Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 132 of 170
Found at i:40064564 original size:41 final size:41
Alignment explanation
Indices: 40064461--40064567 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
40064451 ATCTGAGATT
* * * *
40064461 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
* *
40064502 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGTTGAATTTC
1 TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
40064543 TTCAGACTTTATGTCTAGCAGGCTT
1 TTCAGACTTTATGTCTAGCAGGCTT
40064568 TGTGCCGGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGGCTTGATGTCGGTGAATTAC
Found at i:40071646 original size:22 final size:22
Alignment explanation
Indices: 40071620--40071663 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40071610 TTACAATTCT
*
40071620 TGAATATATCTTAATAATCAAC
1 TGAATATATCTTAACAATCAAC
*
40071642 TGAATATATTTTAACAATCAAC
1 TGAATATATCTTAACAATCAAC
40071664 AGATCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (22 bp):
TGAATATATCTTAACAATCAAC
Found at i:40074569 original size:4 final size:4
Alignment explanation
Indices: 40074560--40074589 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
40074550 GTTTTTAGAT
40074560 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GT
1 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GT
40074590 GTGACTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
GTTA
Found at i:40088735 original size:27 final size:27
Alignment explanation
Indices: 40088697--40088840 Score: 168
Period size: 27 Copynumber: 5.3 Consensus size: 27
40088687 AATCATGGAC
*
40088697 AAATGACCGAATTACCCTCGAAGGGTA
1 AAATGACTGAATTACCCTCGAAGGGTA
*
40088724 AAATGACTGAATTACCCTCAAAGGGTA
1 AAATGACTGAATTACCCTCGAAGGGTA
* *
40088751 AAATGA-TCGAATTACCCCCGAAAGGTA
1 AAATGACT-GAATTACCCTCGAAGGGTA
* *
40088778 AAATGA-TCAAATTACCCCCGAAGGGTA
1 AAATGACT-GAATTACCCTCGAAGGGTA
* *
40088805 AAATGACCGAAATACCCTC-ATAGGGTA
1 AAATGACTGAATTACCCTCGA-AGGGTA
40088832 AAATGACTG
1 AAATGACTG
40088841 TTATACCCCT
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.02
27 100 0.98
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACTGAATTACCCTCGAAGGGTA
Found at i:40088849 original size:54 final size:54
Alignment explanation
Indices: 40088697--40088840 Score: 193
Period size: 54 Copynumber: 2.7 Consensus size: 54
40088687 AATCATGGAC
*
40088697 AAATGACCGAATTACCCTCGAAGGGTAAAATGACTGAATTACCCTCAAAGGGTA
1 AAATGACCGAATTACCCTCGAAGGGTAAAATGACTGAATTACCCCCAAAGGGTA
* * * * *
40088751 AAATGATCGAATTACCCCCGAAAGGTAAAATGA-TCAAATTACCCCCGAAGGGTA
1 AAATGACCGAATTACCCTCGAAGGGTAAAATGACT-GAATTACCCCCAAAGGGTA
*
40088805 AAATGACCGAAATACCCTC-ATAGGGTAAAATGACTG
1 AAATGACCGAATTACCCTCGA-AGGGTAAAATGACTG
40088841 TTATACCCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.03
54 73 0.96
55 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (54 bp):
AAATGACCGAATTACCCTCGAAGGGTAAAATGACTGAATTACCCCCAAAGGGTA
Found at i:40089080 original size:26 final size:26
Alignment explanation
Indices: 40089017--40089080 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
40089007 TGTTACTGGT
* * *
40089017 AGCTTTGCTACATTACTATTAATGGC
1 AGCTTTGCTGCATCACTATTAATAGC
* * *
40089043 AACTTTGTTGCATCACTATTACTAGC
1 AGCTTTGCTGCATCACTATTAATAGC
40089069 AGCTTTGCTGCA
1 AGCTTTGCTGCA
40089081 ATATTGGTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (26 bp):
AGCTTTGCTGCATCACTATTAATAGC
Found at i:40089231 original size:28 final size:29
Alignment explanation
Indices: 40089186--40089245 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
40089176 ACTGCATTGT
* *
40089186 ACTGATTATTGTATTGGGCTAAGGCCCAC
1 ACTGATTACTGTAATGGGCTAAGGCCCAC
40089215 ACTG-TTACTGTAATGGGCTAAGGCCCAC
1 ACTGATTACTGTAATGGGCTAAGGCCCAC
40089243 ACT
1 ACT
40089246 ATACTGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (29 bp):
ACTGATTACTGTAATGGGCTAAGGCCCAC
Found at i:40091088 original size:26 final size:26
Alignment explanation
Indices: 40091047--40091121 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
40091037 AATATTTTCT
40091047 CAAAATTTTACTAGGGGTAAAATCAC
1 CAAAATTTTACTAGGGGTAAAATCAC
*
40091073 CAAAAATTTTAC-AGGGGTAAAATCAT
1 C-AAAATTTTACTAGGGGTAAAATCAC
* *
40091099 CAAAACTTTACTGGGGGTAAAAT
1 CAAAATTTTACTAGGGGTAAAAT
40091122 AGGGATGAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 9 0.20
26 25 0.57
27 10 0.23
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (26 bp):
CAAAATTTTACTAGGGGTAAAATCAC
Found at i:40092783 original size:19 final size:20
Alignment explanation
Indices: 40092759--40092804 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
40092749 GTTGAAAAAG
40092759 TTTCAAT-TGTGTTAAACAT
1 TTTCAATGTGTGTTAAACAT
* *
40092778 TTTCAAATGTGTTTTAACCAT
1 TTTC-AATGTGTGTTAAACAT
40092799 TTTCAA
1 TTTCAA
40092805 ATAAGTCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 5 0.22
21 14 0.61
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (20 bp):
TTTCAATGTGTGTTAAACAT
Found at i:40092982 original size:20 final size:19
Alignment explanation
Indices: 40092947--40092998 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
40092937 GTATCGATCT
*
40092947 AGTATCAATACTTTTCTTAA
1 AGTATCAATA-TTTTCCTAA
40092967 AGTATCAATATATTTCCTAA
1 AGTATCAATAT-TTTCCTAA
* *
40092987 GGTATCGATATT
1 AGTATCAATATT
40092999 CTTGATCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (19 bp):
AGTATCAATATTTTCCTAA
Found at i:40094230 original size:35 final size:35
Alignment explanation
Indices: 40094168--40094253 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
40094158 ATTTTATTTG
*
40094168 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
40094201 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
40094237 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
40094254 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:40094239 original size:25 final size:23
Alignment explanation
Indices: 40094195--40094255 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
40094185 TGATATTTAA
*
40094195 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
40094219 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
40094244 ATATTATTAAAT
1 ATATAATTAAAT
40094256 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:40095571 original size:3 final size:3
Alignment explanation
Indices: 40095557--40095603 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
40095547 GTGAGGTAAG
*
40095557 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40095604 AGATGAATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:40095791 original size:24 final size:27
Alignment explanation
Indices: 40095754--40095817 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
40095744 AATTGCGGAT
*
40095754 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
40095778 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
40095804 TTGTGATTGAATTG
1 TAATGATTGAATTG
40095818 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:40102251 original size:26 final size:26
Alignment explanation
Indices: 40102143--40102278 Score: 150
Period size: 27 Copynumber: 5.1 Consensus size: 26
40102133 TCCAAAATTT
40102143 GTAAAATGA-TCGTAATGCCCCTGTAG
1 GTAAAATGACT-GTAATGCCCCTGTAG
*
40102169 AGTAAAATGA-TCGTAATGCCCATGTAGG
1 -GTAAAATGACT-GTAATGCCCCTGTA-G
* *
40102197 GTAAAATGACCGTAATGCCCCTGCAAG
1 GTAAAATGACTGTAATGCCCCTG-TAG
* *
40102224 GTAAAATGACTGTGATGCCCTTGTAG
1 GTAAAATGACTGTAATGCCCCTGTAG
*
40102250 GTAAAATGACTGTAATACCCCTGTCAG
1 GTAAAATGACTGTAATGCCCCTGT-AG
40102277 GT
1 GT
40102279 GAATTGATCG
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.24
27 69 0.73
28 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (26 bp):
GTAAAATGACTGTAATGCCCCTGTAG
Found at i:40102421 original size:24 final size:24
Alignment explanation
Indices: 40102332--40102423 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
40102322 CCCTCGAGGT
* ** *
40102332 TAAATGATTTATTCATCTGTGATG
1 TAAATGATTGATTTGTCTGTAATG
* *
40102356 TAAGTGATTGATTTGTCCG-AGATG
1 TAAATGATTGATTTGTCTGTA-ATG
* * *
40102380 TAAATGACTAATTTGTCTGTAATT
1 TAAATGATTGATTTGTCTGTAATG
40102404 TAAATGATTGATTTGTCTGT
1 TAAATGATTGATTTGTCTGT
40102424 GATTGGTATA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
24 52 0.98
25 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.45
Consensus pattern (24 bp):
TAAATGATTGATTTGTCTGTAATG
Found at i:40104477 original size:17 final size:19
Alignment explanation
Indices: 40104455--40104490 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40104445 GTTAAAAAAA
40104455 TATTAT-AA-AAATAATAT
1 TATTATAAATAAATAATAT
40104472 TATTATAAATAAATAATAT
1 TATTATAAATAAATAATAT
40104491 AAAATTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATTATAAATAAATAATAT
Found at i:40109747 original size:17 final size:16
Alignment explanation
Indices: 40109727--40109761 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
40109717 GTTTAATATA
40109727 TAATTTTATATAAATTT
1 TAATTTTATAT-AATTT
*
40109744 TAATTTTATGTAATTT
1 TAATTTTATATAATTT
40109760 TA
1 TA
40109762 TATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TAATTTTATATAATTT
Found at i:40123310 original size:25 final size:24
Alignment explanation
Indices: 40123261--40123319 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
40123251 GCTCACATTT
*
40123261 ATATTTTTTATTTCATGTTATTTA
1 ATATTTTTTATTTCATGTTAATTA
* *
40123285 A-ATCTTTTTTTTTCATTTTTAATTA
1 ATAT-TTTTTATTTCA-TGTTAATTA
40123310 ATATTTTTTA
1 ATATTTTTTA
40123320 CTAATCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
23 2 0.07
24 11 0.39
25 13 0.46
26 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (24 bp):
ATATTTTTTATTTCATGTTAATTA
Found at i:40123316 original size:24 final size:25
Alignment explanation
Indices: 40123261--40123319 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
40123251 GCTCACATTT
*
40123261 ATATTTTTTATTTCATGTTATTTAA
1 ATATTTTTTATTTCATGTTAATTAA
* *
40123286 ATCTTTTTT-TTTCATTTTTAATT-A
1 ATATTTTTTATTTCA-TGTTAATTAA
40123310 ATATTTTTTA
1 ATATTTTTTA
40123320 CTAATCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (25 bp):
ATATTTTTTATTTCATGTTAATTAA
Found at i:40123940 original size:17 final size:17
Alignment explanation
Indices: 40123918--40123951 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40123908 ATACTTAACC
*
40123918 TATACATCACTTGGGTA
1 TATACATCACTTAGGTA
40123935 TATACATCACTTAGGTA
1 TATACATCACTTAGGTA
40123952 CATGCCACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (17 bp):
TATACATCACTTAGGTA
Found at i:40125152 original size:45 final size:46
Alignment explanation
Indices: 40125060--40125162 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 46
40125050 GATAGTAGTG
* *
40125060 ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCTGAATCTGTA
1 ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCGGTA
* *
40125106 ACAGTAACGGTAACAGTA-TTCGACACACAAAGTGCCGAATCGGTA
1 ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCGGTA
*
40125151 ACAATAACAGTA
1 ACAGTAACAGTA
40125163 GTCGGTACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 34 0.67
46 17 0.33
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (46 bp):
ACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATCGGTA
Found at i:40126320 original size:4 final size:4
Alignment explanation
Indices: 40126305--40126361 Score: 60
Period size: 4 Copynumber: 13.8 Consensus size: 4
40126295 TAATGTTCTG
* * * *
40126305 TTTC TCTC TTTC TTTC TTTTA TTTC TCTC TTTC TTTC TTTTA TTTC TTTC
1 TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
40126355 TTTC TTT
1 TTTC TTT
40126362 TATTTCTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 37 0.86
5 6 0.14
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:40126329 original size:21 final size:21
Alignment explanation
Indices: 40126305--40126361 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
40126295 TAATGTTCTG
40126305 TTTCTCTCTTTCTTTCTTTTA
1 TTTCTCTCTTTCTTTCTTTTA
40126326 TTTCTCTCTTTCTTTCTTTTA
1 TTTCTCTCTTTCTTTCTTTTA
*
40126347 TTTCTTTCTTTCTTT
1 TTTCTCTCTTTCTTT
40126362 TATTTCTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCTCTCTTTCTTTCTTTTA
Found at i:40126369 original size:17 final size:17
Alignment explanation
Indices: 40126311--40126369 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 17
40126301 TCTGTTTCTC
40126311 TCTTTCTTTCTTTTATTTCT
1 TCTTTCTTTCTTTTA--T-T
40126331 CTCTTTCTTTCTTTTATT
1 -TCTTTCTTTCTTTTATT
40126349 TCTTTCTTTCTTTTATT
1 TCTTTCTTTCTTTTATT
40126366 TCTT
1 TCTT
40126370 GTTTTATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 21 0.55
18 1 0.03
19 1 0.03
21 15 0.39
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTTTCTTTCTTTTATT
Found at i:40126516 original size:5 final size:5
Alignment explanation
Indices: 40126508--40126532 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40126498 ATTTTATCTA
40126508 ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT
40126533 TCTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:40126543 original size:5 final size:5
Alignment explanation
Indices: 40126535--40126560 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40126525 AATATAATTC
40126535 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
40126561 AACTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:40130974 original size:44 final size:44
Alignment explanation
Indices: 40130881--40130977 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
40130871 TCAGTTGTTC
* * *
40130881 GGTTGAATGGAATGGAATAGATATATAATAGCATTCTTGTGTTT
1 GGTTGAATGCAATGGAATAGATATATAATAGCATTATTGTATTT
* * * * * *
40130925 AGTTGAATGCAATTGAATAGATCTGTAATTGTATTATTGTATTT
1 GGTTGAATGCAATGGAATAGATATATAATAGCATTATTGTATTT
40130969 GGTTGAATG
1 GGTTGAATG
40130978 AAATAGATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (44 bp):
GGTTGAATGCAATGGAATAGATATATAATAGCATTATTGTATTT
Found at i:40131288 original size:13 final size:14
Alignment explanation
Indices: 40131247--40131288 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
40131237 AATCCAAGTC
* *
40131247 AAATAAAACAATTA
1 AAATAAAATAACTA
40131261 AAAT-AAATAACTA
1 AAATAAAATAACTA
40131274 AAATAAAATAA-TA
1 AAATAAAATAACTA
40131287 AA
1 AA
40131289 TCAAAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:40131703 original size:25 final size:23
Alignment explanation
Indices: 40131674--40131729 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
40131664 CATAAAATTC
40131674 TTAAATAAATTAAAATACTTAATAA
1 TTAAATAAATTAAAATA--TAATAA
* *
40131699 TTAAAAAAATTAGAATATAATAA
1 TTAAATAAATTAAAATATAATAA
*
40131722 TAAAATAA
1 TTAAATAA
40131730 TAAGAGCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.44
25 15 0.56
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TTAAATAAATTAAAATATAATAA
Found at i:40131705 original size:17 final size:18
Alignment explanation
Indices: 40131666--40131704 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
40131656 CTTGTTAACA
*
40131666 TAAAATTCTTAAATAAAT
1 TAAAATACTTAAATAAAT
40131684 TAAAATACTT-AAT-AAT
1 TAAAATACTTAAATAAAT
40131700 TAAAA
1 TAAAA
40131705 AAATTAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:40137600 original size:43 final size:43
Alignment explanation
Indices: 40137547--40137638 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
40137537 GAAGCGAATA
40137547 AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
1 AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
**
40137590 AAGAAGATAAATGGAAAGATAGAACGTGGCGTGTGGAAGTCCT
1 AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
40137633 AAGAAG
1 AAGAAG
40137639 CCTTGGAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.17
Consensus pattern (43 bp):
AAGAAGATAAATGGAAAGATAGAACGTGAAGTGTGGAAGTCCT
Found at i:40142165 original size:27 final size:26
Alignment explanation
Indices: 40142125--40142385 Score: 213
Period size: 27 Copynumber: 9.7 Consensus size: 26
40142115 GATTCGTGGG
*
40142125 AAAATAACTGAAATACCCCCGAAGGGT
1 AAAATGAC-GAAATACCCCCGAAGGGT
* * *
40142152 AGAATAATCGAAATACCCCCGAATGGT
1 AAAATGA-CGAAATACCCCCGAAGGGT
* *
40142179 AGAATGACTAAAATACCCCCGAAGGGT
1 AAAATGAC-GAAATACCCCCGAAGGGT
* * *
40142206 AAAATGATCAAAATACCCTCGAAGGGC
1 AAAATGA-CGAAATACCCCCGAAGGGT
*
40142233 AAAATGACTGAAATACCCTCGAAGGGT
1 AAAATGAC-GAAATACCCCCGAAGGGT
* *
40142260 AAAATGACTAAAATACCCCCAAAGGGT
1 AAAATGAC-GAAATACCCCCGAAGGGT
*
40142287 AAAATGATC-AGAATACCCCTGAAGGGT
1 AAAATGA-CGA-AATACCCCCGAAGGGT
** *
40142314 AAAATGACCGAAATACCCCTAAAGTGT
1 AAAATGA-CGAAATACCCCCGAAGGGT
** * *
40142341 AAAAT-AAAAAATA-CCCCTATATGGT
1 AAAATGACGAAATACCCCCGA-AGGGT
*
40142366 AAAATAACTGAAATACCCCC
1 AAAATGAC-GAAATACCCCC
40142386 ATAGGATAGA
Statistics
Matches: 197, Mismatches: 26, Indels: 21
0.81 0.11 0.09
Matches are distributed among these distances:
24 4 0.02
25 13 0.07
26 5 0.03
27 167 0.85
28 8 0.04
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (26 bp):
AAAATGACGAAATACCCCCGAAGGGT
Found at i:40142220 original size:54 final size:54
Alignment explanation
Indices: 40142125--40142357 Score: 240
Period size: 54 Copynumber: 4.4 Consensus size: 54
40142115 GATTCGTGGG
* * * * * *
40142125 AAAATAACTGAAATACCCCCGAAGGGTAGAATAATCGAAATACCCCCGAATGGT
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
* * *
40142179 AGAATGACTAAAATACCCCCGAAGGGTAAAATGATCAAAATACCCTCGAAGGGC
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
* * *
40142233 AAAATGACTGAAATACCCTCGAAGGGTAAAATGA-CTAAAATACCCCCAAAGGGT
1 AAAATGACTAAAATACCCCCGAAGGGTAAAATGATC-AAAATACCCCCGAAGGGT
* * * * ** *
40142287 AAAATGA-TCAGAATACCCCTGAAGGGTAAAATGACCGAAATACCCCTAAAGTGT
1 AAAATGACT-AAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
*
40142341 AAAAT-A-AAAAATACCCC
1 AAAATGACTAAAATACCCC
40142358 TATATGGTAA
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
52 9 0.06
53 3 0.02
54 139 0.91
55 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (54 bp):
AAAATGACTAAAATACCCCCGAAGGGTAAAATGATCAAAATACCCCCGAAGGGT
Found at i:40142266 original size:81 final size:80
Alignment explanation
Indices: 40142135--40142357 Score: 272
Period size: 81 Copynumber: 2.8 Consensus size: 80
40142125 AAAATAACTG
* * * *
40142135 AAATACCCCCGAAGGGTAGAAT-AATCGAAATACCCCCGAATGGTAGAATGACTAAAATACCCCC
1 AAATA-CCCCGAAGGGTAAAATGACT-GAAATACCCCCGAAGGGTAAAATGACTAAAATACCCCC
*
40142199 GAAGGGTAAAATGATCA
64 AAAGGGTAAAATGATCA
* *
40142216 AAATACCCTCGAAGGGCAAAATGACTGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCCCA
1 AAATACCC-CGAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACTAAAATACCCCCA
40142281 AAGGGTAAAATGATCA
65 AAGGGTAAAATGATCA
* * ** * *
40142297 GAATACCCCTGAAGGGTAAAATGACCGAAATACCCCTAAAGTGTAAAAT-A-AAAAATACCCC
1 AAATACCCC-GAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACTAAAATACCCC
40142358 TATATGGTAA
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
79 10 0.08
80 5 0.04
81 107 0.86
82 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (80 bp):
AAATACCCCGAAGGGTAAAATGACTGAAATACCCCCGAAGGGTAAAATGACTAAAATACCCCCAA
AGGGTAAAATGATCA
Found at i:40142603 original size:26 final size:26
Alignment explanation
Indices: 40142574--40142630 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
40142564 TTTGCCACAT
*
40142574 ATACTGATACTGGTAGCTTT-GCTGCA
1 ATACTGATACTGGCAG-TTTCGCTGCA
* *
40142600 ATACTGTTACTGGCAGTTTCGCTGCG
1 ATACTGATACTGGCAGTTTCGCTGCA
40142626 ATACT
1 ATACT
40142631 ATTACCAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (26 bp):
ATACTGATACTGGCAGTTTCGCTGCA
Found at i:40142635 original size:26 final size:26
Alignment explanation
Indices: 40142581--40142653 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
40142571 CATATACTGA
* * *
40142581 TACTGGTAGCTTTGCTGCAATACTGT
1 TACTGGCAGCTTTGCTGCGATACTAT
40142607 TACTGGCAG-TTTCGCTGCGATACTAT
1 TACTGGCAGCTTT-GCTGCGATACTAT
**
40142633 TACCAGCAGCTTTGCTGCGAT
1 TACTGGCAGCTTTGCTGCGAT
40142654 GTTGGTTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 3 0.08
26 34 0.85
27 3 0.08
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (26 bp):
TACTGGCAGCTTTGCTGCGATACTAT
Found at i:40149953 original size:15 final size:16
Alignment explanation
Indices: 40149933--40149972 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
40149923 AAAATAATTT
40149933 AAAACTT-AAATTTTG
1 AAAACTTAAAATTTTG
40149948 AAAACTTAAAAATTTTG
1 AAAACTT-AAAATTTTG
40149965 AGAAACTT
1 A-AAACTT
40149973 TGGAACTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (16 bp):
AAAACTTAAAATTTTG
Found at i:40150245 original size:57 final size:57
Alignment explanation
Indices: 40150184--40150352 Score: 275
Period size: 57 Copynumber: 3.0 Consensus size: 57
40150174 AAACTATAGA
* *
40150184 GAATATTTACTGTTTTCACCAGAGAATATTTCCTATTCACTTGTCTTTTCTTGCAGG
1 GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAGG
* * *
40150241 GAATATTTACTTTTTTCGCTAGAGAATATTTCCTGTTCACTTATCTTTTCTTGCAGG
1 GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAGG
* *
40150298 GAATATTTACTGTTTTCGCCAAAGAATATTTCCTGTTCACTCGTCTTTTCTTGCA
1 GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCA
40150353 TCATTTTTTC
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 102 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (57 bp):
GAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTGTCTTTTCTTGCAGG
Found at i:40155899 original size:22 final size:22
Alignment explanation
Indices: 40155874--40155918 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
40155864 TATCCCCACA
*
40155874 TGGAGTGTTG-GGCTGGACTGAG
1 TGGAGTGTAGAGGCTGGA-TGAG
40155896 TGGAGTGTAGAGGCTGGATGAG
1 TGGAGTGTAGAGGCTGGATGAG
40155918 T
1 T
40155919 AGGATTTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.18, C:0.07, G:0.49, T:0.27
Consensus pattern (22 bp):
TGGAGTGTAGAGGCTGGATGAG
Found at i:40163034 original size:57 final size:57
Alignment explanation
Indices: 40162941--40163120 Score: 270
Period size: 57 Copynumber: 3.2 Consensus size: 57
40162931 TATTCATGCG
*
40162941 TCTTTTCTTGCAGGGAATATTTACTGTTTTCGCCAGAGAATATTTCCTGTTCACTTA
1 TCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTTA
* ** *
40162998 TCTTTTCTTGTAGGGAATATTTACTATTTTTTCCAGAGAATATTTCCTGTTCATTTA
1 TCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTTA
* * * **
40163055 TCTTTTCTTGCAGAGAATATTTACTATTTTCGCCAGAGAATATTTCTTATTCACTCG
1 TCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTTA
40163112 TCTTTTCTT
1 TCTTTTCTT
40163121 ACATCATTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 109 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.48
Consensus pattern (57 bp):
TCTTTTCTTGCAGGGAATATTTACTATTTTCGCCAGAGAATATTTCCTGTTCACTTA
Found at i:40164206 original size:15 final size:15
Alignment explanation
Indices: 40164186--40164276 Score: 62
Period size: 15 Copynumber: 6.1 Consensus size: 15
40164176 TTTATGGAAA
40164186 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
40164201 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
40164215 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
40164231 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
40164245 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* *
40164261 ATC-GAGATATTGGT
1 ATCAAAGATATGGGT
40164275 AT
1 AT
40164277 AATAAAATCT
Statistics
Matches: 56, Mismatches: 16, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
14 19 0.34
15 29 0.52
16 8 0.14
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:40164223 original size:30 final size:30
Alignment explanation
Indices: 40164182--40164263 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
40164172 CATATTTATG
*
40164182 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
40164212 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
40164242 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
40164264 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:40168868 original size:15 final size:15
Alignment explanation
Indices: 40168848--40168925 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
40168838 TTTATGGAAA
40168848 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
40168863 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
40168877 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
40168893 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
40168907 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
40168923 ATC
1 ATC
40168926 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:40168885 original size:30 final size:30
Alignment explanation
Indices: 40168844--40168925 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
40168834 CATATTTATG
*
40168844 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
40168874 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
40168904 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
40168926 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:40172126 original size:20 final size:20
Alignment explanation
Indices: 40172064--40172127 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
40172054 AAAAAACTAA
*
40172064 ATTTTTAACGTAATACAAAT
1 ATTTTTAATGTAATACAAAT
40172084 ATTTTTAATGTAATACCAAAT
1 ATTTTTAATGTAATA-CAAAT
* * *
40172105 -TTTCTAATG-GATACTAAT
1 ATTTTTAATGTAATACAAAT
40172123 ATTTT
1 ATTTT
40172128 AAAGGCAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 4 0.11
19 6 0.16
20 22 0.59
21 5 0.14
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (20 bp):
ATTTTTAATGTAATACAAAT
Found at i:40181057 original size:28 final size:28
Alignment explanation
Indices: 40181001--40181060 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
40180991 ACCACCCTAT
*
40181001 TTTATTTTATATTTGAATTATGTTTGAA
1 TTTATTTTATATTTGAATTATGTTAGAA
*
40181029 TTTA-TTTATATGTTAGAATTGTG-TAGAA
1 TTTATTTTATAT-TT-GAATTATGTTAGAA
40181057 TTTA
1 TTTA
40181061 GTGATTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.25
28 14 0.50
29 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TTTATTTTATATTTGAATTATGTTAGAA
Found at i:40181422 original size:30 final size:30
Alignment explanation
Indices: 40181388--40181444 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
40181378 GAGTAACCTC
* *
40181388 GATATACTGTTAGCTTGTGTGAGCAACCCT
1 GATATACTGTCAGCTTGTGTGAACAACCCT
*
40181418 GATATATTGTCAGCTTGTGTGAACAAC
1 GATATACTGTCAGCTTGTGTGAACAAC
40181445 TTTTTCCCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (30 bp):
GATATACTGTCAGCTTGTGTGAACAACCCT
Found at i:40181546 original size:10 final size:11
Alignment explanation
Indices: 40181527--40181555 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
40181517 TAAATGCAAA
40181527 TTTGATATATG
1 TTTGATATATG
40181538 TTT-ATATATG
1 TTTGATATATG
40181548 TTTGATAT
1 TTTGATAT
40181556 TTGATATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (11 bp):
TTTGATATATG
Found at i:40182709 original size:13 final size:11
Alignment explanation
Indices: 40182673--40182703 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40182663 TCATCTGTAT
40182673 TAATTTTTATA
1 TAATTTTTATA
*
40182684 TTATTTTTATA
1 TAATTTTTATA
40182695 TAATTTTTA
1 TAATTTTTA
40182704 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:40182860 original size:30 final size:30
Alignment explanation
Indices: 40182826--40182899 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
40182816 ACTTAACAAG
*
40182826 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
*
40182856 CAAATGCCTTTGAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
40182886 CAAATGCCTTTAAA
1 CAAATGCCTTTAAA
40182900 TTAACAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:40182961 original size:22 final size:22
Alignment explanation
Indices: 40182935--40182983 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40182925 ATATCCAAAC
40182935 AATAACAATAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
* * * *
40182957 CATAATAGTAAAATGGTAGCAA
1 AATAACAATAAAATAGTAGCAA
40182979 AATAA
1 AATAA
40182984 GGAGAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:40185832 original size:13 final size:13
Alignment explanation
Indices: 40185814--40185846 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40185804 ACAAACAAAC
40185814 AAATAAATAAGAT
1 AAATAAATAAGAT
*
40185827 AAATAAATAGGAT
1 AAATAAATAAGAT
40185840 -AATAAAT
1 AAATAAAT
40185847 CAAATATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (13 bp):
AAATAAATAAGAT
Found at i:40186818 original size:23 final size:23
Alignment explanation
Indices: 40186788--40186846 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
40186778 ACAATAGCAT
*
40186788 ATCAACATCATCTTTTTTAAAAA
1 ATCAACATCATCTTTCTTAAAAA
40186811 ATCAACATCATCTTTCTTAAAAA
1 ATCAACATCATCTTTCTTAAAAA
40186834 ATCAACATCATCT
1 ATCAACATCATCT
40186847 CTCCCTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (23 bp):
ATCAACATCATCTTTCTTAAAAA
Found at i:40191429 original size:19 final size:20
Alignment explanation
Indices: 40191350--40191455 Score: 115
Period size: 20 Copynumber: 5.3 Consensus size: 20
40191340 TGAAGAACAT
**
40191350 GAAATTTTGGTATCACATTA
1 GAAATTTTGGTATCATGTTA
* * * * *
40191370 CATATATTGGTATCGTGTCA
1 GAAATTTTGGTATCATGTTA
**
40191390 GAAATTTTGGTATTTTGTTA
1 GAAATTTTGGTATCATGTTA
40191410 GAAATTTTGGTATC-TGTTA
1 GAAATTTTGGTATCATGTTA
*
40191429 GAAATTTTAGTATCATGTTA
1 GAAATTTTGGTATCATGTTA
40191449 GAAATTT
1 GAAATTT
40191456 AGTACATGCT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
19 18 0.26
20 52 0.74
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (20 bp):
GAAATTTTGGTATCATGTTA
Found at i:40191448 original size:39 final size:40
Alignment explanation
Indices: 40191376--40191455 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
40191366 ATTACATATA
* **
40191376 TTGGTATCGTGTCAGAAATTTTGGTATTTTGTTAGAAATT
1 TTGGTATCGTGTCAGAAATTTTAGTATCATGTTAGAAATT
*
40191416 TTGGTATC-TGTTAGAAATTTTAGTATCATGTTAGAAATT
1 TTGGTATCGTGTCAGAAATTTTAGTATCATGTTAGAAATT
40191455 T
1 T
40191456 AGTACATGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (40 bp):
TTGGTATCGTGTCAGAAATTTTAGTATCATGTTAGAAATT
Found at i:40191579 original size:18 final size:18
Alignment explanation
Indices: 40191556--40191600 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
40191546 TCACATTAAA
40191556 AATTTTGGTATTCCA-TAG
1 AATTTTGGTATT-CATTAG
40191574 AATTTTTGGTATTCATTAG
1 AA-TTTTGGTATTCATTAG
*
40191593 AAATTTGG
1 AATTTTGG
40191601 ATATACTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (18 bp):
AATTTTGGTATTCATTAG
Found at i:40191778 original size:20 final size:20
Alignment explanation
Indices: 40191740--40191778 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40191730 TAATGGTTTC
*
40191740 CATTAGAAATATTTTTATTG
1 CATTAGAAATATTTGTATTG
40191760 CATTAGAAAT-TTTGGTATT
1 CATTAGAAATATTT-GTATT
40191779 AACTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (20 bp):
CATTAGAAATATTTGTATTG
Found at i:40208074 original size:22 final size:22
Alignment explanation
Indices: 40208047--40208089 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40208037 ATATCAAAGT
40208047 AACAACCATCAAGAAGGCCAAC
1 AACAACCATCAAGAAGGCCAAC
40208069 AACAACCATCAAGAAGGCCAA
1 AACAACCATCAAGAAGGCCAA
40208090 GGATATCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.30, G:0.14, T:0.05
Consensus pattern (22 bp):
AACAACCATCAAGAAGGCCAAC
Found at i:40213356 original size:50 final size:50
Alignment explanation
Indices: 40213241--40213483 Score: 378
Period size: 50 Copynumber: 4.8 Consensus size: 50
40213231 GATAATAACA
* ** * *
40213241 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
40213292 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
40213342 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
40213392 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
40213442 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40213484 TTACCCAAAT
Statistics
Matches: 177, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
50 144 0.81
51 33 0.19
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40213599 original size:13 final size:13
Alignment explanation
Indices: 40213578--40213608 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40213568 GCTTAGATCA
*
40213578 TCATCAAATAAAT
1 TCATAAAATAAAT
40213591 TCATAAAATAAAT
1 TCATAAAATAAAT
40213604 TCATA
1 TCATA
40213609 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:40213855 original size:30 final size:30
Alignment explanation
Indices: 40213820--40213877 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40213810 CCTCGACTCT
*
40213820 AACTTTTTCAAAATTACAATTTTACCCCTA
1 AACTTTTACAAAATTACAATTTTACCCCTA
* * *
40213850 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTACCCC
40213878 AAGGCTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTACCCCTA
Found at i:40226643 original size:50 final size:50
Alignment explanation
Indices: 40226524--40226665 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 50
40226514 GATAATAACA
* **
40226524 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTCTCATATCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGG
* * * *
40226575 TGCCTATGCCATGTCCCAGACATGGTCCTACATGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
40226625 TGCCAACGCCATGACCCAGACATGGTCTTACATGGGACCTC
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTC
40226666 ATTCCCTTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 47 0.59
51 33 0.41
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:40228438 original size:13 final size:13
Alignment explanation
Indices: 40228422--40228446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40228412 ATATTTTATT
40228422 CTTAATTTTTGTA
1 CTTAATTTTTGTA
40228435 CTTAATTTTTGT
1 CTTAATTTTTGT
40228447 TTGTTTGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
CTTAATTTTTGTA
Found at i:40243554 original size:7 final size:7
Alignment explanation
Indices: 40243542--40243574 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
40243532 TAGTTGATTC
40243542 GTATTTA
1 GTATTTA
40243549 GTATTTA
1 GTATTTA
40243556 GTATTTA
1 GTATTTA
40243563 GTATTTA
1 GTATTTA
40243570 GTATT
1 GTATT
40243575 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:40247916 original size:126 final size:126
Alignment explanation
Indices: 40247691--40247978 Score: 432
Period size: 126 Copynumber: 2.3 Consensus size: 126
40247681 GCCAAATAGG
* ** *
40247691 AACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTTTGTACTTTTGCTGACATTGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* *
40247756 TACTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
66 TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* * *
40247817 AACTACTGTAGCAAAAGAACGTCCATGTGGGAGCTTCTTTCAGTACTTTTGTTGACAATGCATCC
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* * * *
40247882 TGCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTTAGG
66 TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
* * *
40247943 AACTACTATAGTAAAATAGCGTCCACGTGGGAGCTT
1 AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
40247979 TTTTAAATTA
Statistics
Matches: 144, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
126 144 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (126 bp):
AACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
TACTTAAAACGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTCAGA
Found at i:40248350 original size:95 final size:97
Alignment explanation
Indices: 40248010--40248343 Score: 484
Period size: 95 Copynumber: 3.5 Consensus size: 97
40248000 AATTAACCCT
* * *
40248010 AAACCCCAAACCCTAATTTATTT-AATTTTTTCTT-AAAACCCTAAACACTAAACCCTAATCTAA
1 AAACCCTAAACCCTAATTTATTTGATTTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA
40248073 TTTTTTTAAAATTTATAATTAATTTACTCAAG
66 TTTTTTTAAAATTTATAATTAATTTACTCAAG
* * *
40248105 TAACCCTAAACCTTAATTTATTTGATTTTTTTCTTAAAAAACC-TAAACCCTAAACCCTAATCTA
1 AAACCCTAAACCCTAATTTATTTGATTTTTTTCTT-AAAAACCATAAACACTAAACCCTAATCTA
40248169 ATTTTTTTAAAAATTTATAATTAATTTACTCAAG
65 ATTTTTTT-AAAATTTATAATTAATTTACTCAAG
* *
40248203 TAACCCTAAACACTAATTTATTTGA-TTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA
1 AAACCCTAAACCCTAATTTATTTGATTTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA
* * *
40248267 -TTTTTTAAAATTTATAATTAATTGAATTAAG
66 TTTTTTTAAAATTTATAATTAATTTACTCAAG
*
40248298 AAACCCTAAACCCTTATTTATTT-ATTTTTTTCCTT-AAAACCATAAA
1 AAACCCTAAACCCTAATTTATTTGATTTTTTT-CTTAAAAACCATAAA
40248344 ATCTAAAAAC
Statistics
Matches: 218, Mismatches: 14, Indels: 14
0.89 0.06 0.06
Matches are distributed among these distances:
94 1 0.00
95 79 0.36
96 26 0.12
97 58 0.27
98 54 0.25
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (97 bp):
AAACCCTAAACCCTAATTTATTTGATTTTTTTCTTAAAAACCATAAACACTAAACCCTAATCTAA
TTTTTTTAAAATTTATAATTAATTTACTCAAG
Found at i:40249533 original size:41 final size:42
Alignment explanation
Indices: 40249471--40249562 Score: 161
Period size: 41 Copynumber: 2.2 Consensus size: 42
40249461 TGAATATCAA
*
40249471 TCATGCAGTGAAGGCTTTTTGCTTTAAATTTCTAGGTTGATT
1 TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
40249513 T-ATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
1 TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
40249554 TCATG-AGTG
1 TCATGCAGTG
40249563 TACATCATGC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 44 0.92
42 4 0.08
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (42 bp):
TCATGCAGTGAAGGCTGTTTGCTTTAAATTTCTAGGTTGATT
Found at i:40249998 original size:17 final size:17
Alignment explanation
Indices: 40249968--40250000 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40249958 ATTGTTACCC
40249968 TTGTTGATGATGATGAT
1 TTGTTGATGATGATGAT
40249985 TTGTGTGATG-TGATGA
1 TTGT-TGATGATGATGA
40250001 GGCAACGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (17 bp):
TTGTTGATGATGATGAT
Found at i:40252978 original size:6 final size:6
Alignment explanation
Indices: 40252967--40252996 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
40252957 ATAGGCTTTG
40252967 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
40252997 CATGAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:40255690 original size:20 final size:20
Alignment explanation
Indices: 40255661--40255706 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
40255651 ATTTAATAAA
*
40255661 TAAAAATAAAAATCTAAAAC
1 TAAAACTAAAAATCTAAAAC
*
40255681 TAAAACTAAAAGTCTAAAAC
1 TAAAACTAAAAATCTAAAAC
40255701 TAAAAC
1 TAAAAC
40255707 ATAGACATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.65, C:0.13, G:0.02, T:0.20
Consensus pattern (20 bp):
TAAAACTAAAAATCTAAAAC
Found at i:40259707 original size:9 final size:9
Alignment explanation
Indices: 40259693--40259725 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
40259683 ATTCAATGCT
40259693 TTAATTCGG
1 TTAATTCGG
*
40259702 TTAATTTGG
1 TTAATTCGG
40259711 TTAATTCGG
1 TTAATTCGG
40259720 TTAATT
1 TTAATT
40259726 TTTATACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (9 bp):
TTAATTCGG
Found at i:40264788 original size:25 final size:25
Alignment explanation
Indices: 40264741--40264788 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40264731 TTCCGAGCCA
**
40264741 TATAACAGGAAGCTCATCTGAGTTG
1 TATAACAGGAAGCTCATAGGAGTTG
*
40264766 TATAACAGGAAGCTTATAGGAGT
1 TATAACAGGAAGCTCATAGGAGT
40264789 CAATTATCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (25 bp):
TATAACAGGAAGCTCATAGGAGTTG
Found at i:40264847 original size:25 final size:25
Alignment explanation
Indices: 40264819--40264962 Score: 146
Period size: 25 Copynumber: 5.8 Consensus size: 25
40264809 AGAGCCGTTA
*
40264819 ATCGAGAAGCTCATGAGAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCCAAAT
*
40264844 ATCGGGAAGCTCATGAAAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCCAAAT
* * *
40264869 ATCGGGATGCTCATAAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCCAAAT
**
40264894 AAT-GGGAAGCTTGTGAGAGCCAAAT
1 -ATCGGGAAGCTCATGAGAGCCAAAT
* * * *
40264919 ATCGGGATGCTCATAAGCGCTAAAT
1 ATCGGGAAGCTCATGAGAGCCAAAT
* * *
40264944 AACGGAAAGCTCGTGAGAG
1 ATCGGGAAGCTCATGAGAG
40264963 TTATGGTATG
Statistics
Matches: 94, Mismatches: 23, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
24 2 0.02
25 90 0.96
26 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCCAAAT
Found at i:40264881 original size:75 final size:75
Alignment explanation
Indices: 40264793--40264932 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 75
40264783 AGGAGTCAAT
* ***
40264793 TATCTGGAAGCTCAAAAGAGC-CGTTAATCGAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCA
1 TATCGGGAAGCTCAAAAGAGCTAAATAAT-GAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCA
40264857 TGAAAGCCAAA
65 TGAAAGCCAAA
* * * ** *
40264868 TATCGGGATGCTCATAAGAGCTAAATAATGGGAAGCTTGTGAGAGCCAAATATCGGGATGCTCAT
1 TATCGGGAAGCTCAAAAGAGCTAAATAATGAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCAT
40264933 AAGCGCTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 50 0.93
76 4 0.07
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (75 bp):
TATCGGGAAGCTCAAAAGAGCTAAATAATGAGAAGCTCATGAGAGCCAAATATCGGGAAGCTCAT
GAAAGCCAAA
Found at i:40264960 original size:50 final size:50
Alignment explanation
Indices: 40264827--40264962 Score: 191
Period size: 50 Copynumber: 2.7 Consensus size: 50
40264817 TAATCGAGAA
* * * * *
40264827 GCTCATGAGAGCCAAATATCGGGAAGCTCATGAAAGCCAAATATCGGGAT
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCGGGAT
* *
40264877 GCTCATAAGAGCTAAATAATGGGAAGCTTGTGAGAGCCAAATATCGGGAT
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCGGGAT
* *
40264927 GCTCATAAGCGCTAAATAACGGAAAGCTCGTGAGAG
1 GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAG
40264963 TTATGGTATG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (50 bp):
GCTCATAAGAGCTAAATAACGGGAAGCTCGTGAGAGCCAAATATCGGGAT
Found at i:40271015 original size:75 final size:75
Alignment explanation
Indices: 40270951--40271097 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
40270941 AGCTTATACG
* *** *
40270951 AGCCAATTATCTAGAA-GCTCAAAAGAGC-CGTTAATCGGGAAGCTCATGAGAGCCAAATATCGG
1 AGCCAAATATC-AGAATGCTCAAAAGAGCTAAATAAT-GGAAAGCTCATGAGAGCCAAATATCGG
40271014 GAAGCTCATGAA
64 GAAGCTCATGAA
* * *
40271026 AGCCAAATATCGGAATGCTCATAAGAGCTAAATAATGGAAAGCTCGTGAGAGCCAAATATCGGGA
1 AGCCAAATATCAGAATGCTCAAAAGAGCTAAATAATGGAAAGCTCATGAGAGCCAAATATCGGGA
*
40271091 TGCTCAT
66 AGCTCAT
40271098 AAGAGCTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
74 3 0.05
75 54 0.89
76 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (75 bp):
AGCCAAATATCAGAATGCTCAAAAGAGCTAAATAATGGAAAGCTCATGAGAGCCAAATATCGGGA
AGCTCATGAA
Found at i:40271155 original size:25 final size:25
Alignment explanation
Indices: 40270984--40271155 Score: 186
Period size: 25 Copynumber: 6.9 Consensus size: 25
40270974 AGAGCCGTTA
*
40270984 ATCGGGAAGCTCATGAGAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* *
40271009 ATCGGGAAGCTCATGAAAGCCAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
*
40271034 ATC-GGAATGCTCATAAGAGCTAAAT
1 ATCGGGAA-GCTCATGAGAGCTAAAT
* * *
40271059 AAT-GGAAAGCTCGTGAGAGCCAAAT
1 -ATCGGGAAGCTCATGAGAGCTAAAT
* *
40271084 ATCGGGATGCTCATAAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* * *
40271109 AACGGGAAGCTCGTGAGTGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* *
40271134 ATCAGGAAGCTCGTGAGAGCTA
1 ATCGGGAAGCTCATGAGAGCTA
40271156 TGGTGTGTTC
Statistics
Matches: 122, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
24 6 0.05
25 111 0.91
26 5 0.04
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCTAAAT
Found at i:40277977 original size:23 final size:22
Alignment explanation
Indices: 40277951--40277999 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
40277941 ATGCGTATTT
40277951 TTCTATATAGTATATAGACATA-A
1 TTCTATATA-TA-ATAGACATATA
* *
40277974 TTCTTTATATAATATACATATA
1 TTCTATATATAATAGACATATA
40277996 TTCT
1 TTCT
40278000 TAAACCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 7 0.30
23 8 0.35
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (22 bp):
TTCTATATATAATAGACATATA
Found at i:40282503 original size:3 final size:3
Alignment explanation
Indices: 40282495--40282519 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40282485 AGAATAACAT
40282495 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
40282520 CTAAGGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40295604 original size:39 final size:38
Alignment explanation
Indices: 40295554--40295639 Score: 88
Period size: 39 Copynumber: 2.3 Consensus size: 38
40295544 ATGCATTTTT
*
40295554 TTATAT-A-AAATAATAGAACATAAATATTAATAATTACA
1 TTATATAATAAATAAAAGAACATAAATATTAAT-ATTA-A
** * *
40295592 TTATA-AATAAATAAAAGATTATTAATTTTAATATTAA
1 TTATATAATAAATAAAAGAACATAAATATTAATATTAA
40295629 TTATATAATAA
1 TTATATAATAA
40295640 TTGAAAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
37 6 0.15
38 15 0.38
39 19 0.47
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATATAATAAATAAAAGAACATAAATATTAATATTAA
Found at i:40312693 original size:19 final size:19
Alignment explanation
Indices: 40312669--40312710 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
40312659 CGAAATTTGG
40312669 AATAAATAAATAATAAA-AT
1 AATAAA-AAATAATAAATAT
*
40312688 AATAAAACATAATAAATAT
1 AATAAAAAATAATAAATAT
40312707 AATA
1 AATA
40312711 TTGGACTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAATAATAAATAT
Found at i:40314802 original size:20 final size:19
Alignment explanation
Indices: 40314764--40314818 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
40314754 ATTTCAGAAC
40314764 AGTAATTCATCAA-CA-TTT
1 AGTAATT-ATCAATCATTTT
40314782 AGCTAA-TATCATATCATTTT
1 AG-TAATTATCA-ATCATTTT
40314802 AGTAATTATCAATCATT
1 AGTAATTATCAATCATT
40314819 CATATTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 14 0.44
20 10 0.31
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (19 bp):
AGTAATTATCAATCATTTT
Found at i:40315459 original size:15 final size:16
Alignment explanation
Indices: 40315429--40315458 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40315419 ACTTTAACAC
40315429 CCATTTCCCC-ATTTT
1 CCATTTCCCCTATTTT
40315444 CCATTTCCCCTATTT
1 CCATTTCCCCTATTT
40315459 CTCGTTTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.40, G:0.00, T:0.47
Consensus pattern (16 bp):
CCATTTCCCCTATTTT
Found at i:40326511 original size:16 final size:17
Alignment explanation
Indices: 40326490--40326525 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40326480 ATAAAAATAG
40326490 AAATATCTT-TACATTT
1 AAATATCTTATACATTT
*
40326506 AAATATTTTATACATTT
1 AAATATCTTATACATTT
40326523 AAA
1 AAA
40326526 ATTTTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATCTTATACATTT
Found at i:40326532 original size:18 final size:17
Alignment explanation
Indices: 40326490--40326530 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
40326480 ATAAAAATAG
*
40326490 AAATATCTT-TACATTT
1 AAATATTTTATACATTT
40326506 AAATATTTTATACATTT
1 AAATATTTTATACATTT
40326523 AAA-ATTTT
1 AAATATTTT
40326531 TTTGAATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATATTTTATACATTT
Found at i:40331091 original size:15 final size:15
Alignment explanation
Indices: 40331049--40331091 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
40331039 GAAGGCTTCA
*
40331049 CACATACAGGGTTCT
1 CACATATAGGGTTCT
40331064 CACATAT-GGGTTCT
1 CACATATAGGGTTCT
*
40331078 CACATGTAGGGTTC
1 CACATATAGGGTTC
40331092 ACTGTAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (15 bp):
CACATATAGGGTTCT
Found at i:40332966 original size:15 final size:15
Alignment explanation
Indices: 40332946--40332984 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
40332936 TATTGACACT
*
40332946 TATAGGGTT-TGCACG
1 TATAGGGTTAT-CACA
40332961 TATAGGGTTATCACA
1 TATAGGGTTATCACA
40332976 TATAGGGTT
1 TATAGGGTT
40332985 CGAATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (15 bp):
TATAGGGTTATCACA
Found at i:40333005 original size:23 final size:23
Alignment explanation
Indices: 40332973--40333018 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40332963 TAGGGTTATC
* *
40332973 ACATATAGGGTTCGAATATTAAA
1 ACATACAGGGTTCGAATACTAAA
*
40332996 ACATACAGGGTTCGCATACTAAA
1 ACATACAGGGTTCGAATACTAAA
40333019 TCCATAAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (23 bp):
ACATACAGGGTTCGAATACTAAA
Found at i:40333110 original size:16 final size:15
Alignment explanation
Indices: 40333091--40333136 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
40333081 GGGGTCCGGA
40333091 TGCAAGAGGGTTCAC
1 TGCAAGAGGGTTCAC
* *
40333106 TTGCAAGGGGGTTCGC
1 -TGCAAGAGGGTTCAC
*
40333122 TACAAGAGGGTTCAC
1 TGCAAGAGGGTTCAC
40333137 ATATGGGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.22
Consensus pattern (15 bp):
TGCAAGAGGGTTCAC
Found at i:40333132 original size:15 final size:16
Alignment explanation
Indices: 40333093--40333136 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
40333083 GGTCCGGATG
*
40333093 CAAGAGGGTTCACTTG
1 CAAGAGGGTTCACTTA
* *
40333109 CAAGGGGGTTCGC-TA
1 CAAGAGGGTTCACTTA
40333124 CAAGAGGGTTCAC
1 CAAGAGGGTTCAC
40333137 ATATGGGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.20
Consensus pattern (16 bp):
CAAGAGGGTTCACTTA
Found at i:40335616 original size:10 final size:10
Alignment explanation
Indices: 40335570--40335661 Score: 57
Period size: 10 Copynumber: 9.0 Consensus size: 10
40335560 GAGTAATTTC
40335570 TTAAATAATTA
1 TTAAA-AATTA
40335581 TTAAATAATTA
1 TTAAA-AATTA
40335592 -TATAAAATTA
1 TTA-AAAATTA
40335602 TTTAAAAATTA
1 -TTAAAAATTA
* *
40335613 TTAAGAGTTA
1 TTAAAAATTA
40335623 -TAAGAAATTA
1 TTAA-AAATTA
* *
40335633 -CAAATAATGA
1 TTAAA-AATTA
*
40335643 TTAAAAGTT-
1 TTAAAAATTA
40335652 TTAAAAATTA
1 TTAAAAATTA
40335662 CAAAAAAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
9 12 0.19
10 27 0.42
11 23 0.36
12 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:40339438 original size:22 final size:21
Alignment explanation
Indices: 40339413--40339458 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
40339403 TATAATTAAT
40339413 ATATGAATTTGATTCATACTAA
1 ATATGAATTTGATTCATA-TAA
* * *
40339435 ATATTAATTTTATTTATATAA
1 ATATGAATTTGATTCATATAA
40339456 ATA
1 ATA
40339459 GTTATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (21 bp):
ATATGAATTTGATTCATATAA
Found at i:40339638 original size:78 final size:77
Alignment explanation
Indices: 40339505--40339659 Score: 247
Period size: 78 Copynumber: 2.0 Consensus size: 77
40339495 ATAGAAATTA
* * *
40339505 ATATTATTTTGGAAAGAATATATTTCATTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
1 ATATTATTTTGGAAAAAATATAATTCATTTTTTTCTAACTTTCCATTTGCATTCTCTATTAATAA
40339570 GGGAATAATCCT
66 GGGAATAATCCT
* * *
40339582 ATATTCTTTTGGAAAAAATATAATTCTTTTTTTTTCTAACTTTTCATTTGCATTCTCTATTAATA
1 ATATTATTTTGGAAAAAATATAATTC-ATTTTTTTCTAACTTTCCATTTGCATTCTCTATTAATA
40339647 AGGGAATAATCCT
65 AGGGAATAATCCT
40339660 GATTTTCCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 23 0.32
78 48 0.68
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (77 bp):
ATATTATTTTGGAAAAAATATAATTCATTTTTTTCTAACTTTCCATTTGCATTCTCTATTAATAA
GGGAATAATCCT
Found at i:40343856 original size:54 final size:54
Alignment explanation
Indices: 40343778--40343931 Score: 157
Period size: 54 Copynumber: 2.9 Consensus size: 54
40343768 CGAACAAGGG
* ** * **
40343778 ACACACGGCCGTGTCCCAGCCCGTGTCCTCACCCATGTAACTCACTGAGTTGCC
1 ACACACGCCCGTGTGTCAGGCCGTGTCCTAGCCCATGTAACTCACTGAGTTGCC
* * * * *
40343832 CCACATGCCCGTGTGTCAGGCCGTGTGCTAGGCCATGTAACTCTCTGAGTTGCC
1 ACACACGCCCGTGTGTCAGGCCGTGTCCTAGCCCATGTAACTCACTGAGTTGCC
* * * *
40343886 ACACACGCCCGTGTG-CTATGTCGTGTGCTAGGCCATGTAACTCACT
1 ACACACGCCCGTGTGTC-AGGCCGTGTCCTAGCCCATGTAACTCACT
40343932 AACTTGAAAC
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 1 0.01
54 82 0.99
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (54 bp):
ACACACGCCCGTGTGTCAGGCCGTGTCCTAGCCCATGTAACTCACTGAGTTGCC
Found at i:40359609 original size:43 final size:41
Alignment explanation
Indices: 40359543--40359701 Score: 135
Period size: 43 Copynumber: 3.8 Consensus size: 41
40359533 AACTCGTACA
* * * *
40359543 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCATATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACG-AATCA-AAAACG
*
40359586 ATGCCACTGTCCCAGACACGGTCTTACACGAATCAAAAACG
1 ATGCCACTGTCCCAGACATGGTCTTACACGAATCAAAAACG
* * * **
40359627 ATGCCAATGTCCCAGACATGGTCTTTCACG-TTCACATAAGTTG
1 ATGCCACTGTCCCAGACATGGTCTTACACGAATCA-A-AA-ACG
*
40359670 ATGCCAAC-GTCTCAGACATGGTCTTACACGAA
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGAA
40359702 AACACAGATC
Statistics
Matches: 95, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
40 3 0.03
41 32 0.34
42 9 0.09
43 50 0.53
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (41 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGAATCAAAAACG
Found at i:40360868 original size:14 final size:15
Alignment explanation
Indices: 40360849--40360877 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40360839 TCATGAAACT
40360849 TTCACACAT-ATAAA
1 TTCACACATAATAAA
40360863 TTCACACATAATAAA
1 TTCACACATAATAAA
40360878 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:40367134 original size:27 final size:26
Alignment explanation
Indices: 40367087--40367165 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
40367077 TTTCTCATCC
*
40367087 CAATTTTA-CCCCAGTAAAATTTTTGA
1 CAATTTTACCCCCAATAAAA-TTTTGA
* *
40367113 CGATTTTACCCCCAATATAATTTTGA
1 CAATTTTACCCCCAATAAAATTTTGA
* * *
40367139 TAATTTTACCCCTCGATAAAGTTTTGA
1 CAATTTTACCCC-CAATAAAATTTTGA
40367166 GAAAATTCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 23 0.53
27 20 0.47
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (26 bp):
CAATTTTACCCCCAATAAAATTTTGA
Found at i:40367327 original size:12 final size:12
Alignment explanation
Indices: 40367306--40367340 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
40367296 GGATTGCAAG
40367306 TTTCCATTTTTA
1 TTTCCATTTTTA
*
40367318 TTTTCATTTTTA
1 TTTCCATTTTTA
40367330 TTTCCATTTTT
1 TTTCCATTTTT
40367341 GAAAACCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTCCATTTTTA
Found at i:40378429 original size:31 final size:32
Alignment explanation
Indices: 40378366--40378429 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
40378356 ATGTATGGGT
*
40378366 TGCTATGAACATATATGATATTCAGAATAGGC
1 TGCTATAAACATATATGATATTCAGAATAGGC
40378398 TGCTATAAACATATATGATATTCA-AATAGGC
1 TGCTATAAACATATATGATATTCAGAATAGGC
40378429 T
1 T
40378430 TGGGTAGGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (32 bp):
TGCTATAAACATATATGATATTCAGAATAGGC
Found at i:40381657 original size:38 final size:38
Alignment explanation
Indices: 40381615--40381716 Score: 136
Period size: 37 Copynumber: 2.7 Consensus size: 38
40381605 ACAATCTACT
* **
40381615 TTAAGATTTCTACCTAAAATTTTAAGATCGCAACTCCC
1 TTAAGGTTTCTACCTAAAACCTTAAGATCGCAACTCCC
* *
40381653 TTAAGGTTTCTACC-CAAACCTTAAGATTGCAACTCCC
1 TTAAGGTTTCTACCTAAAACCTTAAGATCGCAACTCCC
*
40381690 TTATGGTTTCTACCT-AAACCTTAAGAT
1 TTAAGGTTTCTACCTAAAACCTTAAGAT
40381717 ACAACCCTCT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 44 0.77
38 13 0.23
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (38 bp):
TTAAGGTTTCTACCTAAAACCTTAAGATCGCAACTCCC
Found at i:40382357 original size:20 final size:18
Alignment explanation
Indices: 40382306--40382358 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 18
40382296 ACTTGTTTTA
40382306 AAACAATTTTAACTTCATTG
1 AAAC-ATTTTAAC-TCATTG
40382326 AAA-ATGTTTAACTCATCTG
1 AAACAT-TTTAACTCAT-TG
40382345 AAACTATTTTAACT
1 AAAC-ATTTTAACT
40382359 TGATTTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 6 0.21
19 11 0.38
20 10 0.34
21 2 0.07
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (18 bp):
AAACATTTTAACTCATTG
Found at i:40382416 original size:22 final size:24
Alignment explanation
Indices: 40382388--40382431 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
40382378 ATTTTGTTTA
40382388 ACTTTAACTT-TTAT-TCAAAAAC
1 ACTTTAACTTGTTATATCAAAAAC
*
40382410 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTTGTTATATCAAAA
40382432 TATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (24 bp):
ACTTTAACTTGTTATATCAAAAAC
Found at i:40383053 original size:18 final size:17
Alignment explanation
Indices: 40383032--40383080 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
40383022 AATTTTCTAT
40383032 TTTTAATATTATTTGCAA
1 TTTT-ATATTATTTGCAA
* *
40383050 TTTTTATATTTTTTTCAA
1 -TTTTATATTATTTGCAA
40383068 TTTTATATTATTT
1 TTTTATATTATTT
40383081 TAAATAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 11 0.41
19 4 0.15
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATATTATTTGCAA
Found at i:40383081 original size:18 final size:19
Alignment explanation
Indices: 40383012--40383081 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 19
40383002 AATTTTATAA
*
40383012 AATTTTTA-ATAATTTT-C
1 AATTTTTATATTATTTTGC
*
40383029 TATTTTTAATATTA-TTTGC
1 AATTTTT-ATATTATTTTGC
*
40383048 AATTTTTATATT-TTTTTC
1 AATTTTTATATTATTTTGC
40383066 AA-TTTTATATTATTTT
1 AATTTTTATATTATTTT
40383082 AAATAAGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 15 0.34
18 19 0.43
19 10 0.23
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (19 bp):
AATTTTTATATTATTTTGC
Found at i:40383142 original size:18 final size:18
Alignment explanation
Indices: 40383121--40383184 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
40383111 TTCCTTTTTA
40383121 TAATTTTTTTGAAAATTC
1 TAATTTTTTTGAAAATTC
* * *
40383139 TAATTCTTTT-ACAATTTT
1 TAATTTTTTTGA-AAATTC
*
40383157 TATAATTTTTTGAAAATTC
1 TA-ATTTTTTTGAAAATTC
40383176 TAATTTTTT
1 TAATTTTTT
40383185 AAATAATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
17 1 0.03
18 21 0.60
19 12 0.34
20 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (18 bp):
TAATTTTTTTGAAAATTC
Found at i:40383157 original size:38 final size:36
Alignment explanation
Indices: 40383115--40383260 Score: 136
Period size: 37 Copynumber: 3.9 Consensus size: 36
40383105 TATTTTTTCC
40383115 TTTTTATAATTTTTTTGAAAATTCTAATTCTTTTACAA
1 TTTTTATAA-TTTTTTGAAAATTCTAATT-TTTTACAA
*
40383153 TTTTTATAATTTTTTGAAAATTCTAATTTTTTAAATAA
1 TTTTTATAATTTTTTGAAAATTCTAATTTTTT--ACAA
* * *
40383191 TTTTCTATTATTTTTAGATAAATTTCCATATATTTTTA-AA
1 TTTT-TATAATTTTTTGA-AAA-TTCTA-AT-TTTTTACAA
* *
40383231 TTTTTATAA--TTTTAAAAATTCTATTTTTTT
1 TTTTTATAATTTTTTGAAAATTCTAATTTTTT
40383261 TGAAATTCTA
Statistics
Matches: 92, Mismatches: 9, Indels: 19
0.77 0.08 0.16
Matches are distributed among these distances:
33 5 0.05
34 1 0.01
35 4 0.04
36 7 0.08
37 23 0.25
38 16 0.17
39 15 0.16
40 9 0.10
41 5 0.05
42 2 0.02
43 5 0.05
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (36 bp):
TTTTTATAATTTTTTGAAAATTCTAATTTTTTACAA
Found at i:40383179 original size:17 final size:17
Alignment explanation
Indices: 40383125--40383184 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
40383115 TTTTTATAAT
40383125 TTTTTTGAAAATTCTAA
1 TTTTTTGAAAATTCTAA
* *
40383142 TTCTTTT-ACAATTTTTATAA
1 TT-TTTTGA-AA--ATTCTAA
40383162 TTTTTTGAAAATTCTAA
1 TTTTTTGAAAATTCTAA
40383179 TTTTTT
1 TTTTTT
40383185 AAATAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 14 0.41
18 6 0.18
19 6 0.18
20 8 0.24
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTTTGAAAATTCTAA
Found at i:40383206 original size:21 final size:22
Alignment explanation
Indices: 40383180--40383231 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
40383170 AAATTCTAAT
* *
40383180 TTTTTAAATAATTTTCTAT-TA
1 TTTTTAAATAAATTTCCATATA
*
40383201 TTTTTAGATAAATTTCCATATA
1 TTTTTAAATAAATTTCCATATA
40383223 TTTTTAAAT
1 TTTTTAAAT
40383232 TTTTATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTTAAATAAATTTCCATATA
Found at i:40383214 original size:22 final size:21
Alignment explanation
Indices: 40383180--40383231 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
40383170 AAATTCTAAT
*
40383180 TTTTTAAATAATTTTC-TATTA
1 TTTTTAAATAATTTCCATA-TA
*
40383201 TTTTTAGATAAATTTCCATATA
1 TTTTTAAAT-AATTTCCATATA
40383223 TTTTTAAAT
1 TTTTTAAAT
40383232 TTTTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTTAAATAATTTCCATATA
Found at i:40385918 original size:6 final size:7
Alignment explanation
Indices: 40385901--40385927 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40385891 TCATGTGACA
40385901 AAAAATT
1 AAAAATT
40385908 AAAAATT
1 AAAAATT
40385915 AAAAATT
1 AAAAATT
40385922 AAAAAT
1 AAAAAT
40385928 CCCTAAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:40390829 original size:30 final size:30
Alignment explanation
Indices: 40390794--40390874 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
40390784 TCTTTAACCG
* *
40390794 TTAACCGAACTGAAATTTTTTTTAAAAAAA
1 TTAACCGAACCGAAATTTTTTTAAAAAAAA
40390824 TTAACCGAACCGAAATTTTTTTAAAAAAAA
1 TTAACCGAACCGAAATTTTTTTAAAAAAAA
40390854 TTAACCGAACCGAAATTTTTT
1 TTAACCGAACCGAAATTTTTT
40390875 CGGTTAATTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (30 bp):
TTAACCGAACCGAAATTTTTTTAAAAAAAA
Found at i:40390957 original size:9 final size:9
Alignment explanation
Indices: 40390939--40391017 Score: 113
Period size: 9 Copynumber: 8.8 Consensus size: 9
40390929 TTTGGTTAAA
40390939 AATTAACCG
1 AATTAACCG
*
40390948 AATTACCCG
1 AATTAACCG
40390957 AATTAACCG
1 AATTAACCG
*
40390966 AATTACCCG
1 AATTAACCG
*
40390975 AATTAACCA
1 AATTAACCG
*
40390984 AATTACCCG
1 AATTAACCG
40390993 AATTAACCG
1 AATTAACCG
*
40391002 AATTACCCG
1 AATTAACCG
40391011 AATTAAC
1 AATTAAC
40391018 TAAATTGAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:40390962 original size:18 final size:18
Alignment explanation
Indices: 40390939--40391017 Score: 149
Period size: 18 Copynumber: 4.4 Consensus size: 18
40390929 TTTGGTTAAA
40390939 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
40390957 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
40390975 AATTAACCAAATTACCCG
1 AATTAACCGAATTACCCG
40390993 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
40391011 AATTAAC
1 AATTAAC
40391018 TAAATTGAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.23
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:40392231 original size:29 final size:29
Alignment explanation
Indices: 40392161--40392865 Score: 963
Period size: 29 Copynumber: 23.9 Consensus size: 29
40392151 TTTTGTTAAT
40392161 GGTTAGGGTTTTTAATTAAATTA----AG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
40392186 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
40392216 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
40392245 GGTTTAGGG-TTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
40392274 GGTTAGGGTTTTTACTTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * * *
40392303 GGTTTAGAGTTTTAAAATAAATTAGGGTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
* *
40392333 GGTTTGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
40392362 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
40392391 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
40392420 GGTTTTA-GGTTTTAAAATAAATTAGGTTAG
1 GG--TTAGGGTTTTTAATTAAATTAGGTTAG
*
40392450 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
40392479 GTTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
40392508 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
40392537 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
40392566 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
40392595 GGTTAGGGTTTTAAAATAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
40392624 GGTTAGAGTTAGAGTTTTTAATTAAATTAGGTTAG
1 GGTT--AG---G-GTTTTTAATTAAATTAGGTTAG
40392659 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
40392688 GGTTAAGATTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
**
40392717 GGTTTAGGGTTTTAAAATAAATTAGGTTAGGGTTAG
1 GG-TTAGGGTTTT----T-AATTAAATTA-GGTTAG
*
40392753 GGTTAGGGTTTTTAATTAAATTAGGGTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
40392782 GGTTAGAGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
40392811 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
40392840 GGTTTAGGGTTTTAAAATAAATTAGG
1 GG-TTAGGGTTTTTAATTAAATTAGG
40392866 ATTTTTTTTA
Statistics
Matches: 605, Mismatches: 50, Indels: 45
0.86 0.07 0.06
Matches are distributed among these distances:
25 2 0.00
26 21 0.03
28 9 0.01
29 418 0.69
30 95 0.16
31 6 0.01
33 2 0.00
34 2 0.00
35 42 0.07
36 8 0.01
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:40392327 original size:117 final size:117
Alignment explanation
Indices: 40392161--40392865 Score: 987
Period size: 117 Copynumber: 6.0 Consensus size: 117
40392151 TTTTGTTAAT
40392161 GGTTAGGGTTTTTAATTAAATTA----AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
*
40392222 GGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTT-AATTAAATTAGGTTAG
65 GGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTAAATTAAATTAGGTTAG
* * * * * *
40392274 GGTTAGGGTTTTTACTTAAATTAGGTTAGGGTTTAGAGTTTTAAAATAAATTAGGGTAGGGTTTG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
* *
40392339 GGTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTTTAATTAAATTAGGGTAG
65 GGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTAAATTAAATTAGGTTAG
* *
40392391 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTA-GGTTTTAAAATAAATTAGGTTAGGGTTA
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGG--TTAGGGTTTTTAATTAAATTAGGTTAGGGTTA
* *
40392455 GGGTTTTTAATTAAATTAAGTTA-GGTTTAGGGTTTTTAATTAAATTAGGGTAG
64 GGGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTAAATTAAATTAGGTTAG
* *
40392508 GGTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGGTAGGGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
*
40392573 GTTTTTAATTAAATTAAGTTAGGG-TTAGGGTTTTAAAATAAATTAGGTTAG
66 GTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTAAATTAAATTAGGTTAG
40392624 GGTTAGAGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GGTT--AG---G-GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
* * * *
40392689 GTTAAGATTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTAAAATAAATTAGGTTAGGGTTAG
60 GTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTT-AAATTAA--A--TTA-GGTTAG
* *
40392753 GGTTAGGGTTTTTAATTAAATTAGGGTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
* *
40392818 GTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTAAAATAAATTAGG
66 GTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTAAATTAAATTAGG
40392866 ATTTTTTTTA
Statistics
Matches: 538, Mismatches: 32, Indels: 40
0.88 0.05 0.07
Matches are distributed among these distances:
113 22 0.04
115 3 0.01
116 88 0.16
117 211 0.39
118 9 0.02
120 1 0.00
121 1 0.00
122 82 0.15
123 99 0.18
124 6 0.01
126 1 0.00
127 2 0.00
128 3 0.01
129 10 0.02
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (117 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG
GTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTAAATTAAATTAGGTTAG
Found at i:40395265 original size:22 final size:22
Alignment explanation
Indices: 40395240--40395289 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
40395230 TAATATGGAT
40395240 TTGAGA-GATTTTTAGAAGGAAA
1 TTGAGAGGA-TTTTAGAAGGAAA
40395262 TTGAGAGGATTTTAGAAGGAAA
1 TTGAGAGGATTTTAGAAGGAAA
40395284 TTGAGA
1 TTGAGA
40395290 TAGGATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTGAGAGGATTTTAGAAGGAAA
Found at i:40403880 original size:5 final size:6
Alignment explanation
Indices: 40403846--40403890 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
40403836 TAACAATCGT
*
40403846 TTTTTA TTATTT- TTTTACA TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TT-TTTA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TT
40403891 CCAAATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 2 0.06
6 25 0.74
7 7 0.21
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:40414872 original size:114 final size:114
Alignment explanation
Indices: 40414660--40414889 Score: 415
Period size: 114 Copynumber: 2.0 Consensus size: 114
40414650 CTATAATTAG
*
40414660 TCATTTCTACAATTTAGTCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
1 TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
*
40414725 TATTATTTTTTCTCTAATTATTTGATTTATATATATGTGAAATTACTTC
66 TATTATTTTTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
*
40414774 TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTTACTTGTGAT
1 TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
40414839 TATTATTTTTGTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
66 TATTA-TTTT-TTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
40414890 GGTTATTTAT
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
114 68 0.61
115 4 0.04
116 39 0.35
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (114 bp):
TCATTTCTACAATTTAGCCAGGTAAGTTCATAGTGATTTGTTATTTAATATAATTCACTTGTGAT
TATTATTTTTTCTCTAATTAATTGATTTATATATATGTGAAATTACTTC
Found at i:40415090 original size:40 final size:40
Alignment explanation
Indices: 40415032--40415147 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 40
40415022 AAATGAAGAA
* * *
40415032 GTGCCCCTGTTTGTACTTCGGTACCCCTGAATGCACATTT
1 GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCACATAT
* *
40415072 TTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACATAT
1 GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCACATAT
** * * * *
40415112 GTGCCCCTAATTACATTTCGATGCCCCTGATTGCAC
1 GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCAC
40415148 TTCGGTGCCC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (40 bp):
GTGCCCCTGTTTGCACTTCGATACCCCTGAATGCACATAT
Done.