Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007961.1 Hibiscus syriacus cultivar Beakdansim tig00110388_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: 2700559
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:436081 original size:81 final size:81
Alignment explanation
Indices: 435976--437025 Score: 1699
Period size: 81 Copynumber: 13.0 Consensus size: 81
435966 TGAATAATTA
* * * * * * * *
435976 TTTGAGTAAAAGATTAATGACCTAGATGTGTATTTAACATAAAGGTATCAATTATGCCTGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
*
436041 TGAAATGTTAAATACC
66 TGAAAGGTTAAATACC
* * * *
436057 TTTGAGTAAAATATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
436122 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
436138 TTTGAGTAAAATATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
436203 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
436219 TTTGAGTAAAATATTAATGGCCTAGCTGTTCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
436284 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
436300 TTTGAGTAAAATATTAATGGCCTGGCTGTTCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
*
436365 TGGAAGGTTAAATACC
66 TGAAAGGTTAAATACC
436381 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
436446 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* *
436462 TTTGAGTAAAAGATTAATGGTCTAGCTGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
436527 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
436543 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
436608 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * * *
436624 TTTAAGTAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATACCATTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
436689 TGAAAGGTTAAATACC
66 TGAAAGGTTAAATACC
* * *
436705 TTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGATAG-AATGGTGTCAATTATGGCAGTTAG
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAT-GTGTCAATTATGCCAGTTAG
436769 ATGAAAGGTTAAATACC
65 ATGAAAGGTTAAATACC
* ** * * * *
436786 TTTGAGTAAAAGATTAATGACCTAAATGTGCATTTGACATAAAGGTGTAAATTATGCCAATTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
*
436851 TGAAACGTTAAATACC
66 TGAAAGGTTAAATACC
*
436867 TTAT-AGTAAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAG
1 TT-TGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAG
436931 ATGAAAGGTTAAATACC
65 ATGAAAGGTTAAATACC
*
436948 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGA
1 TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
*
437013 TGAAAGATTAAAT
66 TGAAAGGTTAAAT
437026 GCTTTTGGGG
Statistics
Matches: 908, Mismatches: 57, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
80 4 0.00
81 901 0.99
82 3 0.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (81 bp):
TTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGA
TGAAAGGTTAAATACC
Found at i:437828 original size:81 final size:82
Alignment explanation
Indices: 437688--437853 Score: 226
Period size: 81 Copynumber: 2.0 Consensus size: 82
437678 GAGATGGGTG
* * * *
437688 TTACATCAAAGGCATTTAGCCTTTAATCTAACTTGCAATATTGGCACCTTTCTGCCAAATGCAGA
1 TTACATCAAAGGCATTTAGCCTTTAATCTAACTTGAAATATTGACACCTTTATGCCAAATGCACA
*
437753 ACTAGGCAATTAATCTT
66 ACTAAGCAATTAATCTT
* * * * *
437770 TTAC-TCAAATGCCTTTAGTCTTTCATTTAACTTGAAATATTGACACCTTTATGCCAAATGCACA
1 TTACATCAAAGGCATTTAGCCTTTAATCTAACTTGAAATATTGACACCTTTATGCCAAATGCACA
*
437834 ACTAAGCAATTGATCTT
66 ACTAAGCAATTAATCTT
437851 TTA
1 TTA
437854 TTTTAAGAAC
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 69 0.95
82 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (82 bp):
TTACATCAAAGGCATTTAGCCTTTAATCTAACTTGAAATATTGACACCTTTATGCCAAATGCACA
ACTAAGCAATTAATCTT
Found at i:442168 original size:41 final size:41
Alignment explanation
Indices: 442123--442212 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
442113 GAAGAACCTA
442123 ATTTCTGGTTGGAAAATGTGTTGATCCAATTAAGCTACGCC
1 ATTTCTGGTTGGAAAATGTGTTGATCCAATTAAGCTACGCC
442164 ATTTCTGGTTGGAAAATGTGTTGATCCAATTAAGCTACGCC
1 ATTTCTGGTTGGAAAATGTGTTGATCCAATTAAGCTACGCC
442205 ATTTCTGG
1 ATTTCTGG
442213 ATGCCCAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (41 bp):
ATTTCTGGTTGGAAAATGTGTTGATCCAATTAAGCTACGCC
Found at i:445967 original size:2 final size:2
Alignment explanation
Indices: 445962--445994 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
445952 TTCATATGTG
445962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
445995 CAAAGATGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:446230 original size:2 final size:2
Alignment explanation
Indices: 446187--446211 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
446177 TTTTACTCAA
446187 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
446212 AAAGTTGGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:446567 original size:6 final size:6
Alignment explanation
Indices: 446548--446653 Score: 62
Period size: 6 Copynumber: 18.2 Consensus size: 6
446538 TAATAAAAAT
* *
446548 TTATAA TT-TAA TTATAA TTAT-A TTAAAA TTATAA TTA-AA TTTTAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA
* * ** * *
446593 -TA-AA TGATTAA TTTTAAA TATATCC TTATAA TTATAA TTCT-A TTAAAA
1 TTATAA TTA-TAA TTAT-AA T-TATAA TTATAA TTATAA TTATAA TTATAA
*
446641 TTATAA TTTTAA T
1 TTATAA TTATAA T
446654 ATTTACATAA
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
4 2 0.03
5 18 0.24
6 45 0.61
7 7 0.09
8 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (6 bp):
TTATAA
Found at i:446568 original size:17 final size:17
Alignment explanation
Indices: 446548--446589 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
446538 TAATAAAAAT
446548 TTATAATTTAATTATAA
1 TTATAATTTAATTATAA
*
446565 TTAT-ATTAAAATTATAA
1 TTATAATT-TAATTATAA
446582 TTA-AATTT
1 TTATAATTT
446590 TAATAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATAATTTAATTATAA
Found at i:449685 original size:23 final size:23
Alignment explanation
Indices: 449655--449763 Score: 71
Period size: 23 Copynumber: 4.7 Consensus size: 23
449645 CCCTTTTAGT
449655 CTAAACGAACATGTTCGTCAACA
1 CTAAACGAACATGTTCGTCAACA
* *
449678 CTAAACGAATATATTCG-CAA-A
1 CTAAACGAACATGTTCGTCAACA
* * * *
449699 CGGTAAACAAAAATGTTCATAAACA
1 C--TAAACGAACATGTTCGTCAACA
* * *
449724 CTAAACGAATATATTC-ACAAACA
1 CTAAACGAACATGTTCGTC-AACA
* *
449747 TTAAACGAACACGTTCG
1 CTAAACGAACATGTTCG
449764 CGAACATTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
21 2 0.03
22 3 0.05
23 55 0.86
24 2 0.03
25 2 0.03
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.22
Consensus pattern (23 bp):
CTAAACGAACATGTTCGTCAACA
Found at i:449724 original size:46 final size:46
Alignment explanation
Indices: 449656--449745 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
449646 CCTTTTAGTC
* * * * *
449656 TAAACGAACATGTTCGTCAACACTAAACGAATATATTCGCAAACGG
1 TAAACAAAAATGTTCATAAACACTAAACGAATATATTCACAAACGG
449702 TAAACAAAAATGTTCATAAACACTAAACGAATATATTCACAAAC
1 TAAACAAAAATGTTCATAAACACTAAACGAATATATTCACAAAC
449746 ATTAAACGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (46 bp):
TAAACAAAAATGTTCATAAACACTAAACGAATATATTCACAAACGG
Found at i:456105 original size:4 final size:4
Alignment explanation
Indices: 456098--456131 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
456088 CATCATATAT
456098 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
456132 CATGAATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:460091 original size:40 final size:40
Alignment explanation
Indices: 460047--460176 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
460037 ACCTGACAAC
460047 AGATATTAGATAGTAATGGTATATGATATCACTAAGCATA
1 AGATATTAGATAGTAATGGTATATGATATCACTAAGCATA
* * * * * *
460087 AGATATTATATAGTAATTGTACATGGTATCACTAAGTATC
1 AGATATTAGATAGTAATGGTATATGATATCACTAAGCATA
* ** *
460127 AGATATCGAAGATAGTGGTGGT-TCTGGATATCACTAAGCATCA
1 AGATAT--TAGATAGTAATGGTATAT-GATATCACTAAGCAT-A
460170 AG-TATTA
1 AGATATTA
460177 TTCTCTGTCT
Statistics
Matches: 69, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
40 41 0.59
41 1 0.01
42 25 0.36
43 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (40 bp):
AGATATTAGATAGTAATGGTATATGATATCACTAAGCATA
Found at i:461196 original size:96 final size:97
Alignment explanation
Indices: 461027--461236 Score: 257
Period size: 96 Copynumber: 2.2 Consensus size: 97
461017 TACATTCTAA
** * * * * *
461027 TAATCTTTTATT-CCTTTAATCAAACATAGTAATTTTACATTCATACTAAACCAACCAAATACAA
1 TAATCTTTTATTCCCACTAATCAAACACAATAATCTTAAATTCATACTAAACCAACCAAACACAA
*
461091 AATACAACATTAC-CAG-TAATTATATTCCCTGG
66 AATACAACATT-CTC-GTTAATCATATTCCCTGG
* * *
461123 TAATCTTTTATTCCCACT-ATCAAACACAATAATCTTAAATTCCTGCTAAACTAACCAAACACAA
1 TAATCTTTTATTCCCACTAATCAAACACAATAATCTTAAATTCATACTAAACCAACCAAACACAA
* *
461187 AATATAACATTCTCGTTAATCCTATTCCCTGG
66 AATACAACATTCTCGTTAATCATATTCCCTGG
461219 TAATCTTTTATTCCCACT
1 TAATCTTTTATTCCCACT
461237 GATAATCTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
95 2 0.02
96 93 0.95
97 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (97 bp):
TAATCTTTTATTCCCACTAATCAAACACAATAATCTTAAATTCATACTAAACCAACCAAACACAA
AATACAACATTCTCGTTAATCATATTCCCTGG
Found at i:463073 original size:26 final size:25
Alignment explanation
Indices: 463044--463095 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
463034 TAATTATTAT
463044 TTAAAAACACTAAAATAAAATTGAAA
1 TTAAAAACACTAAAATAAAATT-AAA
* *
463070 TTAAAAATATTAAAATAAAATTAAA
1 TTAAAAACACTAAAATAAAATTAAA
463095 T
1 T
463096 ATTATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (25 bp):
TTAAAAACACTAAAATAAAATTAAA
Found at i:463287 original size:43 final size:43
Alignment explanation
Indices: 463239--463336 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
463229 ATGATCATTT
463239 AAAAACATAAAAGTACTTTAGCCAAACCTAAATTTCTCAAAAG
1 AAAAACATAAAAGTACTTTAGCCAAACCTAAATTTCTCAAAAG
463282 AAAAACATAAAAGTACTTTAGCCAAACCTAAATTTCTCAAAAG
1 AAAAACATAAAAGTACTTTAGCCAAACCTAAATTTCTCAAAAG
*
463325 AAAAACAAAAAA
1 AAAAACATAAAA
463337 TACCGGGTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.20
Consensus pattern (43 bp):
AAAAACATAAAAGTACTTTAGCCAAACCTAAATTTCTCAAAAG
Found at i:463548 original size:21 final size:21
Alignment explanation
Indices: 463522--463566 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
463512 CAAACATTTT
*
463522 AATAA-TTATTGATTACTTCTA
1 AATAATTTAATGATTA-TTCTA
*
463543 AATAATTTAATGATTATTTTA
1 AATAATTTAATGATTATTCTA
463564 AAT
1 AAT
463567 TAAAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (21 bp):
AATAATTTAATGATTATTCTA
Found at i:465591 original size:103 final size:101
Alignment explanation
Indices: 465405--465605 Score: 303
Period size: 103 Copynumber: 2.0 Consensus size: 101
465395 AACAATACCT
* *
465405 TATCAACTAGTAAATGAATGATTGAACTATGGCATTGTAACCAAAGGCCTACCCTTTTCTCATGA
1 TATCAACTAGTAAATGAATGATTGAACTATGGCATTGTAACCAAAGGCCTACACTTCTCTCATGA
* *
465470 AGTGCCTTTTTTTTAAGGGAATAATACCTTAAAGTC
66 AGTGCCTTTATTTGAAGGGAATAATACCTTAAAGTC
* * * * *
465506 TATCAACTTGTAATTGAAATGATTGAACTATGGCATTTGTAAGCAAAGGCCTATACTTCTCTTAT
1 TATCAACTAGTAAATG-AATGATTGAACTATGGCA-TTGTAACCAAAGGCCTACACTTCTCTCAT
465571 GAAGTGCCTTTATTTGAAGGGAATAATACCTTAAA
64 GAAGTGCCTTTATTTGAAGGGAATAATACCTTAAA
465606 TCCTTGCATT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 14 0.16
102 18 0.20
103 57 0.64
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (101 bp):
TATCAACTAGTAAATGAATGATTGAACTATGGCATTGTAACCAAAGGCCTACACTTCTCTCATGA
AGTGCCTTTATTTGAAGGGAATAATACCTTAAAGTC
Found at i:469126 original size:26 final size:25
Alignment explanation
Indices: 469066--469126 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
469056 TCTATACAAA
469066 TATTTTATTA-TATTATATATTTATT
1 TATTTTATTATTATTATATATTTA-T
*
469091 TATTTTTATTATTAGTA-ATATTT-T
1 TA-TTTTATTATTATTATATATTTAT
469115 TATTTTATTATT
1 TATTTTATTATT
469127 TTCACTGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 10 0.30
24 3 0.09
25 2 0.06
26 14 0.42
27 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TATTTTATTATTATTATATATTTAT
Found at i:470643 original size:16 final size:17
Alignment explanation
Indices: 470615--470653 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
470605 CCTCACTAAC
470615 TCTTTTCATTTTTATT-A
1 TCTTTTCATTTTT-TTCA
470632 TCTTTT-ATTTTTTTCA
1 TCTTTTCATTTTTTTCA
470648 TCTTTT
1 TCTTTT
470654 GCATCATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (17 bp):
TCTTTTCATTTTTTTCA
Found at i:472506 original size:17 final size:19
Alignment explanation
Indices: 472475--472509 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
472465 AGATTCAATC
472475 AGAACAAAAAGGAAAAAAG
1 AGAACAAAAAGGAAAAAAG
472494 AGAA-AAAAA-GAAAAAA
1 AGAACAAAAAGGAAAAAA
472510 CAAAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (19 bp):
AGAACAAAAAGGAAAAAAG
Found at i:472537 original size:23 final size:23
Alignment explanation
Indices: 472480--472538 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
472470 CAATCAGAAC
472480 AAAAAGGAAAAAAGAGAAAAAAAG
1 AAAAAGG-AAAAAGAGAAAAAAAG
**
472504 AAAAAACAAAAAGAGAAACAAAA-
1 AAAAAGGAAAAAGAGAAA-AAAAG
*
472527 ACAAAGGAAAAA
1 AAAAAGGAAAAA
472539 ATAAAGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAAAGGAAAAAGAGAAAAAAAG
Found at i:474418 original size:21 final size:22
Alignment explanation
Indices: 474382--474424 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
474372 AATTTACTCA
*
474382 AAACAAAGTTTTATCTCTCTTG
1 AAACAAAGTCTTATCTCTCTTG
474404 AAACAAA-TCTTATCTCTCTTG
1 AAACAAAGTCTTATCTCTCTTG
474425 GGACAGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (22 bp):
AAACAAAGTCTTATCTCTCTTG
Found at i:474447 original size:36 final size:36
Alignment explanation
Indices: 474400--474482 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
474390 TTTTATCTCT
* *
474400 CTTGAAACAAATCTTATCTCTCTTGGGACAGTTTCC
1 CTTGAAACAAATCTTATCTATCTTGAGACAGTTTCC
*
474436 CTTGAAACAAATTTTATCTATCTTGAGACAGTTTCC
1 CTTGAAACAAATCTTATCTATCTTGAGACAGTTTCC
474472 CTTGAAACAAA
1 CTTGAAACAAA
474483 ATATTTGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
CTTGAAACAAATCTTATCTATCTTGAGACAGTTTCC
Found at i:475062 original size:20 final size:20
Alignment explanation
Indices: 475034--475085 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
475024 TCTATAAAAA
475034 TATTTTATTATATTAAATATT
1 TATTTTATTATATT-AATATT
*
475055 TA-TTTATTATTATTATTATT
1 TATTTTATTA-TATTAATATT
475075 TATTTTATTAT
1 TATTTTATTAT
475086 TTGTATAGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTATTATATTAATATT
Found at i:475086 original size:21 final size:22
Alignment explanation
Indices: 475034--475086 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
475024 TCTATAAAAA
475034 TATTTTATTA-TATTAAATATT
1 TATTTTATTATTATTAAATATT
*
475055 TA-TTTATTATTATT-ATTATT
1 TATTTTATTATTATTAAATATT
475075 TATTTTATTATT
1 TATTTTATTATT
475087 TGTATAGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTATTATTATTAAATATT
Found at i:475726 original size:13 final size:13
Alignment explanation
Indices: 475708--475737 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
475698 GATCGAATAC
475708 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
475721 TTTTAATTTTTAA
1 TTTTAAATTTTAA
475734 TTTT
1 TTTT
475738 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:478272 original size:22 final size:22
Alignment explanation
Indices: 478244--478292 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
478234 CCGAAAATGT
*
478244 TAAAAAACATTAATGTTTAAGG
1 TAAAAAACAATAATGTTTAAGG
* *
478266 TAAAAAATAATAATGTTTTAGG
1 TAAAAAACAATAATGTTTAAGG
478288 TAAAA
1 TAAAA
478293 TTTTTTACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (22 bp):
TAAAAAACAATAATGTTTAAGG
Found at i:481401 original size:14 final size:14
Alignment explanation
Indices: 481382--481432 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
481372 AAGTCAATGG
481382 GTTGACTCAGACGA
1 GTTGACTCAGACGA
** *
481396 GTTGACTTGGATGA
1 GTTGACTCAGACGA
*
481410 GTTGACTCA-TCGA
1 GTTGACTCAGACGA
*
481423 GTTGTCTCAG
1 GTTGACTCAG
481433 TTTCTAGAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:483224 original size:6 final size:6
Alignment explanation
Indices: 483213--483240 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
483203 TGCAGAATGC
483213 ATATGG ATATGG ATATGG ATATGG ATAT
1 ATATGG ATATGG ATATGG ATATGG ATAT
483241 ACAATCCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (6 bp):
ATATGG
Found at i:486949 original size:31 final size:32
Alignment explanation
Indices: 486878--486959 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 32
486868 CTAACATGGT
* **
486878 TGAAAGACTAAAACTGAACAAGAGTTAACGGC
1 TGAAAGACTAAAATTGAACAAGAGTTAACAAC
* *
486910 TGAAAGACTAAAATTGAATAA-AGTTAATAAC
1 TGAAAGACTAAAATTGAACAAGAGTTAACAAC
*
486941 TGAGAGACTAAAATTGAAC
1 TGAAAGACTAAAATTGAAC
486960 GAATCGATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 24 0.56
32 19 0.44
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (32 bp):
TGAAAGACTAAAATTGAACAAGAGTTAACAAC
Found at i:487593 original size:21 final size:21
Alignment explanation
Indices: 487568--487617 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
487558 ATTCGGGTCG
*
487568 GGTCGGGTGAAA-TATTATTTT
1 GGTCGAGTGAAACT-TTATTTT
487589 GGTCGAGTGAAACTTTATTTT
1 GGTCGAGTGAAACTTTATTTT
487610 GGTCGAGT
1 GGTCGAGT
487618 CGGGTCGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.08, G:0.30, T:0.40
Consensus pattern (21 bp):
GGTCGAGTGAAACTTTATTTT
Found at i:488078 original size:26 final size:26
Alignment explanation
Indices: 488047--488104 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
488037 ATTCCCCATA
* *
488047 TTCTTTTTCTTCACTTTTCTTCTTCT
1 TTCTTTCTCTTCACTTTTATTCTTCT
488073 TTCTTTCTCTTCACTTTTATTCTT-T
1 TTCTTTCTCTTCACTTTTATTCTTCT
488098 TT-TTTCT
1 TTCTTTCT
488105 TATCACACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 5 0.17
25 3 0.10
26 22 0.73
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.71
Consensus pattern (26 bp):
TTCTTTCTCTTCACTTTTATTCTTCT
Found at i:490506 original size:26 final size:26
Alignment explanation
Indices: 490477--490536 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
490467 TATTTTATGT
490477 TAAAATATTTTGAAGTAAGATAAGAA
1 TAAAATATTTTGAAGTAAGATAAGAA
490503 TAAAATATTTTGAAGTAAGATAAGAA
1 TAAAATATTTTGAAGTAAGATAAGAA
490529 TAAAATAT
1 TAAAATAT
490537 ACTAAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (26 bp):
TAAAATATTTTGAAGTAAGATAAGAA
Found at i:490551 original size:26 final size:26
Alignment explanation
Indices: 490489--490551 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
490479 AAATATTTTG
* ** *
490489 AAGTAAGATAAGAATAAAATATTTTG
1 AAGTAAAATAAGAATAAAATATACTA
*
490515 AAGTAAGATAAGAATAAAATATACTA
1 AAGTAAAATAAGAATAAAATATACTA
*
490541 AATTAAAATAA
1 AAGTAAAATAA
490552 AGTTAGTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (26 bp):
AAGTAAAATAAGAATAAAATATACTA
Found at i:507100 original size:2 final size:2
Alignment explanation
Indices: 507093--507133 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
507083 AGTAATATTA
507093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
507134 ACACTCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:507444 original size:27 final size:27
Alignment explanation
Indices: 507412--507575 Score: 265
Period size: 27 Copynumber: 6.1 Consensus size: 27
507402 CCGCCATCAC
* * * *
507412 CACTTTGAACTTAAAATTTCATAGCAT
1 CACTTTGAACTTGAAAGTCCACAGCAT
*
507439 CACTTTGAACTTGAAAGTCCACAACAT
1 CACTTTGAACTTGAAAGTCCACAGCAT
507466 CACTTTGAACTTGAAAGTCCACAGCAT
1 CACTTTGAACTTGAAAGTCCACAGCAT
507493 CACTTTGAACTTGAAAGTCCACAGCAT
1 CACTTTGAACTTGAAAGTCCACAGCAT
*
507520 CACTTTGAACTTAAAAGTCCACAGCAT
1 CACTTTGAACTTGAAAGTCCACAGCAT
*
507547 CACTTTGAACTTGAAAGTCCACAACAT
1 CACTTTGAACTTGAAAGTCCACAGCAT
507574 CA
1 CA
507576 AAATCTTCAT
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAAGTCCACAGCAT
Found at i:507835 original size:20 final size:19
Alignment explanation
Indices: 507785--507838 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
507775 ACTGAACTTG
507785 CGGTTCACACCGGTTTGGC
1 CGGTTCACACCGGTTTGGC
* *
507804 CGGTTCACACCGGTTTTGT
1 CGGTTCACACCGGTTTGGC
*
507823 CGGTTCCCAACCGGTT
1 CGGTTCAC-ACCGGTT
507839 CTTTGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.11, C:0.31, G:0.28, T:0.30
Consensus pattern (19 bp):
CGGTTCACACCGGTTTGGC
Found at i:509254 original size:19 final size:19
Alignment explanation
Indices: 509230--509271 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
509220 TTCCTATTTT
509230 TAGTGTCAAAAATGTTATA
1 TAGTGTCAAAAATGTTATA
509249 TAGTGTCAAAAATGTTATA
1 TAGTGTCAAAAATGTTATA
509268 TAGT
1 TAGT
509272 AACAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (19 bp):
TAGTGTCAAAAATGTTATA
Found at i:509277 original size:19 final size:19
Alignment explanation
Indices: 509236--509278 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
509226 TTTTTAGTGT
**
509236 CAAAAATGTTATATAGTGT
1 CAAAAATGTTATATAGTAA
509255 CAAAAATGTTATATAGTAA
1 CAAAAATGTTATATAGTAA
509274 CAAAA
1 CAAAA
509279 TATATTGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (19 bp):
CAAAAATGTTATATAGTAA
Found at i:511766 original size:23 final size:23
Alignment explanation
Indices: 511736--511789 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
511726 TAAGTATTTG
511736 TGACAAATAATATTCTTTCACAA
1 TGACAAATAATATTCTTTCACAA
511759 TGACAAATAATATTCTTTCACAA
1 TGACAAATAATATTCTTTCACAA
*
511782 TAACAAAT
1 TGACAAAT
511790 TGTAACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (23 bp):
TGACAAATAATATTCTTTCACAA
Found at i:514622 original size:50 final size:50
Alignment explanation
Indices: 514547--514645 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
514537 CTCACCTTAA
514547 TTCGAGTAATATAGATTCATTGTTTGAATTACTTTCAGGTATGAAACAAT
1 TTCGAGTAATATAGATTCATTGTTTGAATTACTTTCAGGTATGAAACAAT
514597 TTCGAGTAATATAGATTCATTGTTTGAATTACTTTCAGGTATGAAACAA
1 TTCGAGTAATATAGATTCATTGTTTGAATTACTTTCAGGTATGAAACAA
514646 CAGGCATTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (50 bp):
TTCGAGTAATATAGATTCATTGTTTGAATTACTTTCAGGTATGAAACAAT
Found at i:516516 original size:15 final size:14
Alignment explanation
Indices: 516480--516527 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
516470 TAATTTTTTT
* *
516480 ATAAATATTATTTA
1 ATAAATAATATTAA
516494 AT-AATAATATTAA
1 ATAAATAATATTAA
516507 CATAAATAATATTAA
1 -ATAAATAATATTAA
516522 ATAAAT
1 ATAAAT
516528 TATTCTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 9 0.30
14 10 0.33
15 11 0.37
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAATAATATTAA
Found at i:519705 original size:16 final size:16
Alignment explanation
Indices: 519684--519718 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
519674 AAGTGAATTT
519684 GATGGTTGGAAATTGA
1 GATGGTTGGAAATTGA
519700 GATGGTTGGAAATTGA
1 GATGGTTGGAAATTGA
519716 GAT
1 GAT
519719 CATCGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.31
Consensus pattern (16 bp):
GATGGTTGGAAATTGA
Found at i:523913 original size:25 final size:25
Alignment explanation
Indices: 523883--523930 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
523873 ATTGTTGACT
523883 TCTACATGGCCTGATTTGATTAGCG
1 TCTACATGGCCTGATTTGATTAGCG
523908 TCTACATGGCCTGATTTGATTAG
1 TCTACATGGCCTGATTTGATTAG
523931 TGTTCTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (25 bp):
TCTACATGGCCTGATTTGATTAGCG
Found at i:525600 original size:46 final size:46
Alignment explanation
Indices: 525532--525621 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
525522 TTTAAAGTAG
* *
525532 TCGTTCAATTGGCACTTAATCTCGCACGAGGGTCAAATTCCTCTAC
1 TCGTTCAATTGGCACCTAATCTCGCACGAGGGTCAAAGTCCTCTAC
* *
525578 TCGTTCAATTGGCGCCTGATCTCGCACGAGGGTCAAAGTCCTCT
1 TCGTTCAATTGGCACCTAATCTCGCACGAGGGTCAAAGTCCTCT
525622 GCCTTTTCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (46 bp):
TCGTTCAATTGGCACCTAATCTCGCACGAGGGTCAAAGTCCTCTAC
Found at i:528102 original size:288 final size:286
Alignment explanation
Indices: 527502--528156 Score: 839
Period size: 288 Copynumber: 2.3 Consensus size: 286
527492 TTTGTAATTG
* * * * *
527502 TATAGGATTTAGAGTAAATTACAAAAAATAAAAATAATTATGGGTTAATTTTGATAGAAATATAA
1 TATAGGGTTTGGAGTAAATTACAAAAAATAAAAATAATTATGGGCTAATTTCGATAAAAATATAA
* * *
527567 TTTTAAGGACTAATTGAACAAACATGAAATTAGAAACTAAAATTTAAATAAATTAAATAACATGC
66 TTTTAAGGACTAATTAAACAAACATGAAATTACAAACTAAAATTTAAATAAATTAAAGAACATGC
** * *
527632 AGAGATTAAATTGAAACAAGTGTAAAATGTAAAGTTGAAATTAATATCAAATTGGACTAAATTGC
131 AGAGACCAAATTGAAACAAGTGTAAAATGTAAAGCTGAAATTAATATCAAAATGGACTAAATTGC
* * * * *
527697 ATTAATTTTAAAAGTTGGTGAAGAAAAGTTTATTGGGTTCAGGGATTATGATATAATTTATAGGG
196 ATTAATTTGAAAAGTTGGTGAACAAAAGTTTATAGAGTTCAGAGATTATGATATAATTTATAGGG
* ** *
527762 TTTGGAATGAAGTTTATGATGTGATT
261 CTTAAAATAAAGTTTATGATGTGATT
* ** *
527788 TTTAGGGTTTGGAGTAAAAAACAAAAAATAGAAATAATTATGGGCTAATTTCGTATAAAAATATA
1 TATAGGGTTTGGAGTAAATTACAAAAAATAAAAATAATTATGGGCTAATTTCG-ATAAAAATATA
* * * * *
527853 CTTTTAAGGATTAAATTAAACAAACATGAAATTACAAAGTGAAATTTAAATAAATTAAAGAATAT
65 ATTTTAAGGACT-AATTAAACAAACATGAAATTACAAACTAAAATTTAAATAAATTAAAGAACAT
* * * * *
527918 GTAGGGACCAAATTGAAACAATTGTAAAATGTAAAGCT-AAAGTTGATATTAAAATGGACTAAAT
129 GCAGAGACCAAATTGAAACAAGTGTAAAATGTAAAGCTGAAA-TTAATATCAAAATGGACTAAAT
* *
527982 TGCATTCATTTGAAAATTTGGTGAACAAAAGTTTATAGAGTTCAGAGATTATGATATAATTTATA
193 TGCATTAATTTGAAAAGTTGGTGAACAAAAGTTTATAGAGTTCAGAGATTATGATATAATTTATA
*
528047 GGGCTTAAAATAAAGTTTATGATGTTATT
258 GGGCTTAAAATAAAGTTTATGATGTGATT
* * * *
528076 TATAGGGTTTGGAGTAAATTACAAAAAAATATAAATAATT-TGGTG-TCGACTTCAAATAAAAAT
1 TATAGGGTTTGGAGTAAATTAC-AAAAAATAAAAATAATTATGG-GCT-AATTTC-GATAAAAAT
*
528139 ATAGTTTTAAGGACTAAT
62 ATAATTTTAAGGACTAAT
528157 AAGTAATAAA
Statistics
Matches: 315, Mismatches: 47, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
286 45 0.14
287 23 0.07
288 205 0.65
289 42 0.13
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (286 bp):
TATAGGGTTTGGAGTAAATTACAAAAAATAAAAATAATTATGGGCTAATTTCGATAAAAATATAA
TTTTAAGGACTAATTAAACAAACATGAAATTACAAACTAAAATTTAAATAAATTAAAGAACATGC
AGAGACCAAATTGAAACAAGTGTAAAATGTAAAGCTGAAATTAATATCAAAATGGACTAAATTGC
ATTAATTTGAAAAGTTGGTGAACAAAAGTTTATAGAGTTCAGAGATTATGATATAATTTATAGGG
CTTAAAATAAAGTTTATGATGTGATT
Found at i:529136 original size:30 final size:31
Alignment explanation
Indices: 529097--529163 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
529087 GAATGACCTA
* * *
529097 TCCAAAGGTCATAAAGAACCTCGG-AAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
529127 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
529158 TCCATA
1 TCCATA
529164 TGTTCCTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:529159 original size:31 final size:32
Alignment explanation
Indices: 529123--529249 Score: 136
Period size: 32 Copynumber: 4.0 Consensus size: 32
529113 AACCTCGGAA
* *
529123 ACTGTCCATAGGTCCCAAAGAACCTAGGTAA-
1 ACTGTCCATATGTCCCAAAGAACATAGGTAAC
* **
529154 ACTGTCCATATGTTCCTTAGAACATAGGTAATC
1 ACTGTCCATATGTCCCAAAGAACATAGGTAA-C
*
529187 -CTGTCCATATGTCCCGAATG-ACATAGGTAAC
1 ACTGTCCATATGTCCC-AAAGAACATAGGTAAC
*
529218 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAC
1 ACTGTCCATATGTC-CCAAAGAACATAGGTAAC
529250 CCTCGACTCT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
31 27 0.34
32 51 0.64
33 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (32 bp):
ACTGTCCATATGTCCCAAAGAACATAGGTAAC
Found at i:529246 original size:64 final size:63
Alignment explanation
Indices: 529124--529248 Score: 155
Period size: 64 Copynumber: 2.0 Consensus size: 63
529114 ACCTCGGAAA
* **
529124 CTGTCCATAGGTCCCAAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAATC
1 CTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCAAAGAACATAGGTAATC
* * *
529187 CTGTCCATATGTCCCGAATG-ACATAGGTAACACTGTCCATATGTCTCGAAAG-ACATAGGTAA
1 CTGTCCATAGGTCCC-AAAGAACATAGGTAA-ACTGTCCATATGT-TCCAAAGAACATAGGTAA
529249 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 23 0.43
64 26 0.49
65 4 0.08
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (63 bp):
CTGTCCATAGGTCCCAAAGAACATAGGTAAACTGTCCATATGTTCCAAAGAACATAGGTAATC
Found at i:530255 original size:21 final size:21
Alignment explanation
Indices: 530230--530269 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
530220 AAATTGTTCT
530230 TAGTGCATCGATACACATTTA
1 TAGTGCATCGATACACATTTA
*
530251 TAGTGCATCGATGCACATT
1 TAGTGCATCGATACACATT
530270 CTTAGAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
TAGTGCATCGATACACATTTA
Found at i:532047 original size:23 final size:23
Alignment explanation
Indices: 532017--532062 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
532007 AATATGGGAT
532017 AAACTACAAGTCACTCATGAAGG
1 AAACTACAAGTCACTCATGAAGG
532040 AAACTACAAGTCACTCATGAAGG
1 AAACTACAAGTCACTCATGAAGG
532063 CACCGACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (23 bp):
AAACTACAAGTCACTCATGAAGG
Found at i:537954 original size:73 final size:72
Alignment explanation
Indices: 537891--538028 Score: 179
Period size: 73 Copynumber: 1.9 Consensus size: 72
537881 ATCGATGCAA
* *
537891 ATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCA
1 ATACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATGCATCGATGCA
537955 CCAGCCATGC
64 CCAG-CATGC
*** * *
537965 ATTTGATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
1 ATACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCATCGATGCAC
538029 TCTTAGTGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
73 31 0.55
74 22 0.39
75 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (72 bp):
ATACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCATCGATGCACC
AGCATGC
Found at i:537963 original size:65 final size:64
Alignment explanation
Indices: 537810--537966 Score: 178
Period size: 65 Copynumber: 2.4 Consensus size: 64
537800 TTTATCAAAG
*
537810 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTGAACATCGAATGCATT
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACCATGAATTAAATTGAACATCGAATGCATT
* * **
537875 TCATGCATCGATGCA-AATACCATGCATCGATGCA-C-TGAGGATTTTA-TGAAAACATCGAATG
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACCATGA--ATTAAATTG--AACATCGAATG
537936 CATT
61 CATT
*
537940 TGATGCATCGATGCACCAGCCATGCAT
1 TGATGCATCGATGCACCAACCATGCAT
537967 TTGATGCATC
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 20 0.26
65 51 0.65
66 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACCATGAATTAAATTGAACATCGAATGCATT
Found at i:538028 original size:17 final size:19
Alignment explanation
Indices: 538000--538048 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
537990 TATTTTGAAA
538000 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
538018 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
538037 CACCGATGCACT
1 CATCGATGCACT
538049 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:541902 original size:4 final size:4
Alignment explanation
Indices: 541893--542000 Score: 64
Period size: 4 Copynumber: 27.8 Consensus size: 4
541883 TTAATAAATT
* * * * *
541893 ATAC ATAC ATAC GTAT ATA- ATAC ATAC ATTA- ATAA AT-T ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC ATAC ATAC
* * * * * *
541939 ATAT ATAT ATAT ATAC --AC ATATC AAAC ATAC ATAC ATGC ATGC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATA-C ATAC ATAC ATAC ATAC ATAC ATAC
541986 ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATA
542001 TATGATACAT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
2 2 0.02
3 7 0.08
4 72 0.84
5 5 0.06
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:541934 original size:19 final size:19
Alignment explanation
Indices: 541876--541937 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
541866 GAGTTATAAG
*
541876 ACATGCATTAATAAATTAT
1 ACATACATTAATAAATTAT
* * *
541895 ACATACA-TACGTATATAAT
1 ACATACATTA-ATAAATTAT
541914 ACATACATTAATAAATTAT
1 ACATACATTAATAAATTAT
541933 ACATA
1 ACATA
541938 TATATATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
18 2 0.06
19 30 0.88
20 2 0.06
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (19 bp):
ACATACATTAATAAATTAT
Found at i:542040 original size:29 final size:30
Alignment explanation
Indices: 541994--542059 Score: 116
Period size: 29 Copynumber: 2.2 Consensus size: 30
541984 ACATACATAC
*
541994 ATACATATATGATACATGCATTAATAAATT
1 ATACATATATGATACATGCATTAACAAATT
542024 ATACATATAT-ATACATGCATTAACAAATT
1 ATACATATATGATACATGCATTAACAAATT
542053 ATACATA
1 ATACATA
542060 CATAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (30 bp):
ATACATATATGATACATGCATTAACAAATT
Found at i:542087 original size:43 final size:43
Alignment explanation
Indices: 542017--542123 Score: 144
Period size: 43 Copynumber: 2.4 Consensus size: 43
542007 ACATGCATTA
*
542017 ATAAAT-TATACATATATATACATGCATTAACAAATTATACATAC
1 ATAAATATATAC--ATACATACATGCATTAACAAATTATACATAC
* *
542061 ATAAATATATACATACATACATGCATTAATAAATTATACATAT
1 ATAAATATATACATACATACATGCATTAACAAATTATACATAC
*
542104 ATAAATATCATTCATACATA
1 ATAAATAT-ATACATACATA
542124 TGTGTATATG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
43 36 0.63
44 16 0.28
45 5 0.09
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (43 bp):
ATAAATATATACATACATACATGCATTAACAAATTATACATAC
Found at i:542235 original size:20 final size:20
Alignment explanation
Indices: 542205--542251 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
542195 TGGTGCATAT
*
542205 CATATATTAGATC-AAACATA
1 CATACATTAGATCGAAA-ATA
*
542225 CGTACATTAGATCGAAAATA
1 CATACATTAGATCGAAAATA
542245 CATACAT
1 CATACAT
542252 ATCATACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.28
Consensus pattern (20 bp):
CATACATTAGATCGAAAATA
Found at i:542370 original size:12 final size:12
Alignment explanation
Indices: 542349--542436 Score: 77
Period size: 12 Copynumber: 7.3 Consensus size: 12
542339 ATTAATAAAT
542349 TATACATACATA
1 TATACATACATA
*
542361 TATGCATACATA
1 TATACATACATA
* *
542373 CATACATATATA
1 TATACATACATA
* *
542385 TATATATATATA
1 TATACATACATA
* *
542397 TATATATATATA
1 TATACATACATA
* *
542409 TATATATATATA
1 TATACATACATA
* *
542421 TATATATATATA
1 TATACATACATA
542433 TATA
1 TATA
542437 TATCATACAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 70 1.00
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (12 bp):
TATACATACATA
Found at i:542385 original size:2 final size:2
Alignment explanation
Indices: 542378--542439 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
542368 ACATACATAC
542378 AT AT AT 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
542420 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
542440 CATACATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:542942 original size:31 final size:31
Alignment explanation
Indices: 542899--542969 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
542889 TGAGTAATCG
542899 ATTTATTATAAATCAATAACATTAGTGAA-CA
1 ATTTATTATAAATCAATAACATTAGT-AACCA
* * *
542930 ATTTGTTATAAATCTATAATATTAGTAACCA
1 ATTTATTATAAATCAATAACATTAGTAACCA
*
542961 ATTCATTAT
1 ATTTATTAT
542970 TTTTGAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.41
Consensus pattern (31 bp):
ATTTATTATAAATCAATAACATTAGTAACCA
Found at i:544080 original size:2 final size:2
Alignment explanation
Indices: 544071--544155 Score: 154
Period size: 2 Copynumber: 43.0 Consensus size: 2
544061 AAAAAATAAA
*
544071 AT AT -T AT AT AT AT AT TT 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
544112 AT AT AT 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
544154 AT
1 AT
544156 TTGTAACCTA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 79 0.99
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:544252 original size:16 final size:16
Alignment explanation
Indices: 544231--544263 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
544221 AGTCAATTAT
*
544231 AGGTCAGGTTTATAAC
1 AGGTCAGGTTGATAAC
544247 AGGTCAGGTTGATAAC
1 AGGTCAGGTTGATAAC
544263 A
1 A
544264 AGTCGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (16 bp):
AGGTCAGGTTGATAAC
Found at i:556434 original size:15 final size:15
Alignment explanation
Indices: 556416--556447 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
556406 ATATATTCGA
556416 TAAAATATTATTATT
1 TAAAATATTATTATT
*
556431 TAAAATATTATTTTT
1 TAAAATATTATTATT
556446 TA
1 TA
556448 TCAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAAATATTATTATT
Found at i:556483 original size:29 final size:27
Alignment explanation
Indices: 556451--556516 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
556441 TTTTTTATCA
** *
556451 AAAAAATATTAATATTAAATATTTTATT
1 AAAAAATAAAAATATT-AATATTTTAGT
*
556479 GAAAATATTAAAAATATTAATATTTTAGT
1 -AAAA-AATAAAAATATTAATATTTTAGT
556508 AAAAAATAA
1 AAAAAATAA
556517 TTTTTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 4 0.13
28 4 0.13
29 14 0.45
30 9 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (27 bp):
AAAAAATAAAAATATTAATATTTTAGT
Found at i:556528 original size:12 final size:12
Alignment explanation
Indices: 556511--556535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
556501 TTTTAGTAAA
556511 AAATAATTTTTT
1 AAATAATTTTTT
556523 AAATAATTTTTT
1 AAATAATTTTTT
556535 A
1 A
556536 TTAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:558255 original size:21 final size:21
Alignment explanation
Indices: 558205--558262 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 21
558195 AAAATGACCA
*
558205 ACAAAATCGCAGTGCGA-AAT
1 ACAAAATCGCAATGCGATAAT
*
558225 A-AAAATCGCAATGCGATAGT
1 ACAAAATCGCAATGCGATAAT
* *
558245 ACAAATTCGCATTGCGAT
1 ACAAAATCGCAATGCGAT
558263 TTTCCAGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 14 0.44
20 4 0.12
21 14 0.44
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (21 bp):
ACAAAATCGCAATGCGATAAT
Found at i:558298 original size:20 final size:20
Alignment explanation
Indices: 558273--558322 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
558263 TTTCCAGAAC
*
558273 CGCAACGCGAATATGA-AAAT
1 CGCAACGCGAACAT-ATAAAT
*
558293 CGCAACGCAAACATATAAAT
1 CGCAACGCGAACATATAAAT
558313 CGCAACGCGA
1 CGCAACGCGA
558323 TTCTTACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.12
Consensus pattern (20 bp):
CGCAACGCGAACATATAAAT
Found at i:558357 original size:21 final size:20
Alignment explanation
Indices: 558331--558421 Score: 101
Period size: 21 Copynumber: 4.5 Consensus size: 20
558321 GATTCTTACT
558331 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
558352 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* ** *
558372 ATCGCAATGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
558393 ATCACAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
558413 ATCGCAACG
1 ATCGCAACG
558422 CGATTTTTAA
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 25 0.45
21 31 0.55
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:558375 original size:20 final size:20
Alignment explanation
Indices: 558308--558423 Score: 110
Period size: 20 Copynumber: 5.7 Consensus size: 20
558298 CGCAAACATA
* *
558308 TAAATCGCAACGCG-ATTCT
1 TAAATCGCAACGCGTATCCG
* *
558327 TACTATCGCAACGAGTATCCG
1 TA-AATCGCAACGCGTATCCG
558348 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
* * *
558369 TAAATCGCAATGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
*
558389 TAAAATCACAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
558410 TAAATCGCAACGCG
1 TAAATCGCAACGCG
558424 ATTTTTAAAG
Statistics
Matches: 77, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.03
20 38 0.49
21 36 0.47
22 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:558376 original size:41 final size:41
Alignment explanation
Indices: 558289--558421 Score: 146
Period size: 41 Copynumber: 3.3 Consensus size: 41
558279 GCGAATATGA
* * *
558289 AAATCGCAACG-CAA-ACATATAAATCGCAACGCG-ATTCTT
1 AAATCGCAACGACAATACGTA-AAATCGCAACGCGTATCCGT
* ** *
558328 ACTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGT
1 A-AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
* *
558370 AAATCGCAATGACAATACGTAAAATCACAACGCGTATCCGT
1 AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
558411 AAATCGCAACG
1 AAATCGCAACG
558422 CGATTTTTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.01
40 9 0.12
41 58 0.76
42 8 0.11
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (41 bp):
AAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGT
Found at i:560678 original size:63 final size:64
Alignment explanation
Indices: 560600--560726 Score: 202
Period size: 64 Copynumber: 2.0 Consensus size: 64
560590 GCCCATTCTG
*
560600 CTAAACTGTGTATTCTTTAACACTGTGAA-ATAGTATTTATCTTTGTTTTGTCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAAGATAGTATTTATCTTTGTTTTGTCTTTTGGTTGAA
* * * *
560663 CTAAATTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAAGATAGTATTTATCTTTGTTTTGTCTTTTGGTTGAA
560727 GTAATGCAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
63 26 0.45
64 32 0.55
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.51
Consensus pattern (64 bp):
CTAAACTGTGTATTCTTTAACACTCTGAAGATAGTATTTATCTTTGTTTTGTCTTTTGGTTGAA
Found at i:560834 original size:19 final size:19
Alignment explanation
Indices: 560778--560935 Score: 129
Period size: 19 Copynumber: 8.7 Consensus size: 19
560768 TAGTTTACTT
* *
560778 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
560798 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
560819 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
560838 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
560852 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
560871 TCGCAA--CG--AT-AGAA
1 TCGCAACGCGAAATGAAAA
560885 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
560904 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
560923 TCGCAACGCGAAA
1 TCGCAACGCGAAA
560936 CTATAATCGC
Statistics
Matches: 110, Mismatches: 16, Indels: 25
0.73 0.11 0.17
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 56 0.51
20 8 0.07
21 12 0.11
22 3 0.03
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:560855 original size:14 final size:14
Alignment explanation
Indices: 560836--560892 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
560826 GCGAAATGAA
560836 AATCGCAACGAGAG
1 AATCGCAACGAGAG
560850 AATCGCAACGAGAAATG
1 AATCGCAACGAG--A-G
*
560867 AAAATCGCAACGATAG
1 --AATCGCAACGAGAG
560883 AATCGCAACG
1 AATCGCAACG
560893 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 22 0.59
16 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:560865 original size:33 final size:33
Alignment explanation
Indices: 560818--560911 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
560808 AAAAATGACT
560818 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
560851 ATCGCAACGAGAAATGAAAATCGCAACGATAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
560884 ATCGCAACGCGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
560912 CGAAACCAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:560943 original size:19 final size:19
Alignment explanation
Indices: 560883--560945 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
560873 GCAACGATAG
560883 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
*
560902 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACTAA
*
560921 AATCGCAACGCGAAACTAT
1 AATCGCAACGCGAAACTAA
560940 AATCGC
1 AATCGC
560946 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.44, C:0.27, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:560988 original size:33 final size:33
Alignment explanation
Indices: 560945--561038 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
560935 ACTATAATCG
** *
560945 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTAT
1 CGTTGCGATTTTCATTTCACGTTGCGATTCTAT
* * * *
560978 CGTTGTGATTTTTATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCACGTTGCGATTCTAT
561011 CGTTGCGATTTTCATTTCACGTTGCGAT
1 CGTTGCGATTTTCATTTCACGTTGCGAT
561039 AATCATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCACGTTGCGATTCTAT
Found at i:561013 original size:14 final size:14
Alignment explanation
Indices: 560994--561020 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
560984 GATTTTTATT
560994 TCTCGTTGCGATTC
1 TCTCGTTGCGATTC
561008 TCTCGTTGCGATT
1 TCTCGTTGCGATT
561021 TTCATTTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (14 bp):
TCTCGTTGCGATTC
Found at i:561035 original size:19 final size:20
Alignment explanation
Indices: 561011--561062 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
561001 GCGATTCTCT
561011 CGTTGCGATTTTCA-TTTCA
1 CGTTGCGATTTTCATTTTCA
**
561030 CGTTGCGATAATCATTTTTCA
1 CGTTGCGATTTTCA-TTTTCA
561051 CGTTGCGATTTT
1 CGTTGCGATTTT
561063 AAGTTTCGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
21 15 0.56
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:561535 original size:42 final size:42
Alignment explanation
Indices: 561455--561577 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
561445 ACCTGACTCG
* * * * * *
561455 CCTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
*
561497 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
561539 ACTGTCA-TCATTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
561578 CCTGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.16, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:563031 original size:14 final size:14
Alignment explanation
Indices: 563012--563047 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
563002 ATTGTTTAAT
563012 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
563026 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
563040 TGATTTGT
1 TGATTTGT
563048 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:563227 original size:33 final size:33
Alignment explanation
Indices: 563187--563461 Score: 379
Period size: 33 Copynumber: 8.1 Consensus size: 33
563177 CAACGAGTGT
*
563187 GATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
563220 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
563253 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
*
563286 CATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
563319 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
* * * *
563352 GATAGTCATTTCCGCGTTGCGATATTCATATTCACGTTGC
1 GAT--TC---T-CTCGTTGCGATTTTCAT-TTCGCATTGC
* *
563392 GATTTTCACGTTGCGATTTTCATTTCGCATTGC
1 GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
* * *
563425 GATTCTCTTGTTGCGATTGTAATTTTCGCATTGC
1 GATTCTCTCGTTGCGATTTTCA-TTTCGCATTGC
563459 GAT
1 GAT
563462 AGTCAAATGA
Statistics
Matches: 217, Mismatches: 17, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
33 157 0.72
34 29 0.13
35 3 0.01
38 2 0.01
39 15 0.07
40 11 0.05
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
GATTCTCTCGTTGCGATTTTCATTTCGCATTGC
Found at i:563235 original size:14 final size:14
Alignment explanation
Indices: 563216--563336 Score: 71
Period size: 14 Copynumber: 7.6 Consensus size: 14
563206 TCATTTCGCA
563216 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
563230 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
563247 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
563263 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
563280 CATTGCCATTCTCTCG
1 --TTGCGATTCTCTCG
*
563296 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
563313 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
563329 TTGCGATT
1 TTGCGATT
563337 TTCATTTCGC
Statistics
Matches: 84, Mismatches: 8, Indels: 30
0.69 0.07 0.25
Matches are distributed among these distances:
14 25 0.30
16 21 0.25
17 21 0.25
19 17 0.20
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:563373 original size:20 final size:19
Alignment explanation
Indices: 563294--563427 Score: 90
Period size: 19 Copynumber: 7.5 Consensus size: 19
563284 GCCATTCTCT
*
563294 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
563313 CATTGCG--ATTC---TCT
1 CGTTGCGATATTCATTTCG
*
563327 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* *
563346 CATTGCGATAGTCATTTCCG
1 CGTTGCGATATTCATTT-CG
*
563366 CGTTGCGATATTCATATTCA
1 CGTTGCGATATTCAT-TTCG
*
563386 CGTTGCG--A-T--TTTCA
1 CGTTGCGATATTCATTTCG
*
563400 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
*
563419 CATTGCGAT
1 CGTTGCGAT
563428 TCTCTTGTTG
Statistics
Matches: 88, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 3 0.03
17 5 0.06
18 1 0.01
19 34 0.39
20 23 0.26
21 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:563401 original size:14 final size:14
Alignment explanation
Indices: 563382--563413 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
563372 GATATTCATA
563382 TTCACGTTGCGATT
1 TTCACGTTGCGATT
563396 TTCACGTTGCGATT
1 TTCACGTTGCGATT
563410 TTCA
1 TTCA
563414 TTTCGCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (14 bp):
TTCACGTTGCGATT
Found at i:565968 original size:24 final size:24
Alignment explanation
Indices: 565934--565987 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
565924 CTGAAACATC
565934 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
565958 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
565982 ATCAAA
1 ATCAAA
565988 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:566001 original size:24 final size:24
Alignment explanation
Indices: 565934--566001 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
565924 CTGAAACATC
* * *
565934 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
565958 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
565982 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
566002 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:566134 original size:12 final size:12
Alignment explanation
Indices: 566113--566146 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
566103 GGTTGTAGGT
*
566113 TTTGAGATTGTG
1 TTTGATATTGTG
566125 TTTGATATTGTG
1 TTTGATATTGTG
*
566137 TTTGGTATTG
1 TTTGATATTG
566147 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:566832 original size:20 final size:20
Alignment explanation
Indices: 566807--567080 Score: 282
Period size: 20 Copynumber: 13.4 Consensus size: 20
566797 AAAATTTAAG
*
566807 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATTCT
*
566827 CGTTGCGATTTACGGATTAT
1 CGTTGCGATTTACGGATTCT
*
566847 CGTTGCGATTTACGGATTAT
1 CGTTGCGATTTACGGATTCT
566867 CGTTGCGATTTACAGG-TTCT
1 CGTTGCGATTTAC-GGATTCT
* *
566887 CGTTGCGATTAACGTATTCT
1 CGTTGCGATTTACGGATTCT
* * * * *
566907 GGTTGCGA-TAATCAGAATCG
1 CGTTGCGATTTA-CGGATTCT
*
566927 CGTTGCGATTTTACGTATTCT
1 CGTTGCGA-TTTACGGATTCT
* *
566948 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATTCT
*
566968 CGTTGCGATTTTACGTATTCT
1 CGTTGCGA-TTTACGGATTCT
* *
566989 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATTCT
*
567009 CGTTGCGATTTTACGTATTCT
1 CGTTGCGA-TTTACGGATTCT
* *
567030 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATTCT
* *
567050 CGTTGCGATTTTTACGAATACT
1 CGTTGCGA--TTTACGGATTCT
567072 CGTTGCGAT
1 CGTTGCGAT
567081 AGTAAGAACC
Statistics
Matches: 212, Mismatches: 33, Indels: 18
0.81 0.13 0.07
Matches are distributed among these distances:
19 4 0.02
20 140 0.66
21 48 0.23
22 20 0.09
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGGATTCT
Found at i:566955 original size:41 final size:41
Alignment explanation
Indices: 566806--567080 Score: 341
Period size: 41 Copynumber: 6.8 Consensus size: 41
566796 CAAAATTTAA
566806 GCGTTGCGA-TTTACAG-ATTCTCGTTGCGATTTACGGATTA-
1 GCGTTGCGATTTTAC-GTATTCTCGTTGCGATTTACGGA-TAC
* * * *
566846 TCGTTGCGA-TTTACGGATTATCGTTGCGATTTACAGG-TTC
1 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTAC-GGATAC
* * * * *
566886 TCGTTGCGA-TTAACGTATTCTGGTTGCGA-TAATCAGA-ATC
1 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTA-CGGATA-C
566926 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATAC
566967 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATAC
567008 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATAC
* *
567049 GCGTTGCGATTTTTACGAATACTCGTTGCGAT
1 GCGTTGCGA-TTTTACGTATTCTCGTTGCGAT
567081 AGTAAGAACC
Statistics
Matches: 208, Mismatches: 17, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
39 5 0.02
40 65 0.31
41 115 0.55
42 23 0.11
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
GCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATAC
Found at i:567114 original size:20 final size:20
Alignment explanation
Indices: 567090--567141 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
567080 TAGTAAGAAC
*
567090 CGCGTTGCGATTTAT-ATGTT
1 CGCGTTGCGATTT-TCATATT
* *
567110 TGCGTTGTGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
567130 CGCGTTGCGATT
1 CGCGTTGCGATT
567142 CTGGAAACTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.13, C:0.15, G:0.25, T:0.46
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:570907 original size:20 final size:20
Alignment explanation
Indices: 570882--571016 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
570872 AATTGGGAAA
570882 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
570902 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
570922 ATCGCAATGTGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
570943 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
570963 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
570983 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
571003 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
571017 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.68
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:570926 original size:61 final size:61
Alignment explanation
Indices: 570879--571010 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
570869 GCGAATTGGG
* * * * * *
570879 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGTGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
570940 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
571001 ATAATCGCAA
1 AAAATCGCAA
571011 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:571212 original size:22 final size:22
Alignment explanation
Indices: 571184--571227 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
571174 CACTCTCTCA
571184 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* **
571206 CCCATCTCTGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
571228 TATCTCCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:571530 original size:20 final size:20
Alignment explanation
Indices: 571471--571534 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
571461 GCGATTTTAG
*
571471 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
571491 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
571511 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
571531 TTTC
1 TTTC
571535 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:571725 original size:25 final size:24
Alignment explanation
Indices: 571671--571725 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
571661 TGTTTATTAT
* *
571671 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
571695 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
571721 TGTTT
1 TGTTT
571726 ATTGTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:572875 original size:18 final size:18
Alignment explanation
Indices: 572854--572898 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
572844 TCCACTTCGG
*
572854 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
572872 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
572890 GAGCCATCA
1 GAGCCATCA
572899 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:573405 original size:20 final size:20
Alignment explanation
Indices: 573380--573425 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
573370 TAGTTTACTT
573380 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
573400 TCGCAACGTGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
573420 TCGCAA
1 TCGCAA
573426 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:573434 original size:19 final size:19
Alignment explanation
Indices: 573391--573435 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
573381 CGCAACACGA
573391 AAATGACTATCGCAACGTGG
1 AAATGACTATCGCAAC-TGG
*
573411 AAATGGCTATCGCAA-TGCG
1 AAATGACTATCGCAACTG-G
573430 AAATGA
1 AAATGA
573436 AAATCGGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (19 bp):
AAATGACTATCGCAACTGG
Found at i:573454 original size:14 final size:14
Alignment explanation
Indices: 573435--573492 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
573425 ATGCGAAATG
*
573435 AAAATCGGAACGAC
1 AAAATCGCAACGAC
*
573449 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
573465 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
573481 AAAATCGCAACG
1 AAAATCGCAACG
573493 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:573479 original size:32 final size:33
Alignment explanation
Indices: 573419--573509 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
573409 GGAAATGGCT
*
573419 ATCGCAATGCGAAATGAAAATCGGAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
573452 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
573484 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
573510 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:573585 original size:20 final size:20
Alignment explanation
Indices: 573551--573606 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
573541 GTTGCGATTT
*
573551 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
573570 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
*
573590 CATTTTTGCGTTGCGAT
1 CATTTCTGCGTTGCGAT
573607 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 6 0.18
20 27 0.82
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:574067 original size:41 final size:41
Alignment explanation
Indices: 573971--574058 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
573961 GACTCACCTG
* * *
573971 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTA
* *
574013 TCCTCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
574054 TCATC
1 TCATC
574059 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTA
Found at i:575496 original size:14 final size:14
Alignment explanation
Indices: 575477--575526 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
575467 ATTGTTTAAT
575477 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
575491 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
575505 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
575519 TGATTTGT
1 TGATTTGT
575527 TTAATTGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:575685 original size:19 final size:19
Alignment explanation
Indices: 575663--575711 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
575653 ATCGCAACGA
575663 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
*
575682 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
575701 GAAAATCGCAA
1 GAAAATCGCAA
575712 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:575718 original size:19 final size:19
Alignment explanation
Indices: 575663--575718 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
575653 ATCGCAACGA
575663 GAAAATCGCAATGCA-AAAT
1 GAAAATCGCAATG-AGAAAT
*
575682 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGAGAAAT
*
575701 GAAAATCGCAACGAGAAA
1 GAAAATCGCAATGAGAAA
575719 ATCGCAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAAATCGCAATGAGAAAT
Found at i:575794 original size:20 final size:21
Alignment explanation
Indices: 575768--575826 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
575758 TTGTGATAGC
*
575768 CATTTTCGCGTTGCGATTTTT
1 CATTTTCGCGTTGCGATTTGT
** *
575789 CA-TTTCGAATTGCGA-TAGT
1 CATTTTCGCGTTGCGATTTGT
575808 CATTTTCGCGTTGCGATTT
1 CATTTTCGCGTTGCGATTT
575827 CCCCGTTGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.14
20 22 0.76
21 3 0.10
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (21 bp):
CATTTTCGCGTTGCGATTTGT
Found at i:576063 original size:20 final size:20
Alignment explanation
Indices: 576038--576129 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
576028 TTGAAGATGA
576038 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
576058 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
576078 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
576099 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
576119 TTGCGATTTTC
1 TTGCGATTTTC
576130 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:577174 original size:12 final size:12
Alignment explanation
Indices: 577157--577181 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
577147 ATATAATCCT
577157 GAAGAAGAAAAA
1 GAAGAAGAAAAA
577169 GAAGAAGAAAAA
1 GAAGAAGAAAAA
577181 G
1 G
577182 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:578627 original size:22 final size:22
Alignment explanation
Indices: 578597--578639 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
578587 GTTGCCCAGA
*
578597 ATAGAGGAAATCGGTACCCCTTC
1 ATAGAGG-AATCGATACCCCTTC
578620 ATAG-GGAATCGATACCCCTT
1 ATAGAGGAATCGATACCCCTT
578640 TATAATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 2 0.11
23 4 0.21
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (22 bp):
ATAGAGGAATCGATACCCCTTC
Found at i:578705 original size:21 final size:21
Alignment explanation
Indices: 578679--578721 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
578669 CTGTTGAACA
578679 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
578700 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
578721 G
1 G
578722 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:578780 original size:21 final size:21
Alignment explanation
Indices: 578755--578833 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
578745 AAAACCTGCA
578755 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
578776 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
578792 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
578812 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
578833 G
1 G
578834 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:578796 original size:36 final size:36
Alignment explanation
Indices: 578756--578827 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
578746 AAACCTGCAG
* *
578756 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
578792 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
578828 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:578797 original size:15 final size:15
Alignment explanation
Indices: 578777--578806 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
578767 ACCCCCTGGG
578777 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
578792 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
578807 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:578955 original size:29 final size:31
Alignment explanation
Indices: 578923--578982 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
578913 AAACTTTGAA
578923 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
578952 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
578983 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:580783 original size:3 final size:3
Alignment explanation
Indices: 580775--580818 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
580765 TACGTCCTCA
* *
580775 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
580819 CCTTTCTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:581859 original size:34 final size:32
Alignment explanation
Indices: 581806--581875 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
581796 CCTTACAAAC
*
581806 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
581838 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
581872 TCCC
1 TCCC
581876 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:582124 original size:21 final size:21
Alignment explanation
Indices: 582090--582129 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
582080 AGTCGTATAT
*
582090 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTAGGGATGATTTTGG
582110 AGCCGTTTAGGGATGATTTT
1 AGCCG-TTAGGGATGATTTT
582130 TATACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTAGGGATGATTTTGG
Found at i:582183 original size:21 final size:21
Alignment explanation
Indices: 582159--582199 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
582149 CAGAATAGAT
*
582159 GGAATCGGTACCCCTTCATAG
1 GGAATCGATACCCCTTCATAG
582180 GGAATCGATACCCCTTCATA
1 GGAATCGATACCCCTTCATA
582200 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAG
Found at i:582443 original size:30 final size:30
Alignment explanation
Indices: 582409--582468 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
582399 TTGAAACCTT
582409 TTAAAA-ACTTTGAATAAATTCAATT-AAGTC
1 TTAAAACACTTTG--TAAATTCAATTCAAGTC
*
582439 TTAAAACATTTTGTAAATTCAATTCAAGTC
1 TTAAAACACTTTGTAAATTCAATTCAAGTC
582469 CAAAAACCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (30 bp):
TTAAAACACTTTGTAAATTCAATTCAAGTC
Done.