Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008117.1 Hibiscus syriacus cultivar Beakdansim tig00110656_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: 1567030
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:515774 original size:2 final size:2
Alignment explanation
Indices: 515769--515794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
515759 AAAATACATA
515769 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
515795 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:516477 original size:16 final size:16
Alignment explanation
Indices: 516458--516512 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
516448 TAGGGTTGCT
* *
516458 TTCGATTCGGGTTGAC
1 TTCGGTTCGAGTTGAC
* *
516474 TTCGGCTCTAGTTGAC
1 TTCGGTTCGAGTTGAC
*
516490 TTCGGTTCGTGTTGAC
1 TTCGGTTCGAGTTGAC
516506 TTCGGTT
1 TTCGGTT
516513 ATTGTTGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.09, C:0.20, G:0.29, T:0.42
Consensus pattern (16 bp):
TTCGGTTCGAGTTGAC
Found at i:516509 original size:32 final size:32
Alignment explanation
Indices: 516458--516528 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
516448 TAGGGTTGCT
* *
516458 TTCGATTCGGGTTGACTTCGGCTCTAGTTGAC
1 TTCGGTTCGGGTTGACTTCGGCTATAGTTGAC
* * * *
516490 TTCGGTTCGTGTTGACTTCGGTTATTGTTGAT
1 TTCGGTTCGGGTTGACTTCGGCTATAGTTGAC
516522 TTCGGTT
1 TTCGGTT
516529 TAGGTTGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.10, C:0.17, G:0.28, T:0.45
Consensus pattern (32 bp):
TTCGGTTCGGGTTGACTTCGGCTATAGTTGAC
Found at i:516518 original size:16 final size:16
Alignment explanation
Indices: 516468--516528 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
516458 TTCGATTCGG
* *
516468 GTTGACTTCGGCTCTA
1 GTTGACTTCGGTTCTT
*
516484 GTTGACTTCGGTTCGT
1 GTTGACTTCGGTTCTT
*
516500 GTTGACTTCGGTTATT
1 GTTGACTTCGGTTCTT
*
516516 GTTGATTTCGGTT
1 GTTGACTTCGGTT
516529 TAGGTTGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.10, C:0.16, G:0.28, T:0.46
Consensus pattern (16 bp):
GTTGACTTCGGTTCTT
Found at i:516536 original size:32 final size:31
Alignment explanation
Indices: 516467--516536 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 31
516457 TTTCGATTCG
* *
516467 GGTTGACTTCGGCTCTAGTTGACTTCGGTTC
1 GGTTGACTTCGGCTATAGTTGACTTCGGTTA
* * *
516498 GTGTTGACTTCGGTTATTGTTGATTTCGGTTTA
1 G-GTTGACTTCGGCTATAGTTGACTTCGG-TTA
516531 GGTTGA
1 GGTTGA
516537 TTATGGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 1 0.03
32 28 0.88
33 3 0.09
ACGTcount: A:0.11, C:0.14, G:0.30, T:0.44
Consensus pattern (31 bp):
GGTTGACTTCGGCTATAGTTGACTTCGGTTA
Found at i:517666 original size:29 final size:29
Alignment explanation
Indices: 517634--517689 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
517624 ATTCTTAACA
*
517634 TTATCATATATTATTATCATTAATTCTTT
1 TTATCATATAATATTATCATTAATTCTTT
* *
517663 TTATTATATAATATTATCCTTAATTCT
1 TTATCATATAATATTATCATTAATTCT
517690 CATACACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATCATATAATATTATCATTAATTCTTT
Found at i:522484 original size:138 final size:138
Alignment explanation
Indices: 522272--522647 Score: 454
Period size: 138 Copynumber: 2.7 Consensus size: 138
522262 AACTTTTACG
* * * * * *
522272 ACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTGGAATCGACCATCGCACAAGGA
1 ACGAAGGAGAAGAACTTCGTAATGAGAAGAGCTTGTTCAACCTGGAATCGTCTATCGCACAAGGA
* * * ** * *
522337 GATGGATAAATGAAGAGTTCATAATGAGAAGAACTCAT-CTGACGAAGGGTTGGGAATGAGAAGA
66 GGTGGATAAATGAAGAGTTCATAATGAGAAGAACTC-TCCCGAAGAAGGGTTCAGAATAAGAAAA
522401 ACTCGTCCA
130 ACTCGTCCA
**
522410 AC-AAGGAAGAAGAACTTCGTAATGAGAAGAGCTTGTTCAACCTACAATCGTCTATCGCACAAGG
1 ACGAAGG-AGAAGAACTTCGTAATGAGAAGAGCTTGTTCAACCTGGAATCGTCTATCGCACAAGG
* * *
522474 AGGTGGATAAATGAGGATTTCATAATGAGAAGAACTCTCCCGAAGAAGGGTTCATAATAAGAAAA
65 AGGTGGATAAATGAAGAGTTCATAATGAGAAGAACTCTCCCGAAGAAGGGTTCAGAATAAGAAAA
522539 ACTCGTCCA
130 ACTCGTCCA
* * * * * * * * *
522548 ACGATGGAGAAGAAGC-TCGTAATTAGAGGAGTTTGTTTAACCTGGGATTGTCTATCACACAAAG
1 ACGAAGGAGAAGAA-CTTCGTAATGAGAAGAGCTTGTTCAACCTGGAATCGTCTATCGCACAAGG
522612 AGGTGGAT-AATGAAGAGTTCATAATGAGAAGAACTC
65 AGGTGGATAAATGAAGAGTTCATAATGAGAAGAACTC
522648 CCATAGAATA
Statistics
Matches: 203, Mismatches: 31, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
137 30 0.15
138 169 0.83
139 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (138 bp):
ACGAAGGAGAAGAACTTCGTAATGAGAAGAGCTTGTTCAACCTGGAATCGTCTATCGCACAAGGA
GGTGGATAAATGAAGAGTTCATAATGAGAAGAACTCTCCCGAAGAAGGGTTCAGAATAAGAAAAA
CTCGTCCA
Found at i:526013 original size:60 final size:59
Alignment explanation
Indices: 525915--526035 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 59
525905 ATGTGTCCTT
* * *
525915 AATTGTGATTTTCATTTTAAATTAATCCTCAAACTTTTAAACATTTCAATTTCATCTCCA
1 AATTATGATTCTCATTGTAAATTAATCCTCAAACTTTTAAACATTTCAATTTCATC-CCA
*
525975 AATTATGATTCTCATTGTAAATTAATCCTCAAAGTTTTAAACATTTCAATTTCATCCCA
1 AATTATGATTCTCATTGTAAATTAATCCTCAAACTTTTAAACATTTCAATTTCATCCCA
526034 AA
1 AA
526036 CACGCCCTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 5 0.09
60 52 0.91
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (59 bp):
AATTATGATTCTCATTGTAAATTAATCCTCAAACTTTTAAACATTTCAATTTCATCCCA
Found at i:526031 original size:29 final size:28
Alignment explanation
Indices: 525939--526035 Score: 65
Period size: 29 Copynumber: 3.3 Consensus size: 28
525929 TTTTAAATTA
525939 ATCCTCAAACTTTTAAACATTTCAATTTC
1 ATCCTCAAA-TTTTAAACATTTCAATTTC
*** * *
525968 AT-CTCCAAATTATGATTCTCATTGT-AAATTA
1 ATCCT-CAAATT-T--TAAACATT-TCAATTTC
525999 ATCCTCAAAGTTTTAAACATTTCAATTTC
1 ATCCTCAAA-TTTTAAACATTTCAATTTC
526028 ATCC-CAAA
1 ATCCTCAAA
526036 CACGCCCTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 17
0.65 0.13 0.22
Matches are distributed among these distances:
28 9 0.18
29 20 0.40
31 16 0.32
32 5 0.10
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (28 bp):
ATCCTCAAATTTTAAACATTTCAATTTC
Found at i:529375 original size:15 final size:15
Alignment explanation
Indices: 529357--529386 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
529347 AGTTTAGTCC
*
529357 TTTATAATTTAAATT
1 TTTATAAATTAAATT
529372 TTTATAAATTAAATT
1 TTTATAAATTAAATT
529387 AATAATGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATAAATTAAATT
Found at i:531094 original size:21 final size:21
Alignment explanation
Indices: 531068--531107 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
531058 TGAAAGATGA
*
531068 CTTTTAGTGTTGGATATTTTG
1 CTTTTAATGTTGGATATTTTG
531089 CTTTTAATGTTGGATATTT
1 CTTTTAATGTTGGATATTT
531108 ATTTTTCATA
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:0.17, C:0.05, G:0.20, T:0.57
Consensus pattern (21 bp):
CTTTTAATGTTGGATATTTTG
Found at i:537275 original size:19 final size:20
Alignment explanation
Indices: 537251--537322 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
537241 ATGCAAAAAT
*
537251 GGTATCGATACCATAATA-G
1 GGTATCGATACCATAGTAGG
*
537270 GGTATCGCTACCATAGTATGG
1 GGTATCGATACCATAGTA-GG
* *
537291 TAGTATCGATACCATGGTAGG
1 -GGTATCGATACCATAGTAGG
537312 GGTATCGATAC
1 GGTATCGATAC
537323 TGAGGAGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.36
20 10 0.23
21 3 0.07
22 15 0.34
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGG
Found at i:537303 original size:22 final size:19
Alignment explanation
Indices: 537251--537322 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 19
537241 ATGCAAAAAT
*
537251 GGTATCGATACCATAATAG
1 GGTATCGATACCATAGTAG
*
537270 GGTATCGCTACCATAGTATG
1 GGTATCGATACCATAGTA-G
*
537290 GTAGTATCGATACCATGGTAGG
1 G--GTATCGATACCATAGTA-G
537312 GGTATCGATAC
1 GGTATCGATAC
537323 TGAGGAGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 12 0.27
22 17 0.38
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:537731 original size:55 final size:53
Alignment explanation
Indices: 537670--537815 Score: 159
Period size: 55 Copynumber: 2.7 Consensus size: 53
537660 GCAAAAAATT
* * *
537670 AAGAAATCTATACTATGTGTATGAATTTATGTATGGGCACTTTGTATGCAAAACA
1 AAGAAATCTATACTAAGTGTATGAATTT-TGTATGGGCACTATATATGC-AAACA
* * *
537725 AAGAAAT-TCATACTAAGTGTATGAATTTTCGTATGGGCACTATATGTGCGAACT
1 AAGAAATCT-ATACTAAGTGTATGAATTTT-GTATGGGCACTATATATGCAAACA
* * *
537779 AACAAATCCATATTAAGTGTATGAATTTCTGTATGGG
1 AAGAAATCTATACTAAGTGTATGAATTT-TGTATGGG
537816 AAATATATGT
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
54 36 0.46
55 42 0.54
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (53 bp):
AAGAAATCTATACTAAGTGTATGAATTTTGTATGGGCACTATATATGCAAACA
Found at i:537813 original size:54 final size:54
Alignment explanation
Indices: 537673--537826 Score: 166
Period size: 54 Copynumber: 2.8 Consensus size: 54
537663 AAAAATTAAG
* * * * * *
537673 AAATCTATACTATGTGTATGAATTTATGTATGGGCACTTTGTATGCAAAACAAAG
1 AAATCCATACTAAGTGTATGAATTT-TGTATGGGCACTATATGTGCAAAACAAAC
* * *
537728 AAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTATATGTGC-GAACTAAC
1 AAATCCATACTAAGTGTATGAATTTT-GTATGGGCACTATATGTGCAAAACAAAC
* * *
537782 AAATCCATATTAAGTGTATGAATTTCTGTATGGGAAATATATGTG
1 AAATCCATACTAAGTGTATGAATTT-TGTATGGGCACTATATGTG
537827 AAATTATCCG
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
54 45 0.54
55 39 0.46
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (54 bp):
AAATCCATACTAAGTGTATGAATTTTGTATGGGCACTATATGTGCAAAACAAAC
Found at i:538313 original size:81 final size:81
Alignment explanation
Indices: 538096--538800 Score: 923
Period size: 81 Copynumber: 8.7 Consensus size: 81
538086 GTGCCTTTGA
* * * *
538096 GGCCTAACTGTGCA-ATGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
538160 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
538176 GG-CTGAGCTGTGCA-TTGGCAGAAATGTGTCAATTATGACAGTTAGATGAATGGTTAAAGACTG
1 GGCCT-AGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCG
538239 TTGAGTAAAAGATAAAT
65 TTGAGTAAAAGATAAAT
* * * ** * *
538256 GTCCTAGTTGTGCATTTGGTAGAAATATGTCAATTATGCCAGTTACATGAACAGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
538321 TAAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
** * *
538337 GGCCTAGCTGTGCATTTGATAGAAAGATGTCAATTATGCCAGTTAGATGACCGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
538402 TGAGTAAAAGATAAAA
66 TGAGTAAAAGATAAAT
* * * * * * *
538418 GGCCTAGTTATGCAATTGGTAGAAAGGTGTCAATTATGCTAGTTAGATAAATGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
538483 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * *
538499 GGCCTAGTTGTTCA-TTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
538563 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
538579 GGCCTAGCTATGCATTTGGCAAAAAGGTATCAATTATACCAGTTAGATGAACAGTTAAAGATCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
538644 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * *
538660 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATGAATGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
* *
538725 TCAATAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
538741 GGCCTAACTGTGCATTTTGGAAGAAAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAA
1 GGCCTAGCTGTGCA-TTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAA
538801 TACATTTGGG
Statistics
Matches: 548, Mismatches: 72, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
79 2 0.00
80 151 0.28
81 357 0.65
82 38 0.07
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:538557 original size:242 final size:243
Alignment explanation
Indices: 538096--538800 Score: 1015
Period size: 242 Copynumber: 2.9 Consensus size: 243
538086 GTGCCTTTGA
* * *
538096 GGCCTAACTGTGCA-ATGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
538160 TGAGTAAAAGATAAATGG-CTGAGCTGTGC-ATTGGCAGAAATGTGTCAATTATGACAGTTAGAT
66 TGAGTAAAAGATAAATGGCCT-AGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGAT
* * * *
538223 GAATGGTTAAAGACTGTTGAGTAAAAGATAAATGTCCTAGTTGTGCATTTGGTAGAAATATGTCA
130 GAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGAAGAAATGTGTCA
* * *
538288 ATTATGCCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAAT
195 ATTATGCAAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAAT
* * *
538337 GGCCTAGCTGTGCATTTGATAGAAAGATGTCAATTATGCCAGTTAGATGACCGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
* * * *
538402 TGAGTAAAAGATAAAAGGCCTAGTTATGCAATTGGTAGAAAGGTGTCAATTATG-CTAGTTAGAT
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGAC-AGTTAGAT
* * *
538466 AAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTTCA-TTGGCAGAAATGTGTCA
130 GAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGAAGAAATGTGTCA
* *
538530 ATTATGCTAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAAT
195 ATTATGCAAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAAT
* * * * * * *
538579 GGCCTAGCTATGCATTTGGCAAAAAGGTATCAATTATACCAGTTAGATGAACAGTTAAAGATCGT
1 GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
538644 TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATG
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATG
* * ** *
538709 AATGGTTAAAGACCGTTCAATAAAAGATAAATGGCCTAACTGTGCATTTTGGAAGAAAAGTGTCA
131 AATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCA-TTTGGAAGAAATGTGTCA
* *
538774 ATCATGCAAGTTAGATGAAAGGTTAAA
195 ATTATGCAAGTTAGATGAACGGTTAAA
538801 TACATTTGGG
Statistics
Matches: 411, Mismatches: 46, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
241 13 0.03
242 283 0.69
243 76 0.18
244 39 0.09
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (243 bp):
GGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAATGGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGACAGTTAGATG
AATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGAAGAAATGTGTCAA
TTATGCAAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAAT
Found at i:538705 original size:323 final size:322
Alignment explanation
Indices: 538095--538800 Score: 995
Period size: 323 Copynumber: 2.2 Consensus size: 322
538085 AGTGCCTTTG
* * * *
538095 AGGCCTAACTGTGCAA-TGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCG
1 AGGCCTAACTATGCAATTGGTAGAAAGGTGTCAATTATGCAAGTTAGAT-AAAGGTTAAAGACCG
538159 TTGAGTAAAAGATAAATGGCTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGACAGTTAGATG
65 TTGAGTAAAAGATAAATGGCTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGACAGTTAGATG
* * * * * * * * *
538224 AATGGTTAAAGACTGTTGAGTAAAAGATAAATGTCCTAGTTGTGCATTTGGTAGAAATATGTCAA
130 AACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGATATCAA
* *
538289 TTATGCCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCATTT
195 TTATACCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCAATT
* * * * *
538354 GATAGAAAGATGTCAATTATGCCAGTTAGATGACCGGTTAAAGACCGTTGAGTAAAAGATAAA
260 GACAGAAAGATGTCAATTATGACAGTTAGATGAACGGTTAAAGACCGTTCAATAAAAGATAAA
** *
538417 AGGCCTAGTTATGCAATTGGTAGAAAGGTGTCAATTATGCTAGTTAGATAAATGGTTAAAGACCG
1 AGGCCTAACTATGCAATTGGTAGAAAGGTGTCAATTATGCAAGTTAGATAAA-GGTTAAAGACCG
* *
538482 TTGAGTAAAAGATAAATGGCCT-AGTTGTTCATTGGCAGAAATGTGTCAATTATG-CTAGTTAGA
65 TTGAGTAAAAGATAAATGG-CTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGAC-AGTTAGA
*
538545 TGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGGTATC
128 TGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGATATC
* * *
538610 AATTATACCAGTTAGATGAACAGTTAAAGATCGTTGAGTAAAAGATAAATGGCCTAGCTGTGCAA
193 AATTATACCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCAA
* * *
538675 TTGGCAGAAAGGTGTCAATTATGACAGTTAGATGAATGGTTAAAGACCGTTCAATAAAAGATAAA
258 TTGACAGAAAGATGTCAATTATGACAGTTAGATGAACGGTTAAAGACCGTTCAATAAAAGATAAA
* * * * * *
538740 TGGCCTAACTGTGCATTTTGGAAGAAAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAA
1 AGGCCTAACTATGCA-ATTGGTAGAAAGGTGTCAATTATGCAAGTTAGAT-AAAGGTTAAA
538801 TACATTTGGG
Statistics
Matches: 338, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
322 16 0.05
323 281 0.83
324 38 0.11
325 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (322 bp):
AGGCCTAACTATGCAATTGGTAGAAAGGTGTCAATTATGCAAGTTAGATAAAGGTTAAAGACCGT
TGAGTAAAAGATAAATGGCTGAGCTGTGCATTGGCAGAAATGTGTCAATTATGACAGTTAGATGA
ACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTATGCATTTGGCAAAAAGATATCAAT
TATACCAGTTACATGAACAGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCAATTG
ACAGAAAGATGTCAATTATGACAGTTAGATGAACGGTTAAAGACCGTTCAATAAAAGATAAA
Found at i:538994 original size:45 final size:45
Alignment explanation
Indices: 538939--539028 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
538929 AAGGCAAAAC
538939 ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
1 ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
* *
538984 ATATAATAGTGTATAAAAGGCATTAAAGAATGCCATCAATGAAAT
1 ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
539029 GCATATGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.26
Consensus pattern (45 bp):
ATATAATAGTGTATAAAAGGCATGAAAGAATGCCATAAATGAAAT
Found at i:544740 original size:21 final size:21
Alignment explanation
Indices: 544716--544771 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
544706 CAGGGACTCC
*
544716 GGTCTCGATACTGAGACTGGT
1 GGTCTCGATACTGAGACTAGT
*
544737 GGTCTCAATACTGAGACTAGT
1 GGTCTCGATACTGAGACTAGT
*
544758 GGTCTCGAGACTGA
1 GGTCTCGATACTGA
544772 CGGCCCGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (21 bp):
GGTCTCGATACTGAGACTAGT
Found at i:546694 original size:156 final size:156
Alignment explanation
Indices: 546482--546793 Score: 615
Period size: 156 Copynumber: 2.0 Consensus size: 156
546472 TTGGAATATA
*
546482 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCGTGATAAATCGACGGACATTGTCTTGATGTCTT
1 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
546547 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
66 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
546612 TGGCTTGTTCCTTCGTGGGTCATCTC
131 TGGCTTGTTCCTTCGTGGGTCATCTC
546638 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
1 TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
546703 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
66 CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
546768 TGGCTTGTTCCTTCGTGGGTCATCTC
131 TGGCTTGTTCCTTCGTGGGTCATCTC
546794 CAATTTGTCC
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (156 bp):
TCTTCTCAAAGTTCTTCAAGTCATTGATGATCATGATAAATCGACGGACATTGTCTTGATGTCTT
CATCGGGCTTCATCTTGAAGTTCTTATAGTTGAGAGTGAGAATGAAAATCTTTGACTTCTTCACT
TGGCTTGTTCCTTCGTGGGTCATCTC
Found at i:556241 original size:21 final size:21
Alignment explanation
Indices: 556201--556241 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
556191 AATATTATAT
**
556201 ATATTTATTAATTATAATTTA
1 ATATTTATTAAGAATAATTTA
*
556222 ATATTTATTAAGAATTATTT
1 ATATTTATTAAGAATAATTT
556242 CTTCTATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTTATTAAGAATAATTTA
Found at i:556269 original size:73 final size:72
Alignment explanation
Indices: 556185--556343 Score: 248
Period size: 73 Copynumber: 2.2 Consensus size: 72
556175 TATTTTTTGT
* *
556185 TAATTTAATATTATATATATTTATTAATTATAATTTAATATTTATTAAGAATTATTTCTTCTATT
1 TAATTTTATATTATATATATTTATTAATTATAATTTAATATTTATGAAGAATTATTT-TTCTATT
*
556250 -AATTATTA
65 AAATTA-AA
*
556258 TAATTTTATATTATATATATTTATTAATTATAATTTAATATTTATGAAGAATTATTTTTTTATTA
1 TAATTTTATATTATATATATTTATTAATTATAATTTAATATTTATGAAGAATTATTTTTCTATTA
556323 AATTAAA
66 AATTAAA
556330 TAATTTATATATTA
1 TAATTT-TATATTA
556344 AAAATTAAGA
Statistics
Matches: 80, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
72 13 0.16
73 67 0.84
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (72 bp):
TAATTTTATATTATATATATTTATTAATTATAATTTAATATTTATGAAGAATTATTTTTCTATTA
AATTAAA
Found at i:556603 original size:41 final size:41
Alignment explanation
Indices: 556521--556637 Score: 177
Period size: 41 Copynumber: 2.9 Consensus size: 41
556511 CGTTTATTTG
* * **
556521 TTAAATGAACGAACATGAAC-AAGATTTTGCGTTCGTTTAA
1 TTAAATGAACAAACACGAACAAAGAGCTTGCGTTCGTTTAA
556561 TTAAATGAACAAACACGAACAAAGAGCTTGCGTTCGTTTAA
1 TTAAATGAACAAACACGAACAAAGAGCTTGCGTTCGTTTAA
556602 TTAAATGAACAAACACGAACAAAGAGC-T-CGTTCGTT
1 TTAAATGAACAAACACGAACAAAGAGCTTGCGTTCGTT
556638 CATTTACGTT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
39 8 0.11
40 19 0.26
41 45 0.62
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (41 bp):
TTAAATGAACAAACACGAACAAAGAGCTTGCGTTCGTTTAA
Found at i:556701 original size:24 final size:24
Alignment explanation
Indices: 556655--556719 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
556645 GTTCGTGAAC
* *
556655 GTTCGATTATATGTTCGTTCATTTAT
1 GTTC-ATT-TATGTTCGTCCATTCAT
*
556681 GCTT-ATTTATGTTTGTCCATTCAT
1 G-TTCATTTATGTTCGTCCATTCAT
556705 GTTCATTTATGTTCG
1 GTTCATTTATGTTCG
556720 AACAGAGGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.06
24 25 0.76
25 3 0.09
26 1 0.03
27 2 0.06
ACGTcount: A:0.17, C:0.14, G:0.15, T:0.54
Consensus pattern (24 bp):
GTTCATTTATGTTCGTCCATTCAT
Found at i:557012 original size:10 final size:10
Alignment explanation
Indices: 556983--557036 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
556973 GTGTTTGTGT
*
556983 TGTTCGTTTG
1 TGTTCGTTTA
556993 TGTTCGTTTA
1 TGTTCGTTTA
*
557003 TGTTCATTTATTA
1 TGTTC--GT-TTA
557016 TGTTCGTTTA
1 TGTTCGTTTA
*
557026 TGTTCATTTA
1 TGTTCGTTTA
557036 T
1 T
557037 CATTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 27 0.73
11 1 0.03
12 1 0.03
13 8 0.22
ACGTcount: A:0.13, C:0.09, G:0.17, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:557019 original size:23 final size:23
Alignment explanation
Indices: 556993--557036 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
556983 TGTTCGTTTG
556993 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCATTTATTA
557016 TGTTCGTTTATGTTCATTTAT
1 TGTTCGTTTATGTTCATTTAT
557037 CATTTAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTTATTA
Found at i:557081 original size:31 final size:31
Alignment explanation
Indices: 557043--557123 Score: 153
Period size: 31 Copynumber: 2.6 Consensus size: 31
557033 TTATCATTTA
557043 AATGAACGAACATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
557074 AATGAACGAACATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAGCTATATTCCTT
*
557105 AATGAACGAACGTGAACAA
1 AATGAACGAACATGAACAA
557124 AAAAAATTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (31 bp):
AATGAACGAACATGAACAAGCTATATTCCTT
Found at i:557678 original size:37 final size:36
Alignment explanation
Indices: 557637--557710 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
557627 GTTGAAAAAT
*
557637 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTTAAAAT-ATAAA
* * *
557674 ATTTATATATTTTTTTTACAAGATTTAAAATATAAA
1 ATTTATATATTTTCTTTAAAAAATTTAAAATATAAA
557710 A
1 A
557711 AGTTTAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 6 0.18
37 27 0.82
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTTAAAATATAAA
Found at i:558294 original size:19 final size:22
Alignment explanation
Indices: 558254--558296 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
558244 ATGTGTCACG
558254 ATTTTAATTGGAGATCAAATTT
1 ATTTTAATTGGAGATCAAATTT
558276 ATTTTAATT-GA-AT-AAATTT
1 ATTTTAATTGGAGATCAAATTT
558295 AT
1 AT
558297 GACTAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 2 0.10
22 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTTAATTGGAGATCAAATTT
Found at i:558951 original size:13 final size:13
Alignment explanation
Indices: 558892--558970 Score: 70
Period size: 13 Copynumber: 6.1 Consensus size: 13
558882 AAAAATTTAT
558892 TAATATTTTATTA
1 TAATATTTTATTA
**
558905 T-ATATTATTAAAA
1 TAATATT-TTATTA
* * *
558918 TAAGATTATAATA
1 TAATATTTTATTA
**
558931 CCATATTTTATTA
1 TAATATTTTATTA
558944 TAATATTTTATTA
1 TAATATTTTATTA
*
558957 TAATATTATATTA
1 TAATATTTTATTA
558970 T
1 T
558971 TAAAAATATT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
12 5 0.10
13 42 0.82
14 4 0.08
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (13 bp):
TAATATTTTATTA
Found at i:561588 original size:21 final size:21
Alignment explanation
Indices: 561562--561609 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
561552 TACCTCGGAT
* *
561562 CATCAAATGACATCCTTGCGG
1 CATCAAAAGACATCCTGGCGG
*
561583 CATCAAAAGACATCCTGGCTG
1 CATCAAAAGACATCCTGGCGG
561604 CATCAA
1 CATCAA
561610 GGGAAAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
CATCAAAAGACATCCTGGCGG
Found at i:564538 original size:16 final size:17
Alignment explanation
Indices: 564505--564538 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
564495 AATGTTAAAT
564505 AATAAAAATTATCTTTA
1 AATAAAAATTATCTTTA
*
564522 AATAAATATTA-CTTTA
1 AATAAAAATTATCTTTA
564538 A
1 A
564539 TAATTACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAAAATTATCTTTA
Found at i:564540 original size:15 final size:16
Alignment explanation
Indices: 564504--564541 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
564494 CAATGTTAAA
564504 TAATAAAAATTATCTT
1 TAATAAAAATTATCTT
*
564520 TAAATAAATATTA-CTT
1 T-AATAAAAATTATCTT
564536 TAATAA
1 TAATAA
564542 TTACCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 5 0.25
17 10 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAAAAATTATCTT
Found at i:567134 original size:3 final size:3
Alignment explanation
Indices: 567126--567150 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
567116 CTATTTTTAT
567126 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
567151 AAATTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:570301 original size:2 final size:2
Alignment explanation
Indices: 570290--570320 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
570280 TTCGATACGA
570290 AT AT -T 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
570321 TGTGTGTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:572066 original size:2 final size:2
Alignment explanation
Indices: 572061--572094 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
572051 TTTTTTTGAA
572061 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
572095 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:574400 original size:5 final size:5
Alignment explanation
Indices: 574390--574423 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
574380 AGCATTAAAC
*
574390 AATAA AATAA AATAA AATAA AATAA TA-AA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA
574424 GTATGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:580160 original size:26 final size:24
Alignment explanation
Indices: 580137--580185 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
580127 GCTATTTTGA
580137 AATTTGTT-TTTTAAATATAATTTT
1 AATTTGTTATTTTAAATA-AATTTT
*
580161 AATTTTTTAATTTTAAATAAATTTT
1 AATTTGTT-ATTTTAAATAAATTTT
580186 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATTTGTTATTTTAAATAAATTTT
Found at i:580772 original size:37 final size:37
Alignment explanation
Indices: 580710--580814 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
580700 TCTTTTCGTC
* *
580710 CTACTAAGATTCAAACTCCTAAAAATAAGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAAGATAGAATT
* ** * *
580747 TTGTTAGGATTTAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAAGATAGAATT
* *
580784 CTACTATGATTTAAACTCCTAAAGATAAGAT
1 CTACTAGGATTTAAACTCCTAAAAATAAGAT
580815 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAAGATAGAATT
Found at i:581402 original size:24 final size:23
Alignment explanation
Indices: 581375--581482 Score: 95
Period size: 22 Copynumber: 4.9 Consensus size: 23
581365 CTTTGCATTT
581375 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTA-TA
* *
581399 TTATTTTTACTATTATATTT-TC
1 TTATTATTACTATTATATTTATA
* *
581421 TTTTTATT-CTACT-TATTTATA
1 TTATTATTACTATTATATTTATA
581442 TTATATATGTA-TATT-T-TTTATA
1 TTAT-TAT-TACTATTATATTTATA
*
581464 TT-TTATTATTATTATATTT
1 TTATTATTACTATTATATTT
581483 TTTTACTTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.03
20 12 0.17
21 10 0.14
22 21 0.30
23 5 0.07
24 19 0.28
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTATTACTATTATATTTATA
Found at i:581486 original size:27 final size:28
Alignment explanation
Indices: 581434--581485 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
581424 TTATTCTACT
581434 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
581462 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
581486 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:581526 original size:12 final size:11
Alignment explanation
Indices: 581496--581542 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
581486 TACTTTCTCT
*
581496 TTCTTTTATTA
1 TTCTTGTATTA
581507 TTCTTGTATTA
1 TTCTTGTATTA
581518 TTACTTGTATTA
1 TT-CTTGTATTA
* *
581530 TTTTTATATTA
1 TTCTTGTATTA
581541 TT
1 TT
581543 TATTTTGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.68
Consensus pattern (11 bp):
TTCTTGTATTA
Found at i:581669 original size:23 final size:22
Alignment explanation
Indices: 581641--581712 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
581631 TTTTAAGTGT
581641 TATTTTTTATAATATTATACATA
1 TATTTTTTATAATATTATAC-TA
581664 TATTTTTCTATTAAT-TT-T-CTA
1 TATTTTT-TA-TAATATTATACTA
* *
581685 TATTTTTTATTATCATTATATTA
1 TATTTTTTATAAT-ATTATACTA
581708 TATTT
1 TATTT
581713 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
19 3 0.07
20 2 0.05
21 11 0.27
22 2 0.05
23 15 0.37
24 4 0.10
25 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTTATAATATTATACTA
Found at i:582178 original size:27 final size:27
Alignment explanation
Indices: 582115--582178 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
582105 ATTTATTTCC
582115 TTTT-TCTTT-TTCTTTTTTATATATA
1 TTTTATCTTTGTTCTTTTTTATATATA
*
582140 TTTTATTATTTGTT-TTTTTTACT-TACTA
1 TTTTA-TCTTTGTTCTTTTTTA-TATA-TA
582168 TTTTATCTTTG
1 TTTTATCTTTG
582179 CTTTCTTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
25 4 0.12
27 18 0.56
28 10 0.31
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (27 bp):
TTTTATCTTTGTTCTTTTTTATATATA
Found at i:583342 original size:20 final size:20
Alignment explanation
Indices: 583317--583354 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
583307 ACCTTACTAA
583317 CTCTTTTCATTTT-TTTCCCT
1 CTCTTTT-ATTTTATTTCCCT
583337 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
583355 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (20 bp):
CTCTTTTATTTTATTTCCCT
Found at i:586865 original size:31 final size:29
Alignment explanation
Indices: 586790--586876 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 29
586780 AATCAAGAAC
586790 AAAAAAG-AAAAGAAGCAAAAAAACAAAAAA
1 AAAAAAGAAAAAG-AG-AAAAAAACAAAAAA
*
586820 AAACAAAGAAAAAAGAGAAACAATAACAAAAAT
1 AAA-AAAG-AAAAAGAGAAA-AA-AACAAAAAA
* *
586853 CAAAAAGAAAAAGGGAAAAAAACA
1 AAAAAAGAAAAAGAGAAAAAAACA
586877 CATGCAAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
29 4 0.08
30 5 0.10
31 17 0.35
32 8 0.16
33 15 0.31
ACGTcount: A:0.78, C:0.08, G:0.11, T:0.02
Consensus pattern (29 bp):
AAAAAAGAAAAAGAGAAAAAAACAAAAAA
Found at i:587659 original size:22 final size:22
Alignment explanation
Indices: 587631--587681 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
587621 CTACCCCCAT
587631 CAAACCTATGAGCATCAAATGC
1 CAAACCTATGAGCATCAAATGC
*
587653 CAAACCTGTGAGCATCAAATGC
1 CAAACCTATGAGCATCAAATGC
587675 CAAACCT
1 CAAACCT
587682 TTGACCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (22 bp):
CAAACCTATGAGCATCAAATGC
Found at i:588725 original size:106 final size:106
Alignment explanation
Indices: 588510--589864 Score: 1947
Period size: 106 Copynumber: 12.8 Consensus size: 106
588500 ATATCGTACC
* * * * * * *
588510 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * * *
588574 AATTTCGGAGCTAATTTCAACTTCACTGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
588615 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
588680 AATTTCAGATCTAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
588721 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
588786 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
588827 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
588892 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
588933 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
588998 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
589039 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGATTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
589104 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
589145 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
589210 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
589251 ACTCCAAACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
589316 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
589357 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTTAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
589422 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
589463 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* ** *
589528 AATTTCAGAGCCATTTTCAACTTCACAGCCTAGGATATTTG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
589569 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGAGACCACTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
589634 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
589675 AC-CCAAGTCAACACAAGCTCAACTTCACGACGAAGAGG-CGGCTGATTGTCAA-CAA-AA-TT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAATAAACAACTTC
* *
589734 TC-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
589775 ACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCC
** *
589839 CGGTTCCAGAGCCAATTTCAACTTCA
65 CAATTTCAGAGCCAATTTCAACTTCA
589865 TGACGGATGA
Statistics
Matches: 1129, Mismatches: 109, Indels: 23
0.90 0.09 0.02
Matches are distributed among these distances:
99 3 0.00
100 72 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 51 0.05
106 988 0.88
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:590677 original size:37 final size:37
Alignment explanation
Indices: 590615--590719 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
590605 CCTTTTTGTC
* * *
590615 CTACTATGATTCAAACTCCTAAAAATAGGATATAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * * *
590652 TTGCTAGGATTTAAACTTCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
590689 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
590720 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:591325 original size:24 final size:24
Alignment explanation
Indices: 591263--591335 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
591253 TTTTCTTTGC
591263 ATTTTTATTGTTACTATTATA-TTT
1 ATTTTTATT-TTACTATTATATTTT
*
591287 ATTATTATTTTTACTATTATATTTT
1 ATTTTTA-TTTTACTATTATATTTT
* *
591312 CTTTTTATTCTACTTATTTATATT
1 ATTTTTATTTTAC-TA-TTATATT
591336 ATATATGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 22 0.54
25 12 0.29
26 7 0.17
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (24 bp):
ATTTTTATTTTACTATTATATTTT
Found at i:591353 original size:21 final size:21
Alignment explanation
Indices: 591328--591372 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
591318 ATTCTACTTA
591328 TTTATATTATA-TATGTATATT
1 TTTATATTATATTAT-TATATT
*
591349 TTTATATTTTATTATTATATT
1 TTTATATTATATTATTATATT
591370 TTT
1 TTT
591373 TTACTTTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTATATTATATTATTATATT
Found at i:591361 original size:13 final size:13
Alignment explanation
Indices: 591277--591371 Score: 64
Period size: 13 Copynumber: 7.8 Consensus size: 13
591267 TTATTGTTAC
591277 TATTATA-TTTAT
1 TATTATATTTTAT
*
591289 TATTAT-TTTTAC
1 TATTATATTTTAT
*
591301 TATTATATTTTCT
1 TATTATATTTTAT
*
591314 T-TT-TATTCTACT
1 TATTATATTTTA-T
591326 TATT-TA---TAT
1 TATTATATTTTAT
*
591335 TA-TATATGTATAT
1 TATTATAT-TTTAT
*
591348 TTTTATATTTTAT
1 TATTATATTTTAT
591361 TATTATATTTT
1 TATTATATTTT
591372 TTTACTTTCT
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
8 1 0.02
9 5 0.08
10 2 0.03
11 5 0.08
12 20 0.31
13 27 0.42
14 5 0.08
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (13 bp):
TATTATATTTTAT
Found at i:591407 original size:11 final size:11
Alignment explanation
Indices: 591387--591432 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
591377 TTTCTCTTTC
591387 TTTT-TATTAT
1 TTTTGTATTAT
591397 TTTTGTATTAT
1 TTTTGTATTAT
*
591408 TACTTGTATTAT
1 T-TTTGTATTAT
*
591420 TTTTATATTAT
1 TTTTGTATTAT
591431 TT
1 TT
591433 ATTTTGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 4 0.13
11 17 0.55
12 10 0.32
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTGTATTAT
Found at i:591442 original size:23 final size:23
Alignment explanation
Indices: 591388--591431 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
591378 TTCTCTTTCT
*
591388 TTTTATTATTTTTGTATTATTAC
1 TTTTATTATTTTTATATTATTAC
*
591411 TTGTATTATTTTTATATTATT
1 TTTTATTATTTTTATATTATT
591432 TATTTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (23 bp):
TTTTATTATTTTTATATTATTAC
Found at i:591975 original size:33 final size:31
Alignment explanation
Indices: 591906--591977 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 31
591896 TCGTCATTTA
* *
591906 ATTTATTA-ATTTATATATATTTACTTTTTT
1 ATTTATTATATATATATATATTTACTTTGTT
591936 ATTTATTATATATATATATTATTTGTACTTTGTT
1 ATTTATTATATATATATA-TA-TT-TACTTTGTT
591970 A-TTATTAT
1 ATTTATTAT
591978 TTTGTTTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 8 0.22
31 8 0.22
32 2 0.06
33 9 0.25
34 9 0.25
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (31 bp):
ATTTATTATATATATATATATTTACTTTGTT
Found at i:600066 original size:24 final size:24
Alignment explanation
Indices: 600009--600060 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
599999 GCATTAAACA
**
600009 AACATATAGCTGAAAATGTTCAAG
1 AACATATAAATGAAAATGTTCAAG
*
600033 AACATATAAATGAAAATGTTCATG
1 AACATATAAATGAAAATGTTCAAG
600057 AACA
1 AACA
600061 ACTAAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (24 bp):
AACATATAAATGAAAATGTTCAAG
Found at i:600937 original size:15 final size:15
Alignment explanation
Indices: 600917--600945 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
600907 TAGAACAGAC
600917 GCAGTGAGCAGTTTT
1 GCAGTGAGCAGTTTT
600932 GCAGTGAGCAGTTT
1 GCAGTGAGCAGTTT
600946 CAGCAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.34, T:0.31
Consensus pattern (15 bp):
GCAGTGAGCAGTTTT
Found at i:605604 original size:93 final size:93
Alignment explanation
Indices: 605445--605637 Score: 296
Period size: 93 Copynumber: 2.1 Consensus size: 93
605435 TGACAATGAA
* * * * * *
605445 TGCTCAATCGCTCTCGTTACGGTCGATGGTACTCTAACCTGAAACTTTTAAGAATAACAACTATT
1 TGCTCAATCGCTCTCATTACAGTCGATGATACTCCAACCTAAAAATTTTAAGAATAACAACTATT
605510 ATTTTAACCATTAAAGGAATTTCGTGTG
66 ATTTTAACCATTAAAGGAATTTCGTGTG
*
605538 TGCTCAATCGCTCTTATTACAGTCGATGATACTCCAACCTAAAAATTTTAAGAATAACAACTATT
1 TGCTCAATCGCTCTCATTACAGTCGATGATACTCCAACCTAAAAATTTTAAGAATAACAACTATT
* * *
605603 ATTTTAATCGTTAAAGTAATTTCGTGTG
66 ATTTTAACCATTAAAGGAATTTCGTGTG
605631 TGCTCAA
1 TGCTCAA
605638 CCTTTACAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (93 bp):
TGCTCAATCGCTCTCATTACAGTCGATGATACTCCAACCTAAAAATTTTAAGAATAACAACTATT
ATTTTAACCATTAAAGGAATTTCGTGTG
Found at i:607174 original size:19 final size:20
Alignment explanation
Indices: 607159--607198 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
607149 TATAATTGCA
607159 AAAAAATAAAATAATTAAAT
1 AAAAAATAAAATAATTAAAT
607179 AAAAAATAAAA-AA-TAAAT
1 AAAAAATAAAATAATTAAAT
607197 AA
1 AA
607199 TACAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAAATAAAATAATTAAAT
Found at i:607189 original size:26 final size:27
Alignment explanation
Indices: 607159--607216 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
607149 TATAATTGCA
607159 AAAAAATAAAATAATTA-AATAA-AAAAT
1 AAAAAAT-AAATAA-TACAATAATAAAAT
*
607186 AAAAAATAAATAATACAATAATTAAAT
1 AAAAAATAAATAATACAATAATAAAAT
607213 AAAA
1 AAAA
607217 TACTAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 2 0.07
26 11 0.39
27 15 0.54
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (27 bp):
AAAAAATAAATAATACAATAATAAAAT
Found at i:634387 original size:99 final size:99
Alignment explanation
Indices: 634216--634415 Score: 400
Period size: 99 Copynumber: 2.0 Consensus size: 99
634206 AAGTGCGAAT
634216 CCTCAGGCGCGCTTTCAATGGGATTCTGACACGTGCTGGAAGGTGCGGATAATGATATGTGCCTT
1 CCTCAGGCGCGCTTTCAATGGGATTCTGACACGTGCTGGAAGGTGCGGATAATGATATGTGCCTT
634281 CCATTATTCCCCAAAATATCTCCTTTAATACCGC
66 CCATTATTCCCCAAAATATCTCCTTTAATACCGC
634315 CCTCAGGCGCGCTTTCAATGGGATTCTGACACGTGCTGGAAGGTGCGGATAATGATATGTGCCTT
1 CCTCAGGCGCGCTTTCAATGGGATTCTGACACGTGCTGGAAGGTGCGGATAATGATATGTGCCTT
634380 CCATTATTCCCCAAAATATCTCCTTTAATACCGC
66 CCATTATTCCCCAAAATATCTCCTTTAATACCGC
634414 CC
1 CC
634416 AATCTTCCCC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (99 bp):
CCTCAGGCGCGCTTTCAATGGGATTCTGACACGTGCTGGAAGGTGCGGATAATGATATGTGCCTT
CCATTATTCCCCAAAATATCTCCTTTAATACCGC
Found at i:635787 original size:23 final size:22
Alignment explanation
Indices: 635739--635780 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
635729 TTAATTATCG
635739 TTATATAATTAGAATATTTTAT
1 TTATATAATTAGAATATTTTAT
*
635761 TTATAATAATTA-TATATTTT
1 TTAT-ATAATTAGAATATTTT
635781 TTATTATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATATAATTAGAATATTTTAT
Found at i:638921 original size:32 final size:31
Alignment explanation
Indices: 638885--638961 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
638875 TGGGGCCGTG
*
638885 GGGCCTACCTAAGAACACATCTTAAGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAAGGCCGCA
** ** *
638917 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAAGGCCGCA
*
638948 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
638962 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAAGGCCGCA
Found at i:639853 original size:6 final size:7
Alignment explanation
Indices: 639831--639866 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
639821 GTCAAAGAAA
639831 GTCAACG
1 GTCAACG
639838 GTCAACG
1 GTCAACG
639845 GTC-ACG
1 GTCAACG
639851 GTCAA-G
1 GTCAACG
639857 GTCAACG
1 GTCAACG
639864 GTC
1 GTC
639867 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.44
7 15 0.56
ACGTcount: A:0.25, C:0.28, G:0.31, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:639853 original size:13 final size:13
Alignment explanation
Indices: 639831--639866 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
639821 GTCAAAGAAA
639831 GTCAACGGTCAACG
1 GTCAACGGTCAA-G
639845 GTC-ACGGTCAAG
1 GTCAACGGTCAAG
639857 GTCAACGGTC
1 GTCAACGGTC
639867 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 14 0.67
14 3 0.14
ACGTcount: A:0.25, C:0.28, G:0.31, T:0.17
Consensus pattern (13 bp):
GTCAACGGTCAAG
Found at i:639878 original size:17 final size:17
Alignment explanation
Indices: 639856--639913 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
639846 TCACGGTCAA
*
639856 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
639873 GGTCAACAGTAGGGTCG
1 GGTCAACAGTCGGGTCG
639890 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
639907 GGTCAAC
1 GGTCAAC
639914 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:639931 original size:19 final size:19
Alignment explanation
Indices: 639907--639957 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
639897 AGTCGGGTCG
*
639907 GGTCAACCCGGTTC-AGACC
1 GGTCAAACCGGTTCGA-ACC
639926 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
639945 GGTCAAACCGGTT
1 GGTCAAACCGGTT
639958 TTCCAGCAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 29 0.97
20 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCGAACC
Found at i:639944 original size:10 final size:10
Alignment explanation
Indices: 639909--639957 Score: 57
Period size: 9 Copynumber: 5.1 Consensus size: 10
639899 TCGGGTCGGG
*
639909 TCAACCCGGT
1 TCAAACCGGT
*
639919 TCAGACCGG-
1 TCAAACCGGT
639928 TCAAACCGGT
1 TCAAACCGGT
*
639938 TCGAACCGG-
1 TCAAACCGGT
639947 TCAAACCGGT
1 TCAAACCGGT
639957 T
1 T
639958 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:644341 original size:187 final size:187
Alignment explanation
Indices: 644018--644391 Score: 658
Period size: 187 Copynumber: 2.0 Consensus size: 187
644008 TTTTAGAATT
*
644018 CATGGTTGTTTAAACGTTTAAGACGTTTTTGAATATATACCTATATTTTATTGCTATAGTTTAGA
1 CATGATTGTTTAAACGTTTAAGACGTTTTTGAATATATACCTATATTTTATTGCTATAGTTTAGA
* *
644083 ATATAGTAAAATAGGTTTTTGTAACTCATTATATTGTTCTATTAGAAGGAGCATGATAAAGGGTA
66 ATATAGTAAAATAGGTTTTTGTAAATCATTATATTGTTCTATTAAAAGGAGCATGATAAAGGGTA
** * *
644148 TTGTTACATTAGTTAAAGGTGAGTAGCATCTTTATTTATTGATACGTTTGGGTTGAA
131 TTGTTACACGAGTTAAAGGTGAGTAGCATCTTTATTTACTAATACGTTTGGGTTGAA
644205 CATGATTGTTTAAACGTTTAAGACGTTTTTGAATATATACCTATATTTTATTGCTATAGTTTAGA
1 CATGATTGTTTAAACGTTTAAGACGTTTTTGAATATATACCTATATTTTATTGCTATAGTTTAGA
* * *
644270 ATATAGTAATATAGGTTTTTGTAAATCATTATGTTGTTCTATTAAAAGGAGCATGATAAAGGGTG
66 ATATAGTAAAATAGGTTTTTGTAAATCATTATATTGTTCTATTAAAAGGAGCATGATAAAGGGTA
644335 TTGTTACACGAGTTAAAGGTGAGTAGCATCTTTATTTACTAATACGTTTGGGTTGAA
131 TTGTTACACGAGTTAAAGGTGAGTAGCATCTTTATTTACTAATACGTTTGGGTTGAA
644392 ACAATTATAT
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
187 177 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (187 bp):
CATGATTGTTTAAACGTTTAAGACGTTTTTGAATATATACCTATATTTTATTGCTATAGTTTAGA
ATATAGTAAAATAGGTTTTTGTAAATCATTATATTGTTCTATTAAAAGGAGCATGATAAAGGGTA
TTGTTACACGAGTTAAAGGTGAGTAGCATCTTTATTTACTAATACGTTTGGGTTGAA
Found at i:646942 original size:31 final size:31
Alignment explanation
Indices: 646899--646958 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
646889 AAGAGTTTGG
* *
646899 GAGTTCCTAGTGAGAATGACATATTGAATGA
1 GAGTTCCCAGTGAGAAGGACATATTGAATGA
646930 GAGTTCCCAGTGAGAAGGACATATTGAAT
1 GAGTTCCCAGTGAGAAGGACATATTGAAT
646959 TCACCGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (31 bp):
GAGTTCCCAGTGAGAAGGACATATTGAATGA
Found at i:647808 original size:22 final size:22
Alignment explanation
Indices: 647791--647857 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
647781 CTCGTATAAA
647791 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
647813 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
647835 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
647857 T
1 T
647858 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:648118 original size:30 final size:31
Alignment explanation
Indices: 648077--648136 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
648067 TAGACATAGT
*
648077 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
648107 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
648137 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:648194 original size:29 final size:29
Alignment explanation
Indices: 648152--648221 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
648142 TTCTGCATAA
**
648152 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
648181 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
648210 TCATGTCATGTA
1 TCATGTCATGTA
648222 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:648684 original size:21 final size:21
Alignment explanation
Indices: 648654--648695 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
648644 ATTCATTTCG
* *
648654 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
648675 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
648696 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:648695 original size:67 final size:67
Alignment explanation
Indices: 648525--648674 Score: 212
Period size: 67 Copynumber: 2.2 Consensus size: 67
648515 TTTTCTCATG
* *
648525 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
*
648590 GAG
65 GAA
** * * *
648593 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
648657 AA
66 AA
648659 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
648675 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 22 0.30
67 41 0.55
68 11 0.15
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AA
Found at i:654754 original size:22 final size:22
Alignment explanation
Indices: 654737--654803 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
654727 CTCGTATAAA
654737 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
654759 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
654781 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
654803 T
1 T
654804 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:655064 original size:30 final size:31
Alignment explanation
Indices: 655023--655082 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
655013 TAGACATAGT
*
655023 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
655053 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
655083 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:655140 original size:29 final size:29
Alignment explanation
Indices: 655098--655167 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
655088 TTCTGCATAA
**
655098 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
655127 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
655156 TCATGTCATGTA
1 TCATGTCATGTA
655168 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:655565 original size:20 final size:20
Alignment explanation
Indices: 655540--655580 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
655530 ATACGATGAG
*
655540 GGGGTATCGGTTCCCCCCTT
1 GGGGTATCGATTCCCCCCTT
*
655560 GGGGTATCGATTCCCCTCTT
1 GGGGTATCGATTCCCCCCTT
655580 G
1 G
655581 CATTCTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.32, G:0.29, T:0.32
Consensus pattern (20 bp):
GGGGTATCGATTCCCCCCTT
Found at i:655588 original size:67 final size:66
Alignment explanation
Indices: 655470--655621 Score: 196
Period size: 67 Copynumber: 2.3 Consensus size: 66
655460 TTTTTCTCAT
* *
655470 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT--CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACG
655535 ATGA
63 ATGA
* ** * * *
655539 GGGGGTATCGGTTCCCCCCTTGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
655604 A
66 A
*
655605 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
655622 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
66 22 0.30
67 40 0.54
69 12 0.16
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:655631 original size:21 final size:21
Alignment explanation
Indices: 655601--655642 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
655591 ATTCATTTCG
* *
655601 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
655622 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
655643 CAACCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:657843 original size:20 final size:20
Alignment explanation
Indices: 657826--657880 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
657816 CACAAAATGT
*
657826 AAGATTATTAGTGGAAATAA
1 AAGATTATCAGTGGAAATAA
*
657846 AAGATTATCAGTGGGAATAA
1 AAGATTATCAGTGGAAATAA
657866 AAGATTATCAG-GGAA
1 AAGATTATCAGTGGAA
657881 TAGGATTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.25
Consensus pattern (20 bp):
AAGATTATCAGTGGAAATAA
Found at i:663763 original size:2 final size:2
Alignment explanation
Indices: 663756--663785 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
663746 AACAAATCTA
663756 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
663786 TAGGGATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:665584 original size:240 final size:242
Alignment explanation
Indices: 665161--665639 Score: 935
Period size: 240 Copynumber: 2.0 Consensus size: 242
665151 TACTTTAAAG
665161 GGGAAAGGGGAATTTGGCAAGGGAAACATTTGTCTCCTTATATCTTTGTAATGGTCATGAACGTT
1 GGGAAAGGGGAATTTGGCAAGGGAAACATTTGTCTCCTTATATCTTTGTAATGGTCATGAACGTT
665226 TTATCCAACCTTTCGAACCTTGGTGCTAAGGAGGGACTATTCAGATTTCACCAGAAATACAAGAG
66 TTATCCAACCTTTCGAACCTTGGTGCTAAGGAGGGACTATTCAGATTTCACCAGAAATACAAGAG
665291 GATTGATATTACACACGTCTACTTTCATTGATGATTTACTCATTTTTTTTCAAGA-GGTCGTTGG
131 GATTGATATTACACACGTCTACTTTCATTGATGATTTACTCATTTTTTTTCAAGATGGTCGTTGG
665355 ACCCTTTTTGTGGGATTAAGCGTATTCTAGATAGA-TTTATAAGTCT
196 ACCCTTTTTGTGGGATTAAGCGTATTCTAGATAGATTTTATAAGTCT
665401 GGGAAAGGGGAATTTGGCAAGGGAAACATTTGTCTCCTTATATCTTTGTAATGGTCATGAACGTT
1 GGGAAAGGGGAATTTGGCAAGGGAAACATTTGTCTCCTTATATCTTTGTAATGGTCATGAACGTT
665466 TTATCCAACCTTTCGAACCTTGGTGCTAAGGAGGGACTATTCAGATTTCACCAGAAATACAAGAG
66 TTATCCAACCTTTCGAACCTTGGTGCTAAGGAGGGACTATTCAGATTTCACCAGAAATACAAGAG
665531 GATTGATATTACACACGTCTACTTTCATTGATGATTTACTCATTTTTTTTCAAGATGGTCGTTGG
131 GATTGATATTACACACGTCTACTTTCATTGATGATTTACTCATTTTTTTTCAAGATGGTCGTTGG
*
665596 ACTCTTTTTGTGGGATTAAGCGTATTCTAGATAGATTTTATAAG
196 ACCCTTTTTGTGGGATTAAGCGTATTCTAGATAGATTTTATAAG
665640 ATGTCTGGAC
Statistics
Matches: 236, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
240 185 0.78
241 43 0.18
242 8 0.03
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (242 bp):
GGGAAAGGGGAATTTGGCAAGGGAAACATTTGTCTCCTTATATCTTTGTAATGGTCATGAACGTT
TTATCCAACCTTTCGAACCTTGGTGCTAAGGAGGGACTATTCAGATTTCACCAGAAATACAAGAG
GATTGATATTACACACGTCTACTTTCATTGATGATTTACTCATTTTTTTTCAAGATGGTCGTTGG
ACCCTTTTTGTGGGATTAAGCGTATTCTAGATAGATTTTATAAGTCT
Found at i:669415 original size:20 final size:17
Alignment explanation
Indices: 669379--669420 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
669369 AGAAAAAAAG
669379 AAAAAATATTAATATAA
1 AAAAAATATTAATATAA
669396 AAAAAATATTAATATAA
1 AAAAAATATTAATATAA
*
669413 TAAAAATA
1 AAAAAATA
669421 AAAATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATATTAATATAA
Found at i:669538 original size:96 final size:96
Alignment explanation
Indices: 669427--669614 Score: 226
Period size: 96 Copynumber: 2.0 Consensus size: 96
669417 AATAAAAATC
* * *
669427 ATTTTTAAAACTATATATTATATATGC-TTTT-AAAAAT-TGTTTTCAAACCGTATA-A-TATAT
1 ATTTTCAAAACTATATATTATATA--CATTTTCAAAAATAT-TTTCCAAA-AGTATATATTATAT
*
669487 ATATATTCAAAAGT-TGTTTTTAAAACTATATAATTT
62 ATATATTCAAAA-TAT-TTTTAAAAACTATATAATTT
* *
669523 ATTTTCAAAATTATATATTATATACATTTTCAAAAATATTTTCCAAAATTATATATTATATATAT
1 ATTTTCAAAACTATATATTATATACATTTTCAAAAATATTTTCCAAAAGTATATATTATATATAT
669588 ATTCAAAATATTTTTAAAAACTATATA
66 ATTCAAAATATTTTTAAAAACTATATA
669615 TTATATATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
94 1 0.01
95 8 0.10
96 52 0.65
97 19 0.24
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (96 bp):
ATTTTCAAAACTATATATTATATACATTTTCAAAAATATTTTCCAAAAGTATATATTATATATAT
ATTCAAAATATTTTTAAAAACTATATAATTT
Found at i:669565 original size:37 final size:36
Alignment explanation
Indices: 669522--669783 Score: 308
Period size: 37 Copynumber: 7.0 Consensus size: 36
669512 CTATATAATT
* *
669522 TATTTTCAAAATTATATATTATATACATTTTCAAAAA
1 TATTTTCAAAACTATATATTATATATATTTTC-AAAA
* *
669559 TATTTTCCAAAATTATATATTATATATATATTCAAAA
1 TATTTT-CAAAACTATATATTATATATATTTTCAAAA
*
669596 TATTTTTAAAAACTATATATTATATATATTTTTTCAAAA
1 TA-TTTTCAAAACTATATATTATATATA--TTTTCAAAA
*
669635 TGTTTTCAAAAACTATATATTATATATATGTTTTCAAAA
1 TATTTTC-AAAACTATATATTATATATA--TTTTCAAAA
* * *
669674 TATTTTCAAAACTATATAATATATATGTGTTCAAAAA
1 TATTTTCAAAACTATATATTATATATATTTTC-AAAA
* *
669711 TGTTTTCAAAACTATATATTATATATATTTTCAAAC
1 TATTTTCAAAACTATATATTATATATATTTTCAAAA
* *
669747 TGTTTTCAAAAATTATATATTATATATATGTTTCAAA
1 TATTTTC-AAAACTATATATTATATATAT-TTTCAAA
669784 CCGATTTTAA
Statistics
Matches: 199, Mismatches: 18, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
36 14 0.07
37 83 0.42
38 57 0.29
39 45 0.23
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (36 bp):
TATTTTCAAAACTATATATTATATATATTTTCAAAA
Found at i:669805 original size:39 final size:37
Alignment explanation
Indices: 669573--669805 Score: 120
Period size: 39 Copynumber: 6.2 Consensus size: 37
669563 TTCCAAAATT
* *** *
669573 ATATATTATATATATATTCAAAATATTTT-TAAAAAC
1 ATATATTATATATATTTTCAAACCGTTTTAAAAAAAC
** *
669609 TATATATTATATATATTTTTTCAAAATGTTTT-CAAAAAC
1 -ATATATTATATATA--TTTTCAAACCGTTTTAAAAAAAC
*** *
669648 TATATATTATATATATGTTTTCAAAATATTTT--CAAAAC
1 -ATATATTATATATA--TTTTCAAACCGTTTTAAAAAAAC
* ** *
669686 -TATATAATATATATGTGTTCAAAAATGTTTT--CAAAAC
1 ATATATTATATATAT-T-TTC-AAACCGTTTTAAAAAAAC
* * **
669723 TATATATTATATATATTTTCAAACTGTTTTCAAAAATT
1 -ATATATTATATATATTTTCAAACCGTTTTAAAAAAAC
669761 ATATATTATATATATGTTTCAAACCGATTTTAAAAAAAC
1 ATATATTATATATAT-TTTCAAACCG-TTTTAAAAAAAC
*
669800 CTATAT
1 ATATAT
669806 GTTTAAAAAA
Statistics
Matches: 167, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
34 1 0.01
35 1 0.01
36 24 0.14
37 47 0.28
38 18 0.11
39 76 0.46
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAACCGTTTTAAAAAAAC
Found at i:670606 original size:68 final size:68
Alignment explanation
Indices: 670469--670607 Score: 183
Period size: 68 Copynumber: 2.0 Consensus size: 68
670459 ACAGATAGCC
* * *
670469 TTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTGAATGTAATAGAAGTCAAAA
1 TTTCTCGACTTGAGCTATGTTGTAAATTTAATATGCCCTTGAGCTGAATGTAATAGAACTCAAAA
670534 GTT
66 GTT
* * *
670537 TTTCTCGACTT-AGGCTATGTTGTAATTTTAATATGCCCTTGAGTTGAATGTAATCA-AACTCGA
1 TTTCTCGACTTGA-GCTATGTTGTAAATTTAATATGCCCTTGAGCTGAATGTAAT-AGAACTCAA
*
670600 AGGTT
64 AAGTT
670605 TTT
1 TTT
670608 TGTTGACAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
67 1 0.02
68 60 0.97
69 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (68 bp):
TTTCTCGACTTGAGCTATGTTGTAAATTTAATATGCCCTTGAGCTGAATGTAATAGAACTCAAAA
GTT
Found at i:670848 original size:168 final size:169
Alignment explanation
Indices: 670567--670981 Score: 636
Period size: 168 Copynumber: 2.4 Consensus size: 169
670557 TGTAATTTTA
* * * *
670567 ATATGCCCTTGAGTTGAATGTAATCAAACTCGAAGGTTTTTTGTTGACAGATATCCCTTCTCTCC
1 ATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGG--TTTTGTTGACAGATAACCCTTCTCTCC
* * * *
670632 TTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGT
64 TTGAGCTATGCTATAAATTTGATATACCCTTGAGCTGAATGGAATCGAACTCGAAGG-TTTTTAT
670697 TGACAGATAGCCCTTCTCGCCTTGAGTTAT-CTATAAATTTG
128 TGACAGATAGCCCTTCTCGCCTTGAGTTATGCTATAAATTTG
*
670738 ATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGG-TTTGTTGACAGATAACCCTTATCTCCTT
1 ATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGGTTTTGTTGACAGATAACCCTTCTCTCCTT
* *
670802 GAGATATGCTATAAATTTGATATACCCTTGAGTTGAATGGAATCGAACTCGAAGGTTTTTATTGA
66 GAGCTATGCTATAAATTTGATATACCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTATTGA
*
670867 CAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTG
131 CAGATAGCCCTTCTCGCCTTGAGTTATGCTATAAATTTG
* * *
670906 ATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCT
1 ATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGG-TTTTGTTGACAGATAACCCTTCTCTCCT
*
670971 TAAGCTATGCT
65 TGAGCTATGCT
670982 GCGAACAGTT
Statistics
Matches: 223, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
167 36 0.16
168 121 0.54
170 33 0.15
171 33 0.15
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (169 bp):
ATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGGTTTTGTTGACAGATAACCCTTCTCTCCTT
GAGCTATGCTATAAATTTGATATACCCTTGAGCTGAATGGAATCGAACTCGAAGGTTTTTATTGA
CAGATAGCCCTTCTCGCCTTGAGTTATGCTATAAATTTG
Found at i:670982 original size:85 final size:85
Alignment explanation
Indices: 670550--670982 Score: 620
Period size: 85 Copynumber: 5.1 Consensus size: 85
670540 CTCGACTTAG
* * * * *
670550 GCTATGTTGTAATTTTAATATGCCCTTGAGTTGAATGTAATCAAACTCGAAGGTTTTTTGTTGAC
1 GCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG-TTTTTGTTGAC
* *
670615 AGATATCCCTTCTCTCCTTGA
65 AGATAGCCCTTCTCGCCTTGA
670636 GCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGTTGAC
1 GCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG-TTTTTGTTGAC
670701 AGATAGCCCTTCTCGCCTTGA
65 AGATAGCCCTTCTCGCCTTGA
* * *
670722 GTTAT-CTATAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCAAAGG--TTTGTTGACA
1 GCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACA
* * *
670784 GATAACCCTTATCTCCTTGA
66 GATAGCCCTTCTCGCCTTGA
* * * * * *
670804 GATATGCTATAAATTTGATATACCCTTGAGTTGAATGGAATCGAACTCGAAGGTTTTTATTGACA
1 GCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACA
670869 GATAGCCCTTCTCGCCTTGA
66 GATAGCCCTTCTCGCCTTGA
* * *
670889 GTTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGGTTTTTGTTGACA
1 GCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACA
*
670954 GATAGCCCTTCTCGCCTTAA
66 GATAGCCCTTCTCGCCTTGA
670974 GCTATGCTG
1 GCTATGCTG
670983 CGAACAGTTT
Statistics
Matches: 313, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
82 31 0.10
83 43 0.14
85 156 0.50
86 83 0.27
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
GCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACA
GATAGCCCTTCTCGCCTTGA
Found at i:673061 original size:21 final size:21
Alignment explanation
Indices: 673019--673061 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
673009 TTTCTGAGTT
* * *
673019 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
673040 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
673061 A
1 A
673062 CGGATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:673123 original size:67 final size:67
Alignment explanation
Indices: 673042--673191 Score: 228
Period size: 67 Copynumber: 2.2 Consensus size: 67
673032 CCCATTCAAG
*
673042 GGGAACCGATACCCCCTCAACGGATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCAG
1 GGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCAG
673107 GC
66 GC
* * * * *
673109 GGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCAG
1 GGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCAG
*
673174 GG
66 GC
*
673176 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
673192 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (67 bp):
GGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCAG
GC
Found at i:673180 original size:20 final size:20
Alignment explanation
Indices: 673155--673192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
673145 GAATGCTTGT
*
673155 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
673175 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
673193 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:673616 original size:24 final size:26
Alignment explanation
Indices: 673558--673618 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
673548 AGTTATATGA
673558 ACTATGTGATAAAGGTATGTAAATGAT
1 ACTATGTGATAAAGGTATGTAAA-GAT
673585 ATGCCTATGTGATAAAGGTATG-AAA-AT
1 A---CTATGTGATAAAGGTATGTAAAGAT
673612 ACTATGT
1 ACTATGT
673619 CTACGCGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 6 0.19
27 4 0.13
29 3 0.10
30 18 0.58
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (26 bp):
ACTATGTGATAAAGGTATGTAAAGAT
Found at i:673976 original size:149 final size:149
Alignment explanation
Indices: 673706--674009 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
673696 GGGTAGAGGG
673706 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
*
673771 ACTTGATCTATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
673836 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
673855 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
673920 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
673985 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
674004 TCTACG
1 TCTACG
674010 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:674032 original size:23 final size:23
Alignment explanation
Indices: 673988--674032 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
673978 ATTATTATAT
*
673988 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
674011 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
674033 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:680117 original size:21 final size:21
Alignment explanation
Indices: 680075--680117 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
680065 TTTCTGAGTT
* * *
680075 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
680096 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
680117 A
1 A
680118 CGGATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:680178 original size:67 final size:68
Alignment explanation
Indices: 680097--680248 Score: 234
Period size: 67 Copynumber: 2.2 Consensus size: 68
680087 ACCCATTCAA
*
680097 GGGGAACCGATACCCCCTCAACGGATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
680162 -GG
66 GGG
* * * * *
680164 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
680229 GGG
66 GGG
*
680232 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
680249 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 59 0.77
68 18 0.23
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
GGG
Found at i:680673 original size:24 final size:26
Alignment explanation
Indices: 680615--680675 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
680605 AGTTATATGA
680615 ACTATGTGATAAAGGTATGTAAATGAT
1 ACTATGTGATAAAGGTATGTAAA-GAT
680642 ATGCCTATGTGATAAAGGTATG-AAA-AT
1 A---CTATGTGATAAAGGTATGTAAAGAT
680669 ACTATGT
1 ACTATGT
680676 CTACGCGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 6 0.19
27 4 0.13
29 3 0.10
30 18 0.58
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (26 bp):
ACTATGTGATAAAGGTATGTAAAGAT
Found at i:681087 original size:23 final size:23
Alignment explanation
Indices: 681043--681087 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
681033 ATTATTATAT
*
681043 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
681066 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
681088 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:685897 original size:12 final size:13
Alignment explanation
Indices: 685880--685908 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
685870 CTTAATTGCG
685880 AAAATTAAAA-TT
1 AAAATTAAAATTT
685892 AAAATTAAAATTT
1 AAAATTAAAATTT
685905 AAAA
1 AAAA
685909 ACTTGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:690736 original size:26 final size:25
Alignment explanation
Indices: 690707--690769 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
690697 AAAGAAAGGA
*
690707 AAAAAAGAAAAAATATTAATAAAAAT
1 AAAAAACAAAAAATATTAAT-AAAAT
* *
690733 AAAAAACAAATAATATTAATATAAT
1 AAAAAACAAAAAATATTAATAAAAT
*
690758 AAAAAATAAAAA
1 AAAAAACAAAAA
690770 TCATTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (25 bp):
AAAAAACAAAAAATATTAATAAAAT
Found at i:690806 original size:38 final size:36
Alignment explanation
Indices: 690764--690870 Score: 108
Period size: 38 Copynumber: 2.8 Consensus size: 36
690754 TAATAAAAAA
* *
690764 TAAAAATCATTTTTAAAACTATATATTTTATAT-TCTTT
1 TAAAAAT--TTTTTAAAACTATATAATATATATAT-TTT
*
690802 TAAAAATTGTTTTCAAACTCATATAATATATATATTTT
1 TAAAAATT-TTTTAAAACT-ATATAATATATATATTTT
*
690840 AAAAAATTGTTTTTAAAACTATATAATATAT
1 TAAAAA-T-TTTTTAAAACTATATAATATAT
690871 TTTCAAAACT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
36 1 0.02
37 9 0.15
38 37 0.63
39 11 0.19
40 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (36 bp):
TAAAAATTTTTTAAAACTATATAATATATATATTTT
Found at i:690877 original size:59 final size:59
Alignment explanation
Indices: 690811--691027 Score: 174
Period size: 59 Copynumber: 3.5 Consensus size: 59
690801 TTAAAAATTG
**
690811 TTTTC-AAACTCATATAATATATATATTTTAAAAAAT-TGTTTTTAAAACTATATAATATA
1 TTTTCAAAACT-ATATAATATATATATTTTAAAAAATAT-TTTCCAAAACTATATAATATA
* *
690870 TTTTCAAAACTATATATTATATATATTTTCAAAAATATTTTCCAAAACTATATATTATATATA
1 TTTTCAAAACTATATAATATATATATTTTAAAAAATATTTTCCAAAAC--TATA-TA-ATATA
* * * *
690933 TTTTCAAAA-TATTTTTAA-AAACTATATTATATATATATATATTTT-CAAAACTATATGAAATA
1 TTTTCAAAACTA--TATAATATA-TATATT-T-TA-AAAAATATTTTCCAAAACTATAT--AATA
690995 TA
58 TA
*
690997 TGTTTTCAAAACTATATATTATATATATTTT
1 --TTTTCAAAACTATATAATATATATATTTT
691028 CAAACTGTTT
Statistics
Matches: 127, Mismatches: 13, Indels: 32
0.74 0.08 0.19
Matches are distributed among these distances:
59 36 0.28
60 6 0.05
61 4 0.03
62 4 0.03
63 18 0.14
64 19 0.15
65 11 0.09
66 18 0.14
67 11 0.09
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (59 bp):
TTTTCAAAACTATATAATATATATATTTTAAAAAATATTTTCCAAAACTATATAATATA
Found at i:690878 original size:21 final size:21
Alignment explanation
Indices: 690849--690891 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
690839 TAAAAAATTG
*
690849 TTTTTAAAACTATATAATATA
1 TTTTCAAAACTATATAATATA
*
690870 TTTTCAAAACTATATATTATA
1 TTTTCAAAACTATATAATATA
690891 T
1 T
690892 ATATTTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTCAAAACTATATAATATA
Found at i:690881 original size:97 final size:96
Alignment explanation
Indices: 690772--690966 Score: 245
Period size: 97 Copynumber: 2.0 Consensus size: 96
690762 AATAAAAATC
* * * *
690772 ATTTTTAAAACTATATATTTTATAT-TCTTTTAAAAAT-TGTTTTC-AAACTCATATAATATATA
1 ATTTTCAAAACTATATATTATATATAT-TTTCAAAAATAT-TTTCCAAAACT-ATATAATATATA
*
690834 TATTTTAAAAA-ATTGTTTTTAAAACTATATAATAT
63 TATTTTAAAAATA-T-TTTTAAAAACTATATAATAT
*
690869 ATTTTCAAAACTATATATTATATATATTTTCAAAAATATTTTCCAAAACTATATATTATATATAT
1 ATTTTCAAAACTATATATTATATATATTTTCAAAAATATTTTCCAAAACTATATAATATATATAT
* *
690934 TTTCAAAATATTTTTAAAAACTATATTATAT
66 TTTAAAAATATTTTTAAAAACTATATAATAT
690965 AT
1 AT
690967 ATATATATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
96 20 0.23
97 58 0.67
98 8 0.09
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (96 bp):
ATTTTCAAAACTATATATTATATATATTTTCAAAAATATTTTCCAAAACTATATAATATATATAT
TTTAAAAATATTTTTAAAAACTATATAATAT
Found at i:690899 original size:25 final size:25
Alignment explanation
Indices: 690865--691031 Score: 105
Period size: 25 Copynumber: 6.5 Consensus size: 25
690855 AAACTATATA
690865 ATATATTTTCAAAACTATATATTAT
1 ATATATTTTCAAAACTATATATTAT
* *
690890 ATATATTTTCAAAA--ATATTTTCCAAA
1 ATATATTTTCAAAACTATATATT---AT
* * *
690916 ACTATATATT--ATA-TATATTTTCA-
1 A-TATATTTTCAAAACTATATATT-AT
* *
690939 AAATATTTTTAAAAACTATATTATATATAT
1 ATATA-TTTTCAAAAC--TA-TATAT-TAT
*
690969 ATATATTTTCAAAACTATATGA-AAT
1 ATATATTTTCAAAACTATAT-ATTAT
*
690994 ATATGTTTTCAAAACTATATATTAT
1 ATATATTTTCAAAACTATATATTAT
691019 ATATATTTTCAAA
1 ATATATTTTCAAA
691032 CTGTTTTAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 32
0.70 0.09 0.20
Matches are distributed among these distances:
22 3 0.03
23 10 0.09
24 2 0.02
25 53 0.48
26 12 0.11
27 10 0.09
28 2 0.02
29 14 0.13
30 5 0.05
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (25 bp):
ATATATTTTCAAAACTATATATTAT
Found at i:690942 original size:37 final size:37
Alignment explanation
Indices: 690864--691077 Score: 185
Period size: 38 Copynumber: 5.2 Consensus size: 37
690854 AAAACTATAT
690864 AATATATTTTCAAAACTATATATTATATATATTTTCAAA
1 AATAT-TTTTCAAAACTATATATTATATATATTTTC-AA
*
690903 AATATTTTCCAAAACTATATATTATATATATTTTCAA
1 AATATTTTTCAAAACTATATATTATATATATTTTCAA
*
690940 AATATTTTTAAAAACTATATTATATATATATATATTTTCAAAACTATATGAA
1 AATATTTTTCAAAAC--TA-TATAT-TATATATATTTT-----C------AA
690992 ATATATGTTTTCAAAACTATATATTATATATATTTTCAA
1 A-ATAT-TTTTCAAAACTATATATTATATATATTTTCAA
* * **
691031 ACTGTTTTAAAAAACTATATATTATATATATGTTTCAA
1 AATATTTTTCAAAACTATATATTATATATAT-TTTCAA
*
691069 ACTATTTTT
1 AATATTTTT
691078 TTAAAAAAAA
Statistics
Matches: 147, Mismatches: 10, Indels: 37
0.76 0.05 0.19
Matches are distributed among these distances:
37 39 0.27
38 44 0.30
39 10 0.07
40 5 0.03
41 12 0.08
45 1 0.01
46 1 0.01
50 12 0.08
51 5 0.03
52 5 0.03
53 4 0.03
54 9 0.06
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (37 bp):
AATATTTTTCAAAACTATATATTATATATATTTTCAA
Found at i:691028 original size:91 final size:88
Alignment explanation
Indices: 690907--691073 Score: 255
Period size: 91 Copynumber: 1.9 Consensus size: 88
690897 TTCAAAAATA
*
690907 TTTTCCAAAACTATATATTATATATATTTTCAAAATATTTTTAAAAACTATATTATATATATATA
1 TTTTCCAAAACTATATATTATATATATTTTCAAAATATTTTAAAAAACTATA-TAT-TATATATA
*
690972 TATTTTCAAAACTATATGAAATATATG
64 T-GTTTC-AAACTATATGAAATATATG
* *
690999 TTTT-CAAAACTATATATTATATATATTTTCAAACTGTTTTAAAAAACTATATATTATATATATG
1 TTTTCCAAAACTATATATTATATATATTTTCAAAATATTTTAAAAAACTATATATTATATATATG
691063 TTTCAAACTAT
66 TTTCAAACTAT
691074 TTTTTTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
87 7 0.10
88 4 0.06
89 9 0.13
90 3 0.04
91 44 0.62
92 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (88 bp):
TTTTCCAAAACTATATATTATATATATTTTCAAAATATTTTAAAAAACTATATATTATATATATG
TTTCAAACTATATGAAATATATG
Found at i:691028 original size:129 final size:125
Alignment explanation
Indices: 690849--691077 Score: 352
Period size: 129 Copynumber: 1.8 Consensus size: 125
690839 TAAAAAATTG
* **
690849 TTTTTAAAACTATATAATATATTTTCAAAACTATATATTATATATATTTTCAAAAATATTTTCCA
1 TTTTCAAAACTATATAATATATTTTCAAAACTATATATTATATATATTTTC-AAAATATTTTAAA
690914 AAACTATATATTATATATAT-TTTCAAAATATTTTTAAAAACTATATTATATATATATATA
65 AAACTATATATTATATATATGTTTCAAAATATTTTTAAAAACTATATTATATATATATATA
* *
690974 TTTTCAAAACTATATGAAATATATGTTTTCAAAACTATATATTATATATATTTTCAAACTGTTTT
1 TTTTCAAAACTATAT--AATATA--TTTTCAAAACTATATATTATATATATTTTCAAAATATTTT
*
691039 AAAAAACTATATATTATATATATGTTTCAAACTATTTTT
62 AAAAAACTATATATTATATATATGTTTCAAAATATTTTT
691078 TTAAAAAAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
125 14 0.15
127 6 0.06
128 29 0.31
129 44 0.47
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (125 bp):
TTTTCAAAACTATATAATATATTTTCAAAACTATATATTATATATATTTTCAAAATATTTTAAAA
AACTATATATTATATATATGTTTCAAAATATTTTTAAAAACTATATTATATATATATATA
Found at i:694201 original size:3 final size:3
Alignment explanation
Indices: 694193--694246 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
694183 TAAAATTATT
* * * * *
694193 TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TAA TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
694241 TAA TAA
1 TAA TAA
694247 CATCGGGACA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:696007 original size:49 final size:50
Alignment explanation
Indices: 695910--696021 Score: 131
Period size: 49 Copynumber: 2.3 Consensus size: 50
695900 TTTGCAGTAA
* ** **
695910 AGCGCGCCCCCTGCACCGTGTATATGCTGATTTGGCGTCACGTGGGGTA-
1 AGCGCGCCCCCTGCACCGCGTATATGCTGACATGGAATCACGTGGGGTAT
695959 AG-GCGCCCCCTGCACCGCGCTATATGCTGACATGGAATACACGT-GGGTAT
1 AGCGCGCCCCCTGCACCGCG-TATATGCTGACATGGAAT-CACGTGGGGTAT
*
696009 AGCGCGGCCCCTG
1 AGCGCGCCCCCTG
696022 AGCGCGCCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
48 16 0.30
49 21 0.40
50 7 0.13
51 9 0.17
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGTATATGCTGACATGGAATCACGTGGGGTAT
Found at i:696304 original size:35 final size:34
Alignment explanation
Indices: 696219--696305 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
696209 AAAATAATTT
*
696219 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
696253 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
696291 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
696306 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:698655 original size:17 final size:18
Alignment explanation
Indices: 698614--698652 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
698604 ATTATATAAG
698614 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
698631 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
698649 TAAA
1 TAAA
698653 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:698714 original size:10 final size:10
Alignment explanation
Indices: 698691--698740 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
698681 TACCTTAAAC
* *
698691 AGAGAATATA
1 AGAGAATTTG
*
698701 AGAGTATTTG
1 AGAGAATTTG
*
698711 AGAGAAGTTG
1 AGAGAATTTG
*
698721 AGAGAAATTG
1 AGAGAATTTG
698731 AGAGAATTTG
1 AGAGAATTTG
698741 GTGTGATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:721914 original size:4 final size:4
Alignment explanation
Indices: 721905--721949 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
721895 AATTTAAATT
721905 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
721950 CTTTCAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:732162 original size:18 final size:18
Alignment explanation
Indices: 732119--732164 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
732109 TTATTTTTTT
*
732119 AAAAA-AAAAATTATTTG
1 AAAAATAAAAATAATTTG
732136 AAAATATAAAAATAATTTG
1 AAAA-ATAAAAATAATTTG
732155 AAAAATAAAA
1 AAAAATAAAA
732165 TTCCTCTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 7 0.27
19 15 0.58
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (18 bp):
AAAAATAAAAATAATTTG
Found at i:740068 original size:30 final size:28
Alignment explanation
Indices: 740013--740078 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
740003 TAAATACTCA
*
740013 TAATATTATTATTTTATATATTTAATAT
1 TAATATTATCATTTTATATATTTAATAT
*
740041 TAATA-TATCATTTTAGTATCATTTTAATAA
1 TAATATTATCATTTTA-TAT-A-TTTAATAT
*
740071 AAATATTA
1 TAATATTA
740079 ATTATTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 9 0.29
28 8 0.26
29 1 0.03
30 11 0.35
31 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (28 bp):
TAATATTATCATTTTATATATTTAATAT
Done.