Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 3 of 378
Found at i:832669 original size:6 final size:6
Alignment explanation
Indices: 832628--832669 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
832618 GAGTAGTAGT
*
832628 AGGAGT AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
1 AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC AGGAGC
832670 TGCTGAGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.50, T:0.02
Consensus pattern (6 bp):
AGGAGC
Found at i:838385 original size:31 final size:31
Alignment explanation
Indices: 838350--838416 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
838340 GAAAACTTAG
838350 TGACTTAAATAAAAAAATTCAAATAGTTCAA
1 TGACTTAAATAAAAAAATTCAAATAGTTCAA
* ** * *
838381 TGACTTAAATGAAAACTTTTAAATAGTTTAA
1 TGACTTAAATAAAAAAATTCAAATAGTTCAA
838412 TGACT
1 TGACT
838417 ATTTTATAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAAAATTCAAATAGTTCAA
Found at i:845133 original size:2 final size:2
Alignment explanation
Indices: 845126--845163 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
845116 CTCACTCAGG
*
845126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
845164 ATGCAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:847831 original size:135 final size:135
Alignment explanation
Indices: 847589--847855 Score: 507
Period size: 135 Copynumber: 2.0 Consensus size: 135
847579 ATAACCTTTC
* *
847589 ATCCGATGAAATGATATTCCAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCCT
1 ATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCCT
847654 ATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCGCCG
66 ATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCGCCG
847719 GTTAT
131 GTTAT
*
847724 ATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACTGCGCCGGCCT
1 ATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCCT
847789 ATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCGCCG
66 ATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCGCCG
847854 GT
131 GT
847856 GACTTCCCGA
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
135 129 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (135 bp):
ATCCGATGAAATGATAATCAAAATCGTGTGCCACCGTTGCCGGCAAAAGCTAACGGCGCCGGCCT
ATGCCGAGAAAATTACTTGCCCACACTGTGGCCAGGTCAATCCAATTATAAAGAAACCGTCGCCG
GTTAT
Found at i:848858 original size:18 final size:18
Alignment explanation
Indices: 848821--848859 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
848811 ATTTTCTTTA
*
848821 TTTTAAATATGAAATGTT
1 TTTTAAATATGAAATATT
848839 TTTTAAATAATGAAA-ATT
1 TTTTAAAT-ATGAAATATT
848857 TTT
1 TTT
848860 AAAACTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (18 bp):
TTTTAAATATGAAATATT
Found at i:849628 original size:45 final size:45
Alignment explanation
Indices: 849564--849653 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
849554 GCATGTCTAT
849564 GAAAGAGACAAGTAAGTATAAGACACCCTAATTCTTTTTTTTAAG
1 GAAAGAGACAAGTAAGTATAAGACACCCTAATTCTTTTTTTTAAG
*
849609 GAAAGAGACAAGTAAGTATAAGACACCCTATTTCTTTTTTTTAAG
1 GAAAGAGACAAGTAAGTATAAGACACCCTAATTCTTTTTTTTAAG
849654 TTATTTTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (45 bp):
GAAAGAGACAAGTAAGTATAAGACACCCTAATTCTTTTTTTTAAG
Found at i:849771 original size:19 final size:19
Alignment explanation
Indices: 849747--849785 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
849737 TATGAAAGTT
849747 TGTCTTATAACTATACTTA
1 TGTCTTATAACTATACTTA
849766 TGTCTTATAACTATACTTA
1 TGTCTTATAACTATACTTA
849785 T
1 T
849786 CAATAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (19 bp):
TGTCTTATAACTATACTTA
Found at i:850680 original size:2 final size:2
Alignment explanation
Indices: 850675--850703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
850665 TCTAATAACA
850675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
850704 CATGTAGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:850913 original size:2 final size:2
Alignment explanation
Indices: 850906--850946 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
850896 CCAGGTATTC
* *
850906 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AA 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
850947 ATACAATCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:851796 original size:2 final size:2
Alignment explanation
Indices: 851789--851813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
851779 ACAAAGAGGT
851789 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
851814 GCCAATAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:852349 original size:29 final size:29
Alignment explanation
Indices: 852289--852358 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
852279 TTTTTTTTGG
* * *
852289 TCACCTAATTATGAAAAGTTATAAAATAA
1 TCACCCAACTATGAAAAGTTACAAAATAA
* * *
852318 TCATCCAACTATGAAAAGTTACAAGATGA
1 TCACCCAACTATGAAAAGTTACAAAATAA
852347 TCACCCAACTAT
1 TCACCCAACTAT
852359 TCAAATTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.27
Consensus pattern (29 bp):
TCACCCAACTATGAAAAGTTACAAAATAA
Found at i:854312 original size:9 final size:9
Alignment explanation
Indices: 854298--854323 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
854288 AGCCCGCAAC
854298 ATCCACAAT
1 ATCCACAAT
854307 ATCCACAAT
1 ATCCACAAT
854316 ATCCACAA
1 ATCCACAA
854324 CCGCGACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (9 bp):
ATCCACAAT
Found at i:858397 original size:18 final size:19
Alignment explanation
Indices: 858374--858414 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
858364 GAATAGATTT
*
858374 TTAATTAAATAAATTT-AA
1 TTAATTAAAAAAATTTAAA
858392 TTAATTAAAAAAATTTAAA
1 TTAATTAAAAAAATTTAAA
858411 TTAA
1 TTAA
858415 GTACACATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAATTAAAAAAATTTAAA
Found at i:861571 original size:15 final size:15
Alignment explanation
Indices: 861551--861594 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
861541 GAGTATAGTA
861551 AAATATTAAAAATAT
1 AAATATTAAAAATAT
*
861566 AAATATTAAAAAACAT
1 AAATATT-AAAAATAT
861582 AAAT-TTAAAAATA
1 AAATATTAAAAATA
861595 ACTTAAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 6 0.23
15 9 0.35
16 11 0.42
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATTAAAAATAT
Found at i:861577 original size:16 final size:16
Alignment explanation
Indices: 861551--861592 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
861541 GAGTATAGTA
*
861551 AAATATT-AAAAATAT
1 AAATATTAAAAAACAT
861566 AAATATTAAAAAACAT
1 AAATATTAAAAAACAT
861582 AAAT-TTAAAAA
1 AAATATTAAAAA
861593 TAACTTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATTAAAAAACAT
Found at i:867110 original size:126 final size:126
Alignment explanation
Indices: 866946--867195 Score: 333
Period size: 126 Copynumber: 2.0 Consensus size: 126
866936 TTCACTTTGG
* * ** *
866946 AAATAATGAAAGGGGTTGAAGATTTCGAGATTCAAATATCGGATTTGCGGTTGTTTTTTT-AAGA
1 AAATAATGAAAGGGGTCGAAGATTTCGAGATTCAAATATCGAATTTGCAATTGTTTTTTTAAAAA
* *
867010 ATATTAGTTGGTATGAACCAAATTTTGATTACA-ACTCGTATTCGACATTCATTCTATTCCGT
66 AGATTAGTT-GTATGAACCAAACTTTGATTACATACTCGTATTCGACATTCATTCT-TTCCGT
* * * **
867072 AAATAGTGGAAGGGGTCGAAGATTTTGAGATTTGAATATCGAATTTGCAATTGTTTTTTTAAAAA
1 AAATAATGAAAGGGGTCGAAGATTTCGAGATTCAAATATCGAATTTGCAATTGTTTTTTTAAAAA
* * *
867137 AGATTAGTTGTGTGAACTAAACTTTGATTACATACTCGTATTTGACATTCATTCTTTCC
66 AGATTAGTTGTATGAACCAAACTTTGATTACATACTCGTATTCGACATTCATTCTTTCC
867196 CATGAAGGGG
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
126 75 0.70
127 32 0.30
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (126 bp):
AAATAATGAAAGGGGTCGAAGATTTCGAGATTCAAATATCGAATTTGCAATTGTTTTTTTAAAAA
AGATTAGTTGTATGAACCAAACTTTGATTACATACTCGTATTCGACATTCATTCTTTCCGT
Found at i:872048 original size:22 final size:23
Alignment explanation
Indices: 872023--872066 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
872013 GGTAGAGTGA
*
872023 TTTTATTTTTTTTCT-TTAAAAG
1 TTTTATTTTTTTTATGTTAAAAG
872045 TTTTATTTTTTTTATGTTAAAA
1 TTTTATTTTTTTTATGTTAAAA
872067 ACTGTTGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTATTTTTTTTATGTTAAAAG
Found at i:874871 original size:2 final size:2
Alignment explanation
Indices: 874864--874890 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
874854 AAGTTTCTTT
874864 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
874891 TTAAACTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:877441 original size:17 final size:17
Alignment explanation
Indices: 877419--877504 Score: 71
Period size: 17 Copynumber: 5.5 Consensus size: 17
877409 AAGCCCCCCA
877419 AAAAAAAAACCTAACCC
1 AAAAAAAAACCTAACCC
**
877436 AAAAAAAAA-C-AA-AG
1 AAAAAAAAACCTAACCC
*
877450 AAAAAAAAA--GAA---
1 AAAAAAAAACCTAACCC
* *
877462 AAAGAAAAACCTACCCC
1 AAAAAAAAACCTAACCC
877479 AAAAAAAAACCTAACCC
1 AAAAAAAAACCTAACCC
877496 AAAAAAAAA
1 AAAAAAAAA
877505 AAGAAGAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
12 8 0.14
14 12 0.21
15 2 0.04
16 1 0.02
17 33 0.59
ACGTcount: A:0.73, C:0.20, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAAAAACCTAACCC
Found at i:877455 original size:16 final size:16
Alignment explanation
Indices: 877436--877470 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
877426 AACCTAACCC
*
877436 AAAAAAAA-ACAAAGA
1 AAAAAAAAGAAAAAGA
877451 AAAAAAAAGAAAAAGA
1 AAAAAAAAGAAAAAGA
877467 AAAA
1 AAAA
877471 CCTACCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAGA
Found at i:877487 original size:18 final size:18
Alignment explanation
Indices: 877460--877505 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
877450 AAAAAAAAAG
877460 AAAAAGAAAAACCT-ACCC
1 AAAAA-AAAAACCTAACCC
*
877478 CAAAAAAAAACCTAACCC
1 AAAAAAAAAACCTAACCC
877496 AAAAAAAAAA
1 AAAAAAAAAA
877506 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.70, C:0.24, G:0.02, T:0.04
Consensus pattern (18 bp):
AAAAAAAAAACCTAACCC
Found at i:877532 original size:18 final size:17
Alignment explanation
Indices: 877460--877535 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
877450 AAAAAAAAAG
* *
877460 AAAAAGAAAAACCTACC
1 AAAAAAAAAAACCTAAC
**
877477 CCAAAAAAAAACCTAACCC
1 AAAAAAAAAAACCTAA--C
* *
877496 AAAAAAAAAAA--GAAG
1 AAAAAAAAAAACCTAAC
877511 AAAAAAGAAAAACCTAAC
1 AAAAAA-AAAAACCTAAC
877529 AAAAAAA
1 AAAAAAA
877536 GATAAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
15 6 0.14
16 5 0.11
17 15 0.34
18 8 0.18
19 10 0.23
ACGTcount: A:0.72, C:0.18, G:0.05, T:0.04
Consensus pattern (17 bp):
AAAAAAAAAAACCTAAC
Found at i:878115 original size:24 final size:24
Alignment explanation
Indices: 878038--878125 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
878028 ATTTTATATA
* * *
878038 TATTATGTATATATTTTTTAATGC
1 TATTATGTATATATTCTTAAATAC
* ** *
878062 CATTA-GTTATATATTTCTTATGTATT
1 TATTATG-TATATA-TTCTTAAATA-C
878088 TATTATGTATATATTCTTAAATAC
1 TATTATGTATATATTCTTAAATAC
*
878112 TATTATATATATAT
1 TATTATGTATATAT
878126 ATATATATAT
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
23 1 0.02
24 23 0.48
25 13 0.27
26 10 0.21
27 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (24 bp):
TATTATGTATATATTCTTAAATAC
Found at i:878243 original size:2 final size:2
Alignment explanation
Indices: 878231--878278 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
878221 TTTTATGTAC
* * *
878231 AT AT GT AT AT AT AT AT GT AT AT AT AT AT AT AC 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
878273 AT AT AT
1 AT AT AT
878279 TTGTACATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:878301 original size:13 final size:13
Alignment explanation
Indices: 878285--878326 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
878275 ATATTTGTAC
*
878285 ATATTATTATTTT
1 ATATTATTATTGT
*
878298 ATATTATTGTTGT
1 ATATTATTATTGT
*
878311 ATATTTTTA-TGT
1 ATATTATTATTGT
878323 ATAT
1 ATAT
878327 ATTTTTTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (13 bp):
ATATTATTATTGT
Found at i:878329 original size:14 final size:15
Alignment explanation
Indices: 878310--878338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
878300 ATTATTGTTG
878310 TATA-TTTTTATGTA
1 TATATTTTTTATGTA
878324 TATATTTTTTATGTA
1 TATATTTTTTATGTA
878339 CGTTTTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TATATTTTTTATGTA
Found at i:878397 original size:37 final size:37
Alignment explanation
Indices: 878355--878456 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 37
878345 CTAATATTTT
878355 CTTTTATTGTAGATATTATTATTATTATTAT-TACATA
1 CTTTTATT-TAGATATTATTATTATTATTATGTACATA
*
878392 CTTTTATTATATGCATATATATATATGTATTTTTATGTACATA
1 CTTTTATT-TA-G-ATAT-TAT-TAT-TATTATTATGTACATA
*
878435 -TTATTATTT-TATATTATTATTA
1 CTT-TTATTTAGATATTATTATTA
878457 CCAAATATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 8 0.15
40 3 0.05
41 3 0.05
42 11 0.20
43 11 0.20
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (37 bp):
CTTTTATTTAGATATTATTATTATTATTATGTACATA
Found at i:879523 original size:13 final size:14
Alignment explanation
Indices: 879490--879533 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
879480 CGAGCCAAAG
*
879490 ATTTAAAAACTAAAC
1 ATTT-AAAACTACAC
879505 ATTTAAAACTACA-
1 ATTTAAAACTACAC
879518 ATTTAAAACTACAC
1 ATTTAAAACTACAC
879532 AT
1 AT
879534 AACCTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.48
14 10 0.37
15 4 0.15
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTTAAAACTACAC
Found at i:879939 original size:30 final size:30
Alignment explanation
Indices: 879880--879944 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
879870 ATCCCAAAAA
*
879880 AAATTGTTTTTAATAGGGAAAGAAATCTTG
1 AAATTGTTTCTAATAGGGAAAGAAATCTTG
* * *
879910 GAATTGTTTCTAATAGGGAAAGGACTCTTG
1 AAATTGTTTCTAATAGGGAAAGAAATCTTG
879940 AAATT
1 AAATT
879945 TTGCCTTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (30 bp):
AAATTGTTTCTAATAGGGAAAGAAATCTTG
Found at i:886976 original size:36 final size:36
Alignment explanation
Indices: 886936--887008 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
886926 GATAAATTGG
886936 AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
1 AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
* *
886972 AATATGAATTGTAAGCTAATAATTGGGAAATTTTAC
1 AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
887008 A
1 A
887009 TTGTATATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.33
Consensus pattern (36 bp):
AATATGAAATGTAAGCAAATAATTGGGAAATTTTAC
Found at i:887511 original size:37 final size:37
Alignment explanation
Indices: 887436--887517 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
887426 TTAGTGTTGA
* * *
887436 GGCATGCTATTGGTTGGATTAGCTCCTTGGAGCATTT
1 GGCATGTTATTAGTTGGATTAGCTCCTTGAAGCATTT
* * *
887473 GGCGTGTTATTAGTTGGATTAGCT-CTTATAAGCGTTT
1 GGCATGTTATTAGTTGGATTAGCTCCTT-GAAGCATTT
887510 GGCATGTT
1 GGCATGTT
887518 TTGGTTTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
36 3 0.08
37 34 0.92
ACGTcount: A:0.17, C:0.13, G:0.29, T:0.40
Consensus pattern (37 bp):
GGCATGTTATTAGTTGGATTAGCTCCTTGAAGCATTT
Found at i:888992 original size:30 final size:30
Alignment explanation
Indices: 888933--888997 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
888923 CTATCCCAAA
888933 AAATTGTTTTTAATAGGGAAAGAAATCTTG
1 AAATTGTTTTTAATAGGGAAAGAAATCTTG
* * *
888963 GAATTGTTTTTAATAGGGAAAGGACTCTTG
1 AAATTGTTTTTAATAGGGAAAGAAATCTTG
888993 AAATT
1 AAATT
888998 TTTCCTTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (30 bp):
AAATTGTTTTTAATAGGGAAAGAAATCTTG
Found at i:891850 original size:29 final size:30
Alignment explanation
Indices: 891817--891877 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
891807 CCAAAAAAAT
*
891817 TTGTTTTTAATA-GGAAAGAAATCTTGGAA
1 TTGTTTTTAATAGGGAAAGAAATCTTGAAA
* *
891846 TTGTTTTTAATAGGGAACGGAATCTTGAAA
1 TTGTTTTTAATAGGGAAAGAAATCTTGAAA
891876 TT
1 TT
891878 TTGCCTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (30 bp):
TTGTTTTTAATAGGGAAAGAAATCTTGAAA
Found at i:892929 original size:14 final size:14
Alignment explanation
Indices: 892912--892941 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
892902 AAATTTCTTT
892912 AAAAAATATATTCA
1 AAAAAATATATTCA
892926 AAAAAATATATTCA
1 AAAAAATATATTCA
892940 AA
1 AA
892942 TACTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAATATATTCA
Found at i:898002 original size:11 final size:11
Alignment explanation
Indices: 897986--898011 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
897976 TCTTTGCCAA
897986 AGCCCGCCACG
1 AGCCCGCCACG
897997 AGCCCGCCACG
1 AGCCCGCCACG
898008 AGCC
1 AGCC
898012 TATCTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.54, G:0.27, T:0.00
Consensus pattern (11 bp):
AGCCCGCCACG
Found at i:901291 original size:31 final size:30
Alignment explanation
Indices: 901244--901302 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
901234 ATTTAGTTTC
*
901244 AATGTTAAATTAGATATTTGGATTTTTTTTT
1 AATGTTAAATTAGATATTT-AATTTTTTTTT
* *
901275 AATGTTTAATTTGATATTTAATTTTTTT
1 AATGTTAAATTAGATATTTAATTTTTTT
901303 ATCCTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (30 bp):
AATGTTAAATTAGATATTTAATTTTTTTTT
Found at i:901441 original size:30 final size:31
Alignment explanation
Indices: 901375--901447 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
901365 TGCCATTTGG
* *
901375 TTTAGATATCAAATTAAATATTAAAGCGAAA
1 TTTAAATATCAAATTAAATATTAAAACGAAA
* * **
901406 CTTAAATATC-AATTGAATATTAAAATTAAA
1 TTTAAATATCAAATTAAATATTAAAACGAAA
901436 TTTAAATA-CAAA
1 TTTAAATATCAAA
901448 ATGATATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 1 0.03
30 25 0.74
31 8 0.24
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (31 bp):
TTTAAATATCAAATTAAATATTAAAACGAAA
Found at i:901819 original size:10 final size:10
Alignment explanation
Indices: 901804--901841 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
901794 AGAGTAAAAA
901804 ATTTTCTTTC
1 ATTTTCTTTC
*
901814 ATTTTCCTTC
1 ATTTTCTTTC
901824 ATTTTCTTTC
1 ATTTTCTTTC
*
901834 GTTTTCTT
1 ATTTTCTT
901842 CTCTCTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (10 bp):
ATTTTCTTTC
Found at i:903180 original size:41 final size:41
Alignment explanation
Indices: 903130--903215 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
903120 ACACTCAATT
903130 TATT-CTATTAATAAAATCATAAAAAATTCAAACATAATAA
1 TATTACTATTAATAAAATCATAAAAAATTCAAACATAATAA
*
903170 TATTACTATTAATAAAATCATGAAAAATTCAAACATAATAA
1 TATTACTATTAATAAAATCATAAAAAATTCAAACATAATAA
903211 TATTA
1 TATTA
903216 GCAATTCAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (41 bp):
TATTACTATTAATAAAATCATAAAAAATTCAAACATAATAA
Found at i:913828 original size:18 final size:18
Alignment explanation
Indices: 913802--913851 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
913792 ATAAGGTATC
*
913802 ATATAAAAATTAAGAAAT
1 ATATTAAAATTAAGAAAT
* **
913820 ATATTAAAAATATTAAAT
1 ATATTAAAATTAAGAAAT
913838 ATATTAAAAATTAA
1 ATATT-AAAATTAA
913852 AAAAATAACA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
ATATTAAAATTAAGAAAT
Found at i:913834 original size:9 final size:9
Alignment explanation
Indices: 913820--913888 Score: 56
Period size: 9 Copynumber: 8.0 Consensus size: 9
913810 ATTAAGAAAT
913820 ATATTAAAA
1 ATATTAAAA
*
913829 ATATTAAAT
1 ATATTAAAA
913838 ATATT-AAA
1 ATATTAAAA
913846 A-ATTAAAA
1 ATATTAAAA
* *
913854 A-AATAACA
1 ATATTAAAA
*
913862 TTATTTAAAA
1 ATA-TTAAAA
*
913872 AAATTAAAA
1 ATATTAAAA
913881 ATA-TAAAA
1 ATATTAAAA
913889 TACTTGTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.06
8 17 0.36
9 22 0.47
10 5 0.11
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (9 bp):
ATATTAAAA
Found at i:919763 original size:13 final size:13
Alignment explanation
Indices: 919745--919769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
919735 TAATAATTGG
919745 ACTTGATTTTTGA
1 ACTTGATTTTTGA
919758 ACTTGATTTTTG
1 ACTTGATTTTTG
919770 TTTTGCCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
ACTTGATTTTTGA
Found at i:924350 original size:27 final size:26
Alignment explanation
Indices: 924313--924424 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
924303 ATCATGGCTG
* *
924313 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
924339 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
924367 CCAGAATAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
924394 CTAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
924421 CCAG
1 CCAG
924425 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.07
27 52 0.70
28 17 0.23
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:924372 original size:54 final size:54
Alignment explanation
Indices: 924313--924424 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
924303 ATCATGGCTG
*
924313 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * * *
924367 CCAGAATAGATATATGTGGCAGAGCCACTAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
924421 CCAG
1 CCAG
924425 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:924833 original size:8 final size:8
Alignment explanation
Indices: 924817--924846 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
924807 CTCAAAATAC
924817 CGGCTTTT
1 CGGCTTTT
*
924825 CGGCATTT
1 CGGCTTTT
924833 CGGCTTTT
1 CGGCTTTT
924841 CGGCTT
1 CGGCTT
924847 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:929686 original size:2 final size:2
Alignment explanation
Indices: 929679--929706 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
929669 GTACCTAAAT
929679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
929707 CATAAACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:930621 original size:8 final size:8
Alignment explanation
Indices: 930594--930637 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
930584 GGAGGTTAAG
930594 TTTTTTT-
1 TTTTTTTA
930601 TTTTTCTTCA
1 TTTTT-TT-A
930611 TTTTTTTA
1 TTTTTTTA
930619 TTTTTTTA
1 TTTTTTTA
930627 -TTTTTTA
1 TTTTTTTA
930634 TTTT
1 TTTT
930638 GGGTTGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 12 0.36
8 14 0.42
9 2 0.06
10 5 0.15
ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTA
Found at i:940853 original size:27 final size:27
Alignment explanation
Indices: 940815--940927 Score: 124
Period size: 27 Copynumber: 4.2 Consensus size: 27
940805 AGCATGGCTG
* *
940815 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
940841 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
*
940869 CCAGA-ACAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
940896 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
940923 CCAGA
1 CCAGA
940928 ACGCTTCCTC
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
26 5 0.06
27 56 0.73
28 16 0.21
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:940879 original size:54 final size:54
Alignment explanation
Indices: 940815--940929 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
940805 AGCATGGCTG
* *
940815 CCAGAACAGATA-ATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
940869 CCAGAACAGATATTTGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
940923 CCAGAAC
1 CCAGAAC
940930 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:942636 original size:25 final size:25
Alignment explanation
Indices: 942542--942675 Score: 223
Period size: 26 Copynumber: 5.2 Consensus size: 25
942532 CATGAAATTC
*
942542 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCTA
*
942568 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCTA
942594 TTATCATGGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
942620 TTATCATGAACATTTACCTAACCTA
1 TTATCATGAACATTTACCTAACCTA
942645 TTATCATGAACATTTACCTAACCTA
1 TTATCATGAACATTTACCTAACCTA
942670 TTATCA
1 TTATCA
942676 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
25 49 0.46
26 56 0.53
27 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCTA
Found at i:942679 original size:20 final size:22
Alignment explanation
Indices: 942551--942676 Score: 108
Period size: 25 Copynumber: 5.1 Consensus size: 22
942541 CTTATCATGA
*
942551 AACATTTACCTAACCCATTATC
1 AACATTTACCTAACCTATTATC
*
942573 ATGAAACATTTACCTAACCCATTATC
1 ----AACATTTACCTAACCTATTATC
942599 ATGGAACATTTACCTAACCTATTATC
1 ----AACATTTACCTAACCTATTATC
942625 ATGAACATTTACCTAACCTATTATC
1 ---AACATTTACCTAACCTATTATC
942650 ATGAACATTTACCTAACCTATTATC
1 ---AACATTTACCTAACCTATTATC
942675 AA
1 AA
942677 TTTGTATCAA
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
22 2 0.02
25 48 0.50
26 46 0.48
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.33
Consensus pattern (22 bp):
AACATTTACCTAACCTATTATC
Found at i:946655 original size:26 final size:26
Alignment explanation
Indices: 946626--946739 Score: 138
Period size: 27 Copynumber: 4.3 Consensus size: 26
946616 AGCATGGCTG
* *
946626 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
946652 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
946680 CCAGAACAGATATTGTGGCAGAGCCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* * *
946706 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
946733 CCAGAAC
1 CCAGAAC
946740 GCTTCCTCCA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
26 28 0.36
27 34 0.44
28 15 0.19
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:946690 original size:54 final size:53
Alignment explanation
Indices: 946626--946739 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 53
946616 AGCATGGCTG
* *
946626 CCAGAACAGATAATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
946680 CCAGAACAGATATTGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
946733 CCAGAAC
1 CCAGAAC
946740 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 24 0.45
54 29 0.55
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (53 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:946731 original size:27 final size:26
Alignment explanation
Indices: 946626--946737 Score: 125
Period size: 26 Copynumber: 4.2 Consensus size: 26
946616 AGCATGGCTG
* * * *
946626 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGATCAGATATTGTGGCAGAGCCA
* *
946652 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAT-CAGAT-ATTGTGGCAGAGCCA
*
946680 CCAGAACAGATATTGTGGCAGAGCCA
1 CCAGATCAGATATTGTGGCAGAGCCA
*
946706 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGATCAGATA-TTGTGGCAGAGCCA
946733 CCAGA
1 CCAGA
946738 ACGCTTCCTC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
26 30 0.42
27 26 0.36
28 16 0.22
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (26 bp):
CCAGATCAGATATTGTGGCAGAGCCA
Found at i:948389 original size:26 final size:26
Alignment explanation
Indices: 948353--948462 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
948343 CATGAAATTC
948353 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
948379 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
948405 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
948431 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
948457 TTATCA
1 TTATCA
948463 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:960013 original size:31 final size:31
Alignment explanation
Indices: 959978--960073 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 31
959968 TTTCCTTCTC
* * * *
959978 AACGAATCCGATTTGATGTTAGATACGAATT
1 AACGAATCCGAGTCGACGTTAGATACGGATT
*
960009 AACGAATCCGAGCCGACGTTAGATACGGATT
1 AACGAATCCGAGTCGACGTTAGATACGGATT
* *
960040 AACAAATCAGAGTCGACGTTAGATACGGATT
1 AACGAATCCGAGTCGACGTTAGATACGGATT
960071 AAC
1 AAC
960074 ATAAAACATA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (31 bp):
AACGAATCCGAGTCGACGTTAGATACGGATT
Found at i:964085 original size:47 final size:49
Alignment explanation
Indices: 963868--964170 Score: 449
Period size: 49 Copynumber: 6.3 Consensus size: 49
963858 GTATGAGATA
963868 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
963917 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
963966 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
964015 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG-AAG-GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * *
964062 TATATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * * * * *
964109 TATATATGTGATAGGGCCGAGTGGCCAACT-TGATGGATGTGGAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGA-TGTGATGAATGTGAAAGTGTG
*
964156 TATAAATGTGATAAG
1 TATATATGTGATAAG
964171 TCCCGAAGGG
Statistics
Matches: 240, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
47 97 0.40
48 6 0.03
49 137 0.57
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:966543 original size:29 final size:29
Alignment explanation
Indices: 966511--966572 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
966501 ATATTTATAC
966511 TTTAATTAAATCC-TAAATTATTTAATTAA
1 TTTAATTAAA-CCATAAATTATTTAATTAA
* * *
966540 TTTAATTTAACCATAATTTATTTACTTAA
1 TTTAATTAAACCATAAATTATTTAATTAA
966569 TTTA
1 TTTA
966573 TCATTATTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAATTAAACCATAAATTATTTAATTAA
Found at i:968650 original size:32 final size:32
Alignment explanation
Indices: 968614--968674 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
968604 TGCATTTTAA
968614 CATTTTAATAGTTAATGGATGATGGGCATTAG
1 CATTTTAATAGTTAATGGATGATGGGCATTAG
968646 CATTTTAATAGTTAATGGATGATGGGCAT
1 CATTTTAATAGTTAATGGATGATGGGCAT
968675 GGTAAGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.38
Consensus pattern (32 bp):
CATTTTAATAGTTAATGGATGATGGGCATTAG
Found at i:970187 original size:26 final size:26
Alignment explanation
Indices: 970157--970209 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
970147 TTTATAGTTT
*
970157 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCCAAA
*
970183 TACCCCTAGGGTTAAATTGACCCAAA
1 TACCCCTAGGGATAAATTGACCCAAA
970209 T
1 T
970210 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCCAAA
Found at i:973099 original size:24 final size:25
Alignment explanation
Indices: 973044--973099 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
973034 TTGGTGCCGA
*
973044 TTTCTTCTTCCTTTCTTTTTCCTTC
1 TTTCTTCTTCCTTCCTTTTTCCTTC
* * *
973069 ATT-TTCTTTCTTCCTTTTTGCTT-
1 TTTCTTCTTCCTTCCTTTTTCCTTC
973092 TTTCTTCT
1 TTTCTTCT
973100 AGCCAAAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 21 0.84
25 2 0.08
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTCTTCTTCCTTCCTTTTTCCTTC
Found at i:974499 original size:65 final size:65
Alignment explanation
Indices: 974395--974525 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
974385 CCCCTAGGGT
974395 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
*
974460 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
974525 T
1 T
974526 GCATGGGACT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (65 bp):
TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
Found at i:980792 original size:39 final size:39
Alignment explanation
Indices: 980738--980900 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
980728 TGTGTATGAA
*
980738 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
980777 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
980816 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
980855 TGTGCGAGTTGTGATATTCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
980895 TGTGCG
1 TGTGCG
980901 GGTTACCATA
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 96 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:980925 original size:40 final size:39
Alignment explanation
Indices: 980738--980931 Score: 244
Period size: 39 Copynumber: 4.9 Consensus size: 39
980728 TGTGTATGAA
* *
980738 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
980777 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
980816 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * * *
980855 TGTGCGAGTTGTGATATTCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
980895 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGC
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGC
980932 GTTTGAACGA
Statistics
Matches: 136, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 96 0.71
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:983969 original size:46 final size:46
Alignment explanation
Indices: 983909--984178 Score: 443
Period size: 46 Copynumber: 5.9 Consensus size: 46
983899 TTTGACATGA
* * * * * * *
983909 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
*
983955 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
984001 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
984047 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
984093 TGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
984139 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
984179 CCAGAGAGCA
Statistics
Matches: 214, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 4 0.02
46 210 0.98
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:986660 original size:30 final size:30
Alignment explanation
Indices: 986604--986671 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
986594 CACCCTTAAA
* *
986604 ATATTTGCACTATTAGTCCTTCAATTTTTC
1 ATATTTACACTATTAATCCTTCAATTTTTC
* *
986634 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAATTTTTC
986663 AGTATTTAC
1 A-TATTTAC
986672 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAATTTTTC
Found at i:988117 original size:3 final size:3
Alignment explanation
Indices: 988109--988142 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
988099 AGATATTTAC
988109 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
988143 CAAATAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:988384 original size:26 final size:26
Alignment explanation
Indices: 988336--988385 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
988326 GAAACAGAGG
* *
988336 AGAAACAAAATAGAAAGAAAGAAAGA
1 AGAAACAAAAAAGAAAAAAAGAAAGA
988362 AGAAA-AAAAAAGAAAAAAGAGAAA
1 AGAAACAAAAAAGAAAAAA-AGAAA
988386 TTAAGGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (26 bp):
AGAAACAAAAAAGAAAAAAAGAAAGA
Found at i:995143 original size:18 final size:18
Alignment explanation
Indices: 995105--995144 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
995095 GATAAAATGA
*
995105 TTTTTATGAAAATGATAG
1 TTTTTATGAAAATAATAG
* *
995123 TTTTTCTGAAAATAATTG
1 TTTTTATGAAAATAATAG
995141 TTTT
1 TTTT
995145 CAAGGAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (18 bp):
TTTTTATGAAAATAATAG
Found at i:997113 original size:39 final size:39
Alignment explanation
Indices: 997029--997181 Score: 225
Period size: 39 Copynumber: 3.9 Consensus size: 39
997019 TATGGTAACC
** * *
997029 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
997069 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
997108 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
997147 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
997182 TCGAACATTA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 88 0.85
40 15 0.15
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:997154 original size:78 final size:79
Alignment explanation
Indices: 997010--997180 Score: 272
Period size: 78 Copynumber: 2.2 Consensus size: 79
997000 CCCCGGGACA
* **
997010 TAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACA
1 TAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACA
997075 ATTGCCTTCGGGCT
66 ATTGCCTTCGGGCT
* ** *
997089 TAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATTTGCACA
1 TAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACA
997153 ATTGCCTTCGGGCT
66 ATTGCCTTCGGGCT
997167 TAGCCCGGATATCA
1 TAGCCCGGATATCA
997181 CTCGAACATT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 54 0.64
79 31 0.36
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (79 bp):
TAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACA
ATTGCCTTCGGGCT
Found at i:999282 original size:78 final size:78
Alignment explanation
Indices: 999150--999295 Score: 247
Period size: 78 Copynumber: 1.9 Consensus size: 78
999140 CAGAGTGTGG
* * * *
999150 ATGGGCCAACTTCTGGCTTCGCTGATGAGATTGCAGCTTCTCCAGAATCAGAAGTAGAAGTTTCT
1 ATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCAGAAGTAGAAATTGCT
999215 ACTAAATTTATCA
66 ACTAAATTTATCA
*
999228 ATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCGGAAGTAGAAATTGCT
1 ATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCAGAAGTAGAAATTGCT
999293 ACT
66 ACT
999296 GAATCTACCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (78 bp):
ATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCAGAAGTAGAAATTGCT
ACTAAATTTATCA
Found at i:1001658 original size:78 final size:78
Alignment explanation
Indices: 1001522--1001672 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
1001512 CCAAAGTGTG
*
1001522 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1001587 TACTGAATATGCC
66 TACTGAATATGCC
* *
1001600 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCTGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1001665 TACTGAAT
66 TACTGAAT
1001673 CTATTGGCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (78 bp):
GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Found at i:1004041 original size:78 final size:78
Alignment explanation
Indices: 1003905--1004055 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
1003895 CCAAAGTGTG
* *
1003905 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAAAATCGGAAGTAGAAGTTGC
1003970 TACTGAATATGCC
66 TACTGAATATGCC
* *
1003983 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAAAATCTGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAAAATCGGAAGTAGAAGTTGC
1004048 TACTGAAT
66 TACTGAAT
1004056 CTACCGGCGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (78 bp):
GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAAAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Found at i:1006488 original size:12 final size:12
Alignment explanation
Indices: 1006471--1006504 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1006461 CTGTGTACCA
1006471 CTACTGTTACTG
1 CTACTGTTACTG
1006483 CTACTGTTACTG
1 CTACTGTTACTG
* *
1006495 TTACCGTTAC
1 CTACTGTTAC
1006505 GGTGTATTCC
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:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (12 bp):
CTACTGTTACTG
Found at i:1006635 original size:18 final size:18
Alignment explanation
Indices: 1006612--1006655 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1006602 TAAATAAAGG
1006612 TACTGAATAATTAACTGC
1 TACTGAATAATTAACTGC
* * *
1006630 TACTGAATATTTGACTGT
1 TACTGAATAATTAACTGC
1006648 TACTGAAT
1 TACTGAAT
1006656 TACTGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
TACTGAATAATTAACTGC
Found at i:1008847 original size:78 final size:78
Alignment explanation
Indices: 1008711--1008861 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
1008701 CCAAAGTGTG
*
1008711 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1008776 TACTGAATATGCC
66 TACTGAATATGCC
* *
1008789 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCTGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1008854 TACTGAAT
66 TACTGAAT
1008862 CTACTGGCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (78 bp):
GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Found at i:1011294 original size:12 final size:12
Alignment explanation
Indices: 1011277--1011310 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1011267 CTGTGTACCA
1011277 CTACTGTTACTG
1 CTACTGTTACTG
1011289 CTACTGTTACTG
1 CTACTGTTACTG
* *
1011301 TTACCGTTAC
1 CTACTGTTAC
1011311 GGTGTATTCC
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:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (12 bp):
CTACTGTTACTG
Found at i:1011441 original size:18 final size:18
Alignment explanation
Indices: 1011418--1011461 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1011408 TAAATAAAGG
1011418 TACTGAATAATTAACTGC
1 TACTGAATAATTAACTGC
* * *
1011436 TACTGAATATTTGACTGT
1 TACTGAATAATTAACTGC
1011454 TACTGAAT
1 TACTGAAT
1011462 TACTGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
TACTGAATAATTAACTGC
Found at i:1013653 original size:78 final size:78
Alignment explanation
Indices: 1013517--1013667 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
1013507 CCAAAGTGTG
*
1013517 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1013582 TACTGAATATGCC
66 TACTGAATATGCC
* *
1013595 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCTGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1013660 TACTGAAT
66 TACTGAAT
1013668 CTACTGGCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (78 bp):
GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Found at i:1017215 original size:24 final size:24
Alignment explanation
Indices: 1017173--1017220 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1017163 TTATCTAATT
* *
1017173 AACTTAATTTAATCATAATTAAAA
1 AACTTAATCTAATCATAATCAAAA
1017197 AACTTAATCT-ATCATTAATCAAAA
1 AACTTAATCTAATCA-TAATCAAAA
1017221 TAAGTGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (24 bp):
AACTTAATCTAATCATAATCAAAA
Found at i:1017880 original size:17 final size:16
Alignment explanation
Indices: 1017860--1017892 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1017850 TATTTTATAT
1017860 TAATTAAATAAAGTAAA
1 TAATTAAATAAA-TAAA
1017877 TAATTAAATAAATAAA
1 TAATTAAATAAATAAA
1017893 AGAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAATTAAATAAATAAA
Found at i:1017949 original size:19 final size:19
Alignment explanation
Indices: 1017921--1017959 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1017911 TGATATATGG
*
1017921 ATACATATGTACT-AATAAT
1 ATACACATGTA-TAAATAAT
1017940 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
1017959 A
1 A
1017960 AATAAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:1018075 original size:4 final size:4
Alignment explanation
Indices: 1018066--1018095 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1018056 AAAAATAGAG
1018066 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1018096 AGGGAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1021511 original size:78 final size:78
Alignment explanation
Indices: 1021375--1021525 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
1021365 CCAAAGTGTA
*
1021375 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1021440 TACTGAATATGCC
66 TACTGAATATGCC
* *
1021453 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCTGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1021518 TACTGAAT
66 TACTGAAT
1021526 CTACTGCGGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (78 bp):
GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Found at i:1025068 original size:24 final size:24
Alignment explanation
Indices: 1025026--1025073 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1025016 TTATCTAATT
* *
1025026 AACTTAATTTAATCATAATTAAAA
1 AACTTAATCTAATCATAATCAAAA
1025050 AACTTAATCT-ATCATTAATCAAAA
1 AACTTAATCTAATCA-TAATCAAAA
1025074 TAAGTGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (24 bp):
AACTTAATCTAATCATAATCAAAA
Found at i:1025733 original size:17 final size:16
Alignment explanation
Indices: 1025713--1025745 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1025703 TATTTTATAT
1025713 TAATTAAATAAAGTAAA
1 TAATTAAATAAA-TAAA
1025730 TAATTAAATAAATAAA
1 TAATTAAATAAATAAA
1025746 AGAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAATTAAATAAATAAA
Found at i:1025802 original size:19 final size:19
Alignment explanation
Indices: 1025774--1025812 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1025764 TGATATATGG
*
1025774 ATACATATGTACT-AATAAT
1 ATACACATGTA-TAAATAAT
1025793 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
1025812 A
1 A
1025813 AATAAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:1026995 original size:6 final size:6
Alignment explanation
Indices: 1026984--1027009 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1026974 ACTCCGTACC
1026984 TTACTG TTACTG TTACTG TTACTG TT
1 TTACTG TTACTG TTACTG TTACTG TT
1027010 CCGGATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (6 bp):
TTACTG
Found at i:1027006 original size:57 final size:59
Alignment explanation
Indices: 1026939--1027069 Score: 160
Period size: 57 Copynumber: 2.2 Consensus size: 59
1026929 AAGTGCCGCC
* * * *
1026939 TTACTATTACTGTTCTGGATTCATTCCGAAT-AGGTACTC-CGTACC-TTACTGTTACTG
1 TTACTGTTACTGTTCCGGATTCATTCCG-ATGAGGTACTCGCGTACCACTACTGTTACTA
* *
1026996 TTACTGTTACTGTTCCGGATTTATTCCGATGAGGTACTCTGTGTACCACTACTGTTACTA
1 TTACTGTTACTGTTCCGGATTCATTCCGATGAGGTACTC-GCGTACCACTACTGTTACTA
*
1027056 CTACTGTTACTGTT
1 TTACTGTTACTGTT
1027070 ACCGTTACGG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 2 0.03
57 33 0.52
59 5 0.08
60 23 0.37
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (59 bp):
TTACTGTTACTGTTCCGGATTCATTCCGATGAGGTACTCGCGTACCACTACTGTTACTA
Found at i:1029397 original size:78 final size:78
Alignment explanation
Indices: 1029261--1029411 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
1029251 CCAAAGTGTG
*
1029261 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1029326 TACTGAATATGCC
66 TACTGAATATGCC
* *
1029339 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCTGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1029404 TACTGAAT
66 TACTGAAT
1029412 CTACTGGCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (78 bp):
GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Found at i:1032141 original size:31 final size:26
Alignment explanation
Indices: 1032074--1032183 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
1032064 TGATACAAAT
1032074 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1032100 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
1032126 TGATAAT-GGATTAGGTAAATGTTTCA
1 TGATAATAGG-TTAGGTAAATGTTCCA
* *
1032152 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1032178 TGATAA
1 TGATAA
1032184 GAATTTCATG
Statistics
Matches: 81, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
25 2 0.02
26 77 0.95
27 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:1035294 original size:27 final size:27
Alignment explanation
Indices: 1035270--1035502 Score: 297
Period size: 27 Copynumber: 8.6 Consensus size: 27
1035260 TTAGTTTACC
* **
1035270 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
1035297 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
1035324 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
1035351 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
1035378 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
1035405 AAATTATCAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
1035432 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
1035459 AAATTACTAAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*
1035486 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
1035503 TGATTTACAG
Statistics
Matches: 181, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
26 4 0.02
27 175 0.97
28 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:1035550 original size:27 final size:27
Alignment explanation
Indices: 1035498--1035716 Score: 343
Period size: 27 Copynumber: 8.2 Consensus size: 27
1035488 ATTACCAAAG
* *
1035498 TACCCT-GATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
1035524 TACCCTCGACTTACAAAATTATTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
1035551 TACCCTCGATTTAAAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
1035578 T-CCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
1035604 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
1035631 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
1035658 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* **
1035685 TACCCTCGATTTATAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTT
1035712 TACCC
1 TACCC
1035717 CTAGGGTGTT
Statistics
Matches: 180, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
26 31 0.17
27 149 0.83
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:1035556 original size:80 final size:81
Alignment explanation
Indices: 1035471--1035716 Score: 307
Period size: 80 Copynumber: 3.1 Consensus size: 81
1035461 ATTACTAAAA
* ** ** * *
1035471 TACCCTCGACTTGTAAAATTACCAAAGTACCCT-GATTTACAGAATTACCGTTTTACCCTCGACT
1 TACCCTCGATTTAAAAAATTACCAATTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
*
1035535 TACAAAATTATTGTTT
66 TACAAAATTACTGTTT
** * *
1035551 TACCCTCGATTTAAAAAATTA-CTGTTTTCCCTCGATTTACAAAATTACTGTTTTACCCTCGATT
1 TACCCTCGATTTAAAAAATTACCAATTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
1035615 TACAAAATTACTGTTT
66 TACAAAATTACTGTTT
* ***
1035631 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
1 TACCCTCGATTTAAAAAATTACCAATTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
* **
1035696 TATAAAATTACCATTT
66 TACAAAATTACTGTTT
1035712 TACCC
1 TACCC
1035717 CTAGGGTGTT
Statistics
Matches: 143, Mismatches: 21, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
79 6 0.04
80 81 0.57
81 56 0.39
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTAAAAAATTACCAATTTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATT
TACAAAATTACTGTTT
Found at i:1035997 original size:27 final size:26
Alignment explanation
Indices: 1035953--1036003 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1035943 CTCGCTGCAA
*
1035953 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
1035980 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
1036004 AGCAACCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:1036256 original size:31 final size:31
Alignment explanation
Indices: 1036221--1036318 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
1036211 TTGCATTCAC
* * *
1036221 ATTCTGATTTTGATTATGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
* * *
1036252 ATTCTGATTCTAATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACCTGATTCTG
1036283 ATTCTGATTCTGATTCTGATT--CTGATTCTG
1 ATTCTGATTCTGATTCTG-TTACCTGATTCTG
1036313 ATTCTG
1 ATTCTG
1036319 TCACCTGATT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
30 14 0.25
31 42 0.74
32 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTTACCTGATTCTG
Found at i:1036260 original size:6 final size:6
Alignment explanation
Indices: 1036221--1036354 Score: 112
Period size: 6 Copynumber: 21.8 Consensus size: 6
1036211 TTGCATTCAC
* * * *
1036221 ATTCTG ATTTTG ATTATG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
1036270 -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
1036319 -TCACCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
1036355 AGTTTTGATA
Statistics
Matches: 102, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
5 4 0.04
6 88 0.86
7 7 0.07
8 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:1036304 original size:49 final size:49
Alignment explanation
Indices: 1036243--1036354 Score: 179
Period size: 49 Copynumber: 2.3 Consensus size: 49
1036233 ATTATGTTAC
*
1036243 CTGATACTGATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATT
1 CTGATTCTGATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATT
* *
1036292 CTGATTCTGATTCTGATTCTGATTCTGTCACCTGATTCTGATTCTGATT
1 CTGATTCTGATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATT
* *
1036341 CTCATTTTGATTCT
1 CTGATTCTGATTCT
1036355 AGTTTTGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (49 bp):
CTGATTCTGATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATT
Found at i:1038491 original size:25 final size:27
Alignment explanation
Indices: 1038454--1038507 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1038444 TCAAACATGC
1038454 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
1038480 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
1038506 AT
1 AT
1038508 AACTGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:1046878 original size:24 final size:24
Alignment explanation
Indices: 1046836--1046883 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1046826 TTATCTAATT
* *
1046836 AACTTAATTTAATCATAATTAAAA
1 AACTTAATCTAATCATAATCAAAA
1046860 AACTTAATCT-ATCATTAATCAAAA
1 AACTTAATCTAATCA-TAATCAAAA
1046884 TAAGTGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (24 bp):
AACTTAATCTAATCATAATCAAAA
Found at i:1047608 original size:19 final size:19
Alignment explanation
Indices: 1047580--1047618 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1047570 TGATATATGG
*
1047580 ATACATATGTACT-AATAAT
1 ATACACATGTA-TAAATAAT
1047599 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
1047618 A
1 A
1047619 AATAAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:1049013 original size:18 final size:18
Alignment explanation
Indices: 1048972--1049015 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1048962 TAAATAAAGG
1048972 TACTGAATAATTGACTGC
1 TACTGAATAATTGACTGC
* * * *
1048990 TGCTGAATATTTTACTGT
1 TACTGAATAATTGACTGC
1049008 TACTGAAT
1 TACTGAAT
1049016 TACTGATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (18 bp):
TACTGAATAATTGACTGC
Found at i:1049988 original size:28 final size:28
Alignment explanation
Indices: 1049947--1050009 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1049937 GCCATGTGTC
* *
1049947 TGCTGCACCTAAAATTCAACAAAACATAA
1 TGCT-CACCTAAAATGCAACAAAACAGAA
*
1049976 TGCTCACCTAAAATGCAACAAAATAGAA
1 TGCTCACCTAAAATGCAACAAAACAGAA
1050004 TGCTCA
1 TGCTCA
1050010 GGTTTTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.46, C:0.24, G:0.10, T:0.21
Consensus pattern (28 bp):
TGCTCACCTAAAATGCAACAAAACAGAA
Found at i:1051217 original size:78 final size:78
Alignment explanation
Indices: 1051081--1051231 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
1051071 CCAAAGTGTG
*
1051081 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1051146 TACTGAATATGCC
66 TACTGAATATGCC
* *
1051159 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCTGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1051224 TACTGAAT
66 TACTGAAT
1051232 CTACTGGCGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (78 bp):
GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Found at i:1054914 original size:26 final size:26
Alignment explanation
Indices: 1054881--1054988 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1054871 TGATACAAAT
1054881 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
1054907 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1054933 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1054959 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1054985 TGAT
1 TGAT
1054989 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1056494 original size:26 final size:26
Alignment explanation
Indices: 1056465--1056517 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1056455 TTTACAGTTT
*
1056465 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* *
1056491 TACCCATAGGGTTAAATTGACCTAAA
1 TACCCATAGGGATAAATTGACCGAAA
1056517 T
1 T
1056518 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:1058551 original size:17 final size:16
Alignment explanation
Indices: 1058531--1058563 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1058521 TATTTTATAT
1058531 TAATTAAATAAAGTAAA
1 TAATTAAATAAA-TAAA
1058548 TAATTAAATAAATAAA
1 TAATTAAATAAATAAA
1058564 AGAAAGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
TAATTAAATAAATAAA
Found at i:1058620 original size:19 final size:19
Alignment explanation
Indices: 1058592--1058630 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1058582 TGATATATGG
*
1058592 ATACATATGTACT-AATAAT
1 ATACACATGTA-TAAATAAT
1058611 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
1058630 A
1 A
1058631 AATAAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:1060009 original size:18 final size:17
Alignment explanation
Indices: 1059985--1060029 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
1059975 GTAAATAAAG
1059985 GTACTGAATAATTGACT
1 GTACTGAATAATTGACT
*
1060002 GCTACTGAATATTTGACT
1 G-TACTGAATAATTGACT
1060020 GTCACTGAAT
1 GT-ACTGAAT
1060030 TACTAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (17 bp):
GTACTGAATAATTGACT
Found at i:1060715 original size:21 final size:20
Alignment explanation
Indices: 1060676--1060715 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1060666 TGAAAAGATT
*
1060676 TAATTGAAATGAATTTGAAC
1 TAATTGAAATGAATGTGAAC
*
1060696 TAATTGATAATGTATGTGAA
1 TAATTGA-AATGAATGTGAA
1060716 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (20 bp):
TAATTGAAATGAATGTGAAC
Found at i:1064653 original size:26 final size:26
Alignment explanation
Indices: 1064624--1064731 Score: 153
Period size: 26 Copynumber: 4.2 Consensus size: 26
1064614 TGATACAAAT
*
1064624 TGATAATGGGTTAGGTCAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1064650 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1064676 TGATAATGGGTTAGGTAAATGCTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
1064702 CGATAATGGTTTAGGTAAATGTTCCG
1 TGATAATGGGTTAGGTAAATGTTCCA
1064728 TGAT
1 TGAT
1064732 GGGCATTTCA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1065038 original size:10 final size:10
Alignment explanation
Indices: 1065023--1065047 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1065013 GCATTTAGTC
1065023 ATGAATTAAA
1 ATGAATTAAA
1065033 ATGAATTAAA
1 ATGAATTAAA
1065043 ATGAA
1 ATGAA
1065048 GGAAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (10 bp):
ATGAATTAAA
Found at i:1065474 original size:26 final size:25
Alignment explanation
Indices: 1065422--1065474 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
1065412 TTTACAGTTT
1065422 TACCCCTAGTAGGTAAATTACCGAAA
1 TACCCCTAG-AGGTAAATTACCGAAA
*
1065448 TACCCCTAG-GGTTAAATTGACCTAAA
1 TACCCCTAGAGG-TAAATT-ACCGAAA
1065474 T
1 T
1065475 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
25 6 0.25
26 16 0.67
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (25 bp):
TACCCCTAGAGGTAAATTACCGAAA
Found at i:1065966 original size:137 final size:136
Alignment explanation
Indices: 1065721--1066006 Score: 527
Period size: 137 Copynumber: 2.1 Consensus size: 136
1065711 GAGTAGTCTC
*
1065721 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATAGGCCATACT
1 CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATAGGCCATACT
1065786 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
1065851 CTGTTA
131 CTGTTA
*
1065857 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATG-TTACTGATGTTGCATGTATTTTGAAATGGGCCTATAGGCCATAC
1065922 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
1065987 ACTGTTA
130 ACTGTTA
**
1065994 CCTGAATGGGCTT
1 CCCAAATGGGCTT
1066007 AGGCCCAATA
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 20 0.14
137 125 0.86
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTACTGATGTTGCATGTATTTTGAAATGGGCCTATAGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:1070716 original size:16 final size:16
Alignment explanation
Indices: 1070695--1070726 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1070685 CCCTATTTTT
*
1070695 CCTTTTTTTTTCTTTC
1 CCTTTTTCTTTCTTTC
1070711 CCTTTTTCTTTCTTTC
1 CCTTTTTCTTTCTTTC
1070727 TTTCCCTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
CCTTTTTCTTTCTTTC
Found at i:1070766 original size:15 final size:15
Alignment explanation
Indices: 1070692--1070768 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
1070682 AAACCCTATT
*
1070692 TTTCCTTTTTTTTTC
1 TTTCCTTTTTCTTTC
1070707 TTTCCCTTTTTCTTTC
1 TTT-CCTTTTTCTTTC
**
1070723 TTT-CTTTCCCTGTTC
1 TTTCCTTTTTCT-TTC
* **
1070738 TGTTTCGTCCTTCTTTC
1 --TTTCCTTTTTCTTTC
1070755 TTTCCTTTTTCTTT
1 TTTCCTTTTTCTTT
1070769 ATTTTATTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
14 6 0.13
15 17 0.37
16 14 0.30
17 6 0.13
18 3 0.07
ACGTcount: A:0.00, C:0.27, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTCCTTTTTCTTTC
Found at i:1070794 original size:19 final size:19
Alignment explanation
Indices: 1070759--1070801 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1070749 TCTTTCTTTC
*
1070759 CTTTTTCTTTATTTTATTT
1 CTTTTTCTTTATATTATTT
1070778 CTTTATTCTTT-TATTATTT
1 CTTT-TTCTTTATATTATTT
1070797 CTTTT
1 CTTTT
1070802 ATTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 6 0.27
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (19 bp):
CTTTTTCTTTATATTATTT
Found at i:1070811 original size:8 final size:8
Alignment explanation
Indices: 1070800--1070837 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1070790 ATTATTTCTT
1070800 TTATTATA
1 TTATTATA
1070808 TTATTA-A
1 TTATTATA
*
1070815 CTATTATA
1 TTATTATA
1070823 TTATTATAA
1 TTATTAT-A
1070832 TTATTA
1 TTATTA
1070838 ATTTCTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (8 bp):
TTATTATA
Found at i:1073829 original size:78 final size:78
Alignment explanation
Indices: 1073700--1073850 Score: 275
Period size: 78 Copynumber: 1.9 Consensus size: 78
1073690 TCAGAGTGTG
*
1073700 GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGATGTAGAAGTTGC
1 GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1073765 TACTGAATATGCC
66 TACTGAATATGCC
* *
1073778 GATGGGCCAACTTCTGGCTTAGCTGATGAGATTGCAGCTTCTCCAGAATCGGAAGTAGAAGTTGC
1 GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
1073843 TACTGAAT
66 TACTGAAT
1073851 CTGCAGGCAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (78 bp):
GATGGGCCAACTTCTAGCTTAGCTGATGAGATTGCAGCTACTCCAGAATCGGAAGTAGAAGTTGC
TACTGAATATGCC
Done.