Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 255 of 290
Found at i:87909356 original size:14 final size:15
Alignment explanation
Indices: 87909332--87909368 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
87909322 GTTTGTGGTA
87909332 TAAGAGTTTTGAG-TT
1 TAAG-GTTTTGAGATT
87909347 TAAGGTTTTGAGATT
1 TAAGGTTTTGAGATT
87909362 TAAGGTT
1 TAAGGTT
87909369 CAAAGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (15 bp):
TAAGGTTTTGAGATT
Found at i:87909408 original size:41 final size:42
Alignment explanation
Indices: 87909360--87909446 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 42
87909350 GGTTTTGAGA
* *
87909360 TTTAAGGTTCAAAGTTTATGGTTTAGGGTTA-GGGTTTAGGG
1 TTTAAGGTTCAAAGTCTATGGCTTAGGGTTAGGGGTTTAGGG
** * *
87909401 TTTAAGGTTTTATGTCTATGGCTTAGGTTTAGGGGTTTAGGG
1 TTTAAGGTTCAAAGTCTATGGCTTAGGGTTAGGGGTTTAGGG
87909443 TTTA
1 TTTA
87909447 GGGAAGATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 25 0.64
42 14 0.36
ACGTcount: A:0.20, C:0.03, G:0.32, T:0.45
Consensus pattern (42 bp):
TTTAAGGTTCAAAGTCTATGGCTTAGGGTTAGGGGTTTAGGG
Found at i:87909445 original size:7 final size:7
Alignment explanation
Indices: 87909373--87909449 Score: 61
Period size: 7 Copynumber: 11.1 Consensus size: 7
87909363 AAGGTTCAAA
*
87909373 GTTTATG
1 GTTTAGG
87909380 GTTTAGG
1 GTTTAGG
87909387 G-TTAGG
1 GTTTAGG
87909393 GTTTAGG
1 GTTTAGG
87909400 GTTTAAGG
1 GTTT-AGG
* *
87909408 TTTTA-T
1 GTTTAGG
* *
87909414 GTCTATG
1 GTTTAGG
*
87909421 GCTTA-G
1 GTTTAGG
87909427 GTTTAGGG
1 GTTTA-GG
87909435 GTTTAGG
1 GTTTAGG
87909442 GTTTAGG
1 GTTTAGG
87909449 G
1 G
87909450 AAGATCAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
6 14 0.25
7 30 0.54
8 12 0.21
ACGTcount: A:0.16, C:0.03, G:0.38, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:87910727 original size:25 final size:27
Alignment explanation
Indices: 87910676--87910730 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
87910666 AAATTTGTAA
* * *
87910676 CCCAACCTTTTTTCCTCTGCTTTTTTC
1 CCCAACCTTTTCTCCTCTGATTCTTTC
87910703 CCCAACCTTTTCTCCT-T-ATTCTTTC
1 CCCAACCTTTTCTCCTCTGATTCTTTC
87910728 CCC
1 CCC
87910731 CCCCGAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.36
26 1 0.04
27 15 0.60
ACGTcount: A:0.09, C:0.42, G:0.02, T:0.47
Consensus pattern (27 bp):
CCCAACCTTTTCTCCTCTGATTCTTTC
Found at i:87912356 original size:43 final size:42
Alignment explanation
Indices: 87912306--87912397 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
87912296 TCCCAGACGT
* ** * *
87912306 GGTCTTACATGTAATTGAATGTCGATGCCTATGTCCCAAACAA
1 GGTCTTACATGAAATCAAATAT-GATGCCGATGTCCCAAACAA
* *
87912349 GGTCTTACATGAAATCAAATATGATGCCGATGTCCCAGACAT
1 GGTCTTACATGAAATCAAATATGATGCCGATGTCCCAAACAA
87912391 GGTCTTA
1 GGTCTTA
87912398 TACGTAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 24 0.57
43 18 0.43
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (42 bp):
GGTCTTACATGAAATCAAATATGATGCCGATGTCCCAAACAA
Found at i:87912395 original size:42 final size:43
Alignment explanation
Indices: 87912295--87912397 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
87912285 CAATGCTGAC
* * ** * *
87912295 GTCCCAGACGTGGTCTTACATGTAATTGAATGTCGATGCCTAT
1 GTCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCGAT
* *
87912338 GTCCCAAACAAGGTCTTACATGAAATCAAATAT-GATGCCGAT
1 GTCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCGAT
87912380 GTCCCAGACATGGTCTTA
1 GTCCCAGACATGGTCTTA
87912398 TACGTAAATC
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 24 0.48
43 26 0.52
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGAAATCAAATATCGATGCCGAT
Found at i:87914708 original size:13 final size:14
Alignment explanation
Indices: 87914692--87914720 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
87914682 TTTTAAATAT
87914692 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
87914705 TTATAATGGTTTAA
1 TTATAATGGTTTAA
87914719 TT
1 TT
87914721 CATCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:87915566 original size:43 final size:43
Alignment explanation
Indices: 87915499--87915701 Score: 136
Period size: 43 Copynumber: 4.7 Consensus size: 43
87915489 TTTTTAGCGG
**
87915499 CATTTGTGTGAAAAGAGCTGCTAAAGGTCACGTTCTTCAGCAA
1 CATTTGTGTGAAAAGAGCCACTAAAGGTCACGTTCTTCAGCAA
* * **
87915542 CATTTGTGTGAAAAGTGCCACTAAAGGTCACGTTCTTTAGCGG
1 CATTTGTGTGAAAAGAGCCACTAAAGGTCACGTTCTTCAGCAA
* * ** * * * * ***
87915585 CGTTTGTGTGAAAGGCTCCGCTAAAGATCACATTCTTTAGTGG
1 CATTTGTGTGAAAAGAGCCACTAAAGGTCACGTTCTTCAGCAA
* * * * ** * * **
87915628 CTTTTTTGTGAAAGGCGCTGCTCAAGGTCACGTTCTTTAGCGG
1 CATTTGTGTGAAAAGAGCCACTAAAGGTCACGTTCTTCAGCAA
* * *
87915671 CGTTTGTGTGAAAGGAGCCGCTAAAGGTCAC
1 CATTTGTGTGAAAAGAGCCACTAAAGGTCAC
87915702 TTTTTTAACA
Statistics
Matches: 133, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 133 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CATTTGTGTGAAAAGAGCCACTAAAGGTCACGTTCTTCAGCAA
Found at i:87915638 original size:86 final size:86
Alignment explanation
Indices: 87915491--87915701 Score: 246
Period size: 86 Copynumber: 2.5 Consensus size: 86
87915481 GCTCATGTTT
* *
87915491 TTTAGCGGCATTTGTGTGAAAAGAGCT--GCTAAAGGTCACGTTCTTCAGCAACATTTGTGTGAA
1 TTTAGCGGCGTTTGTGTG-AAAG-GCTCCGCTAAAGGTCACATTCTTCAGCAACATTTGTGTGAA
*
87915554 AAGTGCCACTAAAGGTCACGTTC
64 AAGCGCCACTAAAGGTCACGTTC
* * *** * * *
87915577 TTTAGCGGCGTTTGTGTGAAAGGCTCCGCTAAAGATCACATTCTTTAGTGGCTTTTTTGTGAAAG
1 TTTAGCGGCGTTTGTGTGAAAGGCTCCGCTAAAGGTCACATTCTTCAGCAACATTTGTGTGAAAA
** *
87915642 GCGCTGCTCAAGGTCACGTTC
66 GCGCCACTAAAGGTCACGTTC
**
87915663 TTTAGCGGCGTTTGTGTGAAAGGAGCCGCTAAAGGTCAC
1 TTTAGCGGCGTTTGTGTGAAAGGCTCCGCTAAAGGTCAC
87915702 TTTTTTAACA
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
84 3 0.03
85 4 0.04
86 99 0.93
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGTGAAAGGCTCCGCTAAAGGTCACATTCTTCAGCAACATTTGTGTGAAAA
GCGCCACTAAAGGTCACGTTC
Found at i:87916441 original size:86 final size:86
Alignment explanation
Indices: 87916334--87916679 Score: 683
Period size: 86 Copynumber: 4.0 Consensus size: 86
87916324 GTCAAATATG
*
87916334 TTGGACACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
1 TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
87916399 ATTTCATTCCACTTTTCACAT
66 ATTTCATTCCACTTTTCACAT
87916420 TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
1 TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
87916485 ATTTCATTCCACTTTTCACAT
66 ATTTCATTCCACTTTTCACAT
87916506 TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
1 TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
87916571 ATTTCATTCCACTTTTCACAT
66 ATTTCATTCCACTTTTCACAT
87916592 TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
1 TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
87916657 ATTTCATTCCACTTTTCACAT
66 ATTTCATTCCACTTTTCACAT
87916678 TT
1 TT
87916680 CTCAACTTGT
Statistics
Matches: 259, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 259 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (86 bp):
TTGGGCACATAACATCATATGCATGCCAAACAAACATGGATGGGCTTATCACCATATAAACTTTC
ATTTCATTCCACTTTTCACAT
Found at i:87917649 original size:38 final size:38
Alignment explanation
Indices: 87917607--87917684 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
87917597 CTGACTGTAG
87917607 GTTGATTAATCGATCTCTTTCTAATTAAAACCCCTATT
1 GTTGATTAATCGATCTCTTTCTAATTAAAACCCCTATT
87917645 GTTGATTAATCGATCTCTTTCTAATTAAAACCCCTATT
1 GTTGATTAATCGATCTCTTTCTAATTAAAACCCCTATT
87917683 GT
1 GT
87917685 CACATTAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (38 bp):
GTTGATTAATCGATCTCTTTCTAATTAAAACCCCTATT
Found at i:87930595 original size:45 final size:45
Alignment explanation
Indices: 87930544--87930630 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
87930534 CCAAAACATG
87930544 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
* *
87930589 TGTCACATATATCATGAACTCAGACCACAACTCAATGGGTTC
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTC
87930631 AGATTACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
Found at i:87931748 original size:13 final size:13
Alignment explanation
Indices: 87931730--87931780 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
87931720 ACACTTAAAT
*
87931730 TTTTCCAAAGCAC
1 TTTTCAAAAGCAC
*
87931743 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
87931756 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
87931769 TTTTCAAAAGCA
1 TTTTCAAAAGCA
87931781 ATGAAGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 4 0.12
13 26 0.79
14 3 0.09
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:87940771 original size:54 final size:53
Alignment explanation
Indices: 87940685--87940839 Score: 204
Period size: 54 Copynumber: 2.9 Consensus size: 53
87940675 TGGCAACATT
*
87940685 TGATATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGATG
1 TGATATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGTGAGATG
** *
87940738 TGATCATGTGATTTCCATATAAGACCATAGCTGGGCTATGGCATCGGAGAGATG
1 TGAT-ATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGTGAGATG
* * ** *
87940792 TGATTATGTG-CTTCTGTATAATACCATATTTGGGATATGGCATCGGTG
1 TGA-TATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGTG
87940840 CCATATGTGC
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
53 34 0.39
54 53 0.60
55 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (53 bp):
TGATATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGTGAGATG
Found at i:87940895 original size:47 final size:47
Alignment explanation
Indices: 87940796--87940886 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
87940786 GAGATGTGAT
* * * *
87940796 TATGTGCTTCTGTATAATACCATATTTGGGATATGGCATCGGTGCCA
1 TATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAGTGCCA
*
87940843 TATGTGCTACTGTATAAGACCATATCTGGGATATGGTATCAGTG
1 TATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAGTG
87940887 TGGTATGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (47 bp):
TATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAGTGCCA
Found at i:87955490 original size:40 final size:40
Alignment explanation
Indices: 87955446--87955521 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
87955436 ACTATGTTTG
* ** * *
87955446 GCACTTAATGTGCGTTTTATAATAGCTTCGGCTATAAATA
1 GCACTCAATGTGCGAATTAGAATAGCTTCAGCTATAAATA
*
87955486 GCACTCAATGTGTGAATTAGAATAGCTTCAGCTATA
1 GCACTCAATGTGCGAATTAGAATAGCTTCAGCTATA
87955522 TGAGGCACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (40 bp):
GCACTCAATGTGCGAATTAGAATAGCTTCAGCTATAAATA
Found at i:87965297 original size:27 final size:26
Alignment explanation
Indices: 87965207--87965300 Score: 134
Period size: 26 Copynumber: 3.6 Consensus size: 26
87965197 GAAATCTCCA
* *
87965207 ATAGGGTAAAATGACTATAATACACT
1 ATAGGGTAAAATGACTGTAATACCCT
87965233 ATAGGGTAAAATGACTGTAATACCCT
1 ATAGGGTAAAATGACTGTAATACCCT
*
87965259 ATAGGGTGAAATGACTGTAATACCCCT
1 ATAGGGTAAAATGACTGTAATA-CCCT
* *
87965286 GTAAGGTAAAATGAC
1 ATAGGGTAAAATGAC
87965301 AATTTTGCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
26 45 0.74
27 16 0.26
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (26 bp):
ATAGGGTAAAATGACTGTAATACCCT
Found at i:87965377 original size:81 final size:80
Alignment explanation
Indices: 87965292--87965475 Score: 260
Period size: 81 Copynumber: 2.3 Consensus size: 80
87965282 CCCTGTAAGG
*
87965292 TAAAATGACAATTTTGCTCTTATGTGGCAAAATGACTATTTTGCCCTTATATGTTAAAATGACAA
1 TAAAATGACAATTTTGCCCTTATGTGGCAAAATGACTATTTTGCCCTTATATGTTAAAATGACAA
*
87965357 TTTTTCCCTTATGTGA
66 TTTTT-CCTTATCTGA
* * * * * ***
87965373 TAAAATGACGATTTTTCCCTTATGTGGCAAAATGGCTATTTTGTCCTTATGTGTTAAAATGGGGA
1 TAAAATGACAATTTTGCCCTTATGTGGCAAAATGACTATTTTGCCCTTATATGTTAAAATGACAA
*
87965438 TTTTTCCTTATCTGG
66 TTTTTCCTTATCTGA
87965453 TAAAATGACAATTTTGCCCTTAT
1 TAAAATGACAATTTTGCCCTTAT
87965476 ATGGTAGGAT
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 29 0.32
81 61 0.68
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (80 bp):
TAAAATGACAATTTTGCCCTTATGTGGCAAAATGACTATTTTGCCCTTATATGTTAAAATGACAA
TTTTTCCTTATCTGA
Found at i:87965488 original size:27 final size:27
Alignment explanation
Indices: 87965290--87965481 Score: 197
Period size: 27 Copynumber: 7.1 Consensus size: 27
87965280 ACCCCTGTAA
*
87965290 GGTAAAATGACAATTTTGCTCTTATGT
1 GGTAAAATGACAATTTTGCCCTTATGT
* * *
87965317 GGCAAAATGACTATTTTGCCCTTATAT
1 GGTAAAATGACAATTTTGCCCTTATGT
* *
87965344 GTTAAAATGACAATTTTTCCCTTATGT
1 GGTAAAATGACAATTTTGCCCTTATGT
* * *
87965371 GATAAAATGACGATTTTTCCCTTATGT
1 GGTAAAATGACAATTTTGCCCTTATGT
* * * *
87965398 GGCAAAATGGCTATTTTGTCCTTATGT
1 GGTAAAATGACAATTTTGCCCTTATGT
* *** * *
87965425 GTTAAAATGGGGATTTT-TCCTTATCT
1 GGTAAAATGACAATTTTGCCCTTATGT
*
87965451 GGTAAAATGACAATTTTGCCCTTATAT
1 GGTAAAATGACAATTTTGCCCTTATGT
87965478 GGTA
1 GGTA
87965482 GGATGACTTT
Statistics
Matches: 136, Mismatches: 28, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 21 0.15
27 115 0.85
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (27 bp):
GGTAAAATGACAATTTTGCCCTTATGT
Found at i:87965877 original size:18 final size:18
Alignment explanation
Indices: 87965854--87965894 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
87965844 TTACATACTA
*
87965854 TTACTGCTATTGCACTTT
1 TTACTGCTATTGCACTGT
* *
87965872 TTACTGTTATTGTACTGT
1 TTACTGCTATTGCACTGT
87965890 TTACT
1 TTACT
87965895 ATTACTGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (18 bp):
TTACTGCTATTGCACTGT
Found at i:87969150 original size:18 final size:18
Alignment explanation
Indices: 87969123--87969159 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
87969113 GGTTCCTCCA
87969123 ACCTGCATTATAAGTATT
1 ACCTGCATTATAAGTATT
*
87969141 ACCTGTATTATAAGTATT
1 ACCTGCATTATAAGTATT
87969159 A
1 A
87969160 TTGTATGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (18 bp):
ACCTGCATTATAAGTATT
Found at i:87970537 original size:13 final size:13
Alignment explanation
Indices: 87970519--87970543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87970509 GTTGTTTATT
87970519 AAACTAATTAACG
1 AAACTAATTAACG
87970532 AAACTAATTAAC
1 AAACTAATTAAC
87970544 TAACTAAACT
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:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (13 bp):
AAACTAATTAACG
Found at i:87973034 original size:13 final size:12
Alignment explanation
Indices: 87973015--87973046 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
87973005 GGTTGTTTAT
87973015 TAACTAATTAAC
1 TAACTAATTAAC
87973027 TAAACTAATTAAC
1 T-AACTAATTAAC
87973040 TAACTAA
1 TAACTAA
87973047 ACTAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (12 bp):
TAACTAATTAAC
Found at i:87975953 original size:6 final size:6
Alignment explanation
Indices: 87975944--87975982 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
87975934 AATAAAATTG
*
87975944 AAATAA AAATAG AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
87975983 GATAAGAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:87975958 original size:12 final size:12
Alignment explanation
Indices: 87975937--87975978 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
87975927 GGAAAATAAT
*
87975937 AAAATTGAAATA
1 AAAATAGAAATA
87975949 AAAATAGAAATA
1 AAAATAGAAATA
*
87975961 AAAATAAAAATA
1 AAAATAGAAATA
87975973 AAAATA
1 AAAATA
87975979 AAAAGATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (12 bp):
AAAATAGAAATA
Found at i:87988376 original size:26 final size:26
Alignment explanation
Indices: 87988329--87988410 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
87988319 ACTGTTACTA
* *
87988329 GCAGCTTTGCTGCGTTACTATTGCTG
1 GCAGCTTTGCTGCGATATTATTGCTG
* * *
87988355 GTAGCTTTGCTGCGATATTATTACTA
1 GCAGCTTTGCTGCGATATTATTGCTG
* *
87988381 GCAGCTTTGTTGTGATATTAGTGTGCTG
1 GCAGCTTTGCTGCGATATTA-T-TGCTG
87988409 GC
1 GC
87988411 TGGGTGGGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
26 38 0.86
27 1 0.02
28 5 0.11
ACGTcount: A:0.16, C:0.17, G:0.27, T:0.40
Consensus pattern (26 bp):
GCAGCTTTGCTGCGATATTATTGCTG
Found at i:87994688 original size:43 final size:42
Alignment explanation
Indices: 87994590--87994693 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
87994580 TATCGAGTTG
* * * *
87994590 TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTTAA
1 TGATTACATGTAAGACCATGTCTAGGACAGTGGCATCGATAA
* * *
87994632 TCGATTTCGTGTAAGACCTTGTCTAGGACAGTGGCATCGATATA
1 T-GATTACATGTAAGACCATGTCTAGGACAGTGGCATCGATA-A
* *
87994676 TGATAACATGTAAAACCA
1 TGATTACATGTAAGACCA
87994694 CATCTGGGAT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
42 1 0.02
43 45 0.94
44 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (42 bp):
TGATTACATGTAAGACCATGTCTAGGACAGTGGCATCGATAA
Found at i:88004408 original size:43 final size:43
Alignment explanation
Indices: 88004360--88004441 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
88004350 GGTTATCGAG
*
88004360 TTGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTA
1 TTGTGATTACATGTAAGACCATGTCTAGGACATTAGCATTGTA
** *
88004403 TTGTGATTATGTGTAAGACCATGTCTGGGACATTAGCAT
1 TTGTGATTACATGTAAGACCATGTCTAGGACATTAGCAT
88004442 CGTTAATCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (43 bp):
TTGTGATTACATGTAAGACCATGTCTAGGACATTAGCATTGTA
Found at i:88004460 original size:43 final size:43
Alignment explanation
Indices: 88004371--88004475 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 43
88004361 TGTGATTACA
* * * * *
88004371 TGTAAGACCATGTCTAGGACATTGGCATTGTATTGTGATTATG
1 TGTAAGACCATGTCTGGGACATTAGCATCGTAATGCGATTATG
88004414 TGTAAGACCATGTCTGGGACATTAGCATCGTTAAT-CGATT-TCG
1 TGTAAGACCATGTCTGGGACATTAGCATCG-TAATGCGATTAT-G
* *
88004457 TGTAACACCTTGTCTGGGA
1 TGTAAGACCATGTCTGGGA
88004476 TAGTGGCATC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 1 0.02
43 49 0.92
44 3 0.06
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATTAGCATCGTAATGCGATTATG
Found at i:88006320 original size:40 final size:40
Alignment explanation
Indices: 88006175--88006379 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
88006165 CGCTTGGACA
* * * * * *
88006175 AAAAATGCCGCTATAGATTGAGCATTAGTGACGCTTT-T-
1 AAAAACGCCGCTATAGGTCGACCATTAGCGGCGCTTTATG
* * * *
88006213 AAAAACGCCACTATAGGTCAACCATTAGCTGCGCATTT-TT
1 AAAAACGCCGCTATAGGTCGACCATTAGCGGCGC-TTTATG
* *
88006253 AAAAAGCACCGCTATAGGTCGAGCATTAGCGGCGCTTTATG
1 AAAAA-CGCCGCTATAGGTCGACCATTAGCGGCGCTTTATG
* * *
88006294 AAAAACGTCGCTATAGATCGACCATTAGTGGCGCTTTATG
1 AAAAACGCCGCTATAGGTCGACCATTAGCGGCGCTTTATG
* *
88006334 AAAAACGCCACTATAGGTCGACCATTAGAGGCGCTTTATG
1 AAAAACGCCGCTATAGGTCGACCATTAGCGGCGCTTTATG
88006374 AAAAAC
1 AAAAAC
88006380 ACCGAAAAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
38 25 0.18
39 4 0.03
40 80 0.58
41 30 0.22
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGCTATAGGTCGACCATTAGCGGCGCTTTATG
Found at i:88006870 original size:7 final size:7
Alignment explanation
Indices: 88006856--88006888 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
88006846 CTATGTTAAA
88006856 GTTTATG
1 GTTTATG
*
88006863 GATTATG
1 GTTTATG
88006870 GTTTATG
1 GTTTATG
88006877 GTTTATG
1 GTTTATG
88006884 GTTTA
1 GTTTA
88006889 AGGGTTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (7 bp):
GTTTATG
Found at i:88007831 original size:20 final size:20
Alignment explanation
Indices: 88007806--88007845 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
88007796 CAAAAACGCC
88007806 GCAAAAAATCATTTTACTTG
1 GCAAAAAATCATTTTACTTG
88007826 GCAAAAAATCATTTTACTTG
1 GCAAAAAATCATTTTACTTG
88007846 AAAAGAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
GCAAAAAATCATTTTACTTG
Found at i:88007942 original size:13 final size:13
Alignment explanation
Indices: 88007924--88007956 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
88007914 ATCCCTTATT
88007924 AATTTTATCCCCA
1 AATTTTATCCCCA
*
88007937 AATTTTATCCCTA
1 AATTTTATCCCCA
88007950 AATTTTA
1 AATTTTA
88007957 CCCATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTTTATCCCCA
Found at i:88008038 original size:14 final size:14
Alignment explanation
Indices: 88008019--88008048 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88008009 CTAATTTTTC
88008019 CCCCAAATCAAAAT
1 CCCCAAATCAAAAT
*
88008033 CCCCAAATCGAAAT
1 CCCCAAATCAAAAT
88008047 CC
1 CC
88008049 TTCCACCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.13
Consensus pattern (14 bp):
CCCCAAATCAAAAT
Found at i:88008135 original size:14 final size:14
Alignment explanation
Indices: 88008116--88008159 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
88008106 ATTTCCTGCT
88008116 TCTCTAAATCTCCA
1 TCTCTAAATCTCCA
*
88008130 TCTCTAAATCTCCT
1 TCTCTAAATCTCCA
*
88008144 TCTCTAAATTTCCA
1 TCTCTAAATCTCCA
88008158 TC
1 TC
88008160 CCTTTGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (14 bp):
TCTCTAAATCTCCA
Found at i:88010728 original size:46 final size:45
Alignment explanation
Indices: 88010678--88010853 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 45
88010668 TGTTTGGGCA
*
88010678 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AAACG
*** * ** *
88010724 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACT-AGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TGAAACG
* *
88010771 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGA-AACG
* * *
88010817 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
88010854 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
44 1 0.01
45 2 0.02
46 70 0.65
47 33 0.31
48 1 0.01
49 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAACG
Found at i:88010833 original size:93 final size:93
Alignment explanation
Indices: 88010674--88010845 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
88010664 AGGATGTTTG
*** *
88010674 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACACCCGAACTCATTGAG
88010739 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
88010767 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AGAACACCCGAGCTCATTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCA-AACACCCGAACTCATTGA
88010831 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
88010846 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACACCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:88014874 original size:43 final size:43
Alignment explanation
Indices: 88014819--88015004 Score: 216
Period size: 42 Copynumber: 4.4 Consensus size: 43
88014809 AAAACACGAC
* * *
88014819 CTTTATCGGTGTTTTTGTGGAAAGCGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGTTTTTGTGGAAAGCGCCGCTAAAGGTCATGTT
* * *
88014862 CTTTAGCGGTGTTTTTGGGGAAAGCACCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTGTGGAAAGCGCCGCTAAAGGTCATGTT
* *
88014905 CTTTAGCGGCG--TTTGTGGTGAAGCGCTGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTGTGG-AAAGCGCCGCTAAAGGTCATGTT
** * * *
88014947 CTTTAGTAGCATTTGTG-GGAAAGTGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTGTGGAAAGCGCCGCTAAAGGTCATGTT
*
88014989 CTTTAGCGGCTTTTTT
1 CTTTAGCGGCGTTTTT
88015005 TACATAAACG
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
41 6 0.05
42 60 0.50
43 51 0.43
44 3 0.03
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.36
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTGTGGAAAGCGCCGCTAAAGGTCATGTT
Found at i:88014947 original size:42 final size:42
Alignment explanation
Indices: 88014832--88014998 Score: 221
Period size: 42 Copynumber: 4.0 Consensus size: 42
88014822 TATCGGTGTT
* *
88014832 TTTGT-GGAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGTG
1 TTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCG
* *
88014873 TTTTTGGGGAAAGCACCGCTAAAGGTCATGTTCTTTAGCGGCG
1 TTTGT-GGGAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCG
* ** *
88014916 TTTGTGGTG-AAGCGCTGCTAAAGGTCATGTTCTTTAGTAGCA
1 TTTGTGG-GAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCG
*
88014958 TTTGTGGGAAAGTGCCGCTAAAGGTCATGTTCTTTAGCGGC
1 TTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGC
88014999 TTTTTTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.05
42 65 0.60
43 38 0.35
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (42 bp):
TTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCG
Found at i:88015922 original size:2 final size:2
Alignment explanation
Indices: 88015915--88015962 Score: 51
Period size: 2 Copynumber: 22.5 Consensus size: 2
88015905 ACCCTTTATT
* *
88015915 TA TA TA TA TA TA TA TA TCA TA GGA TA TGA TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA -TA TA T-A TA TA TA TA TA TA TA
88015958 TA TA T
1 TA TA T
88015963 CAATCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 34 0.87
3 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:88023405 original size:11 final size:11
Alignment explanation
Indices: 88023389--88023418 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
88023379 CTGATCAAAG
88023389 CTTTTCTGGCA
1 CTTTTCTGGCA
88023400 CTTTTCTGGCA
1 CTTTTCTGGCA
88023411 CTTTTCTG
1 CTTTTCTG
88023419 ACCACTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.07, C:0.27, G:0.17, T:0.50
Consensus pattern (11 bp):
CTTTTCTGGCA
Found at i:88035779 original size:28 final size:28
Alignment explanation
Indices: 88035739--88035847 Score: 139
Period size: 28 Copynumber: 3.9 Consensus size: 28
88035729 TGGGAAGTAG
88035739 TTGGGCCTGATGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
88035767 TTGGGTCC-GATGGGCCATATGAATGTGA
1 TTGGG-CCTGATGGGCCATATGAATGTGA
* * * *
88035795 TTGGGCCTAATGGGCTATGTGAATGAGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
* *
88035823 TTGGGCCTAAATGGGCCAAATGAAT
1 TTGGGCCT-GATGGGCCATATGAAT
88035848 AATTGTGGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
27 2 0.03
28 54 0.76
29 15 0.21
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.28
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAATGTGA
Found at i:88036185 original size:26 final size:27
Alignment explanation
Indices: 88036144--88036390 Score: 252
Period size: 27 Copynumber: 9.2 Consensus size: 27
88036134 TAATAAAGAG
*
88036144 AAATTACTGAAATACCCTCGATTTATA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
88036171 AAATTAC-AAAATACCCCCGATTAGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
88036197 AAATTACTGGAATACCCTC-AATTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* *
88036223 AAATTAGTGAAATACCCTGGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
88036250 AAATTA-TCAAAATA-CCTCCGATTTGTG
1 AAATTACT-GAAATACCCT-CGATTTGTA
* * *
88036277 AAATTACTAAAACACTCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
88036304 AAATTACTGAAATAACCC-CAAATTGTG
1 AAATTACTGAAAT-ACCCTCGATTTGTA
*
88036331 AAATTACTGAAACACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
88036358 AAATTACTGAAATACCCTTGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
88036385 AGAATT
1 A-AATT
88036391 GTTGTTTTTT
Statistics
Matches: 178, Mismatches: 33, Indels: 17
0.78 0.14 0.07
Matches are distributed among these distances:
26 50 0.28
27 118 0.66
28 10 0.06
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:88044001 original size:27 final size:27
Alignment explanation
Indices: 88043983--88044042 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
88043973 TATGTCGGTC
*
88043983 ATTTTACAGTACAAAGGTATTTCAATA
1 ATTTTACAGTACAAAGGTATGTCAATA
* * * *
88044010 ATTTTACATTACAAGGGTATTTCTATA
1 ATTTTACAGTACAAAGGTATGTCAATA
88044037 ATTTTA
1 ATTTTA
88044043 TAAATCGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (27 bp):
ATTTTACAGTACAAAGGTATGTCAATA
Found at i:88044054 original size:27 final size:28
Alignment explanation
Indices: 88043998--88044086 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 28
88043988 ACAGTACAAA
* * *
88043998 GGTATTTC-AATAATTTTAC-ATTACAAG
1 GGTATTTCTAGTAATTTTACAAAT-CGAG
* *
88044025 GGTATTTCTA-TAATTTTATAAATCGGG
1 GGTATTTCTAGTAATTTTACAAATCGAG
*
88044052 GGTGTTT-TAGTAATTTTACAAATCGAG
1 GGTATTTCTAGTAATTTTACAAATCGAG
*
88044079 AGTATTTC
1 GGTATTTC
88044087 GCAAGCACGT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
26 2 0.04
27 44 0.90
28 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (28 bp):
GGTATTTCTAGTAATTTTACAAATCGAG
Found at i:88048813 original size:16 final size:15
Alignment explanation
Indices: 88048792--88048824 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
88048782 TTTGCAATTT
88048792 AATCCTAATTACTCAA
1 AATCCTAATTACT-AA
88048808 AATCCTAATTACTAA
1 AATCCTAATTACTAA
88048823 AA
1 AA
88048825 CGATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCTAATTACTAA
Found at i:88053167 original size:20 final size:22
Alignment explanation
Indices: 88053129--88053170 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
88053119 TAGGAGAGTG
88053129 AAATGAATGAAAAACGGGCCAA
1 AAATGAATGAAAAACGGGCCAA
*
88053151 AAATGAA-G-AAAATGGGCCAA
1 AAATGAATGAAAAACGGGCCAA
88053171 CATACGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.55, C:0.12, G:0.24, T:0.10
Consensus pattern (22 bp):
AAATGAATGAAAAACGGGCCAA
Found at i:88055659 original size:25 final size:26
Alignment explanation
Indices: 88055621--88055674 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
88055611 ATAAAACCTA
*
88055621 AAAATGAAATAGTA-TTAAAGGAAAAT
1 AAAATGAAAAAGTACTTAAA-GAAAAT
*
88055647 AAAA-GAAAAAGTACTTAAAGAAGAT
1 AAAATGAAAAAGTACTTAAAGAAAAT
88055672 AAA
1 AAA
88055675 TAAAGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.19
Consensus pattern (26 bp):
AAAATGAAAAAGTACTTAAAGAAAAT
Found at i:88064218 original size:41 final size:40
Alignment explanation
Indices: 88064133--88064311 Score: 150
Period size: 41 Copynumber: 4.4 Consensus size: 40
88064123 TCGATATCTT
* * * * * *
88064133 ACACACTAAGTGCCAATACATAGTCGAAGCTGTTACAATCTC
1 ACACACTAAGTGCC-ATACTTAGCCAAAGCTATT-CAGTATC
* *
88064175 ACACACTAAGTGCCATACTTAGCCGAAGCTATCTCAGTTTC
1 ACACACTAAGTGCCATACTTAGCCAAAGCTAT-TCAGTATC
* *
88064216 ACACACTAAGTGCCATATTTAGCCAAAGCTATT-ACTGATC
1 ACACACTAAGTGCCATACTTAGCCAAAGCTATTCAGT-ATC
* *
88064256 GCACACTAAGTGCC--ACTATAGCCAAAGCTATCTC-GAATC
1 ACACACTAAGTGCCATACT-TAGCCAAAGCTAT-TCAGTATC
* *
88064295 GCACATTAAGTGCCATA
1 ACACACTAAGTGCCATA
88064312 TATAGTTGAA
Statistics
Matches: 116, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.02
39 31 0.27
40 17 0.15
41 51 0.44
42 15 0.13
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (40 bp):
ACACACTAAGTGCCATACTTAGCCAAAGCTATTCAGTATC
Found at i:88064296 original size:39 final size:39
Alignment explanation
Indices: 88064176--88064312 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 39
88064166 TACAATCTCA
* * *
88064176 CACACTAAGTGCCATACTTAGCCGAAGCTATCTCAGTTTCA
1 CACACTAAGTGCCATA-TTAGCCAAAGCTATCTCAG-ATCG
*
88064217 CACACTAAGTGCCATATTTAGCCAAAGCTAT-TACTGATCG
1 CACACTAAGTGCCATA-TTAGCCAAAGCTATCT-CAGATCG
88064257 CACACTAAGTGCCACTA-TAGCCAAAGCTATCTC-GAATCG
1 CACACTAAGTGCCA-TATTAGCCAAAGCTATCTCAG-ATCG
*
88064296 CACATTAAGTGCCATAT
1 CACACTAAGTGCCATAT
88064313 ATAGTTGAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
38 3 0.04
39 31 0.36
40 18 0.21
41 33 0.39
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (39 bp):
CACACTAAGTGCCATATTAGCCAAAGCTATCTCAGATCG
Found at i:88064329 original size:40 final size:39
Alignment explanation
Indices: 88064176--88064316 Score: 135
Period size: 39 Copynumber: 3.5 Consensus size: 39
88064166 TACAATCTCA
* ** *
88064176 CACACTAAGTGCC-ATACTTAGCCGAAGCTATCTCAGTTTCA
1 CACACTAAGTGCCAATA--TAGCCAAAGCTATCTC-GAATCG
*
88064217 CACACTAAGTGCCATATTTAGCCAAAGCTAT-TACTG-ATCG
1 CACACTAAGTGCCA-ATATAGCCAAAGCTATCT-C-GAATCG
*
88064257 CACACTAAGTGCCACTATAGCCAAAGCTATCTCGAATCG
1 CACACTAAGTGCCAATATAGCCAAAGCTATCTCGAATCG
*
88064296 CACATTAAGTGCCATATATAG
1 CACACTAAGTGCCA-ATATAG
88064317 TTGAAGTTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
38 1 0.01
39 32 0.38
40 23 0.27
41 27 0.32
43 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.26
Consensus pattern (39 bp):
CACACTAAGTGCCAATATAGCCAAAGCTATCTCGAATCG
Found at i:88066324 original size:42 final size:42
Alignment explanation
Indices: 88066243--88066385 Score: 164
Period size: 44 Copynumber: 3.3 Consensus size: 42
88066233 TCCTAGACGT
* * * *
88066243 GGTCTTACATGTAATCAAATATCGATGCCACTATCCCAGACAG
1 GGTCTTACACGAAATCAAATA-CGATGCCAATGTCCCAGACAG
88066286 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGAC-G
1 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGACAG
** *
88066327 TGGTCTTACACGTAAATCATAAGT-CGATGCTGATGTCCCAGACAT
1 -GGTCTTACACG-AAATCA-AA-TACGATGCCAATGTCCCAGACAG
88066372 GGTCTTACACGAAA
1 GGTCTTACACGAAA
88066386 ACACATATCG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
41 1 0.01
42 28 0.32
43 28 0.32
44 30 0.34
45 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGACAG
Found at i:88066356 original size:86 final size:85
Alignment explanation
Indices: 88066227--88066385 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 85
88066217 TAGTACAATT
* *
88066227 CCAACGTCCTAGACGTGGTCTTACATGTAATCAAATATCGATGC-CACTATCCCAGACAGGGTCT
1 CCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCGATGCTCA-TATCCCAGACAGGGTCT
88066291 TACACGAAATCAAATACGATG
65 TACACGAAATCAAATACGATG
* * * * *
88066312 CCAATGTCCCAGACGTGGTCTTACACGTAAATCATAA-GTCGATGCTGATGTCCCAGACATGGTC
1 CCAACGTCCCAGACGTGGTCTTACACGT-AATCA-AATATCGATGCTCATATCCCAGACAGGGTC
88066376 TTACACGAAA
64 TTACACGAAA
88066386 ACACATATCG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
85 25 0.39
86 36 0.56
87 3 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (85 bp):
CCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCGATGCTCATATCCCAGACAGGGTCTT
ACACGAAATCAAATACGATG
Found at i:88071642 original size:42 final size:43
Alignment explanation
Indices: 88071552--88071644 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
88071542 GTCCAAGATG
* * *
88071552 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACA
1 TGGTCTTACACGAAATCAAATATCGACGCCACTGTCCCAGACA
* *
88071595 GGGTCTTACACGAAATCATATA-CGACGCCGA-TGTCCCAGACA
1 TGGTCTTACACGAAATCAAATATCGACGCC-ACTGTCCCAGACA
88071637 TGGTCTTA
1 TGGTCTTA
88071645 TACATAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 24 0.56
43 19 0.44
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
TGGTCTTACACGAAATCAAATATCGACGCCACTGTCCCAGACA
Found at i:88080077 original size:47 final size:47
Alignment explanation
Indices: 88080019--88080140 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
88080009 GCATTGTCCC
*
88080019 TAAGACAAGGATACCGTGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
88080066 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
88080113 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
88080141 CCAAGGCATG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:88082589 original size:47 final size:47
Alignment explanation
Indices: 88082532--88082788 Score: 340
Period size: 47 Copynumber: 5.4 Consensus size: 47
88082522 ATTGATGTAC
* *
88082532 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
88082579 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTATATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
88082628 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
88082675 ACATGCAT-T-TATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-A-GTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
88082722 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
88082769 AAGTGTATAAATGTGATAAG
1 AAGTATATATATGTGATAAG
88082789 TCCCGAAGGG
Statistics
Matches: 188, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
45 2 0.01
46 2 0.01
47 141 0.75
48 1 0.01
49 41 0.22
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:88084765 original size:53 final size:53
Alignment explanation
Indices: 88084637--88084780 Score: 173
Period size: 53 Copynumber: 2.7 Consensus size: 53
88084627 GGGTGTTACA
* * * *
88084637 GTAAGACCATGTCAAGACATGGCATTGATGAGATACTATAAGGCAAAGGTCCCAT
1 GTAAGACCATGTCAAGACATGGCATTGGTGAG-TTC-ATAAGGCAAAGGTACCAC
* *
88084692 GTAAGACCATGCCAATACATGGCATTGGTGAGTTCATAAGGC-AAGGATACCAC
1 GTAAGACCATGTCAAGACATGGCATTGGTGAGTTCATAAGGCAAAGG-TACCAC
* * *
88084745 GTAAGACAATGTCAAGACATGGCAATGGTAAGTTCA
1 GTAAGACCATGTCAAGACATGGCATTGGTGAGTTCA
88084781 AAAAAGAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 4 0.05
53 42 0.55
54 2 0.03
55 29 0.38
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (53 bp):
GTAAGACCATGTCAAGACATGGCATTGGTGAGTTCATAAGGCAAAGGTACCAC
Found at i:88090676 original size:28 final size:29
Alignment explanation
Indices: 88090619--88090676 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
88090609 TACAGGGGTT
*
88090619 TTCACATGGCCTGGCACGCGCCCATGTCC
1 TTCACATGGCCTGGCACACGCCCATGTCC
*
88090648 TTCACATGGCCAT-G-ACACGCCCGTGTCC
1 TTCACATGGCC-TGGCACACGCCCATGTCC
88090676 T
1 T
88090677 AGCCCGTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 12 0.46
30 1 0.04
ACGTcount: A:0.16, C:0.40, G:0.22, T:0.22
Consensus pattern (29 bp):
TTCACATGGCCTGGCACACGCCCATGTCC
Found at i:88091739 original size:46 final size:46
Alignment explanation
Indices: 88091623--88091846 Score: 213
Period size: 46 Copynumber: 4.8 Consensus size: 46
88091613 GGGATAGGAT
88091623 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTA-A-CTCGTA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTACATCTCGTA
* *
88091669 GCCGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCTCG-A
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGTA
* * * *
88091714 GGCTGATGCATGTCCCAGACGTGTCTTACACTAGCTTTCATCTCACTA
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTC-GTA
* * * * * * *
88091762 -TCGATGCCATGTCTCGGACATGGTCTTACACTAGCTTAACTTGTAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTT-ACATCT--CGTA
*
88091812 GCCGATGCATGTCCCATACATGTCTTACACTAGCT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
88091847 CACAATGTCC
Statistics
Matches: 144, Mismatches: 23, Indels: 19
0.77 0.12 0.10
Matches are distributed among these distances:
44 15 0.10
45 15 0.10
46 53 0.37
47 11 0.08
48 16 0.11
49 17 0.12
50 12 0.08
51 5 0.03
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGTA
Found at i:88092210 original size:30 final size:30
Alignment explanation
Indices: 88092174--88092249 Score: 143
Period size: 30 Copynumber: 2.5 Consensus size: 30
88092164 CTATACTTGG
88092174 GCAAAATGACCATTTTGCCCTTAGACTTTT
1 GCAAAATGACCATTTTGCCCTTAGACTTTT
88092204 GCAAAATGACCATTTTGCCCTTAGACTTTT
1 GCAAAATGACCATTTTGCCCTTAGACTTTT
*
88092234 GCAAAATTACCATTTT
1 GCAAAATGACCATTTT
88092250 ACCCCTAGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (30 bp):
GCAAAATGACCATTTTGCCCTTAGACTTTT
Found at i:88093436 original size:19 final size:19
Alignment explanation
Indices: 88093412--88093450 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
88093402 AATGATAAGT
88093412 TTATTTATATAAGGCTTAC
1 TTATTTATATAAGGCTTAC
*
88093431 TTATTTGTATAAGGCTTAC
1 TTATTTATATAAGGCTTAC
88093450 T
1 T
88093451 AAGCTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
TTATTTATATAAGGCTTAC
Found at i:88096304 original size:46 final size:46
Alignment explanation
Indices: 88096254--88096429 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
88096244 TGGTTGAGCA
88096254 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
88096300 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
**
88096345 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
88096393 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
88096430 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 29 0.27
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:88096410 original size:93 final size:93
Alignment explanation
Indices: 88096251--88096422 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
88096241 GGATGGTTGA
***
88096251 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
88096316 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
88096344 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
*
88096409 TGAGTCTGAGTTCG
66 TGAGTCCGAGTTCG
88096423 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:88100844 original size:81 final size:83
Alignment explanation
Indices: 88100695--88100855 Score: 220
Period size: 81 Copynumber: 2.0 Consensus size: 83
88100685 CTACTCAATA
* * *
88100695 TCTCGCACACTAAGTGCCAATACATAGCCAAAGCTATTATAATCTCGCACACTAAGTGCCTTACA
1 TCTCCCACACTAAGTGCCAATACATAGCAAAAGCTATTATAATCTCGCACACTAAGTGCCATACA
*
88100760 TAGTCGAAGTTATCTTAG
66 TAGTCGAAGCTATCTTAG
* * * *
88100778 TCTCCCACACTAAGTGCC-ATATATAGCAAAAGCTATCT-T-GTCTCGCACACTAAGTGTCATAT
1 TCTCCCACACTAAGTGCCAATACATAGCAAAAGCTAT-TATAATCTCGCACACTAAGTGCCATAC
88100840 ATAGTCGAAGCTATCT
65 ATAGTCGAAGCTATCT
88100856 CGAATCACCG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 34 0.49
82 17 0.25
83 18 0.26
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (83 bp):
TCTCCCACACTAAGTGCCAATACATAGCAAAAGCTATTATAATCTCGCACACTAAGTGCCATACA
TAGTCGAAGCTATCTTAG
Found at i:88100851 original size:40 final size:41
Alignment explanation
Indices: 88100695--88100855 Score: 184
Period size: 41 Copynumber: 3.9 Consensus size: 41
88100685 CTACTCAATA
* *
88100695 TCTCGCACACTAAGTGCCAATACATAGCCAAAGCTAT-TATAA
1 TCTCGCACACTAAGTGCC-ATACATAGTCAAAGCTATCT-TAG
* * *
88100737 TCTCGCACACTAAGTGCCTTACATAGTCGAAGTTATCTTAG
1 TCTCGCACACTAAGTGCCATACATAGTCAAAGCTATCTTAG
* *
88100778 TCTCCCACACTAAGTGCCATATATAG-CAAAAGCTATCTT-G
1 TCTCGCACACTAAGTGCCATACATAGTC-AAAGCTATCTTAG
* * *
88100818 TCTCGCACACTAAGTGTCATATATAGTCGAAGCTATCT
1 TCTCGCACACTAAGTGCCATACATAGTCAAAGCTATCT
88100856 CGAATCACCG
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
40 35 0.34
41 49 0.48
42 19 0.18
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (41 bp):
TCTCGCACACTAAGTGCCATACATAGTCAAAGCTATCTTAG
Found at i:88102684 original size:21 final size:21
Alignment explanation
Indices: 88102660--88102699 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
88102650 TATAGCCACA
*
88102660 ACAAAGCTAGATGCACCCATG
1 ACAAAGCCAGATGCACCCATG
*
88102681 ACAAAGCCAGATGCTCCCA
1 ACAAAGCCAGATGCACCCA
88102700 CACCAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (21 bp):
ACAAAGCCAGATGCACCCATG
Found at i:88102706 original size:21 final size:20
Alignment explanation
Indices: 88102655--88102702 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
88102645 TCAGATATAG
*
88102655 CCACAACAAAGCTAGATGCAC
1 CCAC-ACAAAGCCAGATGCAC
* *
88102676 CCATGACAAAGCCAGATGCTC
1 CCA-CACAAAGCCAGATGCAC
88102697 CCACAC
1 CCACAC
88102703 CAAAATCAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.10
Consensus pattern (20 bp):
CCACACAAAGCCAGATGCAC
Found at i:88108252 original size:18 final size:17
Alignment explanation
Indices: 88108221--88108263 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
88108211 ATACGTTTAA
*
88108221 ATTTAATGTTGTATTTG
1 ATTTAATGTGGTATTTG
88108238 ATTTGAATGTGGTATTTG
1 ATTT-AATGTGGTATTTG
88108256 -TTT-ATGTG
1 ATTTAATGTG
88108264 ATTTATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
17 7 0.29
18 12 0.50
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (17 bp):
ATTTAATGTGGTATTTG
Found at i:88115023 original size:40 final size:39
Alignment explanation
Indices: 88114979--88115090 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 39
88114969 ATAACCACAA
*
88114979 GCACAAATGCCCTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATC-ACTC
* *
88115019 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTG
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCACTC
* * *
88115059 GCACAATTGCCTTCGAGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
88115091 CATTCAAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 59 0.92
41 4 0.06
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (39 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCACTC
Found at i:88119893 original size:29 final size:29
Alignment explanation
Indices: 88119851--88119909 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
88119841 AAGGAAAACT
*
88119851 GAGTTAGTTTATTTTATGTTTTAGTTGAA
1 GAGTTAGTTTATTTTAAGTTTTAGTTGAA
88119880 GAGTTAGTTTATTTTAAGTTTTAGTTGAA
1 GAGTTAGTTTATTTTAAGTTTTAGTTGAA
88119909 G
1 G
88119910 TATTCATGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (29 bp):
GAGTTAGTTTATTTTAAGTTTTAGTTGAA
Found at i:88132095 original size:28 final size:28
Alignment explanation
Indices: 88132063--88132132 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
88132053 ATAGTAAGTC
88132063 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
88132091 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
88132119 CGCACACTTAGTGC
1 CGCACACTTAGTGC
88132133 CAATCTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:88137949 original size:30 final size:30
Alignment explanation
Indices: 88137915--88137975 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
88137905 TCCTTAACTC
88137915 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
88137945 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
88137975 A
1 A
88137976 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:88156458 original size:29 final size:28
Alignment explanation
Indices: 88156416--88156513 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
88156406 CATGAGATTG
* * *
88156416 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-AATTATATA
*
88156445 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
88156473 GCACTAAGTGTGCGAGTTTAA-TATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
*
88156500 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
88156514 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 19 0.30
28 26 0.41
29 18 0.29
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATATA
Found at i:88156520 original size:27 final size:27
Alignment explanation
Indices: 88156416--88156526 Score: 107
Period size: 27 Copynumber: 4.0 Consensus size: 27
88156406 CATGAGATTG
* * * *
88156416 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGCTT-AA-TATATA
* *
88156445 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGCTT-AATATATA
*
88156473 GCACTAAGTGTGCGAGTTTAATATATA
1 GCACTAAGTGTGCGAGCTTAATATATA
*
88156500 GCACTGAGTGTGCG-GACTTAATATATA
1 GCACTAAGTGTGCGAG-CTTAATATATA
88156527 CTTTTGAATC
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.01
27 30 0.41
28 23 0.32
29 19 0.26
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTTAATATATA
Found at i:88164391 original size:28 final size:28
Alignment explanation
Indices: 88164323--88164560 Score: 415
Period size: 28 Copynumber: 8.5 Consensus size: 28
88164313 CATGAGATTG
* * * *
88164323 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
88164352 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
88164380 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
88164408 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
88164436 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
88164464 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
88164492 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
88164520 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
88164547 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
88164561 GACTTAATAT
Statistics
Matches: 204, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
27 24 0.12
28 162 0.79
29 18 0.09
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:88169959 original size:22 final size:22
Alignment explanation
Indices: 88169931--88169976 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
88169921 GTTTATTATC
* *
88169931 TATTATTTTCTATTCTTAGTTA
1 TATTATTTTATATTCCTAGTTA
*
88169953 TATTATTTTATTTTCCTAGTTA
1 TATTATTTTATATTCCTAGTTA
88169975 TA
1 TA
88169977 CTTGTCTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.63
Consensus pattern (22 bp):
TATTATTTTATATTCCTAGTTA
Found at i:88171764 original size:6 final size:6
Alignment explanation
Indices: 88171711--88171763 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
88171701 GACCATTAAG
*
88171711 TTTATT TTT-TT ATTTATT TTTATT TTTATT TTTATT TTTATT TTTATG
1 TTTATT TTTATT -TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
88171759 TTTAT
1 TTTAT
88171764 GGTTATTTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
5 2 0.05
6 40 0.91
7 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:88171769 original size:18 final size:18
Alignment explanation
Indices: 88171730--88171772 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
88171720 TTATTTATTT
* **
88171730 TTATTTTTATTTTTATTT
1 TTATTTTTATGTTTATGG
88171748 TTATTTTTATGTTTATGG
1 TTATTTTTATGTTTATGG
88171766 TTATTTT
1 TTATTTT
88171773 CTTAGACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (18 bp):
TTATTTTTATGTTTATGG
Found at i:88185195 original size:27 final size:27
Alignment explanation
Indices: 88185164--88185341 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
88185154 TAAATTGTAC
88185164 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
88185191 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
88185217 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
88185245 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
88185273 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
88185300 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
88185327 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
88185342 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:88185278 original size:82 final size:81
Alignment explanation
Indices: 88185165--88185320 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
88185155 AAATTGTACA
* *
88185165 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
88185229 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
88185246 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
88185311 TGCGAGTTGA
65 TGCGAATTGA
88185321 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:88185332 original size:82 final size:81
Alignment explanation
Indices: 88185161--88185341 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
88185151 GATTAAATTG
* *
88185161 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
88185226 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
88185242 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
88185306 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
88185324 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
88185342 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:88190672 original size:17 final size:17
Alignment explanation
Indices: 88190647--88190687 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
88190637 GGCAATGATG
*
88190647 CATTACTAGATGCCACT
1 CATTGCTAGATGCCACT
88190664 CATTGCTAGATGCCACT
1 CATTGCTAGATGCCACT
88190681 CATTGCT
1 CATTGCT
88190688 TGTAATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (17 bp):
CATTGCTAGATGCCACT
Found at i:88191249 original size:67 final size:67
Alignment explanation
Indices: 88191037--88191249 Score: 157
Period size: 67 Copynumber: 3.1 Consensus size: 67
88191027 TTGATTCATA
**
88191037 CAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATAAATAGTTATATTAATTAATTTTG
1 CAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATAAATAGTTATATTAATTAATTTCA
88191102 GT
66 GT
* **** ***** * * * *
88191104 CAAAATATAAAAAAAATGGAAATTA--ATATTCTTTTGGAA-AGAATATAATTAATATATGAATT
1 CAAAATATTAATTGTATATTTTTTACCAAATT-TATT--AATATAA-ATAGTT-ATAT-T-AA-T
*
88191166 TGA-TTCA-T
58 TAATTTCAGT
88191174 ACAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATAAATAGTTATATTAATTAATTTC
1 -CAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATAAATAGTTATATTAATTAATTTC
88191239 AGT
65 AGT
88191242 CAAAATAT
1 CAAAATAT
88191250 AAAAGACATG
Statistics
Matches: 100, Mismatches: 32, Indels: 28
0.62 0.20 0.17
Matches are distributed among these distances:
65 4 0.04
66 6 0.06
67 32 0.32
68 9 0.09
69 8 0.08
70 9 0.09
71 22 0.22
72 6 0.06
73 4 0.04
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (67 bp):
CAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATAAATAGTTATATTAATTAATTTCA
GT
Found at i:88191298 original size:71 final size:69
Alignment explanation
Indices: 88191223--88191436 Score: 154
Period size: 71 Copynumber: 3.1 Consensus size: 69
88191213 TATAAATAGT
88191223 TATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAATAT
1 TATATTAATTAATTTCAGTCAAAATATAAAAGACATG-AAATTAATATTCTTTT-GAAAGAATAT
88191288 AATTAA
64 AATTAA
* * * ** * * * *** **
88191294 TATATGAATTTGA-TTCA-TACGAAATATTAATTG-TAT-ATATT-TTACTAAATTT--ATTAAT
1 TATATTAA-TTAATTTCAGT-CAAAATA-TAAAAGACATGAAATTAATA-TTCTTTTGAAAGAAT
* *
88191352 ATAAATAGT
62 ATAATTA-A
*
88191361 TATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTAGAAAGAATAT
1 TATATTAATTAATTTCAGTCAAAATATAAAAGACAT-GAAATTAATATTCTTTT-GAAAGAATAT
88191426 AATTAA
64 AATTAA
88191432 TATAT
1 TATAT
88191437 GATTTTTTCA
Statistics
Matches: 98, Mismatches: 31, Indels: 28
0.62 0.20 0.18
Matches are distributed among these distances:
66 17 0.17
67 18 0.18
68 3 0.03
69 16 0.16
70 3 0.03
71 24 0.24
72 17 0.17
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (69 bp):
TATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAATTAATATTCTTTTGAAAGAATATAA
TTAA
Found at i:88191595 original size:274 final size:276
Alignment explanation
Indices: 88190877--88191741 Score: 1411
Period size: 274 Copynumber: 3.1 Consensus size: 276
88190867 ATATATAAAG
88190877 TTAATATATGAATTTGATTT-ATACAAAATATTAATTGTATATATTTTATCGAAA-TTATTAATA
1 TTAATATATGAATTTG-TTTCATACAAAATATTAATTGTATATATTTTATC-AAATTTATTAATA
* *
88190940 TAAAAAATTATATTAATTAATTTCGGTCAAAA-ATAAAAGACATGGAAATTAATATTCTTTTGGA
64 TAAAAAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
* *
88191004 AAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATTTTTTACCAAATT
129 AAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATT
* *
88191069 TATTAATATAAATAGTTATATTAATTAATTTTGGTCAAAATATAAAAAAAATGGAAATTAATATT
194 TATTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAAACATGGAAATTAATATT
88191134 CTTTTGGAAAGAATATAA
259 CTTTTGGAAAGAATATAA
* * *
88191152 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATA
1 TTAATATATGAATTTGTTTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTAATATA
* *
88191217 AATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
66 AAAAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
*
88191282 GAATATAATTAATATATGAATTTGATTCATACGAAATATTAATTGTATATATTTTACTAAATTTA
131 GAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTA
*
88191347 TTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCT
196 TTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAAACATGGAAATTAATATTCT
*
88191412 TTTAGAAAGAATATAA
261 TTTGGAAAGAATATAA
88191428 TTAATATATG-ATTT-TTTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTAATATA
1 TTAATATATGAATTTGTTTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTAATATA
* * ** *
88191491 AACAGTTCTATTAATTAATTTCGGTCAAAATATAAGGGACATGAAAATTAATATTCTTTTGAAAA
66 AAAAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
* *
88191556 GAATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTA
131 GAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTA
* * *
88191621 TTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAATACATGAAAATTATTATTCT
196 TTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAAACATGGAAATTAATATTCT
*
88191686 TTTGGAAAGAAAATAA
261 TTTGGAAAGAATATAA
*
88191702 TTAATATAT-AGATTT-TATTCATCCAAAATATTAATTGTAT
1 TTAATATATGA-ATTTGT-TTCATACAAAATATTAATTGTAT
88191742 TTATATAGAG
Statistics
Matches: 552, Mismatches: 32, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
274 257 0.47
275 91 0.16
276 204 0.37
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (276 bp):
TTAATATATGAATTTGTTTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTAATATA
AAAAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
GAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTA
TTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAAACATGGAAATTAATATTCT
TTTGGAAAGAATATAA
Found at i:88191642 original size:412 final size:413
Alignment explanation
Indices: 88190877--88191741 Score: 1423
Period size: 412 Copynumber: 2.1 Consensus size: 413
88190867 ATATATAAAG
*
88190877 TTAATATATGAATTTGATTTATACAAAATATTAATTGTATATATTTTATCGAAATTATTAATATA
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAAATTATTAATATA
*
88190942 AAAAATTATATTAATTAATTTCGGTCAAAAATAAAAGACATGGAAATTAATATTCTTTTGGAAAG
66 AAAAATTATATTAATTAATTTCGGTCAAAAATAAAAGACATGGAAATTAATATTCTTTTAGAAAG
*
88191007 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATTTTTTACCAAATTTAT
131 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAT
* * *
88191072 TAATATAAATAGTTATATTAATTAATTTTGGTCAAAATATAAAAAAAATGGAAATTAATATTCTT
196 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAAAAATGAAAATTAATATTCTT
* * *
88191137 TTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATTTTTTACC
261 TTGAAAAGAATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACC
88191202 AAATTTATTAATATAAATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTA
326 AAATTTATTAATATAAATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTA
*
88191267 ATATTCTTTTGGAAAGAATATAA
391 ATATTCTTTTGGAAAGAAAATAA
* *
88191290 TTAATATATGAATTTGATTCATACGAAATATTAATTGTATATATTTTA-CTAAATTTATTAATAT
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAAA-TTATTAATAT
* *
88191354 AAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTAGAA
65 AAAAAATTATATTAATTAATTTCGGTCAAAA-ATAAAAGACATGGAAATTAATATTCTTTTAGAA
* *
88191419 AGAATATAATTAATATATG-ATTT-TTTCATACAAAATATTAATTGTATATATTTTATCAAATTT
129 AGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTT
* *** *
88191482 ATTAATATAAACAGTTCTATTAATTAATTTCGGTCAAAATATAAGGGACATGAAAATTAATATTC
194 ATTAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAAAAATGAAAATTAATATTC
88191547 TTTTGAAAAGAATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTA
259 TTTTGAAAAGAATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTA
** * *
88191612 CTGAATTTATTAATATAAATAGTTATATTAATTAATTTCGGTCAAAATATAAAATACATGAAAAT
324 CCAAATTTATTAATATAAATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAAT
*
88191677 TATTATTCTTTTGGAAAGAAAATAA
389 TAATATTCTTTTGGAAAGAAAATAA
* *
88191702 TTAATATAT-AGATTTTATTCATCCAAAATATTAATTGTAT
1 TTAATATATGA-ATTTGATTCATACAAAATATTAATTGTAT
88191742 TTATATAGAG
Statistics
Matches: 420, Mismatches: 29, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
411 1 0.00
412 279 0.66
413 89 0.21
414 51 0.12
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (413 bp):
TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAAATTATTAATATA
AAAAATTATATTAATTAATTTCGGTCAAAAATAAAAGACATGGAAATTAATATTCTTTTAGAAAG
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTAT
TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAAAAATGAAAATTAATATTCTT
TTGAAAAGAATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACC
AAATTTATTAATATAAATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTA
ATATTCTTTTGGAAAGAAAATAA
Found at i:88191763 original size:138 final size:138
Alignment explanation
Indices: 88190877--88191741 Score: 1398
Period size: 138 Copynumber: 6.3 Consensus size: 138
88190867 ATATATAAAG
* *
88190877 TTAATATATGAATTTGATTTATACAAAATATTAATTGTATATATTTTATCGAAA-TTATTAATAT
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTA-CCAAATTTATTAATAT
* * *
88190941 AAAAAATTATATTAATTAATTTCGGTCAAAA-ATAAAAGACATGGAAATTAATATTCTTTTGGAA
65 AAATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAA
88191005 AGAATATAA
130 AGAATATAA
*
88191014 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATA
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
* * * *
88191079 AATAGTTATATTAATTAATTTTGGTCAAAATATAAAAAAAATGGAAATTAATATTCTTTTGGAAA
66 AATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
88191144 GAATATAA
131 GAATATAA
*
88191152 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATTTTTTACCAAATTTATTAATATA
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
*
88191217 AATAGTTATATTAATTAATTTCAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
66 AATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
88191282 GAATATAA
131 GAATATAA
* *
88191290 TTAATATATGAATTTGATTCATACGAAATATTAATTGTATATATTTTACTAAATTTATTAATATA
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
* *
88191355 AATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTAGAAA
66 AATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
88191420 GAATATAA
131 GAATATAA
* *
88191428 TTAATATATG-ATTT-TTTCATACAAAATATTAATTGTATATATTTTATCAAATTTATTAATATA
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
* * ** *
88191491 AACAGTTCTATTAATTAATTTCGGTCAAAATATAAGGGACATGAAAATTAATATTCTTTTGAAAA
66 AATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
88191556 GAATATAA
131 GAATATAA
* **
88191564 TTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATTAATATA
1 TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
* *
88191629 AATAGTTATATTAATTAATTTCGGTCAAAATATAAAATACATGAAAATTATTATTCTTTTGGAAA
66 AATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
*
88191694 GAAAATAA
131 GAATATAA
* *
88191702 TTAATATAT-AGATTTTATTCATCCAAAATATTAATTGTAT
1 TTAATATATGA-ATTTGATTCATACAAAATATTAATTGTAT
88191742 TTATATAGAG
Statistics
Matches: 678, Mismatches: 45, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
136 124 0.18
137 93 0.14
138 461 0.68
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (138 bp):
TTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAATATA
AATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAA
GAATATAA
Found at i:88192238 original size:19 final size:19
Alignment explanation
Indices: 88192214--88192252 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
88192204 TATGGTTTAT
88192214 ATTATCATATTGAATTACA
1 ATTATCATATTGAATTACA
88192233 ATTATCATATTGAATTACA
1 ATTATCATATTGAATTACA
88192252 A
1 A
88192253 GCTATATTAC
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:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTATCATATTGAATTACA
Found at i:88195334 original size:20 final size:21
Alignment explanation
Indices: 88195280--88195319 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
88195270 TATAATCTAA
* *
88195280 ATATTTAAAAATTAATAAAAT
1 ATATGTAAATATTAATAAAAT
88195301 ATATGTAAAT-TTAATAAAA
1 ATATGTAAATATTAATAAAA
88195320 ATTATTCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
ATATGTAAATATTAATAAAAT
Found at i:88197473 original size:18 final size:18
Alignment explanation
Indices: 88197429--88197463 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
88197419 AATATTATTC
*
88197429 TCAAAAGTATTTTTAAAA
1 TCAAAAGCATTTTTAAAA
88197447 TCAAAAGCATTTTTAAA
1 TCAAAAGCATTTTTAAA
88197464 GTAAGAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (18 bp):
TCAAAAGCATTTTTAAAA
Found at i:88197939 original size:34 final size:34
Alignment explanation
Indices: 88197901--88197967 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
88197891 TTTATAATAT
* *
88197901 AATGTTTAAAATAGACATTTTATTTATTAAAAGC
1 AATGTCTAAAATAGACACTTTATTTATTAAAAGC
88197935 AATGTCTAAAATAGACACTTTATTTATTAAAAG
1 AATGTCTAAAATAGACACTTTATTTATTAAAAG
88197968 TATTTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (34 bp):
AATGTCTAAAATAGACACTTTATTTATTAAAAGC
Found at i:88198028 original size:13 final size:13
Alignment explanation
Indices: 88198012--88198073 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
88198002 TAAACTAAAA
88198012 TTTTCAAAAGTAC
1 TTTTCAAAAGTAC
88198025 TTTTCAAAA-TCAC
1 TTTTCAAAAGT-AC
* *
88198038 TTTTCCACAA-CAC
1 TTTT-CAAAAGTAC
*
88198051 TTTTTAAAAGTAC
1 TTTTCAAAAGTAC
*
88198064 TTCTCAAAAG
1 TTTTCAAAAG
88198074 CAATTCTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
12 4 0.10
13 31 0.79
14 4 0.10
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAGTAC
Found at i:88201091 original size:27 final size:27
Alignment explanation
Indices: 88201053--88201104 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
88201043 ACTTCATCAT
88201053 TAGTTTTCATTGTATACACCCAAACAC
1 TAGTTTTCATTGTATACACCCAAACAC
88201080 TAGTTTTCATTGTATACACCCAAAC
1 TAGTTTTCATTGTATACACCCAAAC
88201105 TCTTCTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.35
Consensus pattern (27 bp):
TAGTTTTCATTGTATACACCCAAACAC
Found at i:88201866 original size:20 final size:20
Alignment explanation
Indices: 88201841--88201881 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
88201831 AGTATCTCGC
88201841 TCTATAATACATGCATCTAG
1 TCTATAATACATGCATCTAG
88201861 TCTATAATACATGCATCTAG
1 TCTATAATACATGCATCTAG
88201881 T
1 T
88201882 GCACTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCTATAATACATGCATCTAG
Found at i:88204988 original size:63 final size:63
Alignment explanation
Indices: 88204915--88205040 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
88204905 GTGACAGCGA
*
88204915 CTCATTATATATTGACCAGAACACATTCGACATAATTTATTCACCAATGCTTGTAAATTGATG
1 CTCATTATATATTGACCAGAACACATTCAACATAATTTATTCACCAATGCTTGTAAATTGATG
*
88204978 CTCATTATATATTGACCAGAACACATTCAACATAATTTATTCACCAGTGCTTGTAAATTGATG
1 CTCATTATATATTGACCAGAACACATTCAACATAATTTATTCACCAATGCTTGTAAATTGATG
88205041 TCAAATTAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (63 bp):
CTCATTATATATTGACCAGAACACATTCAACATAATTTATTCACCAATGCTTGTAAATTGATG
Found at i:88205132 original size:28 final size:28
Alignment explanation
Indices: 88205101--88205157 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
88205091 TAGAACGTTG
88205101 AAGTTAATAAAAATAAATATAAGATTTA
1 AAGTTAATAAAAATAAATATAAGATTTA
88205129 AAGTTAATAAAAATAAATATAAGATTTA
1 AAGTTAATAAAAATAAATATAAGATTTA
88205157 A
1 A
88205158 CTATCTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (28 bp):
AAGTTAATAAAAATAAATATAAGATTTA
Found at i:88208225 original size:27 final size:27
Alignment explanation
Indices: 88208171--88208247 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 27
88208161 ACAGAGTCAA
*
88208171 CAGATACAGATATTTTGTGGCAATGCCAC
1 CAGA-ACAGATA-TTTGTGGCAAGGCCAC
* *
88208200 CAGAACAGATATATGTGGCAGGGCCAC
1 CAGAACAGATATTTGTGGCAAGGCCAC
*
88208227 CAGAACATATAATTTGTGGCA
1 CAGAACAGAT-ATTTGTGGCA
88208248 TAACCACCAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 22 0.52
28 16 0.38
29 4 0.10
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (27 bp):
CAGAACAGATATTTGTGGCAAGGCCAC
Found at i:88208254 original size:28 final size:27
Alignment explanation
Indices: 88208196--88208257 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
88208186 TGTGGCAATG
**
88208196 CCACCAGAACAGATATATGTGGCAGGG
1 CCACCAGAACAGATATATGTGGCAGAA
* * *
88208223 CCACCAGAACATATAATTTGTGGCATAA
1 CCACCAGAACAGAT-ATATGTGGCAGAA
88208251 CCACCAG
1 CCACCAG
88208258 GACGCTTCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (27 bp):
CCACCAGAACAGATATATGTGGCAGAA
Found at i:88208694 original size:16 final size:15
Alignment explanation
Indices: 88208673--88208704 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
88208663 CCAAAATACC
88208673 GGCTTTTCGGCATTTT
1 GGCTTTTCGGC-TTTT
88208689 GGCTTTTCGGCTTTT
1 GGCTTTTCGGCTTTT
88208704 G
1 G
88208705 CCGATCTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.03, C:0.19, G:0.28, T:0.50
Consensus pattern (15 bp):
GGCTTTTCGGCTTTT
Found at i:88216300 original size:28 final size:28
Alignment explanation
Indices: 88216253--88216319 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
88216243 AAATTAACCC
*
88216253 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
* *
88216281 TAGGGGTATTATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
88216309 TAGGGGTATAA
1 TAGGGGTATAA
88216320 TAGTACATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:88217017 original size:5 final size:5
Alignment explanation
Indices: 88217001--88217043 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
88216991 TTTTAGGTGG
* *
88217001 AGAAA A-AAA AGAAA AGAAA AGAAA AGAAA GGAAA GGAAA AGAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
88217044 GGAAGAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:88218148 original size:13 final size:13
Alignment explanation
Indices: 88218130--88218161 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
88218120 GTATAGGATT
88218130 CACACGGTCAAGA
1 CACACGGTCAAGA
88218143 CACACGGTCAAGA
1 CACACGGTCAAGA
88218156 CACACG
1 CACACG
88218162 CTCGTGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.34, G:0.22, T:0.06
Consensus pattern (13 bp):
CACACGGTCAAGA
Found at i:88228978 original size:30 final size:30
Alignment explanation
Indices: 88228944--88229031 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
88228934 TTTTCGATCA
*
88228944 TAGGGGTAAAATAGTCATTTTGCCAAAGTC
1 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
* *
88228974 TAGGGATAAAATGGTTATTTTGCCAAAGTC
1 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
* * *
88229004 TTGAGGTAAAATGGTCATTTTACCAAAG
1 TAGGGGTAAAATGGTCATTTTGCCAAAG
88229032 ATGTAAATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (30 bp):
TAGGGGTAAAATGGTCATTTTGCCAAAGTC
Found at i:88229529 original size:47 final size:46
Alignment explanation
Indices: 88229413--88229673 Score: 235
Period size: 47 Copynumber: 5.6 Consensus size: 46
88229403 TATGAGAGCT
* * *
88229413 AGTGTAAGACCATGTCTAGGACATGGCATTGGCATTGAGATG-AGTGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGAGATGTAGT-C
* * * ** * *
88229460 TAGTGCAAGA-CATGCCTAGGACAT-ATATCGGCCTCGAGATGATAGTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGATG-TAGTC
* *
88229507 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGACGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATGT-AGTC
* ** * *
88229554 AGTATAAGA-CATGAGTGGGACAT-GCATCGACTACGAGATGATATTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACT-TGAGATG-TAGTC
*
88229600 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATGT-AGTC
*
88229647 AGTGTAAGACCGTGTCTGGGACATGGC
1 AGTGTAAGACCATGTCTGGGACATGGC
88229674 TTCGGCACCT
Statistics
Matches: 172, Mismatches: 30, Indels: 23
0.76 0.13 0.10
Matches are distributed among these distances:
45 9 0.05
46 46 0.27
47 94 0.55
48 23 0.13
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATGTAGTC
Found at i:88237258 original size:47 final size:47
Alignment explanation
Indices: 88237095--88237408 Score: 189
Period size: 46 Copynumber: 6.7 Consensus size: 47
88237085 TGTGTGGGAT
* * *
88237095 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GATGATAGCC
* * * * ** ** *
88237141 AGTGTAAGTGACCATGTTTAGGACATGGCGTCGGCATTAAGACAAGT-GCT
1 AGTGTAA--GACCATGTCTGGGACAT-GCATCGGCCTCGAGATGA-TAGCC
* * *
88237191 AGTGTAAGA-TATGTCTGGGACATGCGTCGGCCTCGAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
* * * * *
88237237 AGTGTAAGACCATGTTTGGGACATGGCATC-GACTTGATACG-TAAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGAT-AGCC
* * * * *
88237284 AGTGTAAGA-CATGTCTGGGATATGCATCGG-TTACTAGATAATAGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
* * * *
88237330 AATGTAAGACCATGTCTGGGACATGACATC-GACTTGAGATG-TGGCC
1 AGTGTAAGACCATGTCTGGGACATG-CATCGGCCTCGAGATGATAGCC
* *
88237376 AGTGTAAGACCGTGTTTGGGACATTGCATCGGC
1 AGTGTAAGACCATGTCTGGGACA-TGCATCGGC
88237409 ACCTTACCCA
Statistics
Matches: 200, Mismatches: 50, Indels: 35
0.70 0.18 0.12
Matches are distributed among these distances:
45 7 0.04
46 84 0.42
47 65 0.32
48 13 0.06
49 12 0.06
50 18 0.09
51 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
Found at i:88237328 original size:93 final size:92
Alignment explanation
Indices: 88237095--88237408 Score: 303
Period size: 93 Copynumber: 3.3 Consensus size: 92
88237085 TGTGTGGGAT
* * * *
88237095 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGTGACCATGTTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACA-GATGATAGTCAGTGTAA--GACCATGTTT
* * * * *
88237160 AGGACATGGCGTCGGCATTAAGAC--AAGTGCT
63 GGGACATGGCATCGAC-TTGAGACGTAA--GCC
* *
88237191 AGTGTAAGATATGTCTGGGACATGCGTCGGCCT-CGAGATGATAGTCAGTGTAAGACCATGTTTG
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTAC-AGATGATAGTCAGTGTAAGACCATGTTTG
*
88237255 GGACATGGCATCGACTTGATACGTAAGCC
64 GGACATGGCATCGACTTGAGACGTAAGCC
* * * * *
88237284 AGTGTAAGACATGTCTGGGATATGCATCGGTTACTAGATAATAGTCAATGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAC-AGATGATAGTCAGTGTAAGACCATGTTTGG
* * *
88237349 GACATGACATCGACTTGAGATGT-GGCC
65 GACATGGCATCGACTTGAGACGTAAGCC
* *
88237376 AGTGTAAGACCGTGTTTGGGACATTGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCGGC
88237409 ACCTTACCCA
Statistics
Matches: 183, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
92 13 0.07
93 92 0.50
94 31 0.17
95 2 0.01
96 43 0.23
97 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACAGATGATAGTCAGTGTAAGACCATGTTTGGG
ACATGGCATCGACTTGAGACGTAAGCC
Found at i:88243100 original size:27 final size:27
Alignment explanation
Indices: 88243006--88243131 Score: 119
Period size: 27 Copynumber: 4.7 Consensus size: 27
88242996 CATCACGTAG
* * *
88243006 GGGCAAAATAGTCATCTTATCACCTAA
1 GGGCAAAATAGTCATTTTACCACATAA
* *
88243033 GGGTAAATTAGTCATTTTACCACATAA
1 GGGCAAAATAGTCATTTTACCACATAA
* ** *
88243060 GGGGAAAACCGTCATTTTACCACATGA
1 GGGCAAAATAGTCATTTTACCACATAA
* ****
88243087 GGGCAAAATAGTCAGTTTGTTGCATAA
1 GGGCAAAATAGTCATTTTACCACATAA
88243114 GGG-AAAATAGTCATTTTA
1 GGGCAAAATAGTCATTTTA
88243132 TTTTACAGGG
Statistics
Matches: 78, Mismatches: 21, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
26 13 0.17
27 65 0.83
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (27 bp):
GGGCAAAATAGTCATTTTACCACATAA
Found at i:88243201 original size:27 final size:27
Alignment explanation
Indices: 88243122--88243211 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
88243112 AAGGGAAAAT
** * *
88243122 AGTCATTTTATTTTACAGGGGTATTAC
1 AGTCATTTTATCCTACTGGGGTATTTC
* * *
88243149 AATCATTTTATCCTACTAGGGAATTTC
1 AGTCATTTTATCCTACTGGGGTATTTC
*
88243176 AGTCATTTTATCCTA-TGGGGGTATTTT
1 AGTCATTTTATCCTACT-GGGGTATTTC
*
88243203 GGTCATTTT
1 AGTCATTTT
88243212 CAAGTAAATA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 1 0.02
27 49 0.98
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (27 bp):
AGTCATTTTATCCTACTGGGGTATTTC
Found at i:88249713 original size:27 final size:27
Alignment explanation
Indices: 88249652--88249787 Score: 107
Period size: 27 Copynumber: 5.0 Consensus size: 27
88249642 ACACATACAT
* * * * *
88249652 CACATAGGGGCAAAACAGTCATCTTAA
1 CACATAAGGGAAAAATAGTCATTTTAC
* *
88249679 CATC-TAAGGGTAAATTAGTCATTTTAC
1 CA-CATAAGGGAAAAATAGTCATTTTAC
*
88249706 CACATAAGGGCAAAACT-GTCATTTTAC
1 CACATAAGGG-AAAAATAGTCATTTTAC
* * *
88249733 CACATGAGGGCAAAATAGTCAATTT-C
1 CACATAAGGGAAAAATAGTCATTTTAC
* *
88249759 TCGCATAAGGGAAAAACAGTCATTTTAC
1 -CACATAAGGGAAAAATAGTCATTTTAC
88249787 C
1 C
88249788 TTATAGGGGT
Statistics
Matches: 86, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
26 6 0.07
27 74 0.86
28 6 0.07
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (27 bp):
CACATAAGGGAAAAATAGTCATTTTAC
Found at i:88249717 original size:54 final size:54
Alignment explanation
Indices: 88249651--88249781 Score: 140
Period size: 54 Copynumber: 2.4 Consensus size: 54
88249641 TACACATACA
* * * *
88249651 TCACATAGGGGCAAAACAGTCATCTTAACATC-TAAGGGTAAATTAGTCATTTTAC
1 TCACATAAGGGCAAAACAGTCATCTTAACA-CATAAGGGCAAAATAGTCAATTT-C
* * * *
88249706 -CACATAAGGGCAAAACTGTCATTTTACCACATGAGGGCAAAATAGTCAATTTC
1 TCACATAAGGGCAAAACAGTCATCTTAACACATAAGGGCAAAATAGTCAATTTC
* *
88249759 TCGCATAAGGGAAAAACAGTCAT
1 TCACATAAGGGCAAAACAGTCAT
88249782 TTTACCTTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
53 2 0.03
54 61 0.97
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (54 bp):
TCACATAAGGGCAAAACAGTCATCTTAACACATAAGGGCAAAATAGTCAATTTC
Found at i:88250230 original size:8 final size:8
Alignment explanation
Indices: 88250217--88250254 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
88250207 CGACCACTCA
88250217 CTTTTCGG
1 CTTTTCGG
*
88250225 CTTTTCAGC
1 CTTTTC-GG
88250234 CTTTT-GG
1 CTTTTCGG
88250241 CTTTTCGG
1 CTTTTCGG
88250249 CTTTTC
1 CTTTTC
88250255 AACCTTTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 14 0.54
9 6 0.23
ACGTcount: A:0.03, C:0.26, G:0.18, T:0.53
Consensus pattern (8 bp):
CTTTTCGG
Found at i:88253239 original size:18 final size:18
Alignment explanation
Indices: 88253192--88253241 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
88253182 CTTGCCCCAT
88253192 TACAGTAACAGTAAACAG
1 TACAGTAACAGTAAACAG
*
88253210 TACAATAACAGTAAACAG
1 TACAGTAACAGTAAACAG
* *
88253228 TATAGTAGCAGTAA
1 TACAGTAACAGTAA
88253242 CAATATGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (18 bp):
TACAGTAACAGTAAACAG
Found at i:88253617 original size:27 final size:27
Alignment explanation
Indices: 88253578--88253706 Score: 143
Period size: 27 Copynumber: 4.8 Consensus size: 27
88253568 CATCACGTAG
* * *
88253578 GGGCAAAACAGTCATCTTACCACTTAA
1 GGGCAAAATAGTCATTTTACCACATAA
* *
88253605 GGGCAAATTAGTCATTTTACCATATAA
1 GGGCAAAATAGTCATTTTACCACATAA
** *
88253632 GGGC-AAATCCCTCATTTTACCACATGA
1 GGGCAAAAT-AGTCATTTTACCACATAA
* * *
88253659 GGGAAAAATAGTCAGTTTATCACATAA
1 GGGCAAAATAGTCATTTTACCACATAA
88253686 GGGCAAAATAGTCATTTTACC
1 GGGCAAAATAGTCATTTTACC
88253707 TCACAGGGGT
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 3 0.04
27 74 0.91
28 4 0.05
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (27 bp):
GGGCAAAATAGTCATTTTACCACATAA
Found at i:88253753 original size:27 final size:27
Alignment explanation
Indices: 88253713--88253784 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
88253703 TACCTCACAG
** * *
88253713 GGGTATTACAGTCATTTTATCCTATTA
1 GGGTATTTTAGTCATTTTACCCTATGA
* * *
88253740 GGGTATTTTGGTCAATTTACCCTATGG
1 GGGTATTTTAGTCATTTTACCCTATGA
88253767 GGGTATTTTAGTCATTTT
1 GGGTATTTTAGTCATTTT
88253785 CAAGTAAATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (27 bp):
GGGTATTTTAGTCATTTTACCCTATGA
Found at i:88260018 original size:15 final size:16
Alignment explanation
Indices: 88259998--88260027 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88259988 TTTATTTATG
88259998 ACAATCAT-ACATTTC
1 ACAATCATAACATTTC
88260013 ACAATCATAACATTT
1 ACAATCATAACATTT
88260028 AATTTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.33
Consensus pattern (16 bp):
ACAATCATAACATTTC
Found at i:88266509 original size:13 final size:13
Alignment explanation
Indices: 88266491--88266517 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
88266481 TGAATTAAAA
88266491 TGTGTGAAAATTT
1 TGTGTGAAAATTT
88266504 TGTGTGAAAATTT
1 TGTGTGAAAATTT
88266517 T
1 T
88266518 ATCATTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:88267730 original size:43 final size:42
Alignment explanation
Indices: 88267636--88267742 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
88267626 GATGTGTTTC
* * * *
88267636 CATGTAAGACCATGTTTGGGACATTGGCATCGTATATGATTT
1 CATGTAAGACCATGTCTGGGACAGTGGCATCATATATGATTA
*
88267678 CATGTAAGACCTTGTCTGGGACAGTGGCATCA-ATACTTGATTA
1 CATGTAAGACCATGTCTGGGACAGTGGCATCATATA--TGATTA
* *
88267721 CATGTAAGACCACGTCTAGGAC
1 CATGTAAGACCATGTCTGGGAC
88267743 GTTAGCATTG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 3 0.05
42 28 0.51
43 24 0.44
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (42 bp):
CATGTAAGACCATGTCTGGGACAGTGGCATCATATATGATTA
Found at i:88273526 original size:13 final size:13
Alignment explanation
Indices: 88273508--88273532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88273498 AAATTAAAAT
88273508 GTGTGAAAATTTC
1 GTGTGAAAATTTC
88273521 GTGTGAAAATTT
1 GTGTGAAAATTT
88273533 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:88274697 original size:42 final size:43
Alignment explanation
Indices: 88274648--88274762 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
88274638 GATGTGTTTT
*
88274648 CATGTAAGACCATGTCTGGGACA-TCGGCATCG-TATATGATTT
1 CATGTAAGACCATGTCTGGGACAGT-GGCATCGATATATGATTA
** * *
88274690 TTTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATTA
1 CATGTAAGACCATGTCTGGGACAGTGGCATCGATATATGATTA
*
88274733 CATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 CATGTAAGACCATGTCTGGGACAG-TGGCAT
88274763 TGTACGAGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 28 0.46
43 33 0.54
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
CATGTAAGACCATGTCTGGGACAGTGGCATCGATATATGATTA
Found at i:88288626 original size:13 final size:13
Alignment explanation
Indices: 88288608--88288633 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88288598 TATTTGTAAA
88288608 CTTGTTCATTTCC
1 CTTGTTCATTTCC
88288621 CTTGTTCATTTCC
1 CTTGTTCATTTCC
88288634 TTTCTCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.08, T:0.54
Consensus pattern (13 bp):
CTTGTTCATTTCC
Done.