Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008002.1 Hibiscus syriacus cultivar Beakdansim tig00110461_pilon, whole genome shotgun sequence
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: 1031338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:490356 original size:57 final size:57
Alignment explanation
Indices: 490290--490443 Score: 229
Period size: 57 Copynumber: 2.7 Consensus size: 57
490280 TAATGCTCTT
* * *
490290 AGCAACATTGTTCTCATTCTCACTTGCATTCTCGTTGTTGTTGGT-TTGAATCTGAAC
1 AGCAACATTGTTCTCATTCTGACTTGTATTCTCATTGTTGTTGGTATTG-ATCTGAAC
* *
490347 AGCATCATTGTTCTCAATCTGACTTGTATTCTCATTGTTGTTGGTATTGATCTGAAC
1 AGCAACATTGTTCTCATTCTGACTTGTATTCTCATTGTTGTTGGTATTGATCTGAAC
* *
490404 AGCAGCGTTGTTCTCATTCTGACTTGTATTCTCATTGTTG
1 AGCAACATTGTTCTCATTCTGACTTGTATTCTCATTGTTG
490444 CTGTTGTTGC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
57 85 0.97
58 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (57 bp):
AGCAACATTGTTCTCATTCTGACTTGTATTCTCATTGTTGTTGGTATTGATCTGAAC
Found at i:490535 original size:21 final size:21
Alignment explanation
Indices: 490511--490559 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
490501 ACGCTCTGAG
490511 CAGCATTGTTCTCATTTTGCC
1 CAGCATTGTTCTCATTTTGCC
490532 CAGCATTGTTCTCATTTTGCC
1 CAGCATTGTTCTCATTTTGCC
*
490553 TAGCATT
1 CAGCATT
490560 CTCATTGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (21 bp):
CAGCATTGTTCTCATTTTGCC
Found at i:490563 original size:18 final size:19
Alignment explanation
Indices: 490519--490565 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
490509 AGCAGCATTG
490519 TTCTCATTTTGCCCAGCATT
1 TTCTCATTTTGCCCAGCA-T
*
490539 GTTCTCATTTTGCCTAGCA-
1 -TTCTCATTTTGCCCAGCAT
490558 TTCTCATT
1 TTCTCATT
490566 GTTGTTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
21 17 0.68
ACGTcount: A:0.15, C:0.28, G:0.11, T:0.47
Consensus pattern (19 bp):
TTCTCATTTTGCCCAGCAT
Found at i:498106 original size:29 final size:29
Alignment explanation
Indices: 498073--498135 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
498063 AGCGATAAAT
*
498073 ATAATGCT-ATTGAAAATGCAGTTACAAAC
1 ATAATG-TGATTGAAAATGCAGTCACAAAC
*
498102 ATAATGTGATTGAAAATGCAGTCACAATC
1 ATAATGTGATTGAAAATGCAGTCACAAAC
498131 ATAAT
1 ATAAT
498136 TTAAATCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (29 bp):
ATAATGTGATTGAAAATGCAGTCACAAAC
Found at i:508247 original size:16 final size:16
Alignment explanation
Indices: 508226--508284 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
508216 ACATCAACCC
*
508226 TTAATCACTAAGGTCA
1 TTAATCACTAACGTCA
*
508242 TTAATCACTAACGTCG
1 TTAATCACTAACGTCA
*
508258 TTAATCATTAACGTCA
1 TTAATCACTAACGTCA
508274 TTAATCACTAA
1 TTAATCACTAA
508285 AGTTGTTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.34
Consensus pattern (16 bp):
TTAATCACTAACGTCA
Found at i:516221 original size:11 final size:11
Alignment explanation
Indices: 516197--516241 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
516187 TTGGTGTTGG
516197 AAACAAGATAA
1 AAACAAGATAA
* *
516208 AAATAAGATTA
1 AAACAAGATAA
516219 AAACAAGATAA
1 AAACAAGATAA
516230 AGAA-AAGATAA
1 A-AACAAGATAA
516241 A
1 A
516242 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:516225 original size:22 final size:22
Alignment explanation
Indices: 516197--516238 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
516187 TTGGTGTTGG
516197 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
516219 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
516239 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:523636 original size:18 final size:18
Alignment explanation
Indices: 523613--523647 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
523603 AGGAGACATG
*
523613 TCGACCGGATAACAACTA
1 TCGACCGGATAAAAACTA
523631 TCGACCGGATAAAAACT
1 TCGACCGGATAAAAACT
523648 GGATCCCCTT
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:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (18 bp):
TCGACCGGATAAAAACTA
Found at i:524443 original size:18 final size:18
Alignment explanation
Indices: 524420--524454 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
524410 AGGAGACATG
*
524420 TCGACCGGATAACAACTA
1 TCGACCGGATAAAAACTA
524438 TCGACCGGATAAAAACT
1 TCGACCGGATAAAAACT
524455 GGATCCCCTT
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:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (18 bp):
TCGACCGGATAAAAACTA
Found at i:524922 original size:807 final size:807
Alignment explanation
Indices: 523369--524991 Score: 3237
Period size: 807 Copynumber: 2.0 Consensus size: 807
523359 TAATTCCTAA
523369 TAAAATAATAATTCTGATCCTAAAAGATAATTAATCATCCTATATTAAATTATATTACAAATAAT
1 TAAAATAATAATTCTGATCCTAAAAGATAATTAATCATCCTATATTAAATTATATTACAAATAAT
523434 CAATATAAATATTGAAAATTCGTAATATTTACAAAATAACGTATTAATCCCGTATAGGATTTCCT
66 CAATATAAATATTGAAAATTCGTAATATTTACAAAATAACGTATTAATCCCGTATAGGATTTCCT
523499 GCATGCACCATCTTCAGTAAAATGGTCATATCTTGAGTTCCCGATATCGGATTGATGCGATTCAA
131 GCATGCACCATCTTCAGTAAAATGGTCATATCTTGAGTTCCCGATATCGGATTGATGCGATTCAA
523564 AAACCGTTGGAAAGATAAGAGATAGGCGGTTGTATCTCCAGGAGACATGTCGACCGGATAACAAC
196 AAACCGTTGGAAAGATAAGAGATAGGCGGTTGTATCTCCAGGAGACATGTCGACCGGATAACAAC
523629 TATCGACCGGATAAAAACTGGATCCCCTTCAAAAAGTTGTTGCAAATCTGCTGCTATTAGACCCT
261 TATCGACCGGATAAAAACTGGATCCCCTTCAAAAAGTTGTTGCAAATCTGCTGCTATTAGACCCT
523694 TACGGATGAATGCTTGAACTGCGATTTGAAGCTTGTCTTTAAGAAGTTTTTTCCGGCCTCGTGTG
326 TACGGATGAATGCTTGAACTGCGATTTGAAGCTTGTCTTTAAGAAGTTTTTTCCGGCCTCGTGTG
523759 ATAGGGCCAAGTGGTATAGTAAATTCATCATCCTTAGCTTTAGGGCATGTGGTGCATGTATCACT
391 ATAGGGCCAAGTGGTATAGTAAATTCATCATCCTTAGCTTTAGGGCATGTGGTGCATGTATCACT
523824 CGGTCGACGAACCGAAACCACCATCGTGTTCGTTGTCGACCGAGGAACAAAATCCCTTAAACCTT
456 CGGTCGACGAACCGAAACCACCATCGTGTTCGTTGTCGACCGAGGAACAAAATCCCTTAAACCTT
523889 TCGTCATGAATCGTCGCCGTTCGTCGTTAATTTCAGTCGGAAGTATCATCGGTAATAACATGATT
521 TCGTCATGAATCGTCGCCGTTCGTCGTTAATTTCAGTCGGAAGTATCATCGGTAATAACATGATT
523954 TCAGTTGGTTTTTCGTCGATTCACGACGATCCGGTTATCCGTTTACGACACCTCCTGCACCATCG
586 TCAGTTGGTTTTTCGTCGATTCACGACGATCCGGTTATCCGTTTACGACACCTCCTGCACCATCG
524019 TGTTCCTTGTGCCGTTCCGAGTCTGCCGGTGTTCTCCTTGTCTCCGTCGGTGGCGGCGCGTGAGG
651 TGTTCCTTGTGCCGTTCCGAGTCTGCCGGTGTTCTCCTTGTCTCCGTCGGTGGCGGCGCGTGAGG
524084 AGGTGAAATGGTCAAAGTTTTCGACGTTTCGGAATCGAGCTCTCCGCCGTTCAAAATTGTGAACC
716 AGGTGAAATGGTCAAAGTTTTCGACGTTTCGGAATCGAGCTCTCCGCCGTTCAAAATTGTGAACC
524149 GAGCTTGGTAAGTGTCTCAAAATACCT
781 GAGCTTGGTAAGTGTCTCAAAATACCT
524176 TAAAATAATAATTCTGATCCTAAAAGATAATTAATCATCCTATATTAAATTATATTACAAATAAT
1 TAAAATAATAATTCTGATCCTAAAAGATAATTAATCATCCTATATTAAATTATATTACAAATAAT
524241 CAATATAAATATTGAAAATTCGTAATATTTACAAAATAACGTATTAATCCCGTATAGGATTTCCT
66 CAATATAAATATTGAAAATTCGTAATATTTACAAAATAACGTATTAATCCCGTATAGGATTTCCT
524306 GCATGCACCATCTTCAGTAAAATGGTCATATCTTGAGTTCCCGATATCGGATTGATGCGATTCAA
131 GCATGCACCATCTTCAGTAAAATGGTCATATCTTGAGTTCCCGATATCGGATTGATGCGATTCAA
524371 AAACCGTTGGAAAGATAAGAGATAGGCGGTTGTATCTCCAGGAGACATGTCGACCGGATAACAAC
196 AAACCGTTGGAAAGATAAGAGATAGGCGGTTGTATCTCCAGGAGACATGTCGACCGGATAACAAC
524436 TATCGACCGGATAAAAACTGGATCCCCTTCAAAAAGTTGTTGCAAATCTGCTGCTATTAGACCCT
261 TATCGACCGGATAAAAACTGGATCCCCTTCAAAAAGTTGTTGCAAATCTGCTGCTATTAGACCCT
524501 TACGGATGAATGCTTGAACTGCGATTTGAAGCTTGTCTTTAAGAAGTTTTTTCCGGCCTCGTGTG
326 TACGGATGAATGCTTGAACTGCGATTTGAAGCTTGTCTTTAAGAAGTTTTTTCCGGCCTCGTGTG
524566 ATAGGGCCAAGTGGTATAGTAAATTCATCATCCTTAGCTTTAGGGCATGTGGTGCATGTATCACT
391 ATAGGGCCAAGTGGTATAGTAAATTCATCATCCTTAGCTTTAGGGCATGTGGTGCATGTATCACT
524631 CGGTCGACGAACCGAAACCACCATCGTGTTCGTTGTCGACCGAGGAACAAAATCCCTTAAACCTT
456 CGGTCGACGAACCGAAACCACCATCGTGTTCGTTGTCGACCGAGGAACAAAATCCCTTAAACCTT
*
524696 TTGTCATGAATCGTCGCCGTTCGTCGTTAATTTCAGTCGGAAGTATCATCGGTAATAACATGATT
521 TCGTCATGAATCGTCGCCGTTCGTCGTTAATTTCAGTCGGAAGTATCATCGGTAATAACATGATT
524761 TCAGTTGGTTTTTCGTCGATTCACGACGATCCGGTTATCCGTTTACGACACCTCCTGCACCATCG
586 TCAGTTGGTTTTTCGTCGATTCACGACGATCCGGTTATCCGTTTACGACACCTCCTGCACCATCG
524826 TGTTCCTTGTGCCGTTCCGAGTCTGCCGGTGTTCTCCTTGTCTCCGTCGGTGGCGGCGCGTGAGG
651 TGTTCCTTGTGCCGTTCCGAGTCTGCCGGTGTTCTCCTTGTCTCCGTCGGTGGCGGCGCGTGAGG
524891 AGGTGAAATGGTCAAAGTTTTCGACGTTTCGGAATCGAGCTCTCCGCCGTTCAAAATTGTGAACC
716 AGGTGAAATGGTCAAAGTTTTCGACGTTTCGGAATCGAGCTCTCCGCCGTTCAAAATTGTGAACC
524956 GAGCTTGGTAAGTGTCTCAAAATACCT
781 GAGCTTGGTAAGTGTCTCAAAATACCT
524983 TAAAATAAT
1 TAAAATAAT
524992 TTTTAGAAAT
Statistics
Matches: 815, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
807 815 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (807 bp):
TAAAATAATAATTCTGATCCTAAAAGATAATTAATCATCCTATATTAAATTATATTACAAATAAT
CAATATAAATATTGAAAATTCGTAATATTTACAAAATAACGTATTAATCCCGTATAGGATTTCCT
GCATGCACCATCTTCAGTAAAATGGTCATATCTTGAGTTCCCGATATCGGATTGATGCGATTCAA
AAACCGTTGGAAAGATAAGAGATAGGCGGTTGTATCTCCAGGAGACATGTCGACCGGATAACAAC
TATCGACCGGATAAAAACTGGATCCCCTTCAAAAAGTTGTTGCAAATCTGCTGCTATTAGACCCT
TACGGATGAATGCTTGAACTGCGATTTGAAGCTTGTCTTTAAGAAGTTTTTTCCGGCCTCGTGTG
ATAGGGCCAAGTGGTATAGTAAATTCATCATCCTTAGCTTTAGGGCATGTGGTGCATGTATCACT
CGGTCGACGAACCGAAACCACCATCGTGTTCGTTGTCGACCGAGGAACAAAATCCCTTAAACCTT
TCGTCATGAATCGTCGCCGTTCGTCGTTAATTTCAGTCGGAAGTATCATCGGTAATAACATGATT
TCAGTTGGTTTTTCGTCGATTCACGACGATCCGGTTATCCGTTTACGACACCTCCTGCACCATCG
TGTTCCTTGTGCCGTTCCGAGTCTGCCGGTGTTCTCCTTGTCTCCGTCGGTGGCGGCGCGTGAGG
AGGTGAAATGGTCAAAGTTTTCGACGTTTCGGAATCGAGCTCTCCGCCGTTCAAAATTGTGAACC
GAGCTTGGTAAGTGTCTCAAAATACCT
Found at i:525305 original size:22 final size:22
Alignment explanation
Indices: 525254--525305 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
525244 CTTTGACCGG
*
525254 CTTTGACCGGGCATTAAACGAC
1 CTTTGACTGGGCATTAAACGAC
*
525276 CTTTGACTGGGTATTAAACGAC
1 CTTTGACTGGGCATTAAACGAC
525298 CTTTGACT
1 CTTTGACT
525306 TTGACCGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (22 bp):
CTTTGACTGGGCATTAAACGAC
Found at i:525317 original size:28 final size:27
Alignment explanation
Indices: 525254--525317 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 27
525244 CTTTGACCGG
*
525254 CTTTGACCGGGCATTAAACGACCTTTGA
1 CTTTGACC-GGTATTAAACGACCTTTGA
525282 C--TG---GGTATTAAACGACCTTTGA
1 CTTTGACCGGTATTAAACGACCTTTGA
525304 CTTTGACCGAGTAT
1 CTTTGACCG-GTAT
525318 ACCTATCCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
22 19 0.66
24 2 0.07
26 2 0.07
27 1 0.03
28 5 0.17
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (27 bp):
CTTTGACCGGTATTAAACGACCTTTGA
Found at i:526623 original size:27 final size:29
Alignment explanation
Indices: 526593--526656 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 29
526583 AAATGATTGA
526593 AATA-CACCGTAT-ATGTAAAATGAC-CA-G
1 AATATCACC-TATAATG-AAAATGACTCAGG
526620 AATATC-CCTATAATGAAAATGACTCAGG
1 AATATCACCTATAATGAAAATGACTCAGG
526648 AATATCACC
1 AATATCACC
526657 AAGCTCATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
26 11 0.34
27 11 0.34
28 8 0.25
29 2 0.06
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.23
Consensus pattern (29 bp):
AATATCACCTATAATGAAAATGACTCAGG
Found at i:527718 original size:24 final size:25
Alignment explanation
Indices: 527691--527747 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
527681 AATATTTTTA
* *
527691 TCTGATTTC-CGACTTGAATTTTGT
1 TCTGATTTCACGACCTGAATTATGT
* *
527715 TCTGA-TACATGACCTGAATTATGT
1 TCTGATTTCACGACCTGAATTATGT
527739 TCTGATTTC
1 TCTGATTTC
527748 TAATATGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 22 0.85
25 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (25 bp):
TCTGATTTCACGACCTGAATTATGT
Found at i:530027 original size:39 final size:39
Alignment explanation
Indices: 529967--530049 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
529957 AAAATATAAG
* * *
529967 GAATACATGAAAGATATGATAGGTTCCATTGGAATACAT
1 GAATTCATGAAAGATAAGATAGGTTCCATTAGAATACAT
*
530006 GAATTCATGAAAGCTAAGATAGGTTCCATTAGAATACAT
1 GAATTCATGAAAGATAAGATAGGTTCCATTAGAATACAT
530045 GAATT
1 GAATT
530050 ACTTGTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (39 bp):
GAATTCATGAAAGATAAGATAGGTTCCATTAGAATACAT
Found at i:534771 original size:30 final size:30
Alignment explanation
Indices: 534702--534771 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
534692 CTTCAGCAAA
**
534702 TGTAACAGGTGACTCAGACACAGGATCAAC
1 TGTAACATTTGACTCAGACACAGGATCAAC
* *
534732 TGTAACATTTGACTCAGACACTGGATCAGC
1 TGTAACATTTGACTCAGACACAGGATCAAC
*
534762 TGTAGCATTT
1 TGTAACATTT
534772 TCGACAGGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (30 bp):
TGTAACATTTGACTCAGACACAGGATCAAC
Found at i:544396 original size:12 final size:13
Alignment explanation
Indices: 544370--544402 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
544360 TTTAAACTTT
544370 TTTATATTAATTA
1 TTTATATTAATTA
544383 TTTATATT-ATTA
1 TTTATATTAATTA
*
544395 TTGATATT
1 TTTATATT
544403 CATTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TTTATATTAATTA
Found at i:551824 original size:29 final size:30
Alignment explanation
Indices: 551782--551854 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
551772 ATTGTGTCGT
* *
551782 TTATATCACTGAACTTTCAATTT-TTTCAA
1 TTATACCATTGAACTTTCAATTTATTTCAA
* * * *
551811 TTATAGCATTGAACTTTGATTTTCATTTCAG
1 TTATACCATTGAACTTTCAATTT-ATTTCAA
551842 TTATACCATTGAA
1 TTATACCATTGAA
551855 TCGTTAAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (30 bp):
TTATACCATTGAACTTTCAATTTATTTCAA
Found at i:552075 original size:29 final size:30
Alignment explanation
Indices: 552003--552076 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
551993 TGATTTAACG
552003 GTTCAGTGGTATAATTGAAACGAAAATTAAA
1 GTTCAGTGGTATAATTG-AACGAAAATTAAA
* *
552034 GTTC-GATGCTATAATTG-A-TAAAATTGAAA
1 GTTCAG-TGGTATAATTGAACGAAAATT-AAA
552063 GTTCAGTGGTATAA
1 GTTCAGTGGTATAA
552077 ACGATACAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 6 0.16
29 15 0.41
30 2 0.05
31 14 0.38
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (30 bp):
GTTCAGTGGTATAATTGAACGAAAATTAAA
Found at i:552082 original size:29 final size:28
Alignment explanation
Indices: 552025--552082 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
552015 AATTGAAACG
**
552025 AAAATTAAAGTTCGATGCTATAATTGAT
1 AAAATTAAAGTTCGATGCTATAAACGAT
*
552053 AAAATTGAAAGTTC-AGTGGTATAAACGAT
1 AAAATT-AAAGTTCGA-TGCTATAAACGAT
552082 A
1 A
552083 CAACGTCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (28 bp):
AAAATTAAAGTTCGATGCTATAAACGAT
Found at i:555639 original size:20 final size:20
Alignment explanation
Indices: 555616--555654 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
555606 TTTGAAACTT
*
555616 AAATTCGCAAGACGAAAATG
1 AAATTCGCAACACGAAAATG
555636 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACGAAAAT
555655 CGCAACGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:555696 original size:20 final size:20
Alignment explanation
Indices: 555671--555721 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
555661 GTGATTTTAG
555671 TTTCGCGTTGCAGTTTTCAT
1 TTTCGCGTTGCAGTTTTCAT
* * *
555691 TTTCGCGTTACGGTTTTCCT
1 TTTCGCGTTGCAGTTTTCAT
*
555711 TTTCGCTTTGC
1 TTTCGCGTTGC
555722 GATTTTGGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.06, C:0.24, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCAGTTTTCAT
Found at i:555727 original size:20 final size:20
Alignment explanation
Indices: 555671--555727 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
555661 GTGATTTTAG
555671 TTTCGCGTTGC-AGTTTTCAT
1 TTTCGCGTTGCGA-TTTTCAT
* * *
555691 TTTCGCGTTACGGTTTTCCT
1 TTTCGCGTTGCGATTTTCAT
*
555711 TTTCGCTTTGCGATTTT
1 TTTCGCGTTGCGATTTT
555728 GGCGTTGCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.07, C:0.21, G:0.19, T:0.53
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:555746 original size:20 final size:20
Alignment explanation
Indices: 555723--555761 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
555713 TCGCTTTGCG
*
555723 ATTTTGGCGTTGCAAATTTC
1 ATTTTCGCGTTGCAAATTTC
* *
555743 ATTTTCGTGTTGCGAATTT
1 ATTTTCGCGTTGCAAATTT
555762 AAGTTTCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (20 bp):
ATTTTCGCGTTGCAAATTTC
Found at i:557314 original size:42 final size:42
Alignment explanation
Indices: 557255--557351 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
557245 ACCCCCACTT
* * * *
557255 CGAGAGCCATCACCTGATCGAGTCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
*
557297 CGAGAGTCATCACCTGATCGAGCCGATTATACACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
557339 CGAGAGCCATCAC
1 CGAGAGCCATCAC
557352 ATCATCTAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.18
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
Found at i:557994 original size:21 final size:21
Alignment explanation
Indices: 557904--558000 Score: 113
Period size: 21 Copynumber: 4.6 Consensus size: 21
557894 ATTCACCTTT
557904 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
557925 TATTGTTCAAGAGGCCACTCC
1 CATCGTTCAAGAGGCCCCTCC
* * * * *
557946 TATCTTTCAAGAGGTCCATCT
1 CATCGTTCAAGAGGCCCCTCC
557967 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
557988 CACCGTTCAAGAG
1 CATCGTTCAAGAG
558001 CTCGATTCAC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.25
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:559643 original size:15 final size:15
Alignment explanation
Indices: 559623--559657 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
559613 CCGTAGGACC
559623 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
559638 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
559653 ACTAC
1 ACTAC
559658 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:564029 original size:108 final size:108
Alignment explanation
Indices: 563840--564057 Score: 427
Period size: 108 Copynumber: 2.0 Consensus size: 108
563830 ATATGGTGAC
*
563840 ATGGCAATGGGCGTTGTTCCCGGCATTATCTCAATCTGAAATTCTACCTCTCTGTCCGGAGGTAA
1 ATGGCAATGGGCGCTGTTCCCGGCATTATCTCAATCTGAAATTCTACCTCTCTGTCCGGAGGTAA
563905 ACCTGGCAATTCTGCAGGAAATATATCAGAAAACTCTCTAACG
66 ACCTGGCAATTCTGCAGGAAATATATCAGAAAACTCTCTAACG
563948 ATGGCAATGGGCGCTGTTCCCGGCATTATCTCAATCTGAAATTCTACCTCTCTGTCCGGAGGTAA
1 ATGGCAATGGGCGCTGTTCCCGGCATTATCTCAATCTGAAATTCTACCTCTCTGTCCGGAGGTAA
564013 ACCTGGCAATTCTGCAGGAAATATATCAGAAAACTCTCTAACG
66 ACCTGGCAATTCTGCAGGAAATATATCAGAAAACTCTCTAACG
564056 AT
1 AT
564058 AGGAATTTCT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (108 bp):
ATGGCAATGGGCGCTGTTCCCGGCATTATCTCAATCTGAAATTCTACCTCTCTGTCCGGAGGTAA
ACCTGGCAATTCTGCAGGAAATATATCAGAAAACTCTCTAACG
Found at i:566597 original size:15 final size:15
Alignment explanation
Indices: 566577--566611 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
566567 CCGTAGGACC
566577 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
566592 ACTACGTCTCGAAGG
1 ACTACGTCCCGAAGG
566607 ACTAC
1 ACTAC
566612 AGAACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:573442 original size:15 final size:15
Alignment explanation
Indices: 573422--573456 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
573412 CCGTAGGACC
*
573422 ACTACGTCCCGAAGG
1 ACTACGTCCCAAAGG
573437 ACTACGTCCCAAAGG
1 ACTACGTCCCAAAGG
573452 ACTAC
1 ACTAC
573457 AGAACCCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCAAAGG
Found at i:580287 original size:15 final size:15
Alignment explanation
Indices: 580267--580301 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
580257 TCGTAGGACC
580267 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
580282 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
580297 ACTAC
1 ACTAC
580302 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:587147 original size:15 final size:15
Alignment explanation
Indices: 587127--587161 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
587117 CCGTAGGACC
587127 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
587142 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
587157 ACTAC
1 ACTAC
587162 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:589125 original size:20 final size:20
Alignment explanation
Indices: 589097--589139 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
589087 AAGGTACACT
*
589097 TTCATAACGCGAAAATCAAA
1 TTCACAACGCGAAAATCAAA
*
589117 TTCACAACGCGAAAGTCAAA
1 TTCACAACGCGAAAATCAAA
589137 TTC
1 TTC
589140 GCGTTGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (20 bp):
TTCACAACGCGAAAATCAAA
Found at i:589179 original size:20 final size:20
Alignment explanation
Indices: 589154--589207 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
589144 TGTGATTGTT
589154 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
589174 GCGAAAGTAAAATTCGCTAC
1 GCGAAAGTCAAATTCGCAAC
*
589194 GTGAAAGTCAAATT
1 GCGAAAGTCAAATT
589208 TGCGTTGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:589244 original size:20 final size:20
Alignment explanation
Indices: 589219--589303 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
589209 GCGTTGCGAT
*
589219 TTTCGCGTTACGAATTTTAC
1 TTTCGCGTTACGAATTTGAC
*
589239 TTTCGCGTTACGAATTTTAC
1 TTTCGCGTTACGAATTTGAC
* *
589259 TTTCGAGTTTCGAATTTGAC
1 TTTCGCGTTACGAATTTGAC
*
589279 TTTCGCGTTTCGAATTTGAC
1 TTTCGCGTTACGAATTTGAC
589299 TTTCG
1 TTTCG
589304 TAACAATCGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTACGAATTTGAC
Found at i:589582 original size:18 final size:18
Alignment explanation
Indices: 589559--589594 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
589549 AAGCCGGTTG
589559 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
589577 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
589595 CCTTTTGCTT
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:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:592997 original size:41 final size:42
Alignment explanation
Indices: 592947--593029 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 42
592937 TGCGAAAAAG
* *
592947 AAATACGCGTTACGAATT-CAGAAATTAAGTTGCGAATTTGGA
1 AAATACGCGTTACG-ATTGCAGAAACTAAGTTGCGAAATTGGA
* * *
592989 AAAT-CGCGTTGCGATTGTAGAAACTGAGTTGCGAAATTGGA
1 AAATACGCGTTACGATTGCAGAAACTAAGTTGCGAAATTGGA
593030 GTTCGCGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.09
41 28 0.80
42 4 0.11
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (42 bp):
AAATACGCGTTACGATTGCAGAAACTAAGTTGCGAAATTGGA
Found at i:603138 original size:13 final size:13
Alignment explanation
Indices: 603120--603145 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
603110 TCTTCCCATG
603120 CTTAGAGTATGAA
1 CTTAGAGTATGAA
603133 CTTAGAGTATGAA
1 CTTAGAGTATGAA
603146 GAAACCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
CTTAGAGTATGAA
Found at i:614286 original size:22 final size:21
Alignment explanation
Indices: 614252--614292 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
614242 ATAATTATTT
614252 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
614273 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
614293 TTTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:616363 original size:3 final size:3
Alignment explanation
Indices: 616352--616420 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
616342 TTAAATAATA
*
616352 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
616396 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
616421 TTTGCAGGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:621471 original size:106 final size:106
Alignment explanation
Indices: 621228--622073 Score: 1331
Period size: 106 Copynumber: 8.0 Consensus size: 106
621218 AATTTGCTCG
* * * * * * *
621228 AGAGTAAATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATG
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACG
* * * *
621292 ACGAAGGGGCGGCTGATTGTCAACAAAC-ATTTCTCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
621333 AGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
621398 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCGATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
621439 AGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
621504 CGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
621544 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
621609 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
621650 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
621715 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
621756 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
621821 CGAAGGGACCGCTGGCTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
621862 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
621927 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * * **
621968 AGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCTTGACAACGCAAGTTCAACTTCACGA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
622033 CGAAGGGACCGCTGGTTGTCAATAAACAACTT-TCAACTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
622073 A
1 A
622074 CGACGAAGGA
Statistics
Matches: 694, Mismatches: 44, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
105 185 0.27
106 509 0.73
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
Found at i:622266 original size:84 final size:84
Alignment explanation
Indices: 622120--622454 Score: 379
Period size: 84 Copynumber: 4.0 Consensus size: 84
622110 AAAGACCCCC
* * * * * * * * * *
622120 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAGCTCAAGCCTAGGAGGGTTA
1 GAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTCAAGTCGAGAAGGGCTA
622185 TCTGTC-ACCAAAAGACCTTT
65 TCTGTCAACC-AAAGACCTTT
* * * *
622205 GAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGTCGAGAAGGGCTAT
622270 CT-TCCAACCAAAGACCTTT
66 CTGT-CAACCAAAGACCTTT
* * * *
622289 GAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGTCGAGAAGGGCTAT
* *
622354 TTG-CAAACCAAAGACCTTC
66 CTGTC-AACCAAAGACCTTT
* * * *
622373 GAGTTTGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGTCGAGAAGGGCTAT
* *
622438 CTGCCTACCAAAGACCT
66 CTGTCAACCAAAGACCT
622455 GACGAGTTCG
Statistics
Matches: 214, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
83 2 0.01
84 191 0.89
85 21 0.10
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (84 bp):
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTCAAGTCGAGAAGGGCTAT
CTGTCAACCAAAGACCTTT
Found at i:622387 original size:168 final size:169
Alignment explanation
Indices: 622120--622454 Score: 451
Period size: 168 Copynumber: 2.0 Consensus size: 169
622110 AAAGACCCCC
* * * * * * *
622120 GAGTTCGATTACACTCAGCTTCGAGGGTACATCATTTACAGCATAGCTCAAGCCTAGGAGGGTTA
1 GAGTTCGACTACACTCAGCTTCCAAGGTACATCATTTACAACATAGCTCAAGCCAAGAAGGGCTA
* *
622185 TCTGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAA
66 TCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAA
* *
622250 CTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTT
131 CTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTT
* * *
622289 GAGTTCGACTACGCTCAGC-TCCAAGGTACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTA
1 GAGTTCGACTACACTCAGCTTCCAAGGTACATCATTTACAACATAGCTCAAGCCAAGAAGGGCTA
* * *
622353 TTTG-CAAACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCAT
66 TCTGTC--ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCAT
* * *
622416 AGCTTAAGTTGAGAAGGGCTATCTGCCTACCAAAGACCT
129 AACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCT
622455 GACGAGTTCG
Statistics
Matches: 144, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
167 1 0.01
168 123 0.85
169 20 0.14
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (169 bp):
GAGTTCGACTACACTCAGCTTCCAAGGTACATCATTTACAACATAGCTCAAGCCAAGAAGGGCTA
TCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAA
CTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTT
Found at i:622705 original size:3 final size:3
Alignment explanation
Indices: 622694--622762 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
622684 TTAAATAATA
*
622694 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
622738 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
622763 TTTGCAGGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:626386 original size:6 final size:6
Alignment explanation
Indices: 626375--626424 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
626365 AATGCAGAAG
626375 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT
626423 GA
1 GA
626425 TTGATAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
GAGAGT
Found at i:626647 original size:29 final size:29
Alignment explanation
Indices: 626612--626693 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
626602 ACAGTGATCA
626612 TAGGACGCCATGCAATCCAGGCGATCTTG
1 TAGGACGCCATGCAATCCAGGCGATCTTG
*
626641 TAGGACGCCATGCAATCCAGACGATCTTG
1 TAGGACGCCATGCAATCCAGGCGATCTTG
626670 TAGGACGCCATGCAATCCAGGCGA
1 TAGGACGCCATGCAATCCAGGCGA
626694 CATACGGGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (29 bp):
TAGGACGCCATGCAATCCAGGCGATCTTG
Found at i:626744 original size:35 final size:35
Alignment explanation
Indices: 626704--626782 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
626694 CATACGGGAA
626704 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
626739 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
626774 CATACGAGC
1 CATACGAGC
626783 GTTCTCCCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (35 bp):
CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
Found at i:626798 original size:26 final size:26
Alignment explanation
Indices: 626769--626826 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
626759 CCCATGCATA
626769 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
626795 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
626821 CGAGCC
1 CGAGCC
626827 CCATGCATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.19, C:0.40, G:0.24, T:0.17
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:626842 original size:67 final size:67
Alignment explanation
Indices: 626758--626991 Score: 315
Period size: 67 Copynumber: 3.2 Consensus size: 67
626748 CAATGGTTCT
626758 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
626823 AG
66 AG
626825 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
626890 AGGTGG
66 A----G
626896 TTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCG
1 ----CCCCATGCATACGAGCCATACGAG-C----GTTCTCCCCATG----CGAGCCATACGAGCG
626961 TTCTCCCCATGCGAG
53 TTCTCCCCATGCGAG
626976 CCCCATGCATACGAGC
1 CCCCATGCATACGAGC
626992 GTTCTCCCCA
Statistics
Matches: 150, Mismatches: 0, Indels: 25
0.86 0.00 0.14
Matches are distributed among these distances:
67 66 0.44
71 1 0.01
75 24 0.16
76 17 0.11
80 13 0.09
84 29 0.19
ACGTcount: A:0.21, C:0.38, G:0.22, T:0.19
Consensus pattern (67 bp):
CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
AG
Found at i:626867 original size:26 final size:26
Alignment explanation
Indices: 626836--627009 Score: 119
Period size: 26 Copynumber: 6.2 Consensus size: 26
626826 CCCATGCATA
626836 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
626862 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
*
626888 CGAG------GTG-GTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
626907 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 ----CGAGCCATACGAG-C----GTTCTCCCCATG
626942 CATACGAGCCATACGAGCGTTCTCCCCATG
1 ----CGAGCCATACGAGCGTTCTCCCCATG
626972 CGAGCCCCATGCATACGAGCGTTCTCCCCATG
1 CGAG---C---CATACGAGCGTTCTCCCCATG
627004 CGAGCC
1 CGAGCC
627010 CCATGCATAC
Statistics
Matches: 124, Mismatches: 2, Indels: 44
0.73 0.01 0.26
Matches are distributed among these distances:
19 12 0.10
20 2 0.02
23 4 0.03
26 35 0.28
29 4 0.03
30 12 0.10
32 25 0.20
34 1 0.01
35 29 0.23
ACGTcount: A:0.20, C:0.37, G:0.23, T:0.20
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:626939 original size:35 final size:35
Alignment explanation
Indices: 626893--626959 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
626883 CCATGCGAGG
626893 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAA
1 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAA
626928 TGGTTCTCCCCATGCATACGAGCCATACGAGC
1 TGGTTCTCCCCATGCATACGAGCCATACGAGC
626960 GTTCTCCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (35 bp):
TGGTTCTCCCCATGCATACGAGCCATACGAGCCAA
Found at i:626984 original size:41 final size:41
Alignment explanation
Indices: 626935--627050 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 41
626925 CAATGGTTCT
626935 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG
626976 -CCC---CAT----G-CATACGAGCGTTCTCCCCATGCGAG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG
627008 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG
627049 CC
1 CC
627051 ATACGAGCGT
Statistics
Matches: 66, Mismatches: 0, Indels: 18
0.79 0.00 0.21
Matches are distributed among these distances:
32 25 0.38
33 4 0.06
36 3 0.05
37 3 0.05
40 4 0.06
41 27 0.41
ACGTcount: A:0.21, C:0.41, G:0.22, T:0.17
Consensus pattern (41 bp):
CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG
Found at i:626992 original size:32 final size:32
Alignment explanation
Indices: 626951--627023 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
626941 GCATACGAGC
626951 CATACGAGCGTTCTCCCCATGCGAGCCCCATG
1 CATACGAGCGTTCTCCCCATGCGAGCCCCATG
626983 CATACGAGCGTTCTCCCCATGCGAGCCCCATG
1 CATACGAGCGTTCTCCCCATGCGAGCCCCATG
627015 CATACGAGC
1 CATACGAGC
627024 CATACGAGCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.21, C:0.40, G:0.22, T:0.18
Consensus pattern (32 bp):
CATACGAGCGTTCTCCCCATGCGAGCCCCATG
Found at i:627023 original size:73 final size:67
Alignment explanation
Indices: 626935--627074 Score: 226
Period size: 73 Copynumber: 2.0 Consensus size: 67
626925 CAATGGTTCT
626935 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCGTTCTCCC
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG---C---CATACGAGCGTTCTCCC
627000 CATGCGAG
60 CATGCGAG
627008 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
627073 AG
66 AG
627075 GTGGCCATGC
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
67 25 0.37
70 1 0.01
73 41 0.61
ACGTcount: A:0.21, C:0.39, G:0.22, T:0.18
Consensus pattern (67 bp):
CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
AG
Found at i:627050 original size:26 final size:26
Alignment explanation
Indices: 627019--627074 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
627009 CCCATGCATA
627019 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
627045 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
627071 CGAG
1 CGAG
627075 GTGGCCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.18
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:627067 original size:183 final size:177
Alignment explanation
Indices: 626716--627078 Score: 672
Period size: 183 Copynumber: 2.0 Consensus size: 177
626706 TACGAGCCAA
626716 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
1 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
626781 GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
66 GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
626846 GAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
131 GAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
626893 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
1 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
626958 GCGTTCTCCCCATGCGAGCCCCATGCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAG
66 GCGTTCTCCCCATGCGAG---C---CATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAG
627023 CCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
125 CCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
627076 TGG
1 TGG
627079 CCATGCAGTG
Statistics
Matches: 180, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
177 83 0.46
180 1 0.01
183 96 0.53
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.20
Consensus pattern (177 bp):
TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
GAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
Found at i:627150 original size:29 final size:29
Alignment explanation
Indices: 627118--627205 Score: 176
Period size: 29 Copynumber: 3.0 Consensus size: 29
627108 CAGCCTAGGA
627118 GACCTTGTAGGTCGCCATGTAGTCCCGGC
1 GACCTTGTAGGTCGCCATGTAGTCCCGGC
627147 GACCTTGTAGGTCGCCATGTAGTCCCGGC
1 GACCTTGTAGGTCGCCATGTAGTCCCGGC
627176 GACCTTGTAGGTCGCCATGTAGTCCCGGC
1 GACCTTGTAGGTCGCCATGTAGTCCCGGC
627205 G
1 G
627206 CCATTCCCAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.14, C:0.31, G:0.32, T:0.24
Consensus pattern (29 bp):
GACCTTGTAGGTCGCCATGTAGTCCCGGC
Found at i:627224 original size:13 final size:13
Alignment explanation
Indices: 627206--627237 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
627196 AGTCCCGGCG
*
627206 CCATTCCCATCGT
1 CCATTCCCATCAT
627219 CCATTCCCATCAT
1 CCATTCCCATCAT
627232 CCATTC
1 CCATTC
627238 ACATGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.47, G:0.03, T:0.31
Consensus pattern (13 bp):
CCATTCCCATCAT
Found at i:627419 original size:25 final size:25
Alignment explanation
Indices: 627391--627442 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
627381 TGTACAATTA
*
627391 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
627416 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
627441 TT
1 TT
627443 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:627529 original size:21 final size:21
Alignment explanation
Indices: 627505--627557 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
627495 TTGCAGCCGA
627505 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
627526 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
627547 GAAAGTAAGAA
1 GAAAGAAAGAA
627558 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:627551 original size:17 final size:16
Alignment explanation
Indices: 627503--627534 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
627493 GATTGCAGCC
627503 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
627519 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
627535 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:627804 original size:47 final size:47
Alignment explanation
Indices: 627761--627851 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
627751 TTATATAGTT
627761 AAAAAA-TAATTAATTAGTTTGTATT-GTT-AATAGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTTAGTTATATA
* *
627805 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTT-AGTTATAT
627852 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
45 17 0.41
46 3 0.07
47 7 0.17
48 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTTAGTTATATA
Found at i:627823 original size:45 final size:44
Alignment explanation
Indices: 627720--627851 Score: 132
Period size: 45 Copynumber: 3.0 Consensus size: 44
627710 TACATAAATT
*
627720 AAAAATTATTTAATTAGTATATGTTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTGTTAATAGTTAGTTATA-TAA
*
627762 AAAAA-TAATTAATTAGTTTGTATTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGT-TTGTTAATAGTTAGTTATATAA
627806 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TT-GTT-AATAGTT-AGTTATAT
627852 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 3 0.04
40 4 0.05
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 21 0.28
46 3 0.04
47 7 0.09
48 8 0.11
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (44 bp):
AAAAATTATTTAATTAGTTTGTTTGTTAATAGTTAGTTATATAA
Found at i:630725 original size:28 final size:28
Alignment explanation
Indices: 630687--630740 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
630677 TAAATATAAT
*
630687 ATATAACTTAAACTAATAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
630715 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
630741 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:630747 original size:28 final size:28
Alignment explanation
Indices: 630682--630747 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
630672 TTATATAAAT
*
630682 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
630710 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
630738 ATAATTTATA
1 ATAATATATA
630748 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:630750 original size:21 final size:21
Alignment explanation
Indices: 630717--630765 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
630707 CTAATATAAT
630717 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
630738 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
630759 ATTAACT
1 A-TAACT
630766 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:631248 original size:17 final size:17
Alignment explanation
Indices: 631228--631283 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
631218 CATCCCCTCC
631228 CCCATGCATTCCCACGT
1 CCCATGCATTCCCACGT
* * *
631245 CCCATGCATCCCCTC-C
1 CCCATGCATTCCCACGT
631261 CCCATGCATTCCCACGT
1 CCCATGCATTCCCACGT
631278 CCCATG
1 CCCATG
631284 TTGATTGCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.16, C:0.52, G:0.11, T:0.21
Consensus pattern (17 bp):
CCCATGCATTCCCACGT
Found at i:631260 original size:33 final size:34
Alignment explanation
Indices: 631200--631283 Score: 134
Period size: 33 Copynumber: 2.4 Consensus size: 34
631190 CCATGCACAG
*
631200 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCA
1 TTCCCACGTCCCATG--CCATCCCCTCCCCCATGCA
631236 TTCCCACGTCCCATG-CATCCCCTCCCCCATGCA
1 TTCCCACGTCCCATGCCATCCCCTCCCCCATGCA
631269 TTCCCACGTCCCATG
1 TTCCCACGTCCCATG
631284 TTGATTGCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 33 0.70
36 14 0.30
ACGTcount: A:0.17, C:0.52, G:0.10, T:0.21
Consensus pattern (34 bp):
TTCCCACGTCCCATGCCATCCCCTCCCCCATGCA
Found at i:631264 original size:16 final size:16
Alignment explanation
Indices: 631218--631269 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
631208 TCCAATGCAC
631218 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
* * *
631234 CATTCCCACGTCCCATG
1 CATCCCCTC-CCCCATG
631251 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
631267 CAT
1 CAT
631270 TCCCACGTCC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.15, C:0.56, G:0.08, T:0.21
Consensus pattern (16 bp):
CATCCCCTCCCCCATG
Found at i:631354 original size:29 final size:29
Alignment explanation
Indices: 631321--631409 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
631311 TAATACACAC
* *
631321 AGGTCGCCCGGATTCCATGGCGACCTTCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
631350 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
631379 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
631408 AG
1 AG
631410 ACCACTGTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:641398 original size:20 final size:22
Alignment explanation
Indices: 641359--641398 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
641349 AACTACATAT
641359 GTATATTAGAATTATTATTTCA
1 GTATATTAGAATTATTATTTCA
641381 GTATATTAG-ATT-TTATTT
1 GTATATTAGAATTATTATTT
641399 TAAATAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (22 bp):
GTATATTAGAATTATTATTTCA
Found at i:642675 original size:39 final size:40
Alignment explanation
Indices: 642566--642697 Score: 117
Period size: 39 Copynumber: 3.4 Consensus size: 40
642556 TGTTTTTGCA
* * * *
642566 TGGCCTGAAGAGGCCGTGCACTCTTGAAGTC-TATACGTT
1 TGGCCTGAAGACGTCGTGCACTCATGAAGTCTTATACGAT
* * * * * *
642605 TGGCCTGAAGATGTTGTGTACTCCTGGAGTCTTATTC-AT
1 TGGCCTGAAGACGTCGTGCACTCATGAAGTCTTATACGAT
* *
642644 TGGTCTGAAGACGTCGTGCACTCATGAAGTCTT-TACGTT
1 TGGCCTGAAGACGTCGTGCACTCATGAAGTCTTATACGAT
* *
642683 TAGCCTAAAGACGTC
1 TGGCCTGAAGACGTC
642698 AAAAAGTCAT
Statistics
Matches: 72, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
38 2 0.03
39 66 0.92
40 4 0.06
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (40 bp):
TGGCCTGAAGACGTCGTGCACTCATGAAGTCTTATACGAT
Found at i:645448 original size:24 final size:24
Alignment explanation
Indices: 645421--645478 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
645411 ATGTTCATAA
* * * *
645421 ATAAGTTCGTTTATTGACTAATTT
1 ATAAATTCATTTATCGACGAATTT
*
645445 ATAAATTCATTTATCGACGCATTT
1 ATAAATTCATTTATCGACGAATTT
*
645469 ATAAACTCAT
1 ATAAATTCAT
645479 ATGTATACTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (24 bp):
ATAAATTCATTTATCGACGAATTT
Found at i:649066 original size:31 final size:32
Alignment explanation
Indices: 649031--649107 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
649021 AACTGTTGTG
*
649031 GAGAAAATTTGAGACTTTGAAAA-CAATTATA
1 GAGAAAATTTGAGACTTTCAAAATCAATTATA
* * * *
649062 GAGAAAACTTGAGATTTTCAAAATTAGTTATA
1 GAGAAAATTTGAGACTTTCAAAATCAATTATA
*
649094 GATAAAATTTGAGA
1 GAGAAAATTTGAGA
649108 GATTTAATTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 20 0.53
32 18 0.47
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.31
Consensus pattern (32 bp):
GAGAAAATTTGAGACTTTCAAAATCAATTATA
Found at i:653524 original size:59 final size:60
Alignment explanation
Indices: 653419--653546 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 60
653409 AATTAGTCCA
* ** *
653419 TAAATTTTTAAAGGTTTCAATTTCATCCATAAACTATGATTATCATTCTAAATTACTC-C
1 TAAACTTTTAAACATTTCAATTTCATCCACAAACTATGATTATCATTCTAAATTACTCTC
* *
653478 TCAAACTTTTAAACATTTCAA-TTCATCCCCAAACTATGATCT-TCATTCTAAATTAGTCTC
1 T-AAACTTTTAAACATTTCAATTTCATCCACAAACTATGAT-TATCATTCTAAATTACTCTC
653538 TAAACTTTT
1 TAAACTTTT
653547 TGAAAATTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 41 0.68
60 19 0.32
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.41
Consensus pattern (60 bp):
TAAACTTTTAAACATTTCAATTTCATCCACAAACTATGATTATCATTCTAAATTACTCTC
Found at i:653838 original size:58 final size:58
Alignment explanation
Indices: 653755--653865 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
653745 AAAGATGGAT
** * ** *
653755 ATAGTTTAGGGATAAAATTATAATATTCAAAAGTTCAAGGACTGATTTAAAATAAGTC
1 ATAGTTTACAGATAAAATTAAAATATTCAAAAGTTCAAAAACTCATTTAAAATAAGTC
* *
653813 ATAGTTTACAGATGAAATTAAAATATTCAAAAGTTTAAAAACTCATTTAAAAT
1 ATAGTTTACAGATAAAATTAAAATATTCAAAAGTTCAAAAACTCATTTAAAAT
653866 GAGAGTTGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (58 bp):
ATAGTTTACAGATAAAATTAAAATATTCAAAAGTTCAAAAACTCATTTAAAATAAGTC
Found at i:653847 original size:29 final size:28
Alignment explanation
Indices: 653705--653850 Score: 71
Period size: 29 Copynumber: 5.0 Consensus size: 28
653695 TGAAATTGGG
*
653705 GATGAAATTAAAAGATTCAAAAGTTTATA
1 GATGAAATTAAAATATTCAAAAGTTTA-A
** * * ** * *
653734 GACCAACTTAGAAAGATGGATATAGTTTAGG
1 GATGAAATTA-AAATATTCA-AAAGTTTA-A
* * *
653765 GATAAAATTATAATATTCAAAAGTTCAA
1 GATGAAATTAAAATATTCAAAAGTTTAA
* * *
653793 GGACTG-ATTTAAAATAAGTC-ATAGTTTACA
1 -GA-TGAAATTAAAAT-ATTCAAAAGTTTA-A
653823 GATGAAATTAAAATATTCAAAAGTTTAA
1 GATGAAATTAAAATATTCAAAAGTTTAA
653851 AAACTCATTT
Statistics
Matches: 82, Mismatches: 27, Indels: 17
0.65 0.21 0.13
Matches are distributed among these distances:
28 6 0.07
29 45 0.55
30 17 0.21
31 14 0.17
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (28 bp):
GATGAAATTAAAATATTCAAAAGTTTAA
Found at i:654358 original size:3 final size:3
Alignment explanation
Indices: 654350--654382 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
654340 AATAAATAAT
654350 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
654383 TTTAATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:654737 original size:22 final size:22
Alignment explanation
Indices: 654709--654759 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
654699 CCACAAACTT
654709 TTCAAGTTAGATAAATATGAAA
1 TTCAAGTTAGATAAATATGAAA
654731 TTCAAGTTAGATAAATATGAAA
1 TTCAAGTTAGATAAATATGAAA
654753 TTCAAGT
1 TTCAAGT
654760 ATACAAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (22 bp):
TTCAAGTTAGATAAATATGAAA
Found at i:655211 original size:16 final size:16
Alignment explanation
Indices: 655169--655232 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 16
655159 ATAGTTGAAC
* *
655169 CAAAAACAACCCAAAC
1 CAAAAACAACCCGAAT
* ** *
655185 CGAAAGTAACCTGAAT
1 CAAAAACAACCCGAAT
*
655201 CAAAAACAACCCAAAT
1 CAAAAACAACCCGAAT
*
655217 CGAAAACAACCCGAAT
1 CAAAAACAACCCGAAT
655233 TTAATTTACC
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.55, C:0.30, G:0.08, T:0.08
Consensus pattern (16 bp):
CAAAAACAACCCGAAT
Found at i:655324 original size:3 final size:3
Alignment explanation
Indices: 655316--655343 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
655306 ATTGAATAAT
655316 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
655344 ATTTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:656013 original size:31 final size:32
Alignment explanation
Indices: 655941--656055 Score: 90
Period size: 31 Copynumber: 3.7 Consensus size: 32
655931 AAAATCGATC
* * *
655941 GATCCGATATTAACCAAACCCG-AAATCAACC
1 GATCCGATATTAACCCAACCCGAAAACCAACT
* ** * *
655972 AATATGATATTAACCCGACCCGAAAATCAACT
1 GATCCGATATTAACCCAACCCGAAAACCAACT
* * * * *
656004 G-TTCTATATTGATCTAACCCGAAAACCAACT
1 GATCCGATATTAACCCAACCCGAAAACCAACT
*
656035 GATCCGATATTAACCAAACCC
1 GATCCGATATTAACCCAACCC
656056 AACTTACCAT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
31 40 0.65
32 22 0.35
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.22
Consensus pattern (32 bp):
GATCCGATATTAACCCAACCCGAAAACCAACT
Found at i:659793 original size:65 final size:65
Alignment explanation
Indices: 659672--659869 Score: 279
Period size: 65 Copynumber: 3.0 Consensus size: 65
659662 TGTAGAGTGA
* * * * *
659672 ACAAGTACAACTCACTCATATGACTTATATACCTTTGTGGTGCGTGGGATGAAGTGATAATTGAA
1 ACAA-TACAAATCACTCATATGACTTATGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAA
659737 T
65 T
* * * *
659738 ACAATATAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGGGGTGGAGTGATAGTTGAAT
1 ACAATACAAATCACTCATATGACTTATGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAAT
* **
659803 ACAATACAAATCACTCATATGACTTATGTATCTTTGTGGTGCATGAAGTGGAGTGATAATTGAAT
1 ACAATACAAATCACTCATATGACTTATGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAAT
659868 AC
1 AC
659870 TGCAACTATC
Statistics
Matches: 116, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
65 112 0.97
66 4 0.03
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (65 bp):
ACAATACAAATCACTCATATGACTTATGTACCTTTGTGGTGCATGGGGTGGAGTGATAATTGAAT
Found at i:660190 original size:29 final size:29
Alignment explanation
Indices: 660148--660208 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
660138 AAAGAGTAAG
*
660148 TATATGATGTGGAACGGTACAAGTTTAAT
1 TATATGATATGGAACGGTACAAGTTTAAT
*
660177 TATATGATATGGAACGGTTCAAGTTTAAT
1 TATATGATATGGAACGGTACAAGTTTAAT
660206 TAT
1 TAT
660209 TACATTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (29 bp):
TATATGATATGGAACGGTACAAGTTTAAT
Found at i:660894 original size:2 final size:2
Alignment explanation
Indices: 660887--660922 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
660877 CAATAAAACA
660887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
660923 GAAAATTCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:677486 original size:32 final size:32
Alignment explanation
Indices: 677445--677509 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
677435 AGATAATGTG
677445 ATTGCTATAGTGCAAGCTATCAACTTTTTTGA
1 ATTGCTATAGTGCAAGCTATCAACTTTTTTGA
*
677477 ATTGCTATAGTGCAAGCTATCACCTTTTTTGA
1 ATTGCTATAGTGCAAGCTATCAACTTTTTTGA
677509 A
1 A
677510 GAATAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (32 bp):
ATTGCTATAGTGCAAGCTATCAACTTTTTTGA
Found at i:683103 original size:53 final size:53
Alignment explanation
Indices: 683018--683217 Score: 314
Period size: 53 Copynumber: 3.8 Consensus size: 53
683008 TGACGGATCT
* * *
683018 GCTCCCTCTTG-TTCAGGGAGTAGAATTTGAATAATCTTCTGCTTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
* *
683070 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
* *
683123 GCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTTTG-TCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT-TACGGGTTC
683176 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
683218 GTGTGATTCT
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
52 11 0.08
53 126 0.92
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (53 bp):
GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTC
Found at i:683669 original size:42 final size:41
Alignment explanation
Indices: 683584--683675 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 41
683574 ACTATTCCGA
* *
683584 AAAGGCTTA-AAATGGCCCGAAGGACTTATCATCTCACTCG
1 AAAGACTTACAAATGACCCGAAGGACTTATCATCTCACTCG
683624 AAAGACTTACAAATGACCCGAAGGA-TT-TCATCATCATGCTCG
1 AAAGACTTACAAATGACCCGAAGGACTTATCATC-TCA--CTCG
683666 AAAGACTTAC
1 AAAGACTTAC
683676 TGATGAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
39 5 0.11
40 13 0.28
41 14 0.30
42 14 0.30
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAGACTTACAAATGACCCGAAGGACTTATCATCTCACTCG
Found at i:683980 original size:42 final size:41
Alignment explanation
Indices: 683883--683986 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 41
683873 CCCGAAGGTT
* * * * *
683883 TTACAGATGGCCCGAAGGACTCATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTAAGCATCATGCTCGAAAGAC
* *
683924 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGA-CTAAGCATCATGCTCGAAAGAC
*
683966 TTACTGATGGCCCGAAGGACT
1 TTACAGATGGCCCGAAGGACT
683987 TATAAATTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 19 0.37
42 33 0.63
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTAAGCATCATGCTCGAAAGAC
Found at i:684074 original size:214 final size:214
Alignment explanation
Indices: 683705--684095 Score: 692
Period size: 214 Copynumber: 1.8 Consensus size: 214
683695 CTCTTCGGTG
* *
683705 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* *
683770 ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTTGTTTTCAAAAATTTCATCTTCTCAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
*
683835 ATCGTTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACAGATGGCCCGAAG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACAGATGGCCCGAAG
683900 GACTCATCATCTTGCTCTA
196 GACTCATCATCTTGCTCTA
* *
683919 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* *
683984 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
*
684049 ATCATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGT
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGT
684096 CTTATGGATG
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
214 167 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (214 bp):
AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
ACTTATAAATTGTGAAATTTTGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACAGATGGCCCGAAG
GACTCATCATCTTGCTCTA
Found at i:694860 original size:18 final size:18
Alignment explanation
Indices: 694834--694868 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
694824 TCGAAAGGAC
*
694834 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
694852 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
694869 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:711811 original size:2 final size:2
Alignment explanation
Indices: 711800--711846 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
711790 AACACCCATA
711800 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
711841 AT AT AT
1 AT AT AT
711847 TTGTGGGTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:713811 original size:9 final size:9
Alignment explanation
Indices: 713797--713821 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
713787 AAATTCTTAT
713797 ATATTTTAG
1 ATATTTTAG
713806 ATATTTTAG
1 ATATTTTAG
713815 ATATTTT
1 ATATTTT
713822 CTTAAAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (9 bp):
ATATTTTAG
Found at i:716371 original size:29 final size:32
Alignment explanation
Indices: 716337--716410 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 32
716327 TGTCTTTTTT
716337 ATATATTTTTATAATTA-TG-AACAT-AATTA
1 ATATATTTTTATAATTATTGCAACATCAATTA
** *
716366 ATATATTCCTATAATTATTGCCAATATCAATTA
1 ATATATTTTTATAATTATTG-CAACATCAATTA
*
716399 ATATTTTTTTAT
1 ATATATTTTTAT
716411 TAATATCAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 15 0.43
30 2 0.06
32 4 0.11
33 14 0.40
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (32 bp):
ATATATTTTTATAATTATTGCAACATCAATTA
Found at i:725130 original size:17 final size:17
Alignment explanation
Indices: 725110--725142 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
725100 ATATTTATTT
*
725110 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
725127 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
725143 TATGGTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:725194 original size:16 final size:15
Alignment explanation
Indices: 725154--725195 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
725144 ATGGTAGTAA
725154 AATATTATTTTAAAT
1 AATATTATTTTAAAT
*
725169 AAT-TACATTTTACAAT
1 AATAT-TATTTTA-AAT
725185 AATATTATTTT
1 AATATTATTTT
725196 GTAACTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.05
15 9 0.41
16 11 0.50
17 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTATTTTAAAT
Found at i:725256 original size:16 final size:15
Alignment explanation
Indices: 725221--725263 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
725211 ATAAATAGTA
*
725221 AAATATTAAA-TATT
1 AAATATTAAATTATC
725235 AAATATTAAAATTATC
1 AAATATT-AAATTATC
725251 AAATATTTAAATT
1 AAATA-TTAAATT
725264 TTTAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 13 0.52
17 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTAAATTATC
Found at i:725350 original size:14 final size:14
Alignment explanation
Indices: 725331--725372 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
725321 TAATTTTGAG
725331 TAAAATATAAAAAA
1 TAAAATATAAAAAA
*
725345 TAAAATTTAAAAAA
1 TAAAATATAAAAAA
725359 -AAATATTATAAAAA
1 TAAA-A-TATAAAAA
725373 TAATTCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 14 0.58
15 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAATATAAAAAA
Found at i:727642 original size:6 final size:6
Alignment explanation
Indices: 727631--727655 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
727621 TCATTGTCTA
727631 CTGTTT CTGTTT CTGTTT CTGTTT C
1 CTGTTT CTGTTT CTGTTT CTGTTT C
727656 GATGTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.16, T:0.64
Consensus pattern (6 bp):
CTGTTT
Found at i:728554 original size:60 final size:61
Alignment explanation
Indices: 728429--728554 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 61
728419 ATATAATTTG
* * * * *
728429 GGATAAAATTGAAATGTTCAAAAAGTTTGGGGATCAATTTAGAATGAAGATAATAGTTTGG
1 GGATGAAATTGAAATATTCAAAAAGTTTGGGGATCAATTTAGAATCAAGATAATAGATTGA
* *
728490 GGATGAAATTGAAATATT-TAAAAGTTTAGGGG-TCAATTTAGAA-CAAGGATCATA-ATTGAA
1 GGATGAAATTGAAATATTCAAAAAGTTT-GGGGATCAATTTAGAATCAA-GATAATAGATTG-A
728550 GGATG
1 GGATG
728555 TGTGGTATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
59 5 0.09
60 30 0.55
61 20 0.36
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (61 bp):
GGATGAAATTGAAATATTCAAAAAGTTTGGGGATCAATTTAGAATCAAGATAATAGATTGA
Found at i:730490 original size:29 final size:29
Alignment explanation
Indices: 730448--730511 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
730438 TAGACGAATT
*
730448 GAAGAAGGAGAAATGGGTTTATAGAAGAA
1 GAAGAAGAAGAAATGGGTTTATAGAAGAA
* *
730477 GAAGAAGAATAAATGGGTTTATGGAAGAA
1 GAAGAAGAAGAAATGGGTTTATAGAAGAA
*
730506 AAAGAA
1 GAAGAA
730512 AGGTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (29 bp):
GAAGAAGAAGAAATGGGTTTATAGAAGAA
Found at i:730503 original size:23 final size:23
Alignment explanation
Indices: 730448--730719 Score: 185
Period size: 23 Copynumber: 11.5 Consensus size: 23
730438 TAGACGAATT
*
730448 GAAGAAGGAGAAATGGGTTTATAG
1 GAAGAAGAAGAAATGGGTTTAT-G
730472 AAGAAGAAGAAGAATAAATGGGTTTATG
1 --GAAGAAGAAG---AAATGGGTTTATG
* *
730500 GAAGAAAAAGAAA-GGTTTTTATGG
1 GAAGAAGAAGAAATGG-GTTTAT-G
*
730524 AAGAAGAAGAAGAAATGCGTTTATG
1 --GAAGAAGAAGAAATGGGTTTATG
* * * *
730549 GAAGAAAAACATAT-GTTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
*
730571 GAAGAATAAGAAA-GTGGTTTATG
1 GAAGAAGAAGAAATG-GGTTTATG
* * * *
730594 AAAGAAGAATAAACGAGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
* * * *
730617 GAAGAAAAAGCAACGAGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
* * * *
730640 GAAAAAGAAGCAATGAGCTTATG
1 GAAGAAGAAGAAATGGGTTTATG
730663 GAAGAAGAAGAAAAT--GTTTATG
1 GAAGAAGAAG-AAATGGGTTTATG
* * *
730685 GAGGAAGAAAAAATGTGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
730708 GAAGAAGAAGAA
1 GAAGAAGAAGAA
730720 TGGTTCAGAA
Statistics
Matches: 198, Mismatches: 34, Indels: 31
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.02
22 32 0.16
23 107 0.54
24 5 0.03
25 1 0.01
26 35 0.18
27 1 0.01
28 1 0.01
29 12 0.06
ACGTcount: A:0.48, C:0.03, G:0.28, T:0.22
Consensus pattern (23 bp):
GAAGAAGAAGAAATGGGTTTATG
Found at i:730639 original size:117 final size:114
Alignment explanation
Indices: 730478--730716 Score: 277
Period size: 114 Copynumber: 2.1 Consensus size: 114
730468 ATAGAAGAAG
* * * ** *
730478 AAGAAGAATAAATGGGTTTATGGAAGAAAAAGAAAGGTTTTTATGGAAGAAGAAGAAGAAATGCG
1 AAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGG-A-AA-AAGAAGAAATGAG
* * * *
730543 TTTATGGAAGAA-AA-ACATATGTTTTATGGAAGAATAAGAAA-GTGGTTTATGA
63 CTTATGGAAGAAGAAGA-AAATG-TTTATGGAAGAAGAAAAAATGT-GTTTATGA
* *
730595 AAGAAGAATAAACGAGTTTATGGAAGAAAAAGCAACGAGTTTATGGAAAAAGAAGCAATGAGCTT
1 AAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAAAAGAAGAAATGAGCTT
* *
730660 ATGGAAGAAGAAGAAAATGTTTATGGAGGAAGAAAAAATGTGTTTATGG
66 ATGGAAGAAGAAGAAAATGTTTATGGAAGAAGAAAAAATGTGTTTATGA
730709 AAGAAGAA
1 AAGAAGAA
730717 GAATGGTTCA
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
114 53 0.50
115 10 0.10
116 2 0.02
117 40 0.38
ACGTcount: A:0.48, C:0.03, G:0.27, T:0.23
Consensus pattern (114 bp):
AAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAAAAGAAGAAATGAGCTT
ATGGAAGAAGAAGAAAATGTTTATGGAAGAAGAAAAAATGTGTTTATGA
Found at i:730683 original size:68 final size:64
Alignment explanation
Indices: 730492--730722 Score: 194
Period size: 68 Copynumber: 3.4 Consensus size: 64
730482 AGAATAAATG
* * *
730492 GGTTTATGGAAGAAAAAGAAAGGTTTTTATGGAAGAAGAAGAAGAAATGCGTTTATGGAAGAAAA
1 GGTTTATGGAAGAAGAAGAATGG--CTTATGGAAGAAGAAG-A-AAAT--GTTTATGGAAGAAAA
730557 ACATAT
60 ACA-AT
* * * * *
730563 GTTTTATGGAAGAATAAGAAAGTGGTTTATGAAAGAAGAATAAACGA-GTTTATGGAAGAAAAAG
1 GGTTTATGGAAGAAGAAG-AA-TGGCTTATGGAAGAAGAAGAAA--ATGTTTATGGAAGAAAAA-
*
730627 CAAC
61 CAAT
* * *
730631 GAGTTTATGGAAAAAGAAGCAATGAGCTTATGGAAGAAGAAGAAAATGTTTATGGAGGAAGAAAA
1 G-GTTTATGGAAGAAGAAG-AATG-GCTTATGGAAGAAGAAGAAAATGTTTATGGAAGAA-AAAC
730696 AAT
62 AAT
730699 GTGTTTATGGAAGAAGAAGAATGG
1 G-GTTTATGGAAGAAGAAGAATGG
730723 TTCAGAATGG
Statistics
Matches: 133, Mismatches: 18, Indels: 23
0.76 0.10 0.13
Matches are distributed among these distances:
66 1 0.01
67 5 0.04
68 51 0.38
69 40 0.30
70 1 0.01
71 31 0.23
72 2 0.02
73 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.28, T:0.23
Consensus pattern (64 bp):
GGTTTATGGAAGAAGAAGAATGGCTTATGGAAGAAGAAGAAAATGTTTATGGAAGAAAAACAAT
Found at i:730717 original size:117 final size:119
Alignment explanation
Indices: 730474--730720 Score: 285
Period size: 117 Copynumber: 2.1 Consensus size: 119
730464 GTTTATAGAA
* * * **
730474 GAAGAAGAAGAATAAATGGGTTTATGGAAGAAAAAGAAAGGTTTTTATGGAAGAAGAAGAAGAAA
1 GAAGAAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAGAAGAAGAAGAAA
* * * * *
730539 TGCGTTTATGGAAGAAAAACATATGTTTTATGGAAGAATAAGAAAGTGGTTTAT
66 TGAGCTTATGGAAGAAAAACAAATGTTTTATGGAAGAAGAAAAAAGTGGTTTAT
* *
730593 G-A-AAGAAGAATAAACGAGTTTATGGAAGAAAAAGCAACGAGTTTATGG-A-AA-AAGAAGCAA
1 GAAGAAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAGAAGAAGAAGAAA
*
730653 TGAGCTTATGGAAGAAGAAGA-AAATG-TTTATGGAGGAAGAAAAAA-TGTGTTTAT
66 TGAGCTTATGGAAGAA-AA-ACAAATGTTTTATGGAAGAAGAAAAAAGTG-GTTTAT
730707 GGAAGAAGAAGAAT
1 -GAAGAAGAAGAAT
730721 GGTTCAGAAT
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
113 2 0.02
114 44 0.40
115 9 0.08
116 3 0.03
117 49 0.45
118 1 0.01
119 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.27, T:0.22
Consensus pattern (119 bp):
GAAGAAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAGAAGAAGAAGAAA
TGAGCTTATGGAAGAAAAACAAATGTTTTATGGAAGAAGAAAAAAGTGGTTTAT
Found at i:732165 original size:20 final size:20
Alignment explanation
Indices: 732140--732179 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
732130 AGTGCCCATA
732140 TTTTGTTATTT-CATAGTTTT
1 TTTTGTT-TTTGCATAGTTTT
*
732160 TTTTGTTTTTGCATCGTTTT
1 TTTTGTTTTTGCATAGTTTT
732180 GAGCTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.70
Consensus pattern (20 bp):
TTTTGTTTTTGCATAGTTTT
Found at i:736268 original size:31 final size:31
Alignment explanation
Indices: 736233--736454 Score: 390
Period size: 31 Copynumber: 7.2 Consensus size: 31
736223 GGTCACAATA
736233 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
736264 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
736295 CAAACTGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
736326 TAAACTGTTTATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
736357 TAAACTGCTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
736388 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
736419 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
736450 TAAAC
1 TAAAC
736455 CCTCGACTCT
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 179 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:736387 original size:16 final size:16
Alignment explanation
Indices: 736366--736450 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
736356 ATAAACTGCT
736366 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
736382 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
736397 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
736413 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
736428 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
736444 CATATGT
1 CATATGT
736451 AAACCCTCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.27
16 21 0.41
17 4 0.08
18 4 0.08
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:738792 original size:31 final size:31
Alignment explanation
Indices: 738705--738831 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
738695 AGAGTCGAGG
738705 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
738736 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
738768 GTATACCTATGTTCTAAGGAACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * * *
738799 GTTTATCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
738830 GT
1 GT
738832 TGCCAAGGAT
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
31 51 0.65
32 27 0.35
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:740035 original size:64 final size:65
Alignment explanation
Indices: 739927--740104 Score: 225
Period size: 64 Copynumber: 2.8 Consensus size: 65
739917 TAATGAAGGT
* * ** * **
739927 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-AATATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
* ** * *
739991 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
*
740055 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTA
740105 TTTATTTTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
Found at i:740124 original size:64 final size:64
Alignment explanation
Indices: 739990--740151 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 64
739980 ATATTGCTGG
* * *
739990 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
** *
740054 GATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
** *
740117 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
740152 ATTCAAACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 2 0.02
64 79 0.92
65 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
Found at i:743244 original size:31 final size:31
Alignment explanation
Indices: 743209--743461 Score: 443
Period size: 31 Copynumber: 8.2 Consensus size: 31
743199 GGTCACAATA
743209 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
743240 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
743271 CAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* * *
743302 TAAACTGTTTATATATGCCTTTAAATATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
743333 TAAAATGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
743364 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
743395 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
743426 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
743457 TAAAC
1 TAAAC
743462 CCTCGACTCT
Statistics
Matches: 208, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 208 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:744079 original size:64 final size:65
Alignment explanation
Indices: 743971--744148 Score: 225
Period size: 64 Copynumber: 2.8 Consensus size: 65
743961 TAATGAAGGT
* * ** * **
743971 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-AATATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
* ** * *
744035 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
*
744099 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTA
744149 TTTATTTTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
Found at i:744168 original size:64 final size:64
Alignment explanation
Indices: 744034--744195 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 64
744024 ATATTGTTGG
* * *
744034 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
** *
744098 GATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
** *
744161 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
744196 ATTCAAACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 2 0.02
64 79 0.92
65 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
Found at i:749641 original size:12 final size:12
Alignment explanation
Indices: 749626--749655 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
749616 TTATTTAAAA
749626 GGGTATCGGGTC
1 GGGTATCGGGTC
749638 GGGTATCGGGTC
1 GGGTATCGGGTC
749650 GGGTAT
1 GGGTAT
749656 ATATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.13, G:0.50, T:0.27
Consensus pattern (12 bp):
GGGTATCGGGTC
Found at i:749726 original size:2 final size:2
Alignment explanation
Indices: 749719--749756 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
749709 TTATTAAATT
749719 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
749757 ATAATTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:752385 original size:3 final size:3
Alignment explanation
Indices: 752371--752410 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
752361 TTTGCTCCTA
* *
752371 ATG ATT ATG ATG ATG ATA ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
752411 GAGTGAGGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:755794 original size:2 final size:2
Alignment explanation
Indices: 755787--755819 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
755777 AGTATACGTG
*
755787 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
755820 AGTTATTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:756202 original size:30 final size:30
Alignment explanation
Indices: 756166--756268 Score: 145
Period size: 30 Copynumber: 3.4 Consensus size: 30
756156 GGTTTTTCGG
756166 GACCTATGGATAGTTACTGAGGATCTTTAT
1 GACCTATGGATAGTTACTGAGGATCTTTAT
*
756196 GACCTATGGATAGTTA-TCGTGGATCTTTAT
1 GACCTATGGATAGTTACT-GAGGATCTTTAT
* * *
756226 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTATGGATAGTTACTGAGGATCTTTAT
*
756256 GACCTCTGGATAG
1 GACCTATGGATAG
756269 GTCATTCGGG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
29 1 0.02
30 65 0.98
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (30 bp):
GACCTATGGATAGTTACTGAGGATCTTTAT
Found at i:759767 original size:64 final size:63
Alignment explanation
Indices: 759640--759795 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 63
759630 TTCAGTGTGT
* ** * * *
759640 ATCGATGCACAGAAAGTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTGGTGC
* ** *
759703 ATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTGGTGC
* *
759767 ATCGATGCATGGGTACTGCATCGATGCAC
1 ATCGATGCATAGGTAGTGCATCGATGCAC
759796 AAGCTAAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 26 0.33
64 53 0.67
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTGGTGC
Done.