Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 270 of 333
Found at i:89137912 original size:40 final size:42
Alignment explanation
Indices: 89137855--89138007 Score: 170
Period size: 43 Copynumber: 3.7 Consensus size: 42
89137845 TTTATGGAAA
*
89137855 AAACGCCTCTATAGAACATGACCTTTAGTGGCG-TTTCTCAC
1 AAACGACTCTATAGAACATGACCTTTAGTGGCGTTTTCTCAC
* *
89137896 AAA-AACTCTATAGAACATGACCTTTAGCT-GCGTTTTTTCAC
1 AAACGACTCTATAGAACATGACCTTTAG-TGGCGTTTTCTCAC
* * * *
89137937 AAACGA-TGCTATAGAAAAAGACATTTAGTGGCGCTTTTCCCAC
1 AAACGACT-CTATAGAACATGACCTTTAGTGGCG-TTTTCTCAC
* *
89137980 AAACGCCGCTATAGAACATGACCTTTAG
1 AAACGACTCTATAGAACATGACCTTTAG
89138008 CAGCGGTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
40 25 0.27
41 16 0.18
42 21 0.23
43 29 0.32
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (42 bp):
AAACGACTCTATAGAACATGACCTTTAGTGGCGTTTTCTCAC
Found at i:89138478 original size:66 final size:65
Alignment explanation
Indices: 89138399--89138527 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 65
89138389 AAGTTGTAAC
* * *
89138399 TGGAGTTCGTCATATTTTCTGCTT-GCATTTGCTTCTCTCGCTGCTGCCTTTGCTTTAAGTTGAA
1 TGGAGTTCGTCATATTTTCT--TTAGCATCTGCTTCTCTCGATGCTGCCTTCGCTTTAAGTTGAA
89138463 GT
64 GT
* *
89138465 TGGAGTTCTTCATATTTTCTTTGAGCCTCTGCTTCTCTCGATGCTGCCTTCGCTTTAAGTTGA
1 TGGAGTTCGTCATATTTTCTTT-AGCATCTGCTTCTCTCGATGCTGCCTTCGCTTTAAGTTGA
89138528 GCAATTTCCT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 2 0.04
66 54 0.96
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (65 bp):
TGGAGTTCGTCATATTTTCTTTAGCATCTGCTTCTCTCGATGCTGCCTTCGCTTTAAGTTGAAGT
Found at i:89139385 original size:24 final size:24
Alignment explanation
Indices: 89139358--89139405 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
89139348 AACTAAACTT
89139358 CCAAGCATGAATGAAGGATAATTG
1 CCAAGCATGAATGAAGGATAATTG
*
89139382 CCAAGCATGAATGGAGGATAATTG
1 CCAAGCATGAATGAAGGATAATTG
89139406 ATATAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (24 bp):
CCAAGCATGAATGAAGGATAATTG
Found at i:89140237 original size:16 final size:13
Alignment explanation
Indices: 89140216--89140250 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
89140206 AAATAGTTCA
* *
89140216 AAAATAGTATGTT
1 AAAATAATAGGTT
89140229 AAAATAATAGGTT
1 AAAATAATAGGTT
89140242 AAAATAATA
1 AAAATAATA
89140251 ATAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (13 bp):
AAAATAATAGGTT
Found at i:89143805 original size:21 final size:21
Alignment explanation
Indices: 89143766--89143805 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
89143756 TCAACAGGAT
*
89143766 TAATATATATAAAGTTTAAAC
1 TAATATATATAAAGATTAAAC
89143787 TAATATATATTAAA-ATTAA
1 TAATATATA-TAAAGATTAA
89143806 TATTATCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
TAATATATATAAAGATTAAAC
Found at i:89144150 original size:6 final size:6
Alignment explanation
Indices: 89144139--89144166 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
89144129 TTTATGTAAG
89144139 AAAACA AAAACA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAA
89144167 ATTTCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:89147668 original size:17 final size:17
Alignment explanation
Indices: 89147648--89147711 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
89147638 CAATGATATG
89147648 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
89147665 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
*
89147683 CAATCGTAGATATGATA
1 CAATCTTAGATATGATA
89147700 TGCAATCTTAGA
1 --CAATCTTAGA
89147712 AGATATGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
17 16 0.40
18 15 0.38
19 9 0.22
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:89147686 original size:35 final size:37
Alignment explanation
Indices: 89147640--89147718 Score: 112
Period size: 35 Copynumber: 2.2 Consensus size: 37
89147630 ATAATCTTCA
*
89147640 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCGTAGATATGATAGCAATCTTAGAT
89147676 ATGAT-TGCAATCGTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCGTAGATATGATA-GCAATCTTAGAT
89147712 A-GATATG
1 ATGATATG
89147719 ATTTTGTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
35 21 0.54
36 8 0.21
37 10 0.26
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (37 bp):
ATGATATGCAATCGTAGATATGATAGCAATCTTAGAT
Found at i:89147718 original size:17 final size:19
Alignment explanation
Indices: 89147640--89147711 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
89147630 ATAATCTTCA
89147640 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
89147659 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
89147676 ATGAT-TGCAATCGTAGAT
1 ATGATATGCAATCTTAGAT
89147694 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
89147712 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
17 16 0.33
18 15 0.31
19 17 0.35
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:89147733 original size:23 final size:22
Alignment explanation
Indices: 89147640--89147735 Score: 72
Period size: 17 Copynumber: 4.9 Consensus size: 22
89147630 ATAATCTTCA
89147640 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
89147659 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
89147676 ATGAT-TGCAATC---GTAGAT
1 ATGATATGCAATCTTAGAAGAT
89147694 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
89147716 ATGATTTTGTAATCTTAGAA
1 ATGA-TATGCAATCTTAGAA
89147736 ATTTAATTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
17 16 0.25
18 14 0.22
19 13 0.20
22 9 0.14
23 13 0.20
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:89148026 original size:17 final size:17
Alignment explanation
Indices: 89148002--89148036 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
89147992 TGTTTCTCTG
*
89148002 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
89148020 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
89148037 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:89156299 original size:78 final size:78
Alignment explanation
Indices: 89156195--89156427 Score: 387
Period size: 78 Copynumber: 3.0 Consensus size: 78
89156185 TTTTCACATC
* * *
89156195 GAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGAAGCAGATCGAAGACACAGCAGA
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA
89156260 TCTGACCTTCATT
66 TCTGACCTTCATT
* * *
89156273 GAAGCAGATCTAAGATTATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGA
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA
89156338 T-TGGACCTTCATT
66 TCT-GACCTTCATT
*
89156351 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGTAGA
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA
89156416 TCTGACCTTCAT
66 TCTGACCTTCAT
89156428 GTGTTTACAT
Statistics
Matches: 143, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
77 1 0.01
78 141 0.99
79 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (78 bp):
GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGA
TCTGACCTTCATT
Found at i:89156520 original size:45 final size:46
Alignment explanation
Indices: 89156450--89156634 Score: 227
Period size: 45 Copynumber: 4.1 Consensus size: 46
89156440 AAGCAGATCC
*
89156450 AAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG
1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG
* * * *
89156496 -AGATAACAGATTTGGCATTTCTGTATTAGACGAGGAGCAGAT-TG
1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG
* * *
89156540 AAGA-AGCAAATTTGGCGTCTCTGTATTAGACGGGGAGCAAATC-G
1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG
* * * *
89156584 AAGATAACAGATTTGGCGTCTCTGTATTAGATGGAGAGCAGATCA-
1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG
89156629 AAGATA
1 AAGATA
89156635 GCATATATTG
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
44 38 0.32
45 81 0.68
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.25
Consensus pattern (46 bp):
AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCAG
Found at i:89157013 original size:19 final size:19
Alignment explanation
Indices: 89156989--89157025 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
89156979 TATAATCTCA
89156989 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
89157008 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
89157026 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:89157051 original size:22 final size:22
Alignment explanation
Indices: 89156989--89157048 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 22
89156979 TATAATCTCA
89156989 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
89157008 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
89157030 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
89157049 GATTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:89157338 original size:17 final size:17
Alignment explanation
Indices: 89157314--89157348 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
89157304 ATATTTCCCT
*
89157314 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
89157332 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
89157349 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:89162791 original size:327 final size:327
Alignment explanation
Indices: 89162178--89162824 Score: 1005
Period size: 327 Copynumber: 2.0 Consensus size: 327
89162168 AATCTTGAAC
89162178 CTAGAGCCTCATGAAACTTCTTCCAGAACTGAGACATGAAACGAGGATCCCTATCAGAAATGATC
1 CTAGAGCCTCATGAAACTTCTTCCAGAACTGAGACATGAAACGAGGATCCCTATCAGAAATGATC
*
89162243 GAGACAGGTACCCCATACAGTCTTATTATTTCCAAGATGTAGAGCTTAGCTAACTTCTGAAGAGA
66 GAGACAAGTACCCCATACAGTCTTATTATTTCCAAGATGTAGAGCTTAGCTAACTTCTGAAGAGA
* *
89162308 AAAGTCTGTCTTTACCGGGATGAAGTGAGCAGACTTGGTCAATCGATCCACGATGACCCAGACAG
131 AAAGTCTGTCTTTACCGGGATAAAGTGAGCAGACTTGGTCAATCGATCCACGATGACCCAAACAG
* * * *
89162373 AATTCTTTTTAATCAGTGTTAGAGGTAACCCACTAACGAAGTCCATCGTTACTCGTTTCCATTTC
196 AATCCTTCTTAATCAGTGTTAGAAGTAACCCACTAACGAAGTCCATCGTTACTCGCTTCCATTTC
* * * * *
89162438 CATAACTGTATCGACTGTAGCAAACCCGAAGGTAACTAATGCTTAGCCTTAACCTACTGATAAAC
261 CATAACGGTATAGACTGTAACAAACCCGAAAGTAACTAATGCTCAGCCTTAACCTACTGATAAAC
89162503 AG
326 AG
* * **
89162505 CTAGAGCCTCATGAAGCTTCTTCTAGAACTGAGATGTGAAACGAGGAT-CCTAATCAGAAATGAT
1 CTAGAGCCTCATGAAACTTCTTCCAGAACTGAGACATGAAACGAGGATCCCT-ATCAGAAATGAT
89162569 CGAGACAAGTACCCTC-TACAGTCTTATTATTTCCAAGATGTAGAGCTTAGCTAACTTCTGAAGA
65 CGAGACAAGTACCC-CATACAGTCTTATTATTTCCAAGATGTAGAGCTTAGCTAACTTCTGAAGA
* *
89162633 GAAAAGTTTAT-TCTTACCGGGATAAAGTGAGCAGACTTGGTCAATCGATCCACGATGACCCAAA
129 GAAAAGTCTGTCT-TTACCGGGATAAAGTGAGCAGACTTGGTCAATCGATCCACGATGACCCAAA
* *
89162697 CAGAATCCTTCTTAGTC-GATGTTAGAAGTAACCCACTAACGAAGTCCATTGTTACTCGCTTCCA
193 CAGAATCCTTCTTAATCAG-TGTTAGAAGTAACCCACTAACGAAGTCCATCGTTACTCGCTTCCA
** * * *
89162761 TTTCCATAACGGTATAGGTTGTAACAAACCCGAAAGTAATTGATGCTCAGCCTTAACCTGCTGA
257 TTTCCATAACGGTATAGACTGTAACAAACCCGAAAGTAACTAATGCTCAGCCTTAACCTACTGA
89162825 CAAGTCAAAC
Statistics
Matches: 291, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
326 5 0.02
327 285 0.98
328 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (327 bp):
CTAGAGCCTCATGAAACTTCTTCCAGAACTGAGACATGAAACGAGGATCCCTATCAGAAATGATC
GAGACAAGTACCCCATACAGTCTTATTATTTCCAAGATGTAGAGCTTAGCTAACTTCTGAAGAGA
AAAGTCTGTCTTTACCGGGATAAAGTGAGCAGACTTGGTCAATCGATCCACGATGACCCAAACAG
AATCCTTCTTAATCAGTGTTAGAAGTAACCCACTAACGAAGTCCATCGTTACTCGCTTCCATTTC
CATAACGGTATAGACTGTAACAAACCCGAAAGTAACTAATGCTCAGCCTTAACCTACTGATAAAC
AG
Found at i:89171125 original size:52 final size:52
Alignment explanation
Indices: 89171063--89171168 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
89171053 ATAAGTGAAT
89171063 CTTTAAGTTGTTATTCATAGAATAAAATGAAATGCATATTTTTTTTATTTAA
1 CTTTAAGTTGTTATTCATAGAATAAAATGAAATGCATATTTTTTTTATTTAA
89171115 CTTTAAGTTGTTATTCATAGAATAAAATGAAATGCATATTTTTTTTATTTAA
1 CTTTAAGTTGTTATTCATAGAATAAAATGAAATGCATATTTTTTTTATTTAA
89171167 CT
1 CT
89171169 AAGTACTATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (52 bp):
CTTTAAGTTGTTATTCATAGAATAAAATGAAATGCATATTTTTTTTATTTAA
Found at i:89173511 original size:13 final size:13
Alignment explanation
Indices: 89173493--89173517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89173483 GGGTACTCCC
89173493 AATTATGGACCTA
1 AATTATGGACCTA
89173506 AATTATGGACCT
1 AATTATGGACCT
89173518 TACAAAACCC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTATGGACCTA
Found at i:89173752 original size:15 final size:15
Alignment explanation
Indices: 89173729--89173760 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
89173719 CATTTCACTA
89173729 TTATATTTTTTGTAT
1 TTATATTTTTTGTAT
*
89173744 TTATGTTTTTTGTAT
1 TTATATTTTTTGTAT
89173759 TT
1 TT
89173761 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (15 bp):
TTATATTTTTTGTAT
Found at i:89176554 original size:29 final size:29
Alignment explanation
Indices: 89176494--89176567 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
89176484 GTTGTGTAGA
**
89176494 GTGTGACAGCCCGTGTGCGTCACACGGTC
1 GTGTGACAGCCCGTGTGCGTCACACGACC
* * * *
89176523 GTGTGGCAGCCTGTGTGTGTGACACGACC
1 GTGTGACAGCCCGTGTGCGTCACACGACC
*
89176552 GTGTGATAGCCCGTGT
1 GTGTGACAGCCCGTGT
89176568 CCTAGGTCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.14, C:0.26, G:0.36, T:0.24
Consensus pattern (29 bp):
GTGTGACAGCCCGTGTGCGTCACACGACC
Found at i:89180312 original size:21 final size:21
Alignment explanation
Indices: 89180278--89180317 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
89180268 CTTACTTCAA
*
89180278 ATTTTCTTATTTTTACTTTTAT
1 ATTTTCTTAATTTTA-TTTTAT
89180300 ATTTT-TTAATTTTATTTT
1 ATTTTCTTAATTTTATTTT
89180318 GCATTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (21 bp):
ATTTTCTTAATTTTATTTTAT
Found at i:89180464 original size:22 final size:23
Alignment explanation
Indices: 89180416--89180466 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
89180406 ATTATATTTT
**
89180416 AATTTTTATAATAGTAAAAATGT
1 AATTTTTATAATAGTAAAAATAA
* *
89180439 AATTTTTA-AATAGTTAAATTAA
1 AATTTTTATAATAGTAAAAATAA
89180461 AATTTT
1 AATTTT
89180467 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (23 bp):
AATTTTTATAATAGTAAAAATAA
Found at i:89188076 original size:18 final size:18
Alignment explanation
Indices: 89188053--89188087 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
89188043 AAAAGATGTA
89188053 TTAATTAATCAAGCCAAT
1 TTAATTAATCAAGCCAAT
89188071 TTAATTAATCAAGCCAA
1 TTAATTAATCAAGCCAA
89188088 ACAAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (18 bp):
TTAATTAATCAAGCCAAT
Found at i:89188685 original size:19 final size:19
Alignment explanation
Indices: 89188652--89188692 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
89188642 TACTTGGTCT
89188652 AAAAAAATTCAAAAATTATA
1 AAAAAAATTCAAAAATT-TA
*
89188672 AAAAAAATT-TAAAATTTA
1 AAAAAAATTCAAAAATTTA
89188690 AAA
1 AAA
89188693 TTTAAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 6 0.30
20 9 0.45
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAAATTCAAAAATTTA
Found at i:89188687 original size:7 final size:7
Alignment explanation
Indices: 89188675--89188700 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
89188665 AATTATAAAA
89188675 AAAATTT
1 AAAATTT
89188682 AAAATTT
1 AAAATTT
89188689 AAAATTT
1 AAAATTT
89188696 AAAAT
1 AAAAT
89188701 CATTCAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:89190690 original size:19 final size:19
Alignment explanation
Indices: 89190655--89190712 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
89190645 ATATACTTAA
* *
89190655 ATATTAAGTAAACATAT-T
1 ATATTAAATATACATATGT
*
89190673 TTATTAATATATACATATGT
1 ATATTAA-ATATACATATGT
*
89190693 ATATTAAATTTACATATGT
1 ATATTAAATATACATATGT
89190712 A
1 A
89190713 ATCACTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 6 0.18
19 20 0.61
20 7 0.21
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
ATATTAAATATACATATGT
Found at i:89193003 original size:27 final size:27
Alignment explanation
Indices: 89192973--89193027 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
89192963 TATTCAAATT
89192973 CTTCCTTGAGTTAAACCTCTGATCCCC
1 CTTCCTTGAGTTAAACCTCTGATCCCC
* * *
89193000 CTTCTTTGAGTTAAACTTTTGATCCCC
1 CTTCCTTGAGTTAAACCTCTGATCCCC
89193027 C
1 C
89193028 AATCACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (27 bp):
CTTCCTTGAGTTAAACCTCTGATCCCC
Found at i:89196546 original size:21 final size:20
Alignment explanation
Indices: 89196509--89196557 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 20
89196499 GGTTCAAAGC
*
89196509 AAATAAATTATTAAAAATAA
1 AAATAAAATATTAAAAATAA
89196529 AAATAAAAATATTCAAAATTATAA
1 AAAT-AAAATATT-AAAA--ATAA
89196553 AAATA
1 AAATA
89196558 GGTGTCAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 7 0.29
22 4 0.17
23 1 0.04
24 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAATATTAAAAATAA
Found at i:89201272 original size:21 final size:21
Alignment explanation
Indices: 89201246--89201301 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
89201236 AACAGCGGTG
* *
89201246 GCGGTGAGATTAGTTATTGTA
1 GCGGTGAGATTAGATACTGTA
*
89201267 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
89201288 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
89201302 AACAACGGTG
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:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:89205311 original size:46 final size:47
Alignment explanation
Indices: 89205204--89206049 Score: 1118
Period size: 46 Copynumber: 18.4 Consensus size: 47
89205194 CCCTTCGGGA
* *
89205204 CTTATCACATTTATACACTTTCACATCCATCACATTGGCACCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGG--CCATTCGGC
* * * * *
89205253 CTTATCACATATATACACCTTCACA-TCCTCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89205299 CTTATCTCATATATACACTTTC-CATTCATCA-A-T--CCATT-AGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
89205340 CTTATCTCATATATACACTTTGCACATTCATCACATT-GCCATT-GGC
1 CTTATCACATATATACACTTT-CACATTCATCACATTGGCCATTCGGC
89205386 CTTATCACATAT-TACACTTTCACATTCATCAC-TTGGCCATT-GCGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCG-GC
* * *
89205431 CTAATCACATATATACACTTTCACATTCATTCA-ATCGGCCA-T-AGC
1 CTTATCACATATATACACTTTCACATTCA-TCACATTGGCCATTCGGC
*
89205476 CTATATCACATATACACACTTTCACATTCATCACATTGGCCA-TCGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89205523 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTC-GC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89205569 GC-TATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 -CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89205616 CTTATCACATATGTACACTTTCACATTCATCACGTTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCAC-ATTGGCCATTCGGC
89205664 CTTATCACATATATACACTTTCACATTCATCACATTGGCCA-TCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89205710 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
89205757 CTTATCACATATACACACTTT-ACATTCATCACATTGG-CATTCAGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89205802 CTTATCACATATATACACTTTCACATTCATCACATT-GCCATTC-GC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89205847 TTTATCATATATATACACTTTCACATTCATCACCTTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
89205894 CTTATTCACATATGTAC-CTTTCACATTCATCACGTTGGCCA-TCGGC
1 CTTA-TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89205940 CTTATCACATATATACACTTTCACATTCATCACATT-GCCATTCCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATT-CGGC
* * *
89205986 CTTATCACATACATACACTTTCACATTCATCA-ATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
89206032 CTTATCACATATACACAC
1 CTTATCACATATATACAC
89206050 CTTTGTACAT
Statistics
Matches: 716, Mismatches: 51, Indels: 63
0.86 0.06 0.08
Matches are distributed among these distances:
41 23 0.03
42 6 0.01
43 11 0.02
44 20 0.03
45 113 0.16
46 347 0.48
47 110 0.15
48 63 0.09
49 23 0.03
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:89206549 original size:18 final size:17
Alignment explanation
Indices: 89206516--89206549 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
89206506 TCTAGAATAT
*
89206516 AAATTTTTGTCTTTTAA
1 AAATTTTTGTCATTTAA
89206533 AAATTTTTGTACATTTA
1 AAATTTTTGT-CATTTA
89206550 TAATATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
AAATTTTTGTCATTTAA
Found at i:89209141 original size:32 final size:31
Alignment explanation
Indices: 89209058--89209160 Score: 138
Period size: 31 Copynumber: 3.3 Consensus size: 31
89209048 AAAAAATATG
89209058 ATACATTAGGTTACG-TATAAAAAAGTAGATC
1 ATACATTAGGTTA-GATATAAAAAAGTAGATC
* *
89209089 ATACATTA-GTTTGCATATAAAAAAGTAGATA
1 ATACATTAGGTTAG-ATATAAAAAAGTAGATC
*
89209120 ATACATTAGGTTCAGAAATAAAAAAGTAGATC
1 ATACATTAGGTT-AGATATAAAAAAGTAGATC
89209152 ATACATTAG
1 ATACATTAG
89209161 TTTTGCAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 31 0.49
32 27 0.43
33 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.29
Consensus pattern (31 bp):
ATACATTAGGTTAGATATAAAAAAGTAGATC
Found at i:89209201 original size:1 final size:1
Alignment explanation
Indices: 89209197--89209233 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
89209187 AAAAATAGAT
*
89209197 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
89209234 TTTGAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:89209559 original size:26 final size:26
Alignment explanation
Indices: 89209522--89209683 Score: 252
Period size: 26 Copynumber: 6.2 Consensus size: 26
89209512 TGATACAAAT
89209522 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
89209548 CGATAATAGGTTCGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
89209574 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89209600 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89209626 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89209652 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89209678 TGATAA
1 TGATAA
89209684 GAATTTCATG
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 126 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:89210905 original size:8 final size:8
Alignment explanation
Indices: 89210859--89210902 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
89210849 CTAGATTGGC
89210859 AAAAGCCG
1 AAAAGCCG
89210867 AAAAGCCG
1 AAAAGCCG
*
89210875 AAATGCC-
1 AAAAGCCG
89210882 AAAAGCCG
1 AAAAGCCG
* *
89210890 AAATGTCG
1 AAAAGCCG
89210898 AAAAG
1 AAAAG
89210903 TCGGTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:89211359 original size:27 final size:27
Alignment explanation
Indices: 89211318--89211430 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
89211308 GAGGAAGCGT
*
89211318 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
89211345 CCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
89211372 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
89211400 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
89211426 TCTGG
1 TCTGG
89211431 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.73
28 15 0.21
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:89211423 original size:54 final size:54
Alignment explanation
Indices: 89211316--89211430 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
89211306 TGGAGGAAGC
*
89211316 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
* * * * *
89211370 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ACCTGGTGACTCTGCCACATATATCT
89211424 GTTCTGG
1 GTTCTGG
89211431 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
Found at i:89215433 original size:26 final size:26
Alignment explanation
Indices: 89215397--89215600 Score: 275
Period size: 26 Copynumber: 8.2 Consensus size: 26
89215387 TGATACAAAT
89215397 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89215423 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89215449 CGATAATA-G-TAGGT-AAT-TTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89215471 TGAT-ATA--TTA--TAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
89215491 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89215517 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89215543 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
89215569 TGACAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89215595 TGATAA
1 TGATAA
89215601 GAATTTCATG
Statistics
Matches: 162, Mismatches: 7, Indels: 18
0.87 0.04 0.10
Matches are distributed among these distances:
19 1 0.01
20 9 0.06
21 10 0.06
22 7 0.04
23 6 0.04
24 5 0.03
25 9 0.06
26 115 0.71
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:89216801 original size:14 final size:14
Alignment explanation
Indices: 89216782--89216808 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89216772 GCAAAAGCCG
89216782 AAAAGCCGAAATGC
1 AAAAGCCGAAATGC
89216796 AAAAGCCGAAATG
1 AAAAGCCGAAATG
89216809 TCGAAAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.19, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAAGCCGAAATGC
Found at i:89217116 original size:25 final size:25
Alignment explanation
Indices: 89217078--89217126 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
89217068 CCTATGTATG
*
89217078 GAAAATTACTGTTATACCCCTAGGT
1 GAAAATTACCGTTATACCCCTAGGT
89217103 GAAAATTACCGTTATACCCCTAGG
1 GAAAATTACCGTTATACCCCTAGG
89217127 GTTAATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (25 bp):
GAAAATTACCGTTATACCCCTAGGT
Found at i:89217270 original size:27 final size:27
Alignment explanation
Indices: 89217229--89217341 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
89217219 GAGGAAGCGT
*
89217229 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
89217256 CCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
89217283 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
89217311 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
89217337 TCTGG
1 TCTGG
89217342 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.73
28 15 0.21
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:89217334 original size:54 final size:54
Alignment explanation
Indices: 89217227--89217341 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
89217217 TGGAGGAAGC
*
89217227 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
* * * * *
89217281 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ACCTGGTGACTCTGCCACATATATCT
89217335 GTTCTGG
1 GTTCTGG
89217342 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
Found at i:89220309 original size:27 final size:28
Alignment explanation
Indices: 89220254--89220311 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
89220244 AGCACCTGTG
*
89220254 TTAATTCAGCCTGAGTCTGGGAAGGATT
1 TTAATTCAACCTGAGTCTGGGAAGGATT
89220282 TTAATTCAACCTGAGT-TGGGAAGGATT
1 TTAATTCAACCTGAGTCTGGGAAGGATT
89220309 TTA
1 TTA
89220312 GTGTGTACAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (28 bp):
TTAATTCAACCTGAGTCTGGGAAGGATT
Found at i:89221295 original size:26 final size:26
Alignment explanation
Indices: 89221259--89221468 Score: 357
Period size: 26 Copynumber: 8.1 Consensus size: 26
89221249 ACAAATTGAA
89221259 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
*
89221285 AATAGGTTAGGTAAATGTTCCACGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
*
89221311 AATAGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
*
89221337 AATAGGTTTGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
89221363 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
89221389 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
* *
89221415 AATGGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
* *
89221441 AATGGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
89221467 AA
1 AA
89221469 GAATTTCATG
Statistics
Matches: 176, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 176 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
AATAGGTTAGGTAAATGTTCCATGAT
Found at i:89222651 original size:8 final size:8
Alignment explanation
Indices: 89222638--89222688 Score: 75
Period size: 8 Copynumber: 6.4 Consensus size: 8
89222628 CTAGATTGGC
89222638 AAAAGCCG
1 AAAAGCCG
89222646 AAAAGCCG
1 AAAAGCCG
*
89222654 AAATGCCG
1 AAAAGCCG
89222662 AAAAGCCG
1 AAAAGCCG
*
89222670 AAATGCCG
1 AAAAGCCG
*
89222678 AAATGCCG
1 AAAAGCCG
89222686 AAA
1 AAA
89222689 GTCGGTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.47, C:0.24, G:0.24, T:0.06
Consensus pattern (8 bp):
AAAAGCCG
Found at i:89222663 original size:16 final size:16
Alignment explanation
Indices: 89222642--89222688 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
89222632 ATTGGCAAAA
89222642 GCCGAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
89222658 GCCGAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
*
89222674 GCCGAAATGCCGAAA
1 GCCGAAAAGCCGAAA
89222689 GTCGGTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.43, C:0.26, G:0.26, T:0.06
Consensus pattern (16 bp):
GCCGAAAAGCCGAAAT
Found at i:89222670 original size:24 final size:24
Alignment explanation
Indices: 89222638--89222688 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
89222628 CTAGATTGGC
89222638 AAAAGCCGAAAAGCCGAAATGCCG
1 AAAAGCCGAAAAGCCGAAATGCCG
*
89222662 AAAAGCCGAAATGCCGAAATGCCG
1 AAAAGCCGAAAAGCCGAAATGCCG
89222686 AAA
1 AAA
89222689 GTCGGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.24, G:0.24, T:0.06
Consensus pattern (24 bp):
AAAAGCCGAAAAGCCGAAATGCCG
Found at i:89223170 original size:27 final size:26
Alignment explanation
Indices: 89223103--89223216 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
89223093 TGGAGGAAGC
* *
89223103 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
89223130 G-ACTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
89223156 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
89223183 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
89223210 GTTCTGG
1 GTTCTGG
89223217 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
25 1 0.01
26 26 0.34
27 33 0.43
28 17 0.22
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:89223183 original size:53 final size:54
Alignment explanation
Indices: 89223103--89223216 Score: 160
Period size: 53 Copynumber: 2.1 Consensus size: 54
89223093 TGGAGGAAGC
*
89223103 GTTCTGGTGGCTATGCCACAAATATCTG-A-CTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACAT-TATCT
* * * *
89223156 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACATTATCT
89223210 GTTCTGG
1 GTTCTGG
89223217 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
53 25 0.46
54 13 0.24
55 16 0.30
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGTATCTGGTGACTCTGCCACATTATCT
Found at i:89224816 original size:11 final size:11
Alignment explanation
Indices: 89224800--89224825 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
89224790 AAGAGTTTTC
89224800 CAAACTCAGAT
1 CAAACTCAGAT
89224811 CAAACTCAGAT
1 CAAACTCAGAT
89224822 CAAA
1 CAAA
89224826 GACATTATTG
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:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (11 bp):
CAAACTCAGAT
Found at i:89224898 original size:71 final size:72
Alignment explanation
Indices: 89224741--89224933 Score: 300
Period size: 71 Copynumber: 2.7 Consensus size: 72
89224731 TCTATCACAG
* *
89224741 AACTCAGATCAAAAGAAATTATTAAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCAAACT
1 AACTCAGATCAAAAGACATTATTGAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCAAACT
89224806 CAGATCA
66 CAGATCA
* * *
89224813 AACTCAGATC-AAAGACATTATTGAGCTGAAACCTAT-AAAAAGCAGTAAAGAGTTTTCCGAACT
1 AACTCAGATCAAAAGACATTATTGAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCAAACT
89224876 CAGATCA
66 CAGATCA
* *
89224883 AACTCAGATCAAAAGACATTATTGAGCTGGAACCTATCAAAAAAGCACTAA
1 AACTCAGATCAAAAGACATTATTGAGCTGAAACCTAT-AAAAAAACACTAA
89224934 TATATACACA
Statistics
Matches: 111, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
70 41 0.37
71 49 0.44
72 10 0.09
73 11 0.10
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (72 bp):
AACTCAGATCAAAAGACATTATTGAGCTGAAACCTATAAAAAAACACTAAAGAGTTTTCCAAACT
CAGATCA
Found at i:89227030 original size:15 final size:15
Alignment explanation
Indices: 89227002--89227063 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 15
89226992 TTCTTCTAAT
*
89227002 TATTTTTAACTTTATA
1 TATTTTT-ATTTTATA
89227018 TATTTTTATTTTATAAAA
1 TATTTTTATTTTAT---A
*
89227036 TATTATTTATTTCATA
1 TATT-TTTATTTTATA
*
89227052 TATTATTATTTT
1 TATTTTTATTTT
89227064 TAATTAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 12 0.32
16 12 0.32
18 5 0.13
19 9 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTATTTTATA
Found at i:89227046 original size:19 final size:19
Alignment explanation
Indices: 89227017--89227062 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
89227007 TTAACTTTAT
*
89227017 ATATT-TTTATTTTATAAA
1 ATATTATTTATTTCATAAA
*
89227035 ATATTATTTATTTCATATA
1 ATATTATTTATTTCATAAA
*
89227054 TTATTATTT
1 ATATTATTT
89227063 TTAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATATTATTTATTTCATAAA
Found at i:89241572 original size:18 final size:18
Alignment explanation
Indices: 89241549--89241583 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
89241539 AAAAGATGTA
89241549 TTAATTAATCAAGCCAAT
1 TTAATTAATCAAGCCAAT
89241567 TTAATTAATCAAGCCAA
1 TTAATTAATCAAGCCAA
89241584 ACAAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (18 bp):
TTAATTAATCAAGCCAAT
Found at i:89242175 original size:7 final size:7
Alignment explanation
Indices: 89242165--89242190 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
89242155 AAATTATAAA
89242165 AAAATTT
1 AAAATTT
89242172 AAAATTT
1 AAAATTT
89242179 AAAATTT
1 AAAATTT
89242186 AAAAT
1 AAAAT
89242191 CATTCAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:89244177 original size:19 final size:19
Alignment explanation
Indices: 89244142--89244199 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
89244132 ATATACTTAA
* *
89244142 ATATTAAGTAAACATAT-T
1 ATATTAAATATACATATGT
*
89244160 TTATTAATATATACATATGT
1 ATATTAA-ATATACATATGT
*
89244180 ATATTAAATTTACATATGT
1 ATATTAAATATACATATGT
89244199 A
1 A
89244200 ATCACTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 6 0.18
19 20 0.61
20 7 0.21
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
ATATTAAATATACATATGT
Found at i:89246488 original size:27 final size:27
Alignment explanation
Indices: 89246458--89246512 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
89246448 TATTCAAATT
89246458 CTTCCTTGAGTTAAACCTCTGATCCCC
1 CTTCCTTGAGTTAAACCTCTGATCCCC
* * *
89246485 CTTCTTTGAGTTAAACTTTTGATCCCC
1 CTTCCTTGAGTTAAACCTCTGATCCCC
89246512 C
1 C
89246513 AATCACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (27 bp):
CTTCCTTGAGTTAAACCTCTGATCCCC
Found at i:89250034 original size:21 final size:20
Alignment explanation
Indices: 89249997--89250045 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 20
89249987 GGTTCAAAGC
*
89249997 AAATAAATTATTAAAAATAA
1 AAATAAAATATTAAAAATAA
89250017 AAATAAAAATATTCAAAATTATAA
1 AAAT-AAAATATT-AAAA--ATAA
89250041 AAATA
1 AAATA
89250046 GGTGTCAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 7 0.29
22 4 0.17
23 1 0.04
24 8 0.33
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAAATATTAAAAATAA
Found at i:89254769 original size:21 final size:21
Alignment explanation
Indices: 89254743--89254798 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
89254733 AACAGCGGTG
* *
89254743 GCGGTGAGATTAGTTATTGTA
1 GCGGTGAGATTAGATACTGTA
*
89254764 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
89254785 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
89254799 AACAACGGTG
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:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:89258850 original size:47 final size:47
Alignment explanation
Indices: 89258741--89259606 Score: 1399
Period size: 47 Copynumber: 18.4 Consensus size: 47
89258731 CCCTTCGGGA
* *
89258741 CTTATCACATTTATACACTTTCACATCCATCACATTGGCACCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGG--CCATTCGGC
* * * * *
89258790 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89258837 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
89258884 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89258931 CTTATCACATATGTACACTTTCACATTCATCACGTTGGCCATTCAGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89258978 CTAATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
89259025 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89259072 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89259119 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89259166 CTTATCACATATGTACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89259213 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89259260 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
89259307 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCAGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89259354 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
89259401 CTTATCATATATATACACTTTCACATTCATCACCTTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89259448 CTTATCACATATGTACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89259495 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89259542 CTTATCACATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
89259589 CTTATCACATATACACAC
1 CTTATCACATATATACAC
89259607 CTTGTACATC
Statistics
Matches: 761, Mismatches: 56, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
47 726 0.95
49 35 0.05
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:89259244 original size:25 final size:25
Alignment explanation
Indices: 89259216--89259294 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
89259206 ACTCGGCCTT
89259216 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
89259241 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
89259263 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
89259288 ATCACAT
1 ATCACAT
89259295 CGACCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:89259360 original size:22 final size:22
Alignment explanation
Indices: 89259335--89259407 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
89259325 TTTCACATTC
89259335 ATCACATTGGCCATTCAGCCTT
1 ATCACATTGGCCATTCAGCCTT
** * *
89259357 ATCACATATATACACTTTCA-CATT
1 ATCACAT-T-GGC-CATTCAGCCTT
*
89259381 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCAGCCTT
89259404 ATCA
1 ATCA
89259408 TATATATACA
Statistics
Matches: 37, Mismatches: 9, Indels: 10
0.66 0.16 0.18
Matches are distributed among these distances:
22 15 0.41
23 5 0.14
24 5 0.14
25 12 0.32
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCAGCCTT
Found at i:89259526 original size:25 final size:25
Alignment explanation
Indices: 89259498--89259576 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
89259488 ACTCGGCCTT
89259498 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
89259523 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
*
89259545 ATCACATACATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
89259570 ATCACAT
1 ATCACAT
89259577 CGGCCATTAG
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 11 0.29
23 4 0.11
24 5 0.13
25 18 0.47
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:89262832 original size:32 final size:32
Alignment explanation
Indices: 89262792--89262944 Score: 198
Period size: 32 Copynumber: 4.8 Consensus size: 32
89262782 AAAAAATATG
* *
89262792 ATACATTAGGTTTACGTATAAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* *
89262824 ATACATTAGTTTTGCATATAAAAAAGTAGATA
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* * * *
89262856 ATACATTAGGTTCAGAAATAAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
* * *
89262888 ATACATTAGTTTTGCAAATGAAAAAGTAGATC
1 ATACATTAGTTTTACATATAAAAAAGTAGATC
*
89262920 ATGCATTAGTTTTACATATAAAAAA
1 ATACATTAGTTTTACATATAAAAAA
89262945 CTAGCATAAT
Statistics
Matches: 102, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 102 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.31
Consensus pattern (32 bp):
ATACATTAGTTTTACATATAAAAAAGTAGATC
Found at i:89262941 original size:64 final size:64
Alignment explanation
Indices: 89262792--89262944 Score: 225
Period size: 64 Copynumber: 2.4 Consensus size: 64
89262782 AAAAAATATG
* *
89262792 ATACATTAGGTTTACGTATAAAAAAGTAGATCATACATTAGTTTTGCATATAAAAAAGTAGATA
1 ATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
* * * * *
89262856 ATACATTAGGTTCAGAAATAAAAAAGTAGATCATACATTAGTTTTGCAAATGAAAAAGTAGATC
1 ATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
* *
89262920 ATGCATTAGTTTTACATATAAAAAA
1 ATACATTAGGTTTACATATAAAAAA
89262945 CTAGCATAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.31
Consensus pattern (64 bp):
ATACATTAGGTTTACATATAAAAAAGTAGATCATACATTAGTTTTGCAAATAAAAAAGTAGATA
Found at i:89263418 original size:26 final size:26
Alignment explanation
Indices: 89263381--89263541 Score: 252
Period size: 26 Copynumber: 6.2 Consensus size: 26
89263371 TGATACAAAT
89263381 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89263407 CGATAATAGGTTCGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
89263432 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89263458 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89263484 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89263510 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89263536 TGATAA
1 TGATAA
89263542 GAATTTCATG
Statistics
Matches: 126, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
25 22 0.17
26 104 0.83
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:89264758 original size:16 final size:16
Alignment explanation
Indices: 89264719--89264759 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
89264709 ATTGGCAAAA
89264719 GCCGAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
*
89264735 GCCAAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
*
89264751 GTCGAAAAG
1 GCCGAAAAG
89264760 TCGGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.24, T:0.07
Consensus pattern (16 bp):
GCCGAAAAGCCGAAAT
Found at i:89264762 original size:8 final size:8
Alignment explanation
Indices: 89264715--89264759 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
89264705 CTAGATTGGC
89264715 AAAAGCCG
1 AAAAGCCG
89264723 AAAAGCCG
1 AAAAGCCG
* *
89264731 AAATGCCA
1 AAAAGCCG
89264739 AAAAGCCG
1 AAAAGCCG
* *
89264747 AAATGTCG
1 AAAAGCCG
89264755 AAAAG
1 AAAAG
89264760 TCGGTATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:89265215 original size:27 final size:27
Alignment explanation
Indices: 89265174--89265286 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
89265164 GAGGAAGCGT
*
89265174 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
89265201 CCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
89265228 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
89265256 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
89265282 TCTGG
1 TCTGG
89265287 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.73
28 15 0.21
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:89265279 original size:54 final size:54
Alignment explanation
Indices: 89265172--89265286 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
89265162 TGGAGGAAGC
*
89265172 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
* * * * *
89265226 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ACCTGGTGACTCTGCCACATATATCT
89265280 GTTCTGG
1 GTTCTGG
89265287 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
Found at i:89269273 original size:26 final size:26
Alignment explanation
Indices: 89269237--89269423 Score: 304
Period size: 26 Copynumber: 7.2 Consensus size: 26
89269227 TGATACAAAT
89269237 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89269263 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89269289 CGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89269315 TGATAATA-GTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89269340 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
89269366 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
89269392 TGACAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
89269418 TGATAA
1 TGATAA
89269424 GAATTTCATG
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
25 24 0.16
26 128 0.84
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:89269404 original size:103 final size:103
Alignment explanation
Indices: 89269237--89269423 Score: 329
Period size: 103 Copynumber: 1.8 Consensus size: 103
89269227 TGATACAAAT
*
89269237 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCACGATAATAGGTTA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCACGACAATAGGTTA
89269302 GGTAAATGTTTCATGATAATAGTTAGGTAAATGTTCCA
66 GGTAAATGTTTCATGATAATAGTTAGGTAAATGTTCCA
* * * *
89269340 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCATGACAATGGGTTA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCACGACAATAGGTTA
89269405 GGTAAATGTTTCATGATAA
66 GGTAAATGTTTCATGATAA
89269424 GAATTTCATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 79 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (103 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAGGTAAATGTTCCACGACAATAGGTTA
GGTAAATGTTTCATGATAATAGTTAGGTAAATGTTCCA
Found at i:89270641 original size:16 final size:16
Alignment explanation
Indices: 89270602--89270642 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
89270592 ATTGGCAAAA
89270602 GCCGAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
*
89270618 GCCAAAAAGCCGAAAT
1 GCCGAAAAGCCGAAAT
*
89270634 GTCGAAAAG
1 GCCGAAAAG
89270643 TCGGTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.24, T:0.07
Consensus pattern (16 bp):
GCCGAAAAGCCGAAAT
Found at i:89270645 original size:8 final size:8
Alignment explanation
Indices: 89270598--89270642 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
89270588 CTAGATTGGC
89270598 AAAAGCCG
1 AAAAGCCG
89270606 AAAAGCCG
1 AAAAGCCG
* *
89270614 AAATGCCA
1 AAAAGCCG
89270622 AAAAGCCG
1 AAAAGCCG
* *
89270630 AAATGTCG
1 AAAAGCCG
89270638 AAAAG
1 AAAAG
89270643 TCGGTATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.51, C:0.20, G:0.22, T:0.07
Consensus pattern (8 bp):
AAAAGCCG
Found at i:89270939 original size:26 final size:26
Alignment explanation
Indices: 89270879--89270954 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
89270869 TAAAGTAGCT
* * *
89270879 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-GTGGA
89270907 AAATTACTGTTATACCCCTAGGTGGA
1 AAATTACTGTTATACCCCTAGGTGGA
*
89270933 AAATTACCGTTATACCCCTAGG
1 AAATTACTGTTATACCCCTAGG
89270955 GTTAATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 25 0.57
27 1 0.02
28 18 0.41
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGGTGGA
Found at i:89271098 original size:27 final size:27
Alignment explanation
Indices: 89271057--89271169 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
89271047 GAGGAAGCGT
*
89271057 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
89271084 CCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
89271111 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
89271139 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
89271165 TCTGG
1 TCTGG
89271170 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.73
28 15 0.21
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:89271162 original size:54 final size:54
Alignment explanation
Indices: 89271055--89271169 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
89271045 TGGAGGAAGC
*
89271055 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
* * * * *
89271109 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ACCTGGTGACTCTGCCACATATATCT
89271163 GTTCTGG
1 GTTCTGG
89271170 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
Found at i:89274191 original size:28 final size:28
Alignment explanation
Indices: 89274159--89274217 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
89274149 AGCACCTGTG
*
89274159 TTAATTCAGCCTGAGTCTGGGAAGGATT
1 TTAATTCAACCTGAGTCTGGGAAGGATT
89274187 TTAATTCAACCTGAGTCTGGGAAGGATT
1 TTAATTCAACCTGAGTCTGGGAAGGATT
89274215 TTA
1 TTA
89274218 GTGTGTACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (28 bp):
TTAATTCAACCTGAGTCTGGGAAGGATT
Found at i:89275203 original size:26 final size:26
Alignment explanation
Indices: 89275167--89275376 Score: 357
Period size: 26 Copynumber: 8.1 Consensus size: 26
89275157 ACAAATTGAA
89275167 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
*
89275193 AATAGGTTAGGTAAATGTTCCACGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
*
89275219 AATAGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
*
89275245 AATAGGTTTGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
89275271 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
89275297 AATAGGTTAGGTAAATGTTCCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
* *
89275323 AATGGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
* *
89275349 AATGGGTTAGGTAAATGTTTCATGAT
1 AATAGGTTAGGTAAATGTTCCATGAT
89275375 AA
1 AA
89275377 GAATTTCATG
Statistics
Matches: 176, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 176 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
AATAGGTTAGGTAAATGTTCCATGAT
Found at i:89276564 original size:8 final size:8
Alignment explanation
Indices: 89276551--89276603 Score: 79
Period size: 8 Copynumber: 6.6 Consensus size: 8
89276541 CTAGATTGGC
89276551 AAAAGCCG
1 AAAAGCCG
89276559 AAAAGCCG
1 AAAAGCCG
*
89276567 AAATGCCG
1 AAAAGCCG
89276575 AAAAGCCG
1 AAAAGCCG
*
89276583 AAATGCCG
1 AAAAGCCG
*
89276591 AAATGCCG
1 AAAAGCCG
89276599 AAAAG
1 AAAAG
89276604 TCGGTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.47, C:0.23, G:0.25, T:0.06
Consensus pattern (8 bp):
AAAAGCCG
Found at i:89276583 original size:24 final size:24
Alignment explanation
Indices: 89276551--89276603 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
89276541 CTAGATTGGC
89276551 AAAAGCCGAAAAGCCGAAATGCCG
1 AAAAGCCGAAAAGCCGAAATGCCG
*
89276575 AAAAGCCGAAATGCCGAAATGCCG
1 AAAAGCCGAAAAGCCGAAATGCCG
89276599 AAAAG
1 AAAAG
89276604 TCGGTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.25, T:0.06
Consensus pattern (24 bp):
AAAAGCCGAAAAGCCGAAATGCCG
Found at i:89277060 original size:27 final size:27
Alignment explanation
Indices: 89277019--89277131 Score: 120
Period size: 27 Copynumber: 4.2 Consensus size: 27
89277009 GAGGAAGCGT
*
89277019 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * *
89277046 CCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
89277073 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
89277101 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
89277127 TCTGG
1 TCTGG
89277132 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.73
28 15 0.21
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:89277124 original size:54 final size:54
Alignment explanation
Indices: 89277017--89277131 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
89277007 TGGAGGAAGC
*
89277017 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
* * * * *
89277071 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ACCTGGTGACTCTGCCACATATATCT
89277125 GTTCTGG
1 GTTCTGG
89277132 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGACCTGGTGACTCTGCCACATATATCT
Found at i:89278746 original size:11 final size:11
Alignment explanation
Indices: 89278730--89278755 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
89278720 AAGAGTTTTC
89278730 CAAACTCAGAT
1 CAAACTCAGAT
89278741 CAAACTCAGAT
1 CAAACTCAGAT
89278752 CAAA
1 CAAA
89278756 AGACATTATT
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:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (11 bp):
CAAACTCAGAT
Found at i:89278825 original size:72 final size:73
Alignment explanation
Indices: 89278670--89278865 Score: 322
Period size: 72 Copynumber: 2.7 Consensus size: 73
89278660 TCTATCACAG
* * *
89278670 AACTCAGATCAAAAGAAATTATTAAGCTGAAACCTATAAAAAAAACACTAAAGAGTTTTCCAAAC
1 AACTCAGATCAAAAGACATTATTGAGCTGAAACCTATAAAAAAAGCACTAAAGAGTTTTCCAAAC
89278735 TCAGATCA
66 TCAGATCA
* *
89278743 AACTCAGATCAAAAGACATTATTGAGCTGAAACCTAT-AAAAAAGCAGTAAAGAGTTTTCCGAAC
1 AACTCAGATCAAAAGACATTATTGAGCTGAAACCTATAAAAAAAGCACTAAAGAGTTTTCCAAAC
89278807 TCAGATCA
66 TCAGATCA
* *
89278815 AACTCAGATCAAAAGACATTATTGAGCTGGAACCTATCAAAAAAGCACTAA
1 AACTCAGATCAAAAGACATTATTGAGCTGAAACCTATAAAAAAAGCACTAA
89278866 TATATACACA
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
72 68 0.59
73 47 0.41
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.21
Consensus pattern (73 bp):
AACTCAGATCAAAAGACATTATTGAGCTGAAACCTATAAAAAAAGCACTAAAGAGTTTTCCAAAC
TCAGATCA
Found at i:89283580 original size:2 final size:2
Alignment explanation
Indices: 89283575--89283609 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
89283565 TTTTTTCCAT
89283575 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
89283610 TATATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:89289785 original size:13 final size:13
Alignment explanation
Indices: 89289769--89289821 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
89289759 TTTAAACCAA
89289769 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
89289782 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
89289795 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
89289808 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
89289821 A
1 A
89289822 TTGCCAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 26 0.76
14 4 0.12
ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:89290231 original size:25 final size:24
Alignment explanation
Indices: 89290203--89290250 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
89290193 AACAATAGGC
89290203 TTTTTATATATTTT-TAATTGTATAT
1 TTTTTATAT-TTTTATAATT-TATAT
89290228 TTTTTATATTTTTATAATTTATA
1 TTTTTATATTTTTATAATTTATA
89290251 AATTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTATATTTTTATAATTTATAT
Found at i:89290248 original size:15 final size:15
Alignment explanation
Indices: 89290230--89290281 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
89290220 TTGTATATTT
89290230 TTTATATTTTTATAA
1 TTTATATTTTTATAA
**
89290245 TTTATAAATTTATAA
1 TTTATATTTTTATAA
*
89290260 ATTATAACTTTTTATATA
1 TTTAT-A-TTTTTATA-A
89290278 TTTA
1 TTTA
89290282 AAATAATAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 17 0.61
16 1 0.04
17 6 0.21
18 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATATTTTTATAA
Found at i:89290290 original size:24 final size:25
Alignment explanation
Indices: 89290245--89290291 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
89290235 ATTTTTATAA
*
89290245 TTTATAAATTTATAAATTATAACTT
1 TTTATAAATTTATAAATAATAACTT
*
89290270 TTTATATATTTA-AAATAATAAC
1 TTTATAAATTTATAAATAATAAC
89290292 CTAAAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTATAAATTTATAAATAATAACTT
Found at i:89296204 original size:21 final size:22
Alignment explanation
Indices: 89296178--89296231 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
89296168 TAGCCTCCAG
**
89296178 CACGGGCGTGT-CCTAGGGTCA
1 CACGGGCGTGTCCCTAGGACCA
* *
89296199 CACGGGCATGTCCCTTGGACCA
1 CACGGGCGTGTCCCTAGGACCA
89296221 CACGGGCGTGT
1 CACGGGCGTGT
89296232 GAGCCTTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (22 bp):
CACGGGCGTGTCCCTAGGACCA
Found at i:89298696 original size:27 final size:26
Alignment explanation
Indices: 89298640--89298696 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
89298630 CAACCTTAAC
* *
89298640 CCTAGGGGTATATTAGTAATTTTACT
1 CCTAGGGGTAAATTAGTAATTTTACA
*
89298666 CCTAGGGGTAAATCT-GTAAATTTTCCA
1 CCTAGGGGTAAAT-TAGT-AATTTTACA
89298693 CCTA
1 CCTA
89298697 TAAAGGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (26 bp):
CCTAGGGGTAAATTAGTAATTTTACA
Found at i:89309700 original size:13 final size:14
Alignment explanation
Indices: 89309674--89309706 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
89309664 ATAAAATATA
89309674 AATTTATATTTAAT
1 AATTTATATTTAAT
89309688 AATTTAT-TTTAAT
1 AATTTATATTTAAT
89309701 ATATTT
1 A-ATTT
89309707 CATTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTATATTTAAT
Found at i:89332777 original size:14 final size:14
Alignment explanation
Indices: 89332765--89332811 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
89332755 ATCTTATTTG
89332765 TTTATTT-TTATTTA
1 TTTATTTATT-TTTA
89332779 TTTATTTATTTTCATTA
1 TTTATTTA-TTT--TTA
89332796 TTTATTTATTTTTA
1 TTTATTTATTTTTA
89332810 TT
1 TT
89332812 CTTCTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 12 0.41
15 1 0.03
16 5 0.17
17 11 0.38
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTATTTTTA
Found at i:89332780 original size:4 final size:4
Alignment explanation
Indices: 89332758--89332806 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
89332748 TCGATTGATC
*
89332758 TTAT TTGT TTA- TT-T TTAT TTAT TTAT TTAT TT-T CATTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT --TTAT TTAT TTAT
89332805 TT
1 TT
89332807 TTATTCTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 5 0.13
4 30 0.79
5 2 0.05
6 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:89332796 original size:17 final size:18
Alignment explanation
Indices: 89332758--89332807 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
89332748 TCGATTGATC
* *
89332758 TTATTTGTTTATTTTTAT
1 TTATTTATTTATTTTCAT
89332776 TTATTTATTTATTTTCA-
1 TTATTTATTTATTTTCAT
89332793 TTATTTATTTATTTT
1 TTATTTATTTATTTT
89332808 TATTCTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (18 bp):
TTATTTATTTATTTTCAT
Found at i:89335635 original size:47 final size:47
Alignment explanation
Indices: 89335572--89335931 Score: 528
Period size: 47 Copynumber: 7.6 Consensus size: 47
89335562 CCCTTCGGGA
* * *
89335572 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
89335619 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
89335666 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
89335713 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
89335760 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
89335809 CTTATCACATA-ACTACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATA-TACACTTTCACATTCATCACATTGGCCATTCGGC
* *
89335856 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
89335905 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
89335932 TATTCAAATA
Statistics
Matches: 290, Mismatches: 15, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
46 2 0.01
47 198 0.68
49 88 0.30
50 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:89335805 original size:96 final size:96
Alignment explanation
Indices: 89335572--89335931 Score: 536
Period size: 96 Copynumber: 3.8 Consensus size: 96
89335562 CCCTTCGGGA
* * * *
89335572 CTTATCACAT-T-TATACACTTCCACATCCATCACATTGGCCATTCGGCCCTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAC
89335635 ACTTTCACATTCATCACATTGGCCATTCGGC
66 ACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89335666 CTTATCTC--ATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACA
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACA
89335728 CA-TGTTCACATTCATCACATTGGCCATTCGGC
65 CACT-TTCACATTCATCACATTGGCCATTCGGC
89335760 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATA-ACTA
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC-A
* *
89335824 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATTGGCCATTCGGC
* * *
89335856 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAC
89335921 ACTTTCACATT
66 ACTTTCACATT
89335932 TATTCAAATA
Statistics
Matches: 241, Mismatches: 15, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
93 3 0.01
94 87 0.36
95 2 0.01
96 146 0.61
97 3 0.01
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAC
ACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:89335832 original size:143 final size:142
Alignment explanation
Indices: 89335586--89335931 Score: 511
Period size: 143 Copynumber: 2.4 Consensus size: 142
89335576 TCACATTTAT
* * *
89335586 ACACTTCCACATCCATCACATTGGCCATTCGGCCCTATCACATATATACACTTTCACATTCATCA
1 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
* * * *
89335651 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
66 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATCGGCCATTAGGCCTT
89335716 ATCAC-ACATAC
131 ATCACAACATAC
89335727 ACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCA
1 ACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCA
89335791 TCACATTGGCCATTCGGCCTTATCACATA-ACTACACT-TTCACATTCATCACATCGGCCATTAG
63 TCACATTGGCCATTCGGCCTTATCACATATA-TACA-TGTTCACATTCATCACATCGGCCATTAG
* *
89335854 GCCTTATCACATATATAT
126 GCCTTATCACA-ACATAC
* *
89335872 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
1 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATT
89335932 TATTCAAATA
Statistics
Matches: 186, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
140 1 0.01
141 36 0.19
142 1 0.01
143 105 0.56
144 1 0.01
145 41 0.22
146 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (142 bp):
ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATCGGCCATTAGGCCTT
ATCACAACATAC
Found at i:89338334 original size:25 final size:25
Alignment explanation
Indices: 89338299--89338348 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
89338289 GGAATTCGCA
89338299 CACACACAGTGC-CTCTAATCATTCG
1 CACACACAGTGCTCT-TAATCATTCG
* *
89338324 CACACATAGTGCTCTTATTCATTCG
1 CACACACAGTGCTCTTAATCATTCG
89338349 TTATTACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (25 bp):
CACACACAGTGCTCTTAATCATTCG
Found at i:89338581 original size:40 final size:40
Alignment explanation
Indices: 89338511--89338831 Score: 536
Period size: 40 Copynumber: 8.1 Consensus size: 40
89338501 CGAATACACG
* * * ** * *
89338511 TCACCAGCATGATTGCTCTTTGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
89338551 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
89338591 TCACTAGCATGAATGCTCTTCGGGACTTAACCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
89338631 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
89338671 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
89338711 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
89338751 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
89338791 TCACTAGTATGAATGCTCTTCGGGACTTAGCCCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
89338830 TC
1 TC
89338832 GTCGAGACCT
Statistics
Matches: 267, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
39 4 0.01
40 263 0.99
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:89338929 original size:38 final size:38
Alignment explanation
Indices: 89338887--89338959 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
89338877 ATTTTAATCT
*
89338887 GGACATAATCTCTGT-ACATAGCCATCGGGTCTTTACCC
1 GGACATAATCTCT-TCACATAGCCAGCGGGTCTTTACCC
* *
89338925 GGACATAATCTCTTCATATAGTCAGCGGGTCTTTA
1 GGACATAATCTCTTCACATAGCCAGCGGGTCTTTA
89338960 AACTCGGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 1 0.03
38 30 0.97
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (38 bp):
GGACATAATCTCTTCACATAGCCAGCGGGTCTTTACCC
Found at i:89341453 original size:47 final size:47
Alignment explanation
Indices: 89341390--89341892 Score: 758
Period size: 47 Copynumber: 10.6 Consensus size: 47
89341380 CCCTTCGGGA
* * * *
89341390 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
89341437 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* * * *
89341484 CTTATCTCATATATGCA-TGTTCACATTCATTACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTAGGC
* * *
89341531 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTAGGC
*
89341578 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
89341627 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
89341674 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
* *
89341723 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
*
89341770 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
89341817 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTAGGC
89341866 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
89341893 TATTCAAATA
Statistics
Matches: 430, Mismatches: 18, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
46 1 0.00
47 292 0.68
49 136 0.32
50 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:89341624 original size:96 final size:94
Alignment explanation
Indices: 89341390--89341892 Score: 767
Period size: 96 Copynumber: 5.3 Consensus size: 94
89341380 CCCTTCGGGA
* * *
89341390 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
*
89341455 TTTCACATTCATCACATTGGCCATTCGGC
66 TTTCACATTCATCACATTGGCCATTAGGC
* * * * *
89341484 CTTATCTCATATATGCA-TGTTCACATTCATTACATTGGCCATTCGGCCTTATCACACATACACA
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
*
89341548 -TGTTCACATTCATCACATTGGCCATTCGGC
65 CT-TTCACATTCATCACATTGGCCATTAGGC
89341578 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
89341643 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTAGGC
* *
89341674 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
89341739 ACTTTCACATTCATCACATCGGCTATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTAGGC
* *
89341770 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATAC
89341835 ACTTTCACATTCATCACATTGGCCATTAGGC
64 ACTTTCACATTCATCACATTGGCCATTAGGC
89341866 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
89341893 TATTCAAATA
Statistics
Matches: 381, Mismatches: 20, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
93 2 0.01
94 136 0.36
96 241 0.63
97 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATTGGCCATTAGGC
Found at i:89341650 original size:143 final size:142
Alignment explanation
Indices: 89341390--89341892 Score: 780
Period size: 143 Copynumber: 3.5 Consensus size: 142
89341380 CCCTTCGGGA
* * * *
89341390 CTTATCAC-ATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
* * *
89341454 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCA-TGTTCACATTCATTACA
66 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACA
* *
89341518 TTGGCCATTCGGC
130 TCGGCCATTAGGC
* * *
89341531 CTTATCAC-ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACAATATATACACT-TTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATAT
89341594 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
63 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
89341659 CATCGGCCATTAGGC
128 CATCGGCCATTAGGC
*
89341674 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
* * *
89341739 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
65 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
89341804 TCGGCCATTAGGC
130 TCGGCCATTAGGC
89341817 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
89341882 ACTTTCACATT
65 ACTTTCACATT
89341893 TATTCAAATA
Statistics
Matches: 337, Mismatches: 18, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
140 1 0.00
141 48 0.14
143 245 0.73
144 1 0.00
145 41 0.12
146 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (142 bp):
CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGC
Found at i:89343288 original size:85 final size:85
Alignment explanation
Indices: 89343159--89343337 Score: 340
Period size: 85 Copynumber: 2.1 Consensus size: 85
89343149 TATTTTATTG
* *
89343159 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTCATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
89343224 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
89343244 CCCATGCTCTTCATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTCATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
89343309 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
89343329 CCCATGCTC
1 CCCATGCTC
89343338 ATGGCCGGCC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTCATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:89347568 original size:38 final size:38
Alignment explanation
Indices: 89347517--89347756 Score: 354
Period size: 38 Copynumber: 6.3 Consensus size: 38
89347507 ATATTCGATG
*
89347517 TATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
89347555 TATATCCGGGTTAAATCCCGCAGGCTTCATGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
89347593 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
89347631 TATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
* * *
89347671 AATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGGTAC
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
89347709 TATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
89347747 TATATTCGGG
1 TATATCCGGG
89347757 CCTTCGTGCC
Statistics
Matches: 182, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 143 0.79
39 10 0.05
40 29 0.16
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:89347698 original size:78 final size:76
Alignment explanation
Indices: 89347518--89347745 Score: 357
Period size: 78 Copynumber: 3.0 Consensus size: 76
89347508 TATTCGATGT
*
89347518 ATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGTATTATATCCGGGTTAAATCCCGCAGGCTTC
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTC
* *
89347583 ATGCTGGTAAT
66 GTGCTGGTAAA
*
89347594 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGCTTAAAGACCCGCAGGCT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGG-TTAAA-TCCCGCAGGCT
89347659 TCGTGCTGGTAAA
64 TCGTGCTGGTAAA
* * * * *
89347672 ATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGGTACTATATCCGGGATAAATCCCGCAGGCCTA
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTC
89347737 GTGCTGGTA
66 GTGCTGGTA
89347746 TTATATTCGG
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
76 65 0.46
77 9 0.06
78 66 0.47
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (76 bp):
ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTC
GTGCTGGTAAA
Found at i:89347741 original size:116 final size:115
Alignment explanation
Indices: 89347517--89347757 Score: 367
Period size: 116 Copynumber: 2.1 Consensus size: 115
89347507 ATATTCGATG
* **
89347517 TATATCCGGG-TTAAATCCCGCAGGCTTCGTACTGGTATTATATCCGGGTTAAATCCCGCAGGCT
1 TATATCCGGGCTTAAAACCCGCAGGCTTCGTACTGGTAAAATATCCGGGTTAAATCCCGCAGGCT
* * *
89347581 TCATGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
66 TCATGCTGGTAATATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
* *
89347631 TATATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAATATCTGGGTTAAATCCCGCAGGC
1 TATATCCGGGCTTAAA-ACCCGCAGGCTTCGTACTGGTAAAATATCCGGGTTAAATCCCGCAGGC
* *
89347696 TTCGTGCTGGTACTATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
65 TTCATGCTGGTAATATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
*
89347747 TATATTCGGGC
1 TATATCCGGGC
89347758 CTTCGTGCCT
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
114 10 0.09
115 5 0.04
116 99 0.87
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.29
Consensus pattern (115 bp):
TATATCCGGGCTTAAAACCCGCAGGCTTCGTACTGGTAAAATATCCGGGTTAAATCCCGCAGGCT
TCATGCTGGTAATATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
Found at i:89347797 original size:43 final size:43
Alignment explanation
Indices: 89347749--89347860 Score: 197
Period size: 43 Copynumber: 2.6 Consensus size: 43
89347739 GCTGGTATTA
*
89347749 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATG
*
89347792 TATTCGGGCCTTGGTGCCTAGCAGGCTTCGTGCCGGTGATATG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATG
*
89347835 GATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
89347861 GTAATGCCGG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.11, C:0.26, G:0.35, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATATG
Found at i:89349482 original size:28 final size:27
Alignment explanation
Indices: 89349433--89349508 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
89349423 CTTTTTTATC
* *
89349433 TTGTCC-AATGGACTTA-CCCGTGTTT
1 TTGTCCTAACGGACTTATCTCGTGTTT
*
89349458 ATTGTCCTGACGGACTTATCTCGTGTTT
1 -TTGTCCTAACGGACTTATCTCGTGTTT
*
89349486 TTGTCCTAATGGACTTAATCTCG
1 TTGTCCTAACGGACTT-ATCTCG
89349509 GTTCTGTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.14
27 22 0.52
28 14 0.33
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (27 bp):
TTGTCCTAACGGACTTATCTCGTGTTT
Found at i:89349692 original size:44 final size:42
Alignment explanation
Indices: 89349612--89349694 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 42
89349602 TATTAGATGA
* *
89349612 TGCCATAGTCTTTCATCCATGGTCTTACTCATTATACCTGGC
1 TGCCATAGTCTTTCATCCATGGTCTTACACAGTATACCTGGC
* *
89349654 TGCCATAACGTCTTTCATCTATGGTCTTACACCGTATACCT
1 TGCCAT-A-GTCTTTCATCCATGGTCTTACACAGTATACCT
89349695 TATATTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 6 0.17
43 1 0.03
44 28 0.80
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.37
Consensus pattern (42 bp):
TGCCATAGTCTTTCATCCATGGTCTTACACAGTATACCTGGC
Found at i:89351500 original size:40 final size:40
Alignment explanation
Indices: 89351456--89351531 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
89351446 AGTGCCTCGC
* *
89351456 ATAGCCAAAGCTGTTCT-AATTTGCACACTTAGTGCTATTT
1 ATAGCCAAAGCTATTCTGAA-TCGCACACTTAGTGCTATTT
* *
89351496 ATAGCCGAAGCTATTTTGAATCGCACACTTAGTGCT
1 ATAGCCAAAGCTATTCTGAATCGCACACTTAGTGCT
89351532 GAACATAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (40 bp):
ATAGCCAAAGCTATTCTGAATCGCACACTTAGTGCTATTT
Found at i:89355224 original size:50 final size:50
Alignment explanation
Indices: 89355145--89355244 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
89355135 ATGTTTTCGG
*
89355145 AATGTCTGAACCTTTTACTCACAAATGATAATAACCTAATATCAGATCTA
1 AATGTCTGAACCTTTTACTCACAAATGATAATAACCCAATATCAGATCTA
* * * *
89355195 AATGTCTGAATCC-TTTACTCGCAACTGATAATAACCCGATCTCAGATCTA
1 AATGTCTGAA-CCTTTTACTCACAAATGATAATAACCCAATATCAGATCTA
89355245 TCTTTGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 42 0.95
51 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (50 bp):
AATGTCTGAACCTTTTACTCACAAATGATAATAACCCAATATCAGATCTA
Found at i:89366596 original size:12 final size:12
Alignment explanation
Indices: 89366579--89366614 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
89366569 CCAACAATTT
89366579 TCTCCTAAAATC
1 TCTCCTAAAATC
* *
89366591 TCTCCTCATATC
1 TCTCCTAAAATC
89366603 TCTCCTAAAATC
1 TCTCCTAAAATC
89366615 CCTCTTACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTCCTAAAATC
Found at i:89367963 original size:23 final size:22
Alignment explanation
Indices: 89367937--89367979 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
89367927 CCCATGCAAT
89367937 GCAACATA-ATATTATACATGGAG
1 GCAACATACATA-TA-ACATGGAG
89367960 GCAACATACATATAACATGG
1 GCAACATACATATAACATGG
89367980 CATGCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (22 bp):
GCAACATACATATAACATGGAG
Found at i:89368066 original size:27 final size:26
Alignment explanation
Indices: 89368042--89368117 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
89368032 TTACCCTACA
*
89368042 GGGGTATTTCGGTCATTCTATCCTAT
1 GGGGTATTTCGGTCATTTTATCCTAT
* *
89368068 GGAGGTATTTCAGTCATTTTACCCTAT
1 GG-GGTATTTCGGTCATTTTATCCTAT
*
89368095 GAAGGTATTTCGGTCATTTTATC
1 G-GGGTATTTCGGTCATTTTATC
89368118 ACATAAAGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (26 bp):
GGGGTATTTCGGTCATTTTATCCTAT
Found at i:89368126 original size:27 final size:26
Alignment explanation
Indices: 89368044--89368180 Score: 89
Period size: 27 Copynumber: 5.1 Consensus size: 26
89368034 ACCCTACAGG
* **
89368044 GGTATTTCGGTCATTCTATC-CTATGGA
1 GGTATTTC-GTCATTTTATCAC-ATAAA
* *
89368071 GGTATTTCAGTCATTTTA-CCCTATGAA
1 GGTATTTC-GTCATTTTATCAC-ATAAA
89368098 GGTATTTCGGTCATTTTATCACATAAA
1 GGTATTTC-GTCATTTTATCACATAAA
* ** *
89368125 GGCAAAATCGCCATTTTATCACATAAA
1 GG-TATTTCGTCATTTTATCACATAAA
* **
89368152 GGCAAAATCGTCATTTTATCACATAAA
1 GG-TATTTCGTCATTTTATCACATAAA
89368179 GG
1 GG
89368181 CAAAATTGTC
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.01
27 90 0.94
28 5 0.05
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (26 bp):
GGTATTTCGTCATTTTATCACATAAA
Found at i:89368181 original size:27 final size:27
Alignment explanation
Indices: 89368107--89368262 Score: 240
Period size: 27 Copynumber: 5.8 Consensus size: 27
89368097 AGGTATTTCG
89368107 GTCATTTTATCACATAAAGGCAAAATC
1 GTCATTTTATCACATAAAGGCAAAATC
*
89368134 GCCATTTTATCACATAAAGGCAAAATC
1 GTCATTTTATCACATAAAGGCAAAATC
*
89368161 GTCATTTTATCACATAAAGGCAAAATT
1 GTCATTTTATCACATAAAGGCAAAATC
* * *
89368188 GTCATTTTATCATATAAGGGCAAAATT
1 GTCATTTTATCACATAAAGGCAAAATC
* *
89368215 GTCATTTTATCACACAAGGGCAAAATC
1 GTCATTTTATCACATAAAGGCAAAATC
*
89368242 GTCATTTTATCACATGAAGGC
1 GTCATTTTATCACATAAAGGC
89368263 TCAGGTACGT
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 118 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (27 bp):
GTCATTTTATCACATAAAGGCAAAATC
Done.