCTCTCTT Found at i:757608 original size:15 final size:15 Alignment explanation

Indices: 757588--757616 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 757578 AAAGAAGTAG 757588 TTAATATAAAAAAAA 1 TTAATATAAAAAAAA 757603 TTAATATAAAAAAA 1 TTAATATAAAAAAA 757617 TCATAACTAT 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:0.72, C:0.00, G:0.00, T:0.28 Consensus pattern (15 bp): TTAATATAAAAAAAA Found at i:759251 original size:2 final size:2 Alignment explanation

Indices: 759244--759298 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 759234 ACTGACATAC 759244 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 759286 GA GA GA GA GA GA G 1 GA GA GA GA GA GA G 759299 NNNNNNNNNN Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:759963 original size:19 final size:20 Alignment explanation

Indices: 759921--759963 Score: 54 Period size: 20 Copynumber: 2.2 Consensus size: 20 759911 AGGAACAGTG * 759921 AACATTTATGACTACATAAG 1 AACATTTATGACTACATAAA 759941 AACATTTAT-AGCT-CATAAA 1 AACATTTATGA-CTACATAAA 759960 AACA 1 AACA 759964 GCAGCTTTGC Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 19 10 0.48 20 11 0.52 ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28 Consensus pattern (20 bp): AACATTTATGACTACATAAA Found at i:764306 original size:22 final size:23 Alignment explanation

Indices: 764277--764335 Score: 68 Period size: 21 Copynumber: 2.6 Consensus size: 23 764267 AAAACAACAG * 764277 CAACAAAAAAAAAAATTA-CCAA 1 CAACAAAAAAAAAAAATACCCAA * 764299 -AACAAAAAACTAAAAATACCCAA 1 CAACAAAAAA-AAAAAATACCCAA * 764322 CAACAAAAACAAAA 1 CAACAAAAAAAAAA 764336 TATAAAAAGA Statistics Matches: 30, Mismatches: 4, Indels: 5 0.77 0.10 0.13 Matches are distributed among these distances: 21 9 0.30 22 6 0.20 23 7 0.23 24 8 0.27 ACGTcount: A:0.73, C:0.20, G:0.00, T:0.07 Consensus pattern (23 bp): CAACAAAAAAAAAAAATACCCAA Found at i:764307 original size:23 final size:24 Alignment explanation

Indices: 764271--764335 Score: 62 Period size: 24 Copynumber: 2.7 Consensus size: 24 764261 CATAAAAAAA * 764271 CAACAGCAACAAAAAAAAAAATTA-C 1 CAACAACAA-AAAAAAAAAAA-TACC ** 764296 CAA-AACAAAAAACTAAAAATACC 1 CAACAACAAAAAAAAAAAAATACC * 764319 CAACAACAAAAACAAAA 1 CAACAACAAAAAAAAAA 764336 TATAAAAAGA Statistics Matches: 32, Mismatches: 6, Indels: 5 0.74 0.14 0.12 Matches are distributed among these distances: 22 2 0.06 23 13 0.41 24 14 0.44 25 3 0.09 ACGTcount: A:0.71, C:0.22, G:0.02, T:0.06 Consensus pattern (24 bp): CAACAACAAAAAAAAAAAAATACC Found at i:764336 original size:21 final size:20 Alignment explanation

Indices: 764277--764337 Score: 56 Period size: 23 Copynumber: 3.0 Consensus size: 20 764267 AAAACAACAG 764277 CAACAA-AAAAA-AAAATTAC 1 CAACAACAAAAACAAAA-TAC 764296 CAA-AACAAAAAACTAAAAATACC 1 CAACAAC-AAAAAC--AAAATA-C 764319 CAACAACAAAAACAAAATA 1 CAACAACAAAAACAAAATA 764338 TAAAAAGACC Statistics Matches: 35, Mismatches: 0, Indels: 12 0.74 0.00 0.26 Matches are distributed among these distances: 18 2 0.06 19 3 0.09 20 5 0.14 21 6 0.17 22 2 0.06 23 14 0.40 24 3 0.09 ACGTcount: A:0.72, C:0.20, G:0.00, T:0.08 Consensus pattern (20 bp): CAACAACAAAAACAAAATAC Found at i:764399 original size:14 final size:14 Alignment explanation

Indices: 764382--764410 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 764372 CAAAATATTG 764382 AAAAAAAAAAATAA 1 AAAAAAAAAAATAA 764396 AAAAAAAAAAATAA 1 AAAAAAAAAAATAA 764410 A 1 A 764411 GGAAATAAAG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07 Consensus pattern (14 bp): AAAAAAAAAAATAA Found at i:765061 original size:19 final size:20 Alignment explanation

Indices: 765025--765062 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 765015 TAATTTATAA * * 765025 ATTATTAAAAAGAGCAAAAC 1 ATTAATAAAAAGACCAAAAC 765045 ATTAATAAAAA-ACCAAAA 1 ATTAATAAAAAGACCAAAA 765063 TAATTAGCAC Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 19 6 0.38 20 10 0.62 ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18 Consensus pattern (20 bp): ATTAATAAAAAGACCAAAAC Found at i:771849 original size:2 final size:2 Alignment explanation

Indices: 771844--771892 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 771834 TTAAAAATAA 771844 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 771886 CT CT CT C 1 CT CT CT C 771893 CATAAACACA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:796421 original size:24 final size:23 Alignment explanation

Indices: 796381--796428 Score: 62 Period size: 24 Copynumber: 2.0 Consensus size: 23 796371 TTATGTATAG 796381 AATGGACAATATGCGTATTTCTAA 1 AATGGACAATATGCGTATTT-TAA * 796405 AATGGAC-ATAATTCGTATTTTAA 1 AATGGACAAT-ATGCGTATTTTAA 796428 A 1 A 796429 CACTTCTTTA Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 23 6 0.27 24 16 0.73 ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35 Consensus pattern (23 bp): AATGGACAATATGCGTATTTTAA Found at i:798260 original size:21 final size:21 Alignment explanation

Indices: 798236--798280 Score: 54 Period size: 21 Copynumber: 2.1 Consensus size: 21 798226 CTGAGGAAGT 798236 ACAAAACATAACGATAAAAGC 1 ACAAAACATAACGATAAAAGC * * * * 798257 ACAACACATTATGATACAAGC 1 ACAAAACATAACGATAAAAGC 798278 ACA 1 ACA 798281 CCACATAATG Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.56, C:0.22, G:0.09, T:0.13 Consensus pattern (21 bp): ACAAAACATAACGATAAAAGC Found at i:798285 original size:21 final size:21 Alignment explanation

Indices: 798241--798524 Score: 394 Period size: 21 Copynumber: 13.5 Consensus size: 21 798231 GAAGTACAAA * * * 798241 ACATAACGATAAAAGCACAAC 1 ACATAATGATACAAGCACACC * 798262 ACATTATGATACAAGCACACC 1 ACATAATGATACAAGCACACC * 798283 ACATAATGATACAAGGACACC 1 ACATAATGATACAAGCACACC * * 798304 ACACAATGATATAAGCACA-C 1 ACATAATGATACAAGCACACC 798324 ACATAATGATACAAGGACACACC 1 ACATAATGATACAA-G-CACACC 798347 ACATAATGATACAAGCACACC 1 ACATAATGATACAAGCACACC 798368 ACATAATGATACAAGCACACC 1 ACATAATGATACAAGCACACC * 798389 ACATAATGATACAAGAACACC 1 ACATAATGATACAAGCACACC * 798410 ACATAATGATACACTG-ACACC 1 ACATAATGATACA-AGCACACC 798431 ACATAATGATACAAGCACACC 1 ACATAATGATACAAGCACACC * 798452 ACATAATGATACAAGGACACC 1 ACATAATGATACAAGCACACC * 798473 ACATAATGATACAAGCTCACC 1 ACATAATGATACAAGCACACC ** * 798494 ACATAATGATA-AAGCATGCT 1 ACATAATGATACAAGCACACC 798514 ACATAATGATA 1 ACATAATGATA 798525 TATTTGCATA Statistics Matches: 237, Mismatches: 21, Indels: 11 0.88 0.08 0.04 Matches are distributed among these distances: 20 30 0.13 21 186 0.78 22 6 0.03 23 15 0.06 ACGTcount: A:0.48, C:0.25, G:0.11, T:0.16 Consensus pattern (21 bp): ACATAATGATACAAGCACACC Found at i:805228 original size:25 final size:25 Alignment explanation

Indices: 805191--805266 Score: 100 Period size: 25 Copynumber: 3.0 Consensus size: 25 805181 GTCCATCATG * 805191 TCTCTGGTAGTGTGTTGTTTTAAGT 1 TCTCTTGTAGTGTGTTGTTTTAAGT * 805216 TCTCTTG-AGGTGTGTTGTTTAAAGT 1 TCTCTTGTA-GTGTGTTGTTTTAAGT * * 805241 TCTCTTGTACTGTATTGTTTTAAGT 1 TCTCTTGTAGTGTGTTGTTTTAAGT 805266 T 1 T 805267 TTTTTCAATT Statistics Matches: 44, Mismatches: 5, Indels: 4 0.83 0.09 0.08 Matches are distributed among these distances: 24 1 0.02 25 42 0.95 26 1 0.02 ACGTcount: A:0.14, C:0.09, G:0.24, T:0.53 Consensus pattern (25 bp): TCTCTTGTAGTGTGTTGTTTTAAGT Found at i:809683 original size:21 final size:23 Alignment explanation

Indices: 809657--809704 Score: 64 Period size: 24 Copynumber: 2.1 Consensus size: 23 809647 AAAAAGTCTG * 809657 ATTATAT-ATC-GAACTTTATTA 1 ATTATATAATCAGAACTTCATTA 809678 ATTATATCAATCAGAACTTCATTA 1 ATTATAT-AATCAGAACTTCATTA 809702 ATT 1 ATT 809705 TTACCAACCA Statistics Matches: 23, Mismatches: 1, Indels: 3 0.85 0.04 0.11 Matches are distributed among these distances: 21 7 0.30 23 3 0.13 24 13 0.57 ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44 Consensus pattern (23 bp): ATTATATAATCAGAACTTCATTA Found at i:809716 original size:24 final size:24 Alignment explanation

Indices: 809667--809717 Score: 66 Period size: 24 Copynumber: 2.1 Consensus size: 24 809657 ATTATATATC * * * 809667 GAACTTTATTAATTATATCAATCA 1 GAACTTCATTAATTATACCAACCA * 809691 GAACTTCATTAATTTTACCAACCA 1 GAACTTCATTAATTATACCAACCA 809715 GAA 1 GAA 809718 AAGAAAGTCG Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 24 23 1.00 ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35 Consensus pattern (24 bp): GAACTTCATTAATTATACCAACCA Found at i:810850 original size:2 final size:2 Alignment explanation

Indices: 810845--810890 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 810835 GATGATGTGT 810845 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 810887 GA GA 1 GA GA 810891 AGGAATAAAT Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:821516 original size:14 final size:14 Alignment explanation

Indices: 821497--821524 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 821487 ATGTCAACTG 821497 ATATAGATACAAAC 1 ATATAGATACAAAC 821511 ATATAGATACAAAC 1 ATATAGATACAAAC 821525 TTCTATACTA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21 Consensus pattern (14 bp): ATATAGATACAAAC Found at i:829047 original size:65 final size:65 Alignment explanation

Indices: 828943--829073 Score: 262 Period size: 65 Copynumber: 2.0 Consensus size: 65 828933 TGTTTTCACT 828943 CGTGGTGCTATGCCAAAAATGGCCGACTTTTAACTCGTAATTTACGGTGTCTTAAGGTTTGAAGA 1 CGTGGTGCTATGCCAAAAATGGCCGACTTTTAACTCGTAATTTACGGTGTCTTAAGGTTTGAAGA 829008 CGTGGTGCTATGCCAAAAATGGCCGACTTTTAACTCGTAATTTACGGTGTCTTAAGGTTTGAAGA 1 CGTGGTGCTATGCCAAAAATGGCCGACTTTTAACTCGTAATTTACGGTGTCTTAAGGTTTGAAGA 829073 C 1 C 829074 ACGTTTTGAG Statistics Matches: 66, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 65 66 1.00 ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32 Consensus pattern (65 bp): CGTGGTGCTATGCCAAAAATGGCCGACTTTTAACTCGTAATTTACGGTGTCTTAAGGTTTGAAGA Found at i:830966 original size:17 final size:17 Alignment explanation

Indices: 830944--830977 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 830934 AACAATGCAC * * 830944 TGGCGAGAAATGGTCAT 1 TGGCGAAAAATCGTCAT 830961 TGGCGAAAAATCGTCAT 1 TGGCGAAAAATCGTCAT 830978 ATGCCAGTAT Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24 Consensus pattern (17 bp): TGGCGAAAAATCGTCAT Found at i:831430 original size:77 final size:77 Alignment explanation

Indices: 831160--831430 Score: 357 Period size: 77 Copynumber: 3.5 Consensus size: 77 831150 AACCAAACTT ** * * * 831160 AAATCTACATACCCCGTTTATCGATTGGT-GAAAACTCACAACGACTGAAACAAGCTGACCGGAA 1 AAATCTACACGCCCCGTTTATCGATTGGTCGAAACCT-ACAACGACTGAAACTAGCTGACAGGAA 831224 ACTGACAGGACTG 65 ACTGACAGGACTG * * * * * * 831237 AAATCTACATGCCCCTTTTATCTATTGGTGGAAACCTATAACGACTGAATCTAGCTGACAGGAAA 1 AAATCTACACGCCCCGTTTATCGATTGGTCGAAACCTACAACGACTGAAACTAGCTGACAGGAAA 831302 CTGACAGGACTG 66 CTGACAGGACTG * * * 831314 AAATATACACGCCCCGTTTATCGCTTGGTCGAAAGCTACAACGACTGAAACTAGCTGACAGGAAA 1 AAATCTACACGCCCCGTTTATCGATTGGTCGAAACCTACAACGACTGAAACTAGCTGACAGGAAA * 831379 CTGAGAGGACTG 66 CTGACAGGACTG * * 831391 AAATCTACACGTCCCC-TTTATCGATTTGTCGATACCTACA 1 AAATCTACACG-CCCCGTTTATCGATTGGTCGAAACCTACA 831431 GCGATCTACG Statistics Matches: 169, Mismatches: 23, Indels: 4 0.86 0.12 0.02 Matches are distributed among these distances: 77 159 0.94 78 10 0.06 ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23 Consensus pattern (77 bp): AAATCTACACGCCCCGTTTATCGATTGGTCGAAACCTACAACGACTGAAACTAGCTGACAGGAAA CTGACAGGACTG Found at i:832219 original size:32 final size:33 Alignment explanation

Indices: 832153--832229 Score: 138 Period size: 33 Copynumber: 2.4 Consensus size: 33 832143 GATTTTGGTC 832153 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG 1 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG * 832186 TCAATATTCAACGTTGAAAAATGA-CCCCCGGG 1 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG 832218 TCAATTTTCAAC 1 TCAATTTTCAAC 832230 CCGGGTCAAT Statistics Matches: 42, Mismatches: 2, Indels: 1 0.93 0.04 0.02 Matches are distributed among these distances: 32 19 0.45 33 23 0.55 ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26 Consensus pattern (33 bp): TCAATTTTCAACGTTGAAAAATGACCCCCCGGG Found at i:842841 original size:25 final size:25 Alignment explanation

Indices: 842807--842858 Score: 68 Period size: 25 Copynumber: 2.1 Consensus size: 25 842797 AATTATTTTT * * * 842807 ATATATGTGAAGTGTGAGCTAGCTG 1 ATATAAGTGAAATGTGAGATAGCTG * 842832 ATATAAGTGAAATGTGAGATAGTTG 1 ATATAAGTGAAATGTGAGATAGCTG 842857 AT 1 AT 842859 GTTGTCATAA Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 25 23 1.00 ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33 Consensus pattern (25 bp): ATATAAGTGAAATGTGAGATAGCTG Found at i:845659 original size:4 final size:4 Alignment explanation

Indices: 845652--845698 Score: 67 Period size: 4 Copynumber: 11.8 Consensus size: 4 845642 AGAAAAAGAG * * * 845652 AGAC AGAC AGAT GGAC AGAC AGAC AGAC AGAC AGAC AGAG AGAC AGA 1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA 845699 TGCATACACC Statistics Matches: 37, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 4 37 1.00 ACGTcount: A:0.49, C:0.19, G:0.30, T:0.02 Consensus pattern (4 bp): AGAC Found at i:856819 original size:47 final size:47 Alignment explanation

Indices: 856774--857673 Score: 1710 Period size: 47 Copynumber: 19.1 Consensus size: 47 856764 ATGTGATTTT * 856774 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGATTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC * 856821 AGTTTGACTTGTCTTGCAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC * * * * 856868 AGTCTGACTTGTCTAGGAGTACTTGATCTGTAACATTCTGTGATTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 856915 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 856962 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857009 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857056 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857103 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857150 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857197 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857244 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857291 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857338 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857385 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857432 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857479 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC * * 857526 AGTTTGACTTGTGTTGGAGTAATTGATCTGTAACATTCTGTGATTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857573 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC * * 857620 AGTTTGACTTGTGTTGGAGTAATTGATCTGTAACATTCTGTGATTTC 1 AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC 857667 AGTTTGA 1 AGTTTGA 857674 TGCCAATTTA Statistics Matches: 836, Mismatches: 17, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 47 836 1.00 ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44 Consensus pattern (47 bp): AGTTTGACTTGTCTTGGAGTAATTGATCTGTAACATTCTGTGGTTTC Found at i:858510 original size:63 final size:63 Alignment explanation

Indices: 858411--858674 Score: 510 Period size: 63 Copynumber: 4.2 Consensus size: 63 858401 AAGAGATGAG * 858411 GGTATAAACCAGTCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA 1 GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA 858474 GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA 1 GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA 858537 GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA 1 GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA * 858600 GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTCATATA 1 GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA 858663 GGTATAAACCAG 1 GGTATAAACCAG 858675 CGCCCAAGAA Statistics Matches: 199, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 63 199 1.00 ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38 Consensus pattern (63 bp): GGTATAAACCAGGCCATGTCAATTGTGTGTGTGTGATTGAGATTTGATTGATGTCTTGATATA Found at i:869760 original size:19 final size:18 Alignment explanation

Indices: 869738--869773 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 869728 AAATTAGTTA 869738 ACATGTAGTGAGATTGATT 1 ACATGTAGTGAG-TTGATT * 869757 ACATGTATTGAGTTGAT 1 ACATGTAGTGAGTTGAT 869774 CATATGTAAT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 5 0.31 19 11 0.69 ACGTcount: A:0.31, C:0.06, G:0.25, T:0.39 Consensus pattern (18 bp): ACATGTAGTGAGTTGATT Found at i:869780 original size:18 final size:19 Alignment explanation

Indices: 869738--869781 Score: 54 Period size: 18 Copynumber: 2.4 Consensus size: 19 869728 AAATTAGTTA * 869738 ACATGTAGTGAGATTGATT 1 ACATGTAGTGAGATTGATC * 869757 ACATGTATTGAG-TTGATC 1 ACATGTAGTGAGATTGATC * 869775 ATATGTA 1 ACATGTA 869782 ATAAAGTGAT Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 18 11 0.50 19 11 0.50 ACGTcount: A:0.32, C:0.07, G:0.23, T:0.39 Consensus pattern (19 bp): ACATGTAGTGAGATTGATC Found at i:870269 original size:31 final size:31 Alignment explanation

Indices: 870241--871034 Score: 1408 Period size: 31 Copynumber: 25.6 Consensus size: 31 870231 AGATACAATA * * * * 870241 TACAACACCACAGACCATTACAGATACAATG 1 TACAACACCACAGAACGTTACAGTTACAGTG * 870272 TACAACACCACAGAACATTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870303 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * 870334 TACAACACCACAGAACGTTACAGATACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870365 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870396 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870427 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870458 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * 870489 TACAACACCACAGAACGTTACAGATACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * 870520 TACAACACCACAGAACGTTACAGATACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870551 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870582 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870613 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870644 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870675 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870706 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870737 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870768 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870799 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870830 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG 870861 TACAACACCACAGAACGTTACAGTTACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * 870892 TACAACACCACAGAACGTTACAGATACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * 870923 TACAACACCACAGAACGTTACAGATACAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * * ** 870954 TACAACACCACAGAACATTACAGATGTAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * * 870985 TACAACACCACAGAACGTTACAGATGCAGTG 1 TACAACACCACAGAACGTTACAGTTACAGTG * * * * 871016 TTCAAAATCATAGAACGTT 1 TACAACACCACAGAACGTT 871035 TAAGATGCAG Statistics Matches: 745, Mismatches: 18, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 31 745 1.00 ACGTcount: A:0.40, C:0.26, G:0.16, T:0.19 Consensus pattern (31 bp): TACAACACCACAGAACGTTACAGTTACAGTG Found at i:896445 original size:14 final size:14 Alignment explanation

Indices: 896428--896458 Score: 53 Period size: 14 Copynumber: 2.2 Consensus size: 14 896418 TTTGTTTCTG * 896428 TAAGTTTATCCGGA 1 TAAGTGTATCCGGA 896442 TAAGTGTATCCGGA 1 TAAGTGTATCCGGA 896456 TAA 1 TAA 896459 TCTGCAACTG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32 Consensus pattern (14 bp): TAAGTGTATCCGGA Found at i:898301 original size:2 final size:2 Alignment explanation

Indices: 898296--898326 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 898286 TATTTTTTAT 898296 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 898327 TTGGAGTGGG Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:898667 original size:2 final size:2 Alignment explanation

Indices: 898660--898690 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 898650 AACAAACTTT 898660 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 898691 TTAGACATGC 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:922318 original size:18 final size:18 Alignment explanation

Indices: 922295--922331 Score: 74 Period size: 18 Copynumber: 2.1 Consensus size: 18 922285 TTTCCTTAGT 922295 TAGAATAATCTAACTGTG 1 TAGAATAATCTAACTGTG 922313 TAGAATAATCTAACTGTG 1 TAGAATAATCTAACTGTG 922331 T 1 T 922332 CTCGGGAAGG Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35 Consensus pattern (18 bp): TAGAATAATCTAACTGTG Found at i:922971 original size:23 final size:23 Alignment explanation

Indices: 922945--922996 Score: 77 Period size: 23 Copynumber: 2.3 Consensus size: 23 922935 AGTAGTAAAG * 922945 ATTATAGCATTATATAGAATATA 1 ATTATAGCATTATATAAAATATA * * 922968 ATTATCGCATTTTATAAAATATA 1 ATTATAGCATTATATAAAATATA 922991 ATTATA 1 ATTATA 922997 ACCATAAACG Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 23 25 1.00 ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42 Consensus pattern (23 bp): ATTATAGCATTATATAAAATATA Found at i:923679 original size:2 final size:2 Alignment explanation

Indices: 923672--923743 Score: 81 Period size: 2 Copynumber: 35.0 Consensus size: 2 923662 NNNNATAGAT * * * * 923672 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA AA CCA TA CA TC 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA * 923716 TA TA TA TA TA TA TA TC TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 923744 GACCAAACCT Statistics Matches: 59, Mismatches: 9, Indels: 4 0.82 0.12 0.06 Matches are distributed among these distances: 2 57 0.97 3 2 0.03 ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44 Consensus pattern (2 bp): TA Found at i:927950 original size:31 final size:31 Alignment explanation

Indices: 927915--928023 Score: 94 Period size: 32 Copynumber: 3.5 Consensus size: 31 927905 ATTATTCCTG 927915 GTACGACTTAACAAAACCCGAATGATTTTAA 1 GTACGACTTAACAAAACCCGAATGATTTTAA * **** * 927946 GTACGATTTAACAAAAACCTTTTTGATTTCAA 1 GTACGACTTAAC-AAAACCCGAATGATTTTAA * * * * 927978 GAACGACTTTAAAAAAATCCGAATG-TGTTTGA 1 GTACGAC-TTAACAAAACCCGAATGAT-TTTAA 928010 GTACGACTTAACAA 1 GTACGACTTAACAA 928024 TTATTTTTGG Statistics Matches: 57, Mismatches: 18, Indels: 6 0.70 0.22 0.07 Matches are distributed among these distances: 31 18 0.32 32 35 0.61 33 4 0.07 ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29 Consensus pattern (31 bp): GTACGACTTAACAAAACCCGAATGATTTTAA Found at i:929051 original size:436 final size:433 Alignment explanation

Indices: 928197--929179 Score: 1348 Period size: 436 Copynumber: 2.3 Consensus size: 433 928187 AGCTGCTTTG * * * * * * 928197 TTGCTTTATAATAAATATC-AAATTTTGGTCAGAAAAGAGTTATCGTAAAAAGACTTAGTAGCCC 1 TTGCTTTATAATTAATAACAAAATATTGTTCAGTAAAGAGTTATTGTAAAAAGACTTAG-AGCCC * ** * * 928261 TTGTACCCCCTAATTTGTGGAGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCTCGCTAATA 65 TTTTGGCCCCTAATTTGAGG-GCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCTCGCAAATA * * 928326 TAAACATATTTTGTTCTACAAGTGTTCATGAATTGTAAACCGTTCTCGAGATATATGTACAAATG 129 TAAACATATTTTGTTCAACAAGTGTTCATGAAATGTAAACCGTTCTCGAGATATATGTACAAATG * * ** * 928391 TGTTTTAAGGGCCGACCCTTTAACCCCTTACCGGGGCCACTAACAACAAAATTTTTGGTTTAATA 194 TGTTTTAAGGGCCGACCCTTTAACCCCTAAACGGGGCCACTAACAACAAAATTTAAGGTATAATA * ** 928456 TTGTTCAGAACATTATTTTGAACAACTTTTGTTCTACACTGCTTTTTAAAATATTTCTCCTTTTT 259 TTGTACAGAACACCATTTTGAACAACTTTTGTTCTACACTGCTTTTTAAAATATTTCTCCTTTTT * * * * * 928521 CAGATATTAATGATCATAGTTTTGAGTTCTGGCCCCTTGAAACCCCTAATTAGGTAATATATGAC 324 CAGATATTAATGATAAAAGTTTTGACTTCTGGCCCCTTGAAACCCCTAATTACGTAACATATGAC * * * * 928586 TTAGGTATGGTACTGTATAGTTGAACAGCTGTACAATGAACATTT 389 TTAAGTATGATACTGTATAGATAAACAGCTGTACAATGAACATTT 928631 TTGCTTCTATAATTAATAACAAAATATTGTTCAGTAAAGAGTTATTGTAAAAAGACATTAGAGCC 1 TTGCTT-TATAATTAATAACAAAATATTGTTCAGTAAAGAGTTATTGTAAAAAGAC-TTAGAGCC ** * 928696 CTTTTGGCCCCTAATTTGAGAGGCCAGCCCCTTTTTCTTGATATCAAATTTAAGGTCTTGCAAAT 64 CTTTTGGCCCCTAATTTGAG-GGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCTCGCAAAT * * * * * 928761 TTAAACATATTTTGTTCAACAAGTGTTCATGAAATGTTAACCGTTCTTGAGATATCTGTACGAAT 128 ATAAACATATTTTGTTCAACAAGTGTTCATGAAATGTAAACCGTTCTCGAGATATATGTACAAAT * * * * * 928826 GTGTTTTAGGGGCCGACCCTTTAACTCCTAAATGGGGTCA-TAAACAA-AAACATTTAAGGTATC 193 GTGTTTTAAGGGCCGACCCTTTAACCCCTAAACGGGGCCACT-AACAACAAA-ATTTAAGGTATA * 928889 ATATTG-ACAAGAACACCATTTT-AAGCAACTTTTGTTCTACATTGC-TTTTAAAATATTTCTCC 256 ATATTGTAC-AGAACACCATTTTGAA-CAACTTTTGTTCTACACTGCTTTTTAAAATATTTCTCC 928951 TTTTTCAGATATTAATGATAAAAGTTTTGAACTTCTGGCCCCTTGAAACCCCTAATTACGTAACA 319 TTTTTCAGATATTAATGATAAAAGTTTTG-ACTTCTGGCCCCTTGAAACCCCTAATTACGTAACA 929016 TATGACTTAAGTATGATACTGTATAGATAAACAGCTGTACAATGAACATTT 383 TATGACTTAAGTATGATACTGTATAGATAAACAGCTGTACAATGAACATTT * * * 929067 TTGCTTATATAATTAATAACAAATTATTGTTCAGTAAAGAGTTATTGTAAGAGGACTTTAGAGCC 1 TTGCTT-TATAATTAATAACAAAATATTGTTCAGTAAAGAGTTATTGTAAAAAGAC-TTAGAGCC ** * * 929132 CCCTTGGCCCCTTATTTGAGGGGTCAGCCCCTTTTTCTTGATATCAAA 64 CTTTTGGCCCCTAATTTGA-GGGCCAGCCCCTTTTTCTTGATATCAAA 929180 GGAAAGCTCG Statistics Matches: 486, Mismatches: 53, Indels: 18 0.87 0.10 0.03 Matches are distributed among these distances: 434 6 0.01 435 62 0.13 436 412 0.85 437 6 0.01 ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36 Consensus pattern (433 bp): TTGCTTTATAATTAATAACAAAATATTGTTCAGTAAAGAGTTATTGTAAAAAGACTTAGAGCCCT TTTGGCCCCTAATTTGAGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCTCGCAAATATA AACATATTTTGTTCAACAAGTGTTCATGAAATGTAAACCGTTCTCGAGATATATGTACAAATGTG TTTTAAGGGCCGACCCTTTAACCCCTAAACGGGGCCACTAACAACAAAATTTAAGGTATAATATT GTACAGAACACCATTTTGAACAACTTTTGTTCTACACTGCTTTTTAAAATATTTCTCCTTTTTCA GATATTAATGATAAAAGTTTTGACTTCTGGCCCCTTGAAACCCCTAATTACGTAACATATGACTT AAGTATGATACTGTATAGATAAACAGCTGTACAATGAACATTT Found at i:930998 original size:437 final size:436 Alignment explanation

Indices: 930174--931099 Score: 1214 Period size: 437 Copynumber: 2.1 Consensus size: 436 930164 ATGACTTTGT * * * 930174 AGCCCTTTTAGCCCCTTATTTGAGGGGCTGACCCCTTTTTCTTGATATCAAATGAAAGGTCTTGA 1 AGCCCTTTTAGCCCCTTATTTGAGGGGC-CAGCCCTTTTTCTTGATATCAAATAAAAGGTCTTGA * * * * 930239 AAATATAAACATATTTTGTTACACAAGTATTCACGAATTGCTAACCGTTCTAGAGATATCCAAAC 65 AAATATAAACACATTTTGTCACACAAGTATTCACGAACTGCTAACCGTTCTAAAGATATCCAAAC * * * * 930304 AACTGTGTTTCAGGGGCCGACCCTTAAACTCCTTACCAGGGCCACCAAAAAAATATTTTTAGATC 130 AACTGTGTTTCAGGGGCCGACCCTTAAAATCCTTACCAGGGCCACCAAAAAAATATATTAAGATA ** * * * 930369 CCATATTGTTAAGAACATTTTTTTGAGCAACTTTTCTTCTACAAGGCTTTTCAAAATATTTCTCC 195 CCATATTGTTAAGAACATCATTCTAAGCAACTTTTCTTCTACAAGGCTTATCAAAATATTTCTCC * * * * * * 930434 TTTTCTAGATATTAAAATGAAATTTTTTAGACCTCTGGCCCCTTGAAACCCCTAATTACGTATCA 260 TTTTCTAGAAACTAAAATCAAAGTTTTGAGACCTCTGGCCCCTTGAAACCCCTAATTACGTAACA * * * * * * 930499 TATGTCTTAAGTATGGTACCGTATAGATAAACAGATGTTCAATTAACATTTTTGGTTCTATAACT 325 TATGACTTAAGCATGGTACCGTATAAATAAACAGATATACAATGAACATTTTTGGTTCTATAACT ** 930564 GATAACAAATTATTTTTCAGTAAAGAGTTATTATTAAAAGACTTAAG 390 GATAACAAATTATTTTTCAGTAAAGAGTTATTACCAAAAGACTTAAG * * * * 930611 AGCCCTCTTGGCCCCTTATTTGAGGGGCCAGCCCTTATTCCTTGATATCAAATAAAAGGTCTTGT 1 AGCCCTTTTAGCCCCTTATTTGAGGGGCCAGCCCTT-TTTCTTGATATCAAATAAAAGGTCTTGA * * * ** 930676 AAATATAAAGACATTTTGCTCA-ACAAGTGA-TCA-GAAACTGTTGACCGTTCTAAAGATATCTG 65 AAATATAAACACATTTTG-TCACACAAGT-ATTCACG-AACTGCTAACCGTTCTAAAGATATCCA * * ** 930738 AACAATTGTGTTTTAGGGGCCGACCCTTAAAATCCTTACTGGGGCCACCAACAAAAAT-TATTAA 127 AACAACTGTGTTTCAGGGGCCGACCCTTAAAATCCTTACCAGGGCCACCAA-AAAAATATATTAA * * ** * * * 930802 GGTAGCATATTGTTAAGAACATCATTCTAAGCATTTTTTGTTCTATAATGCTTATCAAAATATTT 191 GATACCATATTGTTAAGAACATCATTCTAAGCAACTTTTCTTCTACAAGGCTTATCAAAATATTT * 930867 CTCCTTTTCTAGAAACTAAAGATCAAAGTTTTGA-ACTTCTGGCCCCTTGAAACCCCTAATTACG 256 CTCCTTTTCTAGAAACTAAA-ATCAAAGTTTTGAGACCTCTGGCCCCTTGAAACCCCTAATTACG * * 930931 TAACATATGACTTAGGCATGGTACTGTATAAATAAACAGATATACAATGAACATTTTTGGTTCTA 320 TAACATATGACTTAAGCATGGTACCGTATAAATAAACAGATATACAATGAACATTTTTGGTTCTA * * * 930996 TAATTGATTACAAATTATTTTTCAGTAAAGAGTTATTGCCAAAAGACTTAAG 385 TAACTGATAACAAATTATTTTTCAGTAAAGAGTTATTACCAAAAGACTTAAG * * * 931048 AGCCATTTTTGCCCCTTATTTGAGGGGCCAGCCCCTTTTTCTTGAAATCAAA 1 AGCCCTTTTAGCCCCTTATTTGAGGGGCCAG-CCCTTTTTCTTGATATCAAA 931100 CGCATGTCCT Statistics Matches: 421, Mismatches: 61, Indels: 14 0.85 0.12 0.03 Matches are distributed among these distances: 436 7 0.02 437 390 0.93 438 24 0.06 ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34 Consensus pattern (436 bp): AGCCCTTTTAGCCCCTTATTTGAGGGGCCAGCCCTTTTTCTTGATATCAAATAAAAGGTCTTGAA AATATAAACACATTTTGTCACACAAGTATTCACGAACTGCTAACCGTTCTAAAGATATCCAAACA ACTGTGTTTCAGGGGCCGACCCTTAAAATCCTTACCAGGGCCACCAAAAAAATATATTAAGATAC CATATTGTTAAGAACATCATTCTAAGCAACTTTTCTTCTACAAGGCTTATCAAAATATTTCTCCT TTTCTAGAAACTAAAATCAAAGTTTTGAGACCTCTGGCCCCTTGAAACCCCTAATTACGTAACAT ATGACTTAAGCATGGTACCGTATAAATAAACAGATATACAATGAACATTTTTGGTTCTATAACTG ATAACAAATTATTTTTCAGTAAAGAGTTATTACCAAAAGACTTAAG Found at i:932880 original size:433 final size:435 Alignment explanation

Indices: 932055--932938 Score: 1153 Period size: 433 Copynumber: 2.0 Consensus size: 435 932045 AGGGATCAGA * * 932055 CCCTTTTTCTTGATATCAAATAAAAGATCTCGCTAATATAAACATATTTTGTTCTACAAATGTTC 1 CCCTTTTTCTTGATATCAAATAAAAGATCTCGCAAATATAAACATATTTTGTTCAACAAATGTTC * * * 932120 ACGAATGGTTATCCGTTACCGAGATATCTAAACAACTGTATTTTAGGGGCCGACCCTTTAACTCT 66 ACGAATGGTTAACCGTTACCGAGATATCTAAACAAATGTATTTTAGGGGCCGACCCTTTAACTCC *** * * * * 932185 TTGCCGGGGCCACTAACAACAAAATTTATGGCATCATATTGTTCAGAACATTATTTTGAACAACT 131 TAAACGGGGCCACTAACAACAAAATTTAAGGCAGCATATTGTACAAAACATTATTTTGAACAACT * * 932250 TTTGTTCTACATTGCTTTTAAAAATATTTCTCCTTTTTCAGATATTAATGATCAAAGTTTTGAAT 196 TTAGTTCTACAATGCTTTTAAAAATATTTCTCCTTTTTCAGATATTAATGATCAAAGTTTTGAAT * * 932315 TCTGGCCCCTTGAAATCCCTAATTACGTAAAATATGACTTAGTATGATACTGTATAGATAAACAG 261 TCTGGCCACTTGAAACCCCTAATTACGTAAAATATGACTTAGTATGATACTGTATAGATAAACAG * * * 932380 TCCAACAATGAACATTTTTGCTTCTATAATTAATAACAAATTATTGTTCAATAAAGAGTTCTTGT 326 CCCAACAATGAACATTTTTGCTTCTATAATTAATAACAAATTATTATTCAATAAAGAGTTATTGT * 932445 AAGAAG-TTTTA-AGACCCCTCTTGACCCCTAAATGGAGGGGCCAGC 391 AAGAAGACTTTACAG--CCCTCTTGACCCCTAAATGGAGGGGCCAGC * * * * * * 932490 CCCTTTTTCTTGATATCAACTGAAAGGTCTTGCAAATATAAACATGTTTTGTTCAACAAGTGTTC 1 CCCTTTTTCTTGATATCAAATAAAAGATCTCGCAAATATAAACATATTTTGTTCAACAAATGTTC ** ** * * * 932555 ACGAAAT-GTTAACCGTT-CTTAGGATATCTTTACAAATG-GTTTTAGGGGCCGGCCCTTTATCT 66 ACG-AATGGTTAACCGTTACCGA-GATATCTAAACAAATGTATTTTAGGGGCCGACCCTTTAACT * * * ** 932617 CCTAAATGGGGTCA-TGAGCAA-AAAGATTTAAGGTGGCATATTGTACAAAACATTATTTT-AAG 129 CCTAAACGGGGCCACT-AACAACAAA-ATTTAAGGCAGCATATTGTACAAAACATTATTTTGAA- ** * 932679 CAACTTTAGTTCTACAATGCTTTTTGAAATA-TT-T-CTTTTTCATATATTAATGATCGAAA-TT 191 CAACTTTAGTTCTACAATGCTTTTAAAAATATTTCTCCTTTTTCAGATATTAATGATC-AAAGTT * * * * 932740 TTGAATTTCTGGCCACTTGAAACCCCTTATTACGTAACATATGACTTAAGTATGGTACTGTTTAG 255 TTGAA-TTCTGGCCACTTGAAACCCCTAATTACGTAAAATATGACTT-AGTATGATACTGTATAG * 932805 ATAAACAGCCCAACAATGAACATTTTTGCTTCTATAATTAATAACAAATTATTATTCAGTAAAGA 318 ATAAACAGCCCAACAATGAACATTTTTGCTTCTATAATTAATAACAAATTATTATTCAATAAAGA * * * 932870 GTTATTGTAAGAAGACTTTACAGCCCTCTTGGCCCCTAATTTGAGGGGCCAGC 383 GTTATTGTAAGAAGACTTTACAGCCCTCTTGACCCCTAAATGGAGGGGCCAGC 932923 CCCTTTTTCTTGATAT 1 CCCTTTTTCTTGATAT 932939 TAAACGAAAG Statistics Matches: 390, Mismatches: 49, Indels: 22 0.85 0.11 0.05 Matches are distributed among these distances: 431 27 0.07 432 41 0.11 433 141 0.36 434 94 0.24 435 84 0.22 436 3 0.01 ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36 Consensus pattern (435 bp): CCCTTTTTCTTGATATCAAATAAAAGATCTCGCAAATATAAACATATTTTGTTCAACAAATGTTC ACGAATGGTTAACCGTTACCGAGATATCTAAACAAATGTATTTTAGGGGCCGACCCTTTAACTCC TAAACGGGGCCACTAACAACAAAATTTAAGGCAGCATATTGTACAAAACATTATTTTGAACAACT TTAGTTCTACAATGCTTTTAAAAATATTTCTCCTTTTTCAGATATTAATGATCAAAGTTTTGAAT TCTGGCCACTTGAAACCCCTAATTACGTAAAATATGACTTAGTATGATACTGTATAGATAAACAG CCCAACAATGAACATTTTTGCTTCTATAATTAATAACAAATTATTATTCAATAAAGAGTTATTGT AAGAAGACTTTACAGCCCTCTTGACCCCTAAATGGAGGGGCCAGC Found at i:934658 original size:16 final size:16 Alignment explanation

Indices: 934637--934668 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 934627 AGTTGCGTCT 934637 ACAGACAGACGGACAG 1 ACAGACAGACGGACAG 934653 ACAGACAGACGGACAG 1 ACAGACAGACGGACAG 934669 GGTGAAANNN Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.44, C:0.25, G:0.31, T:0.00 Consensus pattern (16 bp): ACAGACAGACGGACAG Found at i:939334 original size:1 final size:1 Alignment explanation

Indices: 939328--939357 Score: 51 Period size: 1 Copynumber: 30.0 Consensus size: 1 939318 TATTCAATGT * 939328 AAAAAAAAAAACAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 939358 CAGTCGGCGG Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:942226 original size:17 final size:17 Alignment explanation

Indices: 942204--942237 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 942194 TGCTAAAACG 942204 CGGAACGGAAAACGGAA 1 CGGAACGGAAAACGGAA 942221 CGGAACGGAAAACGGAA 1 CGGAACGGAAAACGGAA 942238 AAAAACTTAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.47, C:0.18, G:0.35, T:0.00 Consensus pattern (17 bp): CGGAACGGAAAACGGAA Found at i:943775 original size:12 final size:12 Alignment explanation

Indices: 943754--943806 Score: 88 Period size: 12 Copynumber: 4.4 Consensus size: 12 943744 ATATGATATT 943754 TTCCGTTTTCCG 1 TTCCGTTTTCCG ** 943766 TTCCACTTTCCG 1 TTCCGTTTTCCG 943778 TTCCGTTTTCCG 1 TTCCGTTTTCCG 943790 TTCCGTTTTCCG 1 TTCCGTTTTCCG 943802 TTCCG 1 TTCCG 943807 CGTTCTAAGG Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 12 37 1.00 ACGTcount: A:0.02, C:0.36, G:0.15, T:0.47 Consensus pattern (12 bp): TTCCGTTTTCCG Found at i:945298 original size:13 final size:13 Alignment explanation

Indices: 945280--945319 Score: 71 Period size: 13 Copynumber: 3.1 Consensus size: 13 945270 ACAACAGGGT 945280 AGGTAACAGTTGA 1 AGGTAACAGTTGA 945293 AGGTAACAGTTGA 1 AGGTAACAGTTGA * 945306 GGGTAACAGTTGA 1 AGGTAACAGTTGA 945319 A 1 A 945320 ATTGACACCC Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 13 25 1.00 ACGTcount: A:0.38, C:0.07, G:0.33, T:0.23 Consensus pattern (13 bp): AGGTAACAGTTGA Found at i:947826 original size:18 final size:18 Alignment explanation

Indices: 947803--947838 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 947793 GATAGAATGT 947803 TCTATCGTTAAAATGACA 1 TCTATCGTTAAAATGACA 947821 TCTATCGTTAAAATGACA 1 TCTATCGTTAAAATGACA 947839 GATGTTCTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33 Consensus pattern (18 bp): TCTATCGTTAAAATGACA Found at i:951088 original size:20 final size:20 Alignment explanation

Indices: 951026--951088 Score: 54 Period size: 20 Copynumber: 3.1 Consensus size: 20 951016 ACATGATTCC * * * * 951026 TATGATATAGTATTCTATGA 1 TATGATACAATATTATATAA * * * 951046 TATGATACACTATTGTTTAA 1 TATGATACAATATTATATAA * 951066 TATGATACAATATTATATCA 1 TATGATACAATATTATATAA 951086 TAT 1 TAT 951089 AATAATATTG Statistics Matches: 34, Mismatches: 9, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 20 34 1.00 ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44 Consensus pattern (20 bp): TATGATACAATATTATATAA Found at i:951280 original size:20 final size:20 Alignment explanation

Indices: 951255--951295 Score: 57 Period size: 20 Copynumber: 2.0 Consensus size: 20 951245 ATCATGCATA 951255 TACAATATCATA-CTATATGT 1 TACAATATCATATC-ATATGT * 951275 TACAATATTATATCATATGT 1 TACAATATCATATCATATGT 951295 T 1 T 951296 TAAATATTGT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 18 0.95 21 1 0.05 ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44 Consensus pattern (20 bp): TACAATATCATATCATATGT Found at i:951797 original size:145 final size:143 Alignment explanation

Indices: 951534--951962 Score: 478 Period size: 145 Copynumber: 3.0 Consensus size: 143 951524 AAATTTGTAA * * 951534 AGAAAAAGTGCAAAATTCGTGTCCGGTCCATATCTTTCTTTTG-GACAAATGTTGATGTTCTTAC 1 AGAAAAAGTGCAAAATTCGTGTCC-GTCCATATCTTTCTTATGAGA-AAAT-TTGAAGTTCTTAC * 951598 TTTACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGAC-CAAAGGTCATTT-GGAC 63 TTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTC-AAGGTCATTTGGGA- * * 951661 AAGGTGAAGGTCACTGGC 126 AAGGTCAAGGTCACTGAC ** 951679 AGAAAAAGTGCAAACGTCG-GTCCGCTCCATATCTTTCTTATGAAGAAACATTTGAAGTTCTTAC 1 AGAAAAAGTGCAAAATTCGTGTCCG-TCCATATCTTTCTTATG-AGAAA-ATTTGAAGTTCTTAC ** * ** * 951743 TTCATGCAAAGATTGTTTATGGTCTAAGGGTGTGTCATGACCTTGACTCGAGGTCATTTGGGAAA 63 TTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTTGGGAAA 951808 GGTCAAGGTCACTGAC 128 GGTCAAGGTCACTGAC * * * 951824 AG-AAAAGTGCAAAATTTGTGTCCAGTCCATATCTTTCCTATG-GACAGATATTGGAAGTTCTTA 1 AGAAAAAGTGCAAAATTCGTGTCC-GTCCATATCTTTCTTATGAGA-A-A-ATTTGAAGTTCTTA * * * * * * 951887 ATTCACATAAAGATTGCTTATAACCTGACGGTGTGTCATGACCTTGACTTAAGGTCA-TTGAGG- 62 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTTG-GGA * 951950 AAGTTCAAGGTCA 126 AAGGTCAAGGTCA 951963 TTTTAAAAAA Statistics Matches: 241, Mismatches: 32, Indels: 23 0.81 0.11 0.08 Matches are distributed among these distances: 143 3 0.01 144 49 0.20 145 180 0.75 146 9 0.04 ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31 Consensus pattern (143 bp): AGAAAAAGTGCAAAATTCGTGTCCGTCCATATCTTTCTTATGAGAAAATTTGAAGTTCTTACTTC ACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACCTTGACTCAAGGTCATTTGGGAAAGGT CAAGGTCACTGAC Found at i:954869 original size:29 final size:29 Alignment explanation

Indices: 954827--954887 Score: 122 Period size: 29 Copynumber: 2.1 Consensus size: 29 954817 AGTTAAAGGC 954827 AGGGGGTCCTGAAATCTAGATATTTTGAA 1 AGGGGGTCCTGAAATCTAGATATTTTGAA 954856 AGGGGGTCCTGAAATCTAGATATTTTGAA 1 AGGGGGTCCTGAAATCTAGATATTTTGAA 954885 AGG 1 AGG 954888 CAAAATCATG Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 32 1.00 ACGTcount: A:0.31, C:0.10, G:0.30, T:0.30 Consensus pattern (29 bp): AGGGGGTCCTGAAATCTAGATATTTTGAA Found at i:956786 original size:162 final size:161 Alignment explanation

Indices: 956356--956823 Score: 521 Period size: 162 Copynumber: 2.8 Consensus size: 161 956346 TTGCTGCTCG * * * * 956356 GAAACTAATCAGCCAGGAGAGCCGAAACCTGTGTTGAAGTATCCTCAGTTAGCGTAGATTCAAAG 1 GAAACTAATCAGCCAGGAAAGCTGAAACCTGTGTAGAAGTATCCTCAGTTAGTGTAGATTCAAAG * * * * * * 956421 TTATGAAAATCATGACCCCCAGGGGATAGGG-TG-GCGCAACCATGGGGA-TTGAATTTTTACCT 66 TTTTGAAAATCATGACCCCCA-GGG-T-GGGATGAG-GCCACAATGGGGAGTCGAATTATTACAT * * 956483 AGGAATATATCAAGTAAATCTTCTTAAGTCTTCTCA 127 AGGAATATAT-GAGTAAACCTTCTTAAGTCTTCTCA * * * * * * * * * 956519 GAAACAAATCAGCCATTTACCTGGGAAGCTGGAACTTG-GAAGGAAGCATCCGCAGGTAGTTTAG 1 GAAACTAATCAGCC----A---GGAAAGCTGAAACCTGTGTA-GAAGTATCCTCAGTTAGTGTAG * * 956583 ATTCAAAGTTTAGAAAATCATGACCCCCAGGATGGGATGAGGCCACAATGGGGAGTCGAATTATT 58 ATTCAAAGTTTTGAAAATCATGACCCCCAGGGTGGGATGAGGCCACAATGGGGAGTCGAATTATT 956648 ACATAGGAATATAGTGAGTAAACCTTCTTAAGTCTTCTCA 123 ACATAGGAATATA-TGAGTAAACCTTCTTAAGTCTTCTCA * 956688 GAAACTAACCAGCCAGGAAAGCTGAAACCTGTGTAGAAGTATCCTCAGTTAGTGTAGATTCAAAG 1 GAAACTAATCAGCCAGGAAAGCTGAAACCTGTGTAGAAGTATCCTCAGTTAGTGTAGATTCAAAG * * * * * 956753 TTTTGAAAATCAAGACCCTCAGGGTGGGATGAGGCCACAATGGGGAGTCGAATTACTACTTAGGG 66 TTTTGAAAATCATGACCCCCAGGGTGGGATGAGGCCACAATGGGGAGTCGAATTATTACATAGGA 956818 ATATAT 131 ATATAT 956824 TGAGAAAAAT Statistics Matches: 252, Mismatches: 40, Indels: 28 0.79 0.12 0.09 Matches are distributed among these distances: 161 1 0.00 162 102 0.40 163 15 0.06 165 1 0.00 167 4 0.02 168 14 0.06 169 59 0.23 170 56 0.22 ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25 Consensus pattern (161 bp): GAAACTAATCAGCCAGGAAAGCTGAAACCTGTGTAGAAGTATCCTCAGTTAGTGTAGATTCAAAG TTTTGAAAATCATGACCCCCAGGGTGGGATGAGGCCACAATGGGGAGTCGAATTATTACATAGGA ATATATGAGTAAACCTTCTTAAGTCTTCTCA Found at i:958594 original size:152 final size:153 Alignment explanation

Indices: 958317--958825 Score: 622 Period size: 152 Copynumber: 3.3 Consensus size: 153 958307 TTTACTGTAG * * * * ** 958317 TGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGA-GGAAATTTTGGCT 1 TGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAATTCTTTGACAAAAATTTTGGCT * * * * 958381 -AAAATAAACAAAGT-ACTCATTTAACAGGAAGTTAACGTCTGATTGGTCCGAAAATACATCCCA 66 AAAAATAAAC-AAGTCA-TCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCA * 958444 CAATATAGCATGCCTTAACAAACAC 129 CAATATGGCATGCCTTAACAAACAC 958469 TGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAATTCTTTGACAAAAATTTTGGCT 1 TGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAATTCTTTGACAAAAATTTTGGCT * * 958534 AAAAATAAAC-AGTCATCATTTAACAGGAAGTTGACGTCTGATTGGAACAAAAATATATCCCACG 66 AAAAATAAACAAGTCATCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACA ** 958598 ATATGGCATGCC-TATACAAATTC 131 ATATGGCATGCCTTA-ACAAACAC * 958621 T-TGGTAAAAATTTCAAGCATCTGCGATGAACAGTTGCTGAGAATTCTTTGACAAAAATTTGTTT 1 TGT-GTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAATTCTTTGACAAAAA--T-TTT ** * 958685 GAAAATTTTTGCTAAAAATAAACAAAGTCGGCATTTAAGAGGAAGTTGACG--TGATTGGTACAA 62 G---------GCTAAAAATAAAC-AAGTCATCATTTAACAGGAAGTTGACGTCTGATTGGTACAA 958748 AAATATATCCCACAATATGGCATGCCTTAACAAACAC 117 AAATATATCCCACAATATGGCATGCCTTAACAAACAC * 958785 TGTGTAAAAATTTCAA-CATCTGCGATAAATAGTTGCTGAGA 1 TGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA 958826 TAAATGCGAC Statistics Matches: 311, Mismatches: 25, Indels: 31 0.85 0.07 0.08 Matches are distributed among these distances: 151 3 0.01 152 164 0.53 153 12 0.04 154 10 0.03 155 4 0.01 163 23 0.07 164 69 0.22 165 3 0.01 166 23 0.07 ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29 Consensus pattern (153 bp): TGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAATTCTTTGACAAAAATTTTGGCT AAAAATAAACAAGTCATCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACA ATATGGCATGCCTTAACAAACAC Found at i:958794 original size:164 final size:162 Alignment explanation

Indices: 958522--958825 Score: 443 Period size: 164 Copynumber: 1.9 Consensus size: 162 958512 TTCTTTGACA * 958522 AAAATTTTGGCTAAAAATAAACAGTCATCATTTAACAGGAAGTTGACGTCTGATTGGAACAAAAA 1 AAAATTTTGGCTAAAAATAAACAGTCAGCATTTAACAGGAAGTTGACG-CTGATTGGAACAAAAA * ** * 958587 TATATCCCACGATATGGCATGCCTATACAAATTCTTGGTAAAAATTTCAAGCATCTGCGATGAAC 65 TATATCCCACAATATGGCATGCCTATACAAACACTTGGTAAAAATTTCAA-CATCTGCGATAAAC 958652 AGTTGCTGAGAATTCTTTGACAAAAATTTGTTTG 129 AGTTGCTGAGAATTCTTTGACAAAAATTTGTTTG * * * * 958686 AAAATTTTTGCTAAAAATAAACAAAGTCGGCATTTAAGAGGAAGTTGACG-TGATTGGTACAAAA 1 AAAATTTTGGCTAAAAATAAAC--AGTCAGCATTTAACAGGAAGTTGACGCTGATTGGAACAAAA 958750 ATATATCCCACAATATGGCATGCCT-TAACAAACAC-TGTGTAAAAATTTCAACATCTGCGATAA 64 ATATATCCCACAATATGGCATGCCTAT-ACAAACACTTG-GTAAAAATTTCAACATCTGCGATAA * 958813 ATAGTTGCTGAGA 127 ACAGTTGCTGAGA 958826 TAAATGCGAC Statistics Matches: 126, Mismatches: 10, Indels: 9 0.87 0.07 0.06 Matches are distributed among these distances: 163 26 0.21 164 77 0.61 166 23 0.18 ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29 Consensus pattern (162 bp): AAAATTTTGGCTAAAAATAAACAGTCAGCATTTAACAGGAAGTTGACGCTGATTGGAACAAAAAT ATATCCCACAATATGGCATGCCTATACAAACACTTGGTAAAAATTTCAACATCTGCGATAAACAG TTGCTGAGAATTCTTTGACAAAAATTTGTTTG Found at i:961420 original size:18 final size:18 Alignment explanation

Indices: 961397--961434 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 961387 ATACATCATT * 961397 GTTGAGAAAAGAAGTTAA 1 GTTGAGAAAAGAAGTAAA 961415 GTTGAGAAAAGAAGTAAA 1 GTTGAGAAAAGAAGTAAA 961433 GT 1 GT 961435 ATGGCACAAA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21 Consensus pattern (18 bp): GTTGAGAAAAGAAGTAAA Found at i:969513 original size:2 final size:2 Alignment explanation

Indices: 969502--969534 Score: 52 Period size: 2 Copynumber: 17.5 Consensus size: 2 969492 AATGAAAGAT 969502 AG AG AG -G AG AG AG AG AG AG AG -G AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 969535 AATACACAGG Statistics Matches: 29, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 1 2 0.07 2 27 0.93 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): AG Found at i:969520 original size:13 final size:12 Alignment explanation

Indices: 969502--969534 Score: 52 Period size: 11 Copynumber: 2.9 Consensus size: 12 969492 AATGAAAGAT 969502 AGAGAG-GAGAG 1 AGAGAGAGAGAG 969513 AGAGAGAGAG-G 1 AGAGAGAGAGAG 969524 AGAGAGAGAGA 1 AGAGAGAGAGA 969535 AATACACAGG Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 11 17 0.85 12 3 0.15 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (12 bp): AGAGAGAGAGAG Found at i:969522 original size:15 final size:15 Alignment explanation

Indices: 969502--969534 Score: 66 Period size: 15 Copynumber: 2.2 Consensus size: 15 969492 AATGAAAGAT 969502 AGAGAGGAGAGAGAG 1 AGAGAGGAGAGAGAG 969517 AGAGAGGAGAGAGAG 1 AGAGAGGAGAGAGAG 969532 AGA 1 AGA 969535 AATACACAGG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (15 bp): AGAGAGGAGAGAGAG Found at i:971551 original size:57 final size:57 Alignment explanation

Indices: 971463--972088 Score: 906 Period size: 57 Copynumber: 11.0 Consensus size: 57 971453 GAGTTGGAGG * 971463 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCATTCCAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * 971520 GAAACACTGAAGACAGGGCTAGTGTACCCACAGTACGACCTTTGACCTTTCTAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * * * * 971577 GAAACACTTAAGACAGGGCTAGTGTACCTACAGAACGACCTCTGACCATCCCAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA ** * 971634 GAAACACTGAAGACAGGGCGGGCTAGTGTACCCACATTACGACCTTTGACCTTTCTAGGTA 1 GAAACACTGAAGACA----GGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * 971695 G-AA-AC-----ACAGGGCTAGTGTACCCACAGAACGACCTCTGACCATTCCAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * 971745 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTCTGACCATTCCAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * * 971802 GAAACACTGAAGACAGGGCTAGCGTACCCACAGTACGACCTTTGACCTTTCTAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * * * * 971859 GAAACATTTAAGACAGGGCTAGTGTAACCACAGAACGACCTTAGACCATTCCAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * 971916 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCTAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * 971973 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAGCGACCTTTGACCTTTCTAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA * * * 972030 GAAACATTTAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTTCAGGTA 1 GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA 972087 GA 1 GA 972089 CAAAGGAAGC Statistics Matches: 510, Mismatches: 48, Indels: 22 0.88 0.08 0.04 Matches are distributed among these distances: 50 38 0.07 51 2 0.00 52 2 0.00 54 3 0.01 57 425 0.83 59 2 0.00 60 2 0.00 61 36 0.07 ACGTcount: A:0.32, C:0.26, G:0.23, T:0.20 Consensus pattern (57 bp): GAAACACTGAAGACAGGGCTAGTGTACCCACAGAACGACCTTTGACCTTTCCAGGTA Found at i:978240 original size:16 final size:16 Alignment explanation

Indices: 978219--978250 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 978209 ATTTAAAAAT 978219 AACTGCATGCACATGC 1 AACTGCATGCACATGC 978235 AACTGCATGCACATGC 1 AACTGCATGCACATGC 978251 TGTACAATTA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19 Consensus pattern (16 bp): AACTGCATGCACATGC Found at i:981358 original size:1 final size:1 Alignment explanation

Indices: 981352--981381 Score: 60 Period size: 1 Copynumber: 30.0 Consensus size: 1 981342 GTGTGTGTGT 981352 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 981382 CTGGACAACT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 29 1.00 ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00 Consensus pattern (1 bp): G Found at i:986877 original size:14 final size:15 Alignment explanation

Indices: 986860--986889 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 986850 TTGTTCTTTC 986860 TTTGAA-TTTCTGAA 1 TTTGAATTTTCTGAA 986874 TTTGAATTTTCTGAA 1 TTTGAATTTTCTGAA 986889 T 1 T 986890 AATGAATATG Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.40 15 9 0.60 ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53 Consensus pattern (15 bp): TTTGAATTTTCTGAA Found at i:995550 original size:2 final size:2 Alignment explanation

Indices: 995543--995593 Score: 102 Period size: 2 Copynumber: 25.5 Consensus size: 2 995533 CCACCCATAC 995543 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 995585 AG AG AG AG A 1 AG AG AG AG A 995594 ATTATACGAT Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 49 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1000896 original size:2 final size:2 Alignment explanation

Indices: 1000889--1000913 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 1000879 CCTACGTGCC 1000889 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 C 1000914 CGTCATTTAC 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:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:1002291 original size:19 final size:19 Alignment explanation

Indices: 1002256--1002292 Score: 51 Period size: 18 Copynumber: 2.0 Consensus size: 19 1002246 TGTGTGTCTG 1002256 GTTTGGTTTTTTGTTTTTT 1 GTTTGGTTTTTTGTTTTTT 1002275 GTTT-GTTTATTT-TTTTTT 1 GTTTGGTTT-TTTGTTTTTT 1002293 ATTGTCGGTT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 18 10 0.59 19 7 0.41 ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81 Consensus pattern (19 bp): GTTTGGTTTTTTGTTTTTT Found at i:1010795 original size:12 final size:12 Alignment explanation

Indices: 1010778--1010803 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 1010768 CTACATGTTG 1010778 TCTAATAGAAAT 1 TCTAATAGAAAT 1010790 TCTAATAGAAAT 1 TCTAATAGAAAT 1010802 TC 1 TC 1010804 AAATGAGATT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35 Consensus pattern (12 bp): TCTAATAGAAAT Found at i:1015038 original size:20 final size:20 Alignment explanation

Indices: 1015013--1015056 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 1015003 ACCACTAGCC 1015013 CTCATTCATTCAT-TCTTTCT 1 CTCATTCATTC-TCTCTTTCT * 1015033 CTCATTCGTTCTCTCTTTCT 1 CTCATTCATTCTCTCTTTCT 1015053 CTCA 1 CTCA 1015057 AAAATTAAAA Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 19 1 0.05 20 21 0.95 ACGTcount: A:0.11, C:0.34, G:0.02, T:0.52 Consensus pattern (20 bp): CTCATTCATTCTCTCTTTCT Found at i:1029235 original size:18 final size:18 Alignment explanation

Indices: 1029214--1029248 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 1029204 ACTAAAGAGC 1029214 AAACAACAACCGCAGAAA 1 AAACAACAACCGCAGAAA * 1029232 AAACCACAACCGCAGAA 1 AAACAACAACCGCAGAA 1029249 CAACCAATAA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.57, C:0.31, G:0.11, T:0.00 Consensus pattern (18 bp): AAACAACAACCGCAGAAA Found at i:1030721 original size:18 final size:18 Alignment explanation

Indices: 1030651--1030730 Score: 70 Period size: 18 Copynumber: 4.4 Consensus size: 18 1030641 AAAAACAAGC * * * 1030651 CAGAGCAAACCACAACCA 1 CAGAACAAACAACAACCG * * * 1030669 CAAAACAAACAATAACTG 1 CAGAACAAACAACAACCG * * * 1030687 CGGAGCTAACAACAACCG 1 CAGAACAAACAACAACCG * 1030705 CAGAACAAACCACAACCG 1 CAGAACAAACAACAACCG 1030723 CAGAACAA 1 CAGAACAA 1030731 CCAATAACTA Statistics Matches: 46, Mismatches: 16, Indels: 0 0.74 0.26 0.00 Matches are distributed among these distances: 18 46 1.00 ACGTcount: A:0.51, C:0.33, G:0.12, T:0.04 Consensus pattern (18 bp): CAGAACAAACAACAACCG Found at i:1047787 original size:11 final size:11 Alignment explanation

Indices: 1047771--1047797 Score: 54 Period size: 11 Copynumber: 2.5 Consensus size: 11 1047761 CAATTGAGAA 1047771 CATTGGAATAT 1 CATTGGAATAT 1047782 CATTGGAATAT 1 CATTGGAATAT 1047793 CATTG 1 CATTG 1047798 CGTCTGATTT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 16 1.00 ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37 Consensus pattern (11 bp): CATTGGAATAT Found at i:1057895 original size:13 final size:13 Alignment explanation

Indices: 1057877--1057925 Score: 64 Period size: 13 Copynumber: 3.8 Consensus size: 13 1057867 AGAGTGTCAA 1057877 TTTTGTTTTTTTG 1 TTTTGTTTTTTTG 1057890 TTTTGTTTTTTT- 1 TTTTGTTTTTTTG * 1057902 TTTCGGTTTTTTTG 1 TTT-TGTTTTTTTG * 1057916 CTTTGTTTTT 1 TTTTGTTTTT 1057926 GTTTTGTGTT Statistics Matches: 31, Mismatches: 3, Indels: 4 0.82 0.08 0.11 Matches are distributed among these distances: 12 3 0.10 13 26 0.84 14 2 0.06 ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82 Consensus pattern (13 bp): TTTTGTTTTTTTG Found at i:1057936 original size:26 final size:27 Alignment explanation

Indices: 1057880--1057936 Score: 82 Period size: 26 Copynumber: 2.2 Consensus size: 27 1057870 GTGTCAATTT * * 1057880 TGTTTTTTTGTTTTGTTTTTTTTTTCG 1 TGTTTTTTTGCTTTGTTTTTGTTTTCG 1057907 -GTTTTTTTGCTTTGTTTTTGTTTT-G 1 TGTTTTTTTGCTTTGTTTTTGTTTTCG 1057932 TGTTT 1 TGTTT 1057937 GTATGTTTGT Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 25 1 0.04 26 26 0.96 ACGTcount: A:0.00, C:0.04, G:0.18, T:0.79 Consensus pattern (27 bp): TGTTTTTTTGCTTTGTTTTTGTTTTCG Found at i:1067987 original size:16 final size:16 Alignment explanation

Indices: 1067948--1067987 Score: 53 Period size: 16 Copynumber: 2.5 Consensus size: 16 1067938 TTTCCTCTGC * * 1067948 GTCCGTCAGTCCGTCT 1 GTCCGTCCGTCCGGCT 1067964 GTCCGTCCGTCCGGCT 1 GTCCGTCCGTCCGGCT * 1067980 GTCTGTCC 1 GTCCGTCC 1067988 CACTTCAGTT Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.03, C:0.40, G:0.28, T:0.30 Consensus pattern (16 bp): GTCCGTCCGTCCGGCT Found at i:1073127 original size:17 final size:17 Alignment explanation

Indices: 1073105--1073137 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 1073095 CTGGTACTGT 1073105 ACCAGTTATCGGCTAAG 1 ACCAGTTATCGGCTAAG 1073122 ACCAGTTATCGGCTAA 1 ACCAGTTATCGGCTAA 1073138 ACTGAGAGTT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24 Consensus pattern (17 bp): ACCAGTTATCGGCTAAG Found at i:1084594 original size:46 final size:46 Alignment explanation

Indices: 1084541--1084700 Score: 302 Period size: 46 Copynumber: 3.5 Consensus size: 46 1084531 TGTATACTTT 1084541 TAACCCAATGCTATCTCTACCATTATCGTTAGGCTGTAACCTTAAA 1 TAACCCAATGCTATCTCTACCATTATCGTTAGGCTGTAACCTTAAA 1084587 TAACCCAATGCTATCTCTACCATTATCGTTAGGCTGTAACCTTAAA 1 TAACCCAATGCTATCTCTACCATTATCGTTAGGCTGTAACCTTAAA * * 1084633 AAACCCAATGCTATCTCTACCATTATCGTTAGGCTGTAACCTTAAG 1 TAACCCAATGCTATCTCTACCATTATCGTTAGGCTGTAACCTTAAA 1084679 TAACCCAATGCTATCTCTACCA 1 TAACCCAATGCTATCTCTACCA 1084701 AGAGCTGTGT Statistics Matches: 111, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 46 111 1.00 ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31 Consensus pattern (46 bp): TAACCCAATGCTATCTCTACCATTATCGTTAGGCTGTAACCTTAAA Found at i:1086623 original size:59 final size:59 Alignment explanation

Indices: 1086558--1086806 Score: 286 Period size: 59 Copynumber: 4.0 Consensus size: 59 1086548 CAAGTTAGTT * 1086558 GTGTCAAGTGTACATTGGCCCTATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGAC 1 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGAC 1086617 GTGTCAAGTGTACATTGGCCCAATG-TGTGCCCAACGCTGTGTTCCCAACTAATATTGAC 1 GTGTCAAGTGTACATTGGCCCAATGTTG-GCCCAACGCTGTGTTCCCAACTAATATTGAC * * * * * * 1086676 -TCTCAACTTAGATGTGTCAAGTGTACATTGGCCCAATGTTGGTCCAACGCTGTGTTCCCAACTA 1 GTGTC-A---AG-TGT-AC-ATTG-GC----CC--AATGTTGGCCCAACGCTGTGTTCCCAACTA 1086740 ATATTGAC 52 ATATTGAC 1086748 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGAC 1 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGAC 1086807 TCTGAACTTA Statistics Matches: 160, Mismatches: 13, Indels: 34 0.77 0.06 0.16 Matches are distributed among these distances: 58 5 0.03 59 93 0.58 61 1 0.01 62 2 0.01 63 3 0.02 64 1 0.01 65 4 0.03 66 4 0.03 67 1 0.01 68 3 0.02 69 2 0.01 70 1 0.01 72 35 0.22 73 5 0.03 ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30 Consensus pattern (59 bp): GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGAC Found at i:1086760 original size:131 final size:131 Alignment explanation

Indices: 1086508--1086971 Score: 651 Period size: 131 Copynumber: 3.4 Consensus size: 131 1086498 TTGACCCAAT * * * * * * 1086508 ATGTTGGCCCGACGTTGCGTTCCCAACTAACATTGACTCTCAAGTTAGTTGTGTCAAGTGTACAT 1 ATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAACTTAGATGTGTCAAGTGTACAT * 1086573 TGGCCCTATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACGTGTCAAGTGTACATTGGCCC 66 TGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACGTGTCAAGTGTACATTGGCCC 1086638 A 131 A 1086639 ATG-TGTGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAACTTAGATGTGTCAAGTGTACA 1 ATGTTG-GCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAACTTAGATGTGTCAAGTGTACA * 1086703 TTGGCCCAATGTTGGTCCAACGCTGTGTTCCCAACTAATATTGACGTGTCAAGTGTACATTGGCC 65 TTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACGTGTCAAGTGTACATTGGCC 1086768 CA 130 CA * * 1086770 ATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTGAACTTAGATGGGTCAAGTGTACAT 1 ATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAACTTAGATGTGTCAAGTGTACAT * * * 1086835 TGGCCCAATGTTGGCCCAACGTTGCGTTCCCAACTAACATTGACTCTCAAGTTAGTTGTGTCAAG 66 TGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACT-A-A-T-A-T-T---G--A--CGTGTCAAG 1086900 TGTACATTGGCCCA 118 TGTACATTGGCCCA * * * 1086914 ATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAAGTTAGTTGTATCAAG 1 ATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAACTTAGATGTGTCAAG 1086972 CCAACGCCAA Statistics Matches: 299, Mismatches: 19, Indels: 17 0.89 0.06 0.05 Matches are distributed among these distances: 130 2 0.01 131 212 0.71 132 3 0.01 133 1 0.00 134 1 0.00 135 1 0.00 136 1 0.00 137 1 0.00 140 1 0.00 142 1 0.00 144 75 0.25 ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31 Consensus pattern (131 bp): ATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAACTTAGATGTGTCAAGTGTACAT TGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACGTGTCAAGTGTACATTGGCCC A Found at i:1086962 original size:72 final size:72 Alignment explanation

Indices: 1086748--1086971 Score: 376 Period size: 72 Copynumber: 3.1 Consensus size: 72 1086738 TAATATTGAC * 1086748 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTGAA 1 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAA * * 1086813 CTTAGAT 66 GTTAGTT * * * * 1086820 GGGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGTTGCGTTCCCAACTAACATTGACTCTCAA 1 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAA 1086885 GTTAGTT 66 GTTAGTT 1086892 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAA 1 GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAA 1086957 GTTAGTT 66 GTTAGTT * 1086964 GTATCAAG 1 GTGTCAAG 1086972 CCAACGCCAA Statistics Matches: 140, Mismatches: 12, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 72 140 1.00 ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30 Consensus pattern (72 bp): GTGTCAAGTGTACATTGGCCCAATGTTGGCCCAACGCTGTGTTCCCAACTAATATTGACTCTCAA GTTAGTT Found at i:1095275 original size:23 final size:23 Alignment explanation

Indices: 1095230--1095277 Score: 62 Period size: 22 Copynumber: 2.1 Consensus size: 23 1095220 TGTTTTCTTT * * 1095230 TGGGTTTTTTTTTTCATTTTTCA 1 TGGGTTTTTTTTTTCAATATTCA 1095253 TGGG-TTTTTTTTTCAGATATTCA 1 TGGGTTTTTTTTTTCA-ATATTCA 1095276 TG 1 TG 1095278 CATAACAATG Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 22 11 0.50 23 11 0.50 ACGTcount: A:0.12, C:0.08, G:0.17, T:0.62 Consensus pattern (23 bp): TGGGTTTTTTTTTTCAATATTCA Found at i:1105011 original size:2 final size:2 Alignment explanation

Indices: 1105004--1105035 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 1104994 TAGAACTTTT 1105004 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1105036 NNNNNNNNNN Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1116899 original size:11 final size:11 Alignment explanation

Indices: 1116828--1116890 Score: 83 Period size: 11 Copynumber: 5.8 Consensus size: 11 1116818 TTCTGTGTCC 1116828 ACTCTGGGTTT 1 ACTCTGGGTTT * 1116839 ACTTTGGGTTT 1 ACTCTGGGTTT * 1116850 ACTCT-GGTCT 1 ACTCTGGGTTT * 1116860 AATCTGGGTTT 1 ACTCTGGGTTT * 1116871 ACTTTGGGTTT 1 ACTCTGGGTTT 1116882 ACTCTGGGT 1 ACTCTGGGT 1116891 CCACTCTGGT Statistics Matches: 43, Mismatches: 8, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 10 8 0.19 11 35 0.81 ACGTcount: A:0.11, C:0.16, G:0.27, T:0.46 Consensus pattern (11 bp): ACTCTGGGTTT Found at i:1119366 original size:27 final size:27 Alignment explanation

Indices: 1119334--1119414 Score: 110 Period size: 27 Copynumber: 3.0 Consensus size: 27 1119324 AACTGTATTG 1119334 CACAATCAATCTACAAAAATGTATTAA 1 CACAATCAATCTACAAAAATGTATTAA 1119361 CACAATCAATCTACAAAAATGTAATT-A 1 CACAATCAATCTACAAAAATGT-ATTAA * * * 1119388 CACCATGAATCTACAAAACTGTTATTA 1 CACAATCAATCTACAAAAATG-TATTA 1119415 GTATACAGAA Statistics Matches: 48, Mismatches: 3, Indels: 5 0.86 0.05 0.09 Matches are distributed among these distances: 27 44 0.92 28 4 0.08 ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27 Consensus pattern (27 bp): CACAATCAATCTACAAAAATGTATTAA Found at i:1124762 original size:18 final size:18 Alignment explanation

Indices: 1124739--1124811 Score: 112 Period size: 18 Copynumber: 4.1 Consensus size: 18 1124729 AATATAATAA 1124739 TGTAATGAATTAGTGTAT 1 TGTAATGAATTAGTGTAT 1124757 TGTAATGAATTAGTGTAT 1 TGTAATGAATTAGTGTAT * 1124775 TGTAATAAATTAGTGTAT 1 TGTAATGAATTAGTGTAT * 1124793 TGTGAT-AGATTAGTGTAT 1 TGTAATGA-ATTAGTGTAT 1124811 T 1 T 1124812 ATCATTAAGT Statistics Matches: 52, Mismatches: 2, Indels: 2 0.93 0.04 0.04 Matches are distributed among these distances: 17 1 0.02 18 51 0.98 ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45 Consensus pattern (18 bp): TGTAATGAATTAGTGTAT Found at i:1125191 original size:18 final size:18 Alignment explanation

Indices: 1125101--1125202 Score: 84 Period size: 18 Copynumber: 5.7 Consensus size: 18 1125091 AAATCAGATG * * * 1125101 AGTGTATTGTGATAAATT 1 AGTGTATTGTAATGAATA * 1125119 AGTGTAGTGTAATG-ATA 1 AGTGTATTGTAATGAATA * * 1125136 AGTGTTTTGTAA-GAAAA 1 AGTGTATTGTAATGAATA * 1125153 ATGTGCTA-TGAAATGAATA 1 A-GTG-TATTGTAATGAATA * 1125172 AGTGTATTGTAATGAGTA 1 AGTGTATTGTAATGAATA * 1125190 AGTGTATTCTAAT 1 AGTGTATTGTAAT 1125203 TTATTGATAA Statistics Matches: 66, Mismatches: 13, Indels: 10 0.74 0.15 0.11 Matches are distributed among these distances: 16 1 0.02 17 17 0.26 18 42 0.64 19 6 0.09 ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38 Consensus pattern (18 bp): AGTGTATTGTAATGAATA Found at i:1127370 original size:2 final size:2 Alignment explanation

Indices: 1127363--1127406 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 1127353 AACTTACCAA 1127363 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1127405 TC 1 TC 1127407 ATAATGAATA Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1128861 original size:24 final size:24 Alignment explanation

Indices: 1128829--1128925 Score: 194 Period size: 24 Copynumber: 4.0 Consensus size: 24 1128819 TAAAACAGTT 1128829 TCTGAGATATCAACAATACCAATA 1 TCTGAGATATCAACAATACCAATA 1128853 TCTGAGATATCAACAATACCAATA 1 TCTGAGATATCAACAATACCAATA 1128877 TCTGAGATATCAACAATACCAATA 1 TCTGAGATATCAACAATACCAATA 1128901 TCTGAGATATCAACAATACCAATA 1 TCTGAGATATCAACAATACCAATA 1128925 T 1 T 1128926 GTAATTTTAA Statistics Matches: 73, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 73 1.00 ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26 Consensus pattern (24 bp): TCTGAGATATCAACAATACCAATA Found at i:1130309 original size:2 final size:2 Alignment explanation

Indices: 1130302--1130353 Score: 97 Period size: 2 Copynumber: 26.5 Consensus size: 2 1130292 ATATAACACA 1130302 TC TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1130343 TC TC TC TC TC T 1 TC TC TC TC TC T 1130354 GCACATTTTT Statistics Matches: 49, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 1 1 0.02 2 48 0.98 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:1141602 original size:22 final size:20 Alignment explanation

Indices: 1141577--1141633 Score: 53 Period size: 22 Copynumber: 2.7 Consensus size: 20 1141567 GGTGGGTCAA 1141577 TTGTGTGGACTATCTTGGTCTT 1 TTGTGTGGACTATCTT-GTC-T * 1141599 TTGTATGG-CATATTCTTGTCT 1 TTGTGTGGAC-TA-TCTTGTCT * 1141620 TTGTGTGAACTATC 1 TTGTGTGGACTATC 1141634 CAATACCTTA Statistics Matches: 29, Mismatches: 3, Indels: 8 0.73 0.08 0.20 Matches are distributed among these distances: 20 2 0.07 21 10 0.34 22 13 0.45 23 4 0.14 ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49 Consensus pattern (20 bp): TTGTGTGGACTATCTTGTCT Found at i:1144350 original size:63 final size:63 Alignment explanation

Indices: 1144251--1144376 Score: 252 Period size: 63 Copynumber: 2.0 Consensus size: 63 1144241 TCAGGGTAAT 1144251 GCTTTATATTCCTTGTAAAGTTTATCAAATTTAAAATAACAACTGTATAATTCATTATTGGAA 1 GCTTTATATTCCTTGTAAAGTTTATCAAATTTAAAATAACAACTGTATAATTCATTATTGGAA 1144314 GCTTTATATTCCTTGTAAAGTTTATCAAATTTAAAATAACAACTGTATAATTCATTATTGGAA 1 GCTTTATATTCCTTGTAAAGTTTATCAAATTTAAAATAACAACTGTATAATTCATTATTGGAA 1144377 ATATTGACAA Statistics Matches: 63, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 63 63 1.00 ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41 Consensus pattern (63 bp): GCTTTATATTCCTTGTAAAGTTTATCAAATTTAAAATAACAACTGTATAATTCATTATTGGAA Found at i:1150036 original size:27 final size:27 Alignment explanation

Indices: 1150006--1150250 Score: 400 Period size: 27 Copynumber: 9.1 Consensus size: 27 1149996 GGTCAGGCTT * * 1150006 AGGGGTCATATGACCAAGGTCAAATAC 1 AGGGGTCACATGACCATGGTCAAATAC * 1150033 AGGGGTCACATGAACATGGTCAAATAC 1 AGGGGTCACATGACCATGGTCAAATAC 1150060 AGGGGTCACATGACCATGGTCAAATAC 1 AGGGGTCACATGACCATGGTCAAATAC * 1150087 AGGGGTCACATGACCATGGTCAAACAC 1 AGGGGTCACATGACCATGGTCAAATAC * 1150114 AGGGGTCACATGAACATGGTCAAATAC 1 AGGGGTCACATGACCATGGTCAAATAC * 1150141 AGGGGTCACATGACCATGGTCAAAAAC 1 AGGGGTCACATGACCATGGTCAAATAC * 1150168 AGGGGTCACATGACCATGGTCAAACAC 1 AGGGGTCACATGACCATGGTCAAATAC * 1150195 AGGGGTCACATGACCAAGGTCAAATAC 1 AGGGGTCACATGACCATGGTCAAATAC * * 1150222 AGGGGTCACATGACCAAGGTTAAATAC 1 AGGGGTCACATGACCATGGTCAAATAC 1150249 AG 1 AG 1150251 AGGAGAATAT Statistics Matches: 205, Mismatches: 13, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 27 205 1.00 ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17 Consensus pattern (27 bp): AGGGGTCACATGACCATGGTCAAATAC Found at i:1150470 original size:32 final size:32 Alignment explanation

Indices: 1150406--1150470 Score: 87 Period size: 32 Copynumber: 2.0 Consensus size: 32 1150396 TGGTAAAGGT * * 1150406 TGGATTCATTTTCATACAAATCGTGCAGAATA 1 TGGATTCATTTTCATACAAATCATGCACAATA * 1150438 TGGATTTATTTTCATAC-AATGCATGCACAATA 1 TGGATTCATTTTCATACAAAT-CATGCACAATA 1150470 T 1 T 1150471 ATACATAGCA Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 31 3 0.10 32 26 0.90 ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37 Consensus pattern (32 bp): TGGATTCATTTTCATACAAATCATGCACAATA Found at i:1158560 original size:22 final size:20 Alignment explanation

Indices: 1158491--1158567 Score: 82 Period size: 20 Copynumber: 3.7 Consensus size: 20 1158481 GAACTCACTG * 1158491 TGTACGGTGATATCTGTCTC 1 TGTACTGTGATATCTGTCTC * * * * 1158511 TCTACAGTGACATTTGGTCTC 1 TGTACTGTGATATCT-GTCTC 1158532 TGTACTGTGATATCTGTCTC 1 TGTACTGTGATATCTGTCTC 1158552 TGTGTACTGTGATATC 1 --TGTACTGTGATATC 1158568 CATCTGTTCA Statistics Matches: 46, Mismatches: 8, Indels: 4 0.79 0.14 0.07 Matches are distributed among these distances: 20 16 0.35 21 16 0.35 22 14 0.30 ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42 Consensus pattern (20 bp): TGTACTGTGATATCTGTCTC Found at i:1159824 original size:8 final size:8 Alignment explanation

Indices: 1159803--1159844 Score: 68 Period size: 8 Copynumber: 5.4 Consensus size: 8 1159793 GATCACATTT 1159803 TGTCCGTC 1 TGTCCGTC 1159811 -GTCCGTC 1 TGTCCGTC 1159818 TGTCCGTC 1 TGTCCGTC * 1159826 CGTCCGTC 1 TGTCCGTC 1159834 TGTCCGTC 1 TGTCCGTC 1159842 TGT 1 TGT 1159845 AAACTTTTTA Statistics Matches: 31, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 7 7 0.23 8 24 0.77 ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36 Consensus pattern (8 bp): TGTCCGTC Found at i:1159826 original size:4 final size:4 Alignment explanation

Indices: 1159804--1159841 Score: 51 Period size: 4 Copynumber: 9.8 Consensus size: 4 1159794 ATCACATTTT * * 1159804 GTCC GT-C GTCC GTCT GTCC GTCC GTCC GTCT GTCC GTC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC 1159842 TGTAAACTTT Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 3 3 0.10 4 26 0.90 ACGTcount: A:0.00, C:0.42, G:0.26, T:0.32 Consensus pattern (4 bp): GTCC Done.