Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 49 of 163
Found at i:12116831 original size:3 final size:3
Alignment explanation
Indices: 12116825--12116862 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
12116815 GAAGAAGATA
*
12116825 TCT TCT TCT TCT TCT TCT TCA TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
12116863 ACTTTTCCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:12118783 original size:169 final size:171
Alignment explanation
Indices: 12118403--12118821 Score: 533
Period size: 169 Copynumber: 2.4 Consensus size: 171
12118393 ACTGTCATCT
*
12118403 GGCTCTTGTAGCTCAGTTGGTTAGAGCACTCGTTTAGTAAGCGGGAGGTCTTGAGTTCGACTCTC
1 GGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCGACTCTC
* * ** * * *
12118468 ACCAAGAGCAAGTTATACTTTATTTTCTCTTTTGGGTTCTGACATGTAATTTACTTTAGTCATGA
66 AACAAGAGCAAATTATACTTTATTTTCTCTTACGAGTTATGACATG--A-CTACTTTAGTCATGA
* ** * *
12118533 AAATTATGGCTCTATATAGTTGCTCTTTATTGAGTACTCAACAA
128 AAATTATGACTCTATATAAATACTCTTTATCGAGTACTCAACAA
12118577 GGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCGACTCTC
1 GGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCGACTCTC
* ** * **
12118642 AACAAGAGCAAATTGTTTTTTTATTTTTTCTTACGAGTTATTCCATG-CTACTTTAGTCATGAAA
66 AACAAGAGCAAATT-ATACTTTATTTTCTCTTACGAGTTATGACATGACTACTTTAGTCATGAAA
* * * *
12118706 CTT-TGATTCTTTA-AAATACT-TTCTATCGAGCT-TTCAACAA
130 ATTATGACTCTATATAAATACTCTT-TATCGAG-TACTCAACAA
12118746 GGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCGACTCTC
1 GGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCGACTCTC
*
12118811 AACAAGGGCAA
66 AACAAGAGCAA
12118822 CCCCATTTAT
Statistics
Matches: 218, Mismatches: 24, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
168 2 0.01
169 92 0.42
170 8 0.04
171 18 0.08
174 76 0.35
175 22 0.10
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (171 bp):
GGCTCTTGTAGCTCAGTTGGTTAGAGCACCCGTTTAGTAAGCGGGAGGTCTTGAGTTCGACTCTC
AACAAGAGCAAATTATACTTTATTTTCTCTTACGAGTTATGACATGACTACTTTAGTCATGAAAA
TTATGACTCTATATAAATACTCTTTATCGAGTACTCAACAA
Found at i:12119641 original size:6 final size:6
Alignment explanation
Indices: 12119605--12119708 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
12119595 GATTTTTTTT
* * * *
12119605 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAGA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
12119649 TCTTAAA TTTAAA TTTATTTA TTTAAA TTT-AC TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12119698 -TTAAA TTTAAA
1 TTTAAA TTTAAA
12119709 AATAATATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.05
5 18 0.23
6 49 0.63
7 2 0.03
8 5 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:12119642 original size:17 final size:16
Alignment explanation
Indices: 12119617--12119708 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
12119607 TAAGTTTAAA
*
12119617 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
*
12119634 TTAGATTTAAATTTAT
1 TTAAATTTAAATTTAT
12119650 CTTAAATTTAAATTTAT
1 -TTAAATTTAAATTTAT
12119667 TT--ATTTAAATTTACT
1 TTAAATTTAAATTTA-T
*
12119682 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
12119698 TTAAATTTAAA
1 TTAAATTTAAA
12119709 AATAATATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.16
15 3 0.04
16 18 0.27
17 35 0.52
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:12119699 original size:11 final size:11
Alignment explanation
Indices: 12119605--12119708 Score: 68
Period size: 11 Copynumber: 9.0 Consensus size: 11
12119595 GATTTTTTTT
12119605 TTTAAGTTTAAA
1 TTTAA-TTTAAA
12119617 -TTAATTTTAAA
1 TTTAA-TTTAAA
* *
12119628 TTTTATTTAGA
1 TTTAATTTAAA
**
12119639 TTTAAATTTATC
1 TTT-AATTTAAA
*
12119651 TTAAATTTAAA
1 TTTAATTTAAA
12119662 TTTATTTATTTAAA
1 TTTA---ATTTAAA
*
12119676 TTTACTTTAAA
1 TTTAATTTAAA
12119687 TTTAAATTT-AA
1 TTT-AATTTAAA
*
12119698 TTAAATTTAAA
1 TTTAATTTAAA
12119709 AATAATATTA
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
10 5 0.07
11 42 0.58
12 14 0.19
14 11 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:12121505 original size:30 final size:29
Alignment explanation
Indices: 12121471--12121702 Score: 203
Period size: 30 Copynumber: 7.7 Consensus size: 29
12121461 AGTTATCCAG
*
12121471 AAATTACATTTTGACCCCGAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTT-TAA
* ** *
12121501 AAATTACATTTTAACCTAAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTT-AA
*
12121531 AAATTATATTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTGACCCCAAAACTTT-TAA
* * *
12121561 AAATTACATTTTAACCCTAAAACTTTTTTA
1 AAATTACATTTTGACCCCAAAAC-TTTTAA
* *
12121591 AAATTACATTTTGACCCCGAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTT-AA
* * *
12121621 AAATTACATTTTGACTCAAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTT-AA
* * * * * *
12121651 AAATTATACTTTAACCTCGAAACTTTCAA
1 AAATTACATTTTGACCCCAAAACTTTTAA
*
12121680 AAATTACCATTTTTACCCTCAAA
1 AAATTA-CATTTTGACCC-CAAA
12121703 CTTCCCTAAA
Statistics
Matches: 161, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
29 12 0.07
30 142 0.88
31 7 0.04
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATTACATTTTGACCCCAAAACTTTTAA
Found at i:12121542 original size:60 final size:60
Alignment explanation
Indices: 12121466--12121692 Score: 291
Period size: 60 Copynumber: 3.8 Consensus size: 60
12121456 CCCTAAGTTA
12121466 TCCAGAAATTACATTTTGACCCCGAAACTTTCTAAAAATTACATTTTAACCTAAAAACTTT
1 TCCA-AAATTACATTTTGACCCCGAAACTTTCTAAAAATTACATTTTAACCTAAAAACTTT
* *
12121527 TCCAAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCT-AAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAACTTTCTAAAAATTACATTTTAA-CCTAAAAACTTT
** * *
12121587 TTTAAAATTACATTTTGACCCCGAAACTTT-TCCAAAATTACATTTTGA-CTCAAAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAACTTTCT-AAAAATTACATTTTAACCT-AAAAACTTT
* * * *
12121647 TCCAAAATTATACTTTAACCTCGAAACTTTC-AAAAATTACCATTTT
1 TCCAAAATTACATTTTGACCCCGAAACTTTCTAAAAATTA-CATTTT
12121693 TACCCTCAAA
Statistics
Matches: 145, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
58 2 0.01
59 8 0.06
60 128 0.88
61 7 0.05
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.37
Consensus pattern (60 bp):
TCCAAAATTACATTTTGACCCCGAAACTTTCTAAAAATTACATTTTAACCTAAAAACTTT
Found at i:12121624 original size:90 final size:90
Alignment explanation
Indices: 12121471--12121697 Score: 260
Period size: 90 Copynumber: 2.5 Consensus size: 90
12121461 AGTTATCCAG
* * *
12121471 AAATTACATTTTGACCCCGAAACTTTCTAAAAATTACATTTTAACCTAAAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAAACTTTTCCAAAATT
* *
12121536 ATATTTTGACCCCAAAACTTTCTAA
66 ACATTTTGACCCAAAAACTTTCTAA
* * * * **
12121561 AAATTACATTTTAACCCTAAAACTTTTTTAAAATTACATTTTGACCCCGAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAAACTTTTCCAAAATT
* *
12121626 ACATTTTGACTCAAAAACTTT-TCCA
66 ACATTTTGACCCAAAAACTTTCT-AA
* * * * *
12121651 AAATTATACTTTAACCTCGAAACTTTC-AAAAATTACCATTTTTACCC
1 AAATTACATTTTAACCCCAAAACTTTCTAAAAATTA-CATTTTAACCC
12121698 TCAAACTTCC
Statistics
Matches: 114, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
89 8 0.07
90 106 0.93
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.37
Consensus pattern (90 bp):
AAATTACATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAAACTTTTCCAAAATT
ACATTTTGACCCAAAAACTTTCTAA
Found at i:12132640 original size:3 final size:3
Alignment explanation
Indices: 12132632--12132667 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
12132622 ACATAATCAA
12132632 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12132668 CGGAGAGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12133623 original size:68 final size:68
Alignment explanation
Indices: 12133507--12134179 Score: 1166
Period size: 68 Copynumber: 9.9 Consensus size: 68
12133497 ATCATTTCCA
* * *
12133507 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACATGTCTTTATCTCTGAAATCGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
12133572 CGTC
65 CGTC
*
12133576 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCGCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
12133641 GTC
66 GTC
* *
12133644 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATATCTGAAATTGAAGTAAGAGCAAT
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
12133709 GTC
66 GTC
*
12133712 ATCCTCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
12133777 GTC
66 GTC
*
12133780 ATCCTCTTGAAGTTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
12133845 GTC
66 GTC
*
12133848 ATCCTCTTGAAGTTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
12133913 GTC
66 GTC
* *
12133916 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATATCTGAAATTGAAGTAAGAGCAAT
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
12133981 GTC
66 GTC
* *
12133984 ATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
12134049 GTC
66 GTC
* * *
12134052 ATCCTCTTGAAGTTGAAGTAGAGTGGATAATACATCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
*
12134117 ATC
66 GTC
* *
12134120 ATCCTCTTGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAGTTGAAGTAAGA
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGA
12134180 ACAAGATTAT
Statistics
Matches: 576, Mismatches: 28, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
68 554 0.96
69 22 0.04
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (68 bp):
ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:12134604 original size:28 final size:28
Alignment explanation
Indices: 12134573--12134653 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
12134563 TTAGACTTTG
*
12134573 ATTTTTTTTAAGTTTAAATTAATTTTAA
1 ATTTTATTTAAGTTTAAATTAATTTTAA
* *
12134601 ATTTTATTT-AGATTTAAATTTATCTTAA
1 ATTTTATTTAAG-TTTAAATTAATTTTAA
*
12134629 A-TTTACTTTAAATTTAAATTTAATT
1 ATTTTA-TTTAAGTTTAAA-TTAATT
12134654 AAATTTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 6 0.14
28 32 0.74
29 5 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTATTTAAGTTTAAATTAATTTTAA
Found at i:12134615 original size:6 final size:6
Alignment explanation
Indices: 12134579--12134662 Score: 65
Period size: 6 Copynumber: 15.0 Consensus size: 6
12134569 TTTGATTTTT
* * * *
12134579 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAGA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
12134623 TCTTAAA TTT-AC TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA
1 T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12134663 AATAATATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.06
5 18 0.29
6 38 0.61
7 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:12134632 original size:17 final size:17
Alignment explanation
Indices: 12134591--12134651 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
12134581 TAAGTTTAAA
*
12134591 TTAATTTTAAATTTTAT
1 TTAAATTTAAATTTTAT
*
12134608 TTAGATTTAAA-TTTAT
1 TTAAATTTAAATTTTAT
* *
12134624 CTTAAATTT-ACTTTAAAT
1 -TTAAATTTAAATTT-TAT
12134642 TTAAATTTAA
1 TTAAATTTAA
12134652 TTAAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.17
17 26 0.74
18 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTAAATTTTAT
Found at i:12134653 original size:11 final size:11
Alignment explanation
Indices: 12134579--12134662 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
12134569 TTTGATTTTT
*
12134579 TTTAAGTTTAA
1 TTTAAATTTAA
* *
12134590 ATTAATTTTAAA
1 TTTAAATTT-AA
*
12134602 TTT-TATTTAGA
1 TTTAAATTTA-A
12134613 TTTAAATTT-A
1 TTTAAATTTAA
*
12134623 TCTTAAATTTAC
1 T-TTAAATTTAA
12134635 TTTAAATTTAAA
1 TTTAAATTT-AA
*
12134647 TTT-AATTAAA
1 TTTAAATTTAA
12134657 TTTAAA
1 TTTAAA
12134663 AATAATATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
10 8 0.14
11 36 0.63
12 13 0.23
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:12134655 original size:16 final size:17
Alignment explanation
Indices: 12134625--12134662 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
12134615 TAAATTTATC
*
12134625 TTAAATTTACTTTAAAT
1 TTAAATTTACATTAAAT
12134642 TTAAATTTA-ATTAAAT
1 TTAAATTTACATTAAAT
12134658 TTAAA
1 TTAAA
12134663 AATAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATTTACATTAAAT
Found at i:12136465 original size:30 final size:29
Alignment explanation
Indices: 12136426--12136601 Score: 181
Period size: 30 Copynumber: 5.9 Consensus size: 29
12136416 AAGTTGTCCA
* * *
12136426 AAAAATACATTTTGACCCCGAAACTTTCTG
1 AAAATTACATTTTGACCCCAAAACTTT-TC
* **
12136456 AAAATTACATTTTAACCATAAAACTTTTC
1 AAAATTACATTTTGACCCCAAAACTTTTC
*
12136485 TGAAATTACATTTTGACCCCAAAACTTTTCC
1 -AAAATTACATTTTGACCCCAAAACTTTT-C
*
12136516 AAAATTACATTTTGACTCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTT-C
* * * *
12136546 AAAATTATACTTTGACCCCGAAACTTTTA
1 AAAATTACATTTTGACCCCAAAACTTTTC
* *
12136575 AAAATTACCATTTTTACCCCCAAACTT
1 AAAATTA-CATTTTGACCCCAAAACTT
12136602 CCCTAAATCC
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
29 8 0.07
30 113 0.93
31 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAAACTTTTC
Found at i:12136677 original size:59 final size:56
Alignment explanation
Indices: 12136575--12136769 Score: 167
Period size: 59 Copynumber: 3.3 Consensus size: 56
12136565 GAAACTTTTA
* * * *
12136575 AAAATTACCATTTTTACCCCCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTT-GCCCCAAACTTTCC-AAATTCCATTTTTAACCTCGATTTCACC
* * * * * * **
12136634 AAAACTTACCGTTTTGCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGCC
1 AAAA-TTACCATTTTGCC-CCAAACTTTCC-AAATTCCATTTTTAACCTCGATTTCACC
* *
12136693 AAAAGTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCTCGATTTCA-C
1 AAAA-TTACCA-TTT-TGCCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCACC
*
12136751 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTGCCCC
12136770 TAAAAACCCA
Statistics
Matches: 107, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
55 5 0.05
56 3 0.03
57 6 0.06
58 7 0.07
59 65 0.61
60 18 0.17
61 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.37
Consensus pattern (56 bp):
AAAATTACCATTTTGCCCCAAACTTTCCAAATTCCATTTTTAACCTCGATTTCACC
Found at i:12137751 original size:12 final size:12
Alignment explanation
Indices: 12137729--12137817 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
12137719 AACATCAAAA
*
12137729 CAACCAAAATAG
1 CAACAAAAATAG
*
12137741 CAGCAAAAATAG
1 CAACAAAAATAG
*
12137753 CAACAAAAACAG
1 CAACAAAAATAG
* *
12137765 TAACAAAAATAA
1 CAACAAAAATAG
12137777 CAACAAAAATAG
1 CAACAAAAATAG
* *
12137789 AAACAAAAACAG
1 CAACAAAAATAG
* *
12137801 TAACAAAAATAA
1 CAACAAAAATAG
12137813 CAACA
1 CAACA
12137818 TCAAAACAGT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.08
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:12137784 original size:36 final size:36
Alignment explanation
Indices: 12137734--12137817 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
12137724 CAAAACAACC
* * *
12137734 AAAATAGCAGCAAAAATAGCAACAAAAACAGTAACA
1 AAAATAACAACAAAAATAGAAACAAAAACAGTAACA
12137770 AAAATAACAACAAAAATAGAAACAAAAACAGTAACA
1 AAAATAACAACAAAAATAGAAACAAAAACAGTAACA
12137806 AAAATAACAACA
1 AAAATAACAACA
12137818 TCAAAACAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.69, C:0.15, G:0.07, T:0.08
Consensus pattern (36 bp):
AAAATAACAACAAAAATAGAAACAAAAACAGTAACA
Found at i:12137817 original size:24 final size:25
Alignment explanation
Indices: 12137778--12137834 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 25
12137768 CAAAAATAAC
12137778 AACAAAAATAGAAACA-AAAACAGT
1 AACAAAAATAGAAACACAAAACAGT
12137802 AACAAAAATA-ACAACATCAAAACAGT
1 AACAAAAATAGA-AACA-CAAAACAGT
12137828 AA-AAAAA
1 AACAAAAA
12137835 GCACCAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 1 0.03
24 14 0.47
25 5 0.17
26 10 0.33
ACGTcount: A:0.72, C:0.14, G:0.05, T:0.09
Consensus pattern (25 bp):
AACAAAAATAGAAACACAAAACAGT
Found at i:12137833 original size:36 final size:35
Alignment explanation
Indices: 12137757--12137865 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 35
12137747 AAATAGCAAC
* *
12137757 AAAAACAGTAACAAAAATAACAACA-AAAATAGAAA
1 AAAAACAGTAACAAAAATAACAACACAAAACAG-TA
12137792 CAAAAACAGTAACAAAAATAACAACATCAAAACAGTA
1 -AAAAACAGTAACAAAAATAACAACA-CAAAACAGTA
* * *
12137829 AAAAA-AG-CACCAAAACAACAAC-CAAAACAGTA
1 AAAAACAGTAACAAAAATAACAACACAAAACAGTA
12137861 AAAAA
1 AAAAA
12137866 ACCAAAACAG
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
32 15 0.23
34 12 0.18
35 2 0.03
36 30 0.45
37 1 0.02
38 6 0.09
ACGTcount: A:0.70, C:0.17, G:0.06, T:0.07
Consensus pattern (35 bp):
AAAAACAGTAACAAAAATAACAACACAAAACAGTA
Found at i:12137848 original size:23 final size:23
Alignment explanation
Indices: 12137822--12137939 Score: 59
Period size: 23 Copynumber: 5.2 Consensus size: 23
12137812 ACAACATCAA
12137822 AACAGTAAAAAAAGCACCAAAAC
1 AACAGTAAAAAAAGCACCAAAAC
*** * * **
12137845 AACAACCAAAACAGTAAAAAAACC
1 AACAGTAAAAAAAGCACCAAAA-C
12137869 AAAACAGTAAAAAAA--ACCAAAAC
1 --AACAGTAAAAAAAGCACCAAAAC
* * *
12137892 AACA--AAAAATAGCAAC-GAA-
1 AACAGTAAAAAAAGCACCAAAAC
12137911 AACAGTAAAAAAATAGCACCAAAAC
1 AACAGT-AAAAAA-AGCACCAAAAC
12137936 AACA
1 AACA
12137940 ATATAAATTT
Statistics
Matches: 65, Mismatches: 19, Indels: 20
0.62 0.18 0.19
Matches are distributed among these distances:
19 10 0.15
20 2 0.03
21 6 0.09
22 5 0.08
23 21 0.32
24 8 0.12
25 4 0.06
26 9 0.14
ACGTcount: A:0.68, C:0.20, G:0.07, T:0.05
Consensus pattern (23 bp):
AACAGTAAAAAAAGCACCAAAAC
Found at i:12137870 original size:17 final size:18
Alignment explanation
Indices: 12137848--12137892 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
12137838 CCAAAACAAC
12137848 AACCAAAACAGT-AAAAA
1 AACCAAAACAGTAAAAAA
12137865 AACCAAAACAGTAAAAAA
1 AACCAAAACAGTAAAAAA
12137883 AACCAAAACA
1 AACCAAAACA
12137893 ACAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.71, C:0.20, G:0.04, T:0.04
Consensus pattern (18 bp):
AACCAAAACAGTAAAAAA
Found at i:12137898 original size:17 final size:16
Alignment explanation
Indices: 12137848--12137900 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
12137838 CCAAAACAAC
*
12137848 AACCAAAACAGTAAAAA
1 AACCAAAACA-AAAAAA
12137865 AACCAAAACAGTAAAAAA
1 AACCAAAACA--AAAAAA
12137883 AACCAAAACAACAAAAA
1 AACCAAAACAA-AAAAA
12137900 A
1 A
12137901 TAGCAACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 1 0.03
17 16 0.50
18 15 0.47
ACGTcount: A:0.74, C:0.19, G:0.04, T:0.04
Consensus pattern (16 bp):
AACCAAAACAAAAAAA
Found at i:12137898 original size:18 final size:18
Alignment explanation
Indices: 12137860--12137900 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
12137850 CCAAAACAGT
**
12137860 AAAAAAACCAAAACAGTA
1 AAAAAAACCAAAACAACA
12137878 AAAAAAACCAAAACAACA
1 AAAAAAACCAAAACAACA
12137896 AAAAA
1 AAAAA
12137901 TAGCAACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.78, C:0.17, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAAACCAAAACAACA
Found at i:12137934 original size:22 final size:22
Alignment explanation
Indices: 12137866--12137936 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
12137856 CAGTAAAAAA
12137866 ACCAAAACAGT-AAAAAA-A--
1 ACCAAAACAGTAAAAAAATAGC
12137884 ACCAAAACA--ACAAAAAATAGC
1 ACCAAAACAGTA-AAAAAATAGC
*
12137905 AACGAAAACAGTAAAAAAATAGC
1 -ACCAAAACAGTAAAAAAATAGC
12137928 ACCAAAACA
1 ACCAAAACA
12137937 ACAATATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 15 0.35
19 1 0.02
22 16 0.37
23 10 0.23
24 1 0.02
ACGTcount: A:0.68, C:0.20, G:0.07, T:0.06
Consensus pattern (22 bp):
ACCAAAACAGTAAAAAAATAGC
Found at i:12137947 original size:23 final size:22
Alignment explanation
Indices: 12137883--12137940 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
12137873 CAGTAAAAAA
12137883 AACCAAAACAACAAAAAATAGC
1 AACCAAAACAACAAAAAATAGC
*
12137905 AACGAAAACAGTA-AAAAAATAGC
1 AACCAAAACA--ACAAAAAATAGC
12137928 -ACCAAAACAACAA
1 AACCAAAACAACAA
12137941 TATAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 17 0.55
23 10 0.32
24 1 0.03
ACGTcount: A:0.67, C:0.21, G:0.07, T:0.05
Consensus pattern (22 bp):
AACCAAAACAACAAAAAATAGC
Found at i:12138832 original size:334 final size:334
Alignment explanation
Indices: 12138221--12138886 Score: 1161
Period size: 334 Copynumber: 2.0 Consensus size: 334
12138211 GAGTTCTAGC
* *
12138221 AGAAAAAGTGAGTACGTAAGTGTGTATGAGTTATTTGCATGGTCTTTTTATAATGGGAGATAAGC
1 AGAAAAAATGAGTACGTAAGTGTGTATGAGTTATTTGCATGGTCTTTTTATAATGAGAGATAAGC
*
12138286 TTAGTTACGTGTCTTGAGGCAATTGACATTCAAGTCTGATTTGATACTTTTAGTAGTGACGGTGA
66 TTAGTTACGTGTCATGAGGCAATTGACATTCAAGTCTGATTTGATACTTTTAGTAGTGACGGTGA
* * * *
12138351 TGCTATGTCCTAGGATAGGACGCTTTAAGATGACTAGTAATTAATGACTTTAGACTTTCACGTGA
131 TGCTACGTCCTAGGATAGGACGCTTTAAGACGACTAGTAATTAATAACTTTAGACTTTCACATGA
12138416 TCCTCATGTAGTCTTAACAAAGATGCTTAGTCTCGAGGTTCACAAGGCTGAGGTTTGCAAGCTAA
196 TCCTCATGTAGTCTTAACAAAGATGCTTAGTCTCGAGGTTCACAAGGCTGAGGTTTGCAAGCTAA
* * *
12138481 CTAAATGTTCGCTAGTTGGTAGGTTGAATATGCATGGTCCTTTGTGATGTTGGTTTCGTTTAGAA
261 CTAAATGTTCGCTAGTTGGTAGGTTGAATATGCATGGTCCTTTGTGATATTAGTTTCGTCTAGAA
12138546 ACACGTGCT
326 ACACGTGCT
* * * *
12138555 AGAAAAAATGTGTATGTGAGTGTGTATGAGTTATTTGCATGGTCTTTTTATAATGAGAGATAAGT
1 AGAAAAAATGAGTACGTAAGTGTGTATGAGTTATTTGCATGGTCTTTTTATAATGAGAGATAAGC
* *
12138620 TTAGTTACGTGTCATGAGGCAATTGACATTGAAGTCTGATTTGATACTTTTAGTAGTGAGGGTGA
66 TTAGTTACGTGTCATGAGGCAATTGACATTCAAGTCTGATTTGATACTTTTAGTAGTGACGGTGA
* *
12138685 TGCTACGTCCTAGGATAGGACGCTTTAAGACGATTAGTAATTAATAACTTTAGACTTTCACATGG
131 TGCTACGTCCTAGGATAGGACGCTTTAAGACGACTAGTAATTAATAACTTTAGACTTTCACATGA
12138750 TCCTCATGTAGTCTTAACAAAGATGCTTAGTCTCGAGGTTCACAAGGCTGAGGTTTGCAAGCTAA
196 TCCTCATGTAGTCTTAACAAAGATGCTTAGTCTCGAGGTTCACAAGGCTGAGGTTTGCAAGCTAA
*
12138815 CTAAATGTTCTCTAGTTGGTAGGTTGAATATGCATGGTCCTTTGTGATATTAGTTTCGTCTAGAA
261 CTAAATGTTCGCTAGTTGGTAGGTTGAATATGCATGGTCCTTTGTGATATTAGTTTCGTCTAGAA
12138880 ACACGTG
326 ACACGTG
12138887 TTAAGTTCTC
Statistics
Matches: 313, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
334 313 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (334 bp):
AGAAAAAATGAGTACGTAAGTGTGTATGAGTTATTTGCATGGTCTTTTTATAATGAGAGATAAGC
TTAGTTACGTGTCATGAGGCAATTGACATTCAAGTCTGATTTGATACTTTTAGTAGTGACGGTGA
TGCTACGTCCTAGGATAGGACGCTTTAAGACGACTAGTAATTAATAACTTTAGACTTTCACATGA
TCCTCATGTAGTCTTAACAAAGATGCTTAGTCTCGAGGTTCACAAGGCTGAGGTTTGCAAGCTAA
CTAAATGTTCGCTAGTTGGTAGGTTGAATATGCATGGTCCTTTGTGATATTAGTTTCGTCTAGAA
ACACGTGCT
Found at i:12139465 original size:23 final size:23
Alignment explanation
Indices: 12139423--12139466 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12139413 TAAATGGTTT
* *
12139423 TTGCTTTAACTTATTTTATCATA
1 TTGCTTTAACATATTGTATCATA
*
12139446 TTGCTTTAACATGTTGTATCA
1 TTGCTTTAACATATTGTATCA
12139467 CATGTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (23 bp):
TTGCTTTAACATATTGTATCATA
Found at i:12139807 original size:20 final size:20
Alignment explanation
Indices: 12139782--12139819 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12139772 AAGTCACTCT
12139782 AAATGAACTCAATTTGATTA
1 AAATGAACTCAATTTGATTA
* *
12139802 AAATGAATTGAATTTGAT
1 AAATGAACTCAATTTGAT
12139820 AATATTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (20 bp):
AAATGAACTCAATTTGATTA
Found at i:12140459 original size:60 final size:60
Alignment explanation
Indices: 12140354--12140527 Score: 217
Period size: 60 Copynumber: 2.9 Consensus size: 60
12140344 TTAATATAAC
* * * *
12140354 ATTTGGTATCTGAACTTGACA-TTTTTTCCTAATTTGGTACTTAAACTTTTTTTCACTCA
1 ATTTGGAAACTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAACTTTTTTTCACCCA
* **
12140413 ATTT-GACAATTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAACTTTTTTGGACCCA
1 ATTTGGA-AACTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAACTTTTTTTCACCCA
* * **
12140473 ATTTGGAACCTAAACTTGACATTTTTTTTCCTAATTTGGTACCTAAGTTTTTTTT
1 ATTTGGAAACTGAACTTGACA-TTTTTTTCCTAATTTGGTACCTAAACTTTTTTT
12140528 AGATTCAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 1 0.01
59 16 0.16
60 49 0.50
61 32 0.33
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.48
Consensus pattern (60 bp):
ATTTGGAAACTGAACTTGACATTTTTTTCCTAATTTGGTACCTAAACTTTTTTTCACCCA
Found at i:12140771 original size:66 final size:65
Alignment explanation
Indices: 12140636--12140760 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 65
12140626 ATTTTAGAAA
12140636 AAATTCATGTTAAAAATAGGTATTGAGCGATGCTTAACGAATTAATATTAAAAAGATTAGATACC
1 AAATTCATGTTAAAAATAGGTATTGAGCGATGCTTAACGAATTAATATTAAAAAGATTAGATACC
* *
12140701 AAATTCATGTTAAAAAATAGGTATTGAGCGTTGCTTAATGAATTAATATTAAAAAGATTA
1 AAATTCATGTT-AAAAATAGGTATTGAGCGATGCTTAACGAATTAATATTAAAAAGATTA
12140761 AGTATTAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 11 0.19
66 46 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (65 bp):
AAATTCATGTTAAAAATAGGTATTGAGCGATGCTTAACGAATTAATATTAAAAAGATTAGATACC
Found at i:12141389 original size:17 final size:17
Alignment explanation
Indices: 12141367--12141409 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
12141357 CTTCTTTGAC
* *
12141367 CTTTAACTTTTCATCTT
1 CTTTAACTTCTCATATT
12141384 CTTTAACTTCTCATATT
1 CTTTAACTTCTCATATT
12141401 CTTGTAACT
1 CTT-TAACT
12141410 ACTTTTCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.53
Consensus pattern (17 bp):
CTTTAACTTCTCATATT
Found at i:12147276 original size:19 final size:19
Alignment explanation
Indices: 12147252--12147299 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
12147242 TTAAATTTAT
12147252 TTAATAAAATATATTAAAA
1 TTAATAAAATATATTAAAA
*** *
12147271 TTAATATTTTATATTTAAA
1 TTAATAAAATATATTAAAA
*
12147290 TTAATTAAAT
1 TTAATAAAAT
12147300 TCATCAATTA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATAAAATATATTAAAA
Found at i:12153828 original size:21 final size:21
Alignment explanation
Indices: 12153803--12153842 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12153793 AAATATTATT
12153803 TTTGTAACTCTCCCCATAATG
1 TTTGTAACTCTCCCCATAATG
*
12153824 TTTGTAACTCTCCTCATAA
1 TTTGTAACTCTCCCCATAA
12153843 ATTTTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTGTAACTCTCCCCATAATG
Found at i:12153852 original size:21 final size:20
Alignment explanation
Indices: 12153802--12153853 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
12153792 AAAATATTAT
12153802 TTTTGTAACTCTCCCCATAA
1 TTTTGTAACTCTCCCCATAA
*
12153822 TGTTTGTAACTCTCCTCATAAA
1 T-TTTGTAACTCTCCCCAT-AA
*
12153844 TTTTATAACT
1 TTTTGTAACT
12153854 TTCATCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (20 bp):
TTTTGTAACTCTCCCCATAA
Found at i:12156467 original size:17 final size:17
Alignment explanation
Indices: 12156434--12156488 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
12156424 TTGAATTGAT
*
12156434 TTTAAATTT-TTTAAAA
1 TTTAAATTTGTTTTAAA
12156450 TTTAAATTTGTTTTAAA
1 TTTAAATTTGTTTTAAA
*
12156467 TCTAAATTTAG--TTAAA
1 TTTAAATTT-GTTTTAAA
12156483 TTTAAA
1 TTTAAA
12156489 ATGGTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 19 0.56
17 14 0.41
18 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTGTTTTAAA
Found at i:12157074 original size:3 final size:3
Alignment explanation
Indices: 12157066--12157094 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12157056 TGTCTTGATT
12157066 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12157095 TTGTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12158042 original size:29 final size:29
Alignment explanation
Indices: 12157973--12158178 Score: 234
Period size: 30 Copynumber: 6.9 Consensus size: 29
12157963 TAAAGTCCCT
* * * *
12157973 AAACTATCTAAAAATAGTATTTTGACCCCC
1 AAACTTTCTAAAATTA-TATTTTAACCCCA
*
12158003 AAACTTCTCTAAAATTATATTTTGACCCCA
1 AAACTT-TCTAAAATTATATTTTAACCCCA
* *
12158033 AAACTTTCTAAAAATTACA-TTTAACCCCT
1 AAACTTTCT-AAAATTATATTTTAACCCCA
*
12158062 AAACTTCTCCAAAATTATATTTTAACCCCA
1 AAACTT-TCTAAAATTATATTTTAACCCCA
* * *
12158092 AAACTTTCTAAAATTACATTTTGACCCCT
1 AAACTTTCTAAAATTATATTTTAACCCCA
*
12158121 AAACTTCTCTAAAATTATATTTTAACCCTA
1 AAACTT-TCTAAAATTATATTTTAACCCCA
*
12158151 AAACTTTCTAAAAATTACATTTTAACCC
1 AAACTTTCT-AAAATTATATTTTAACCC
12158179 TTAAGTGTTC
Statistics
Matches: 152, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
29 53 0.35
30 90 0.59
31 9 0.06
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTTCTAAAATTATATTTTAACCCCA
Found at i:12158070 original size:59 final size:60
Alignment explanation
Indices: 12157973--12158178 Score: 310
Period size: 59 Copynumber: 3.5 Consensus size: 60
12157963 TAAAGTCCCT
* * * * *
12157973 AAACTATCTAAAAA-TAGTATTTTGACCCCCAAACTTCTCTAAAATTATATTTTGACCCCA
1 AAACTTTCTAAAAATTA-CATTTTAACCCCTAAACTTCTCTAAAATTATATTTTAACCCCA
*
12158033 AAACTTTCTAAAAATTACA-TTTAACCCCTAAACTTCTCCAAAATTATATTTTAACCCCA
1 AAACTTTCTAAAAATTACATTTTAACCCCTAAACTTCTCTAAAATTATATTTTAACCCCA
* *
12158092 AAACTTTCT-AAAATTACATTTTGACCCCTAAACTTCTCTAAAATTATATTTTAACCCTA
1 AAACTTTCTAAAAATTACATTTTAACCCCTAAACTTCTCTAAAATTATATTTTAACCCCA
12158151 AAACTTTCTAAAAATTACATTTTAACCC
1 AAACTTTCTAAAAATTACATTTTAACCC
12158179 TTAAGTGTTC
Statistics
Matches: 133, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
58 9 0.07
59 91 0.68
60 31 0.23
61 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.35
Consensus pattern (60 bp):
AAACTTTCTAAAAATTACATTTTAACCCCTAAACTTCTCTAAAATTATATTTTAACCCCA
Found at i:12158179 original size:30 final size:28
Alignment explanation
Indices: 12157969--12158202 Score: 200
Period size: 30 Copynumber: 7.9 Consensus size: 28
12157959 CCCTTAAAGT
* * *
12157969 CCCTAAACTATCTAAAAATAGTATTTTGAC
1 CCCTAAACTTTCTAAAATTA-TATTTT-AA
* *
12157999 CCCCAAACTTCTCTAAAATTATATTTTGAC
1 CCCTAAACTT-TCTAAAATTATATTTT-AA
* *
12158029 CCCAAAACTTTCTAAAAATTACA-TTTAA
1 CCCTAAACTTTCT-AAAATTATATTTTAA
*
12158057 CCCCTAAACTTCTCCAAAATTATATTTTAA
1 -CCCTAAACTT-TCTAAAATTATATTTTAA
* * *
12158087 CCCCAAAACTTTCTAAAATTACATTTTGAC
1 -CCCTAAACTTTCTAAAATTATATTTT-AA
12158117 CCCTAAACTTCTCTAAAATTATATTTTAA
1 CCCTAAACTT-TCTAAAATTATATTTTAA
*
12158146 CCCTAAAACTTTCTAAAAATTACATTTTAA
1 CCCT-AAACTTTCT-AAAATTATATTTTAA
* * * *
12158176 CCCTTAAGTGTTCCAAAATTCTATTTT
1 CCCTAAACT-TTCTAAAATTATATTTT
12158203 TGACCTTGAT
Statistics
Matches: 172, Mismatches: 22, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.01
29 68 0.40
30 94 0.55
31 9 0.05
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTTCTAAAATTATATTTTAA
Found at i:12158194 original size:59 final size:59
Alignment explanation
Indices: 12158003--12158202 Score: 280
Period size: 59 Copynumber: 3.4 Consensus size: 59
12157993 TTTGACCCCC
* *
12158003 AAACTTCTCTAAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACA-TTTAACCCCT
1 AAACTTCTCCAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAA-CCCT
*
12158062 AAACTTCTCCAAAATTATATTTTAACCCCAAAACTTTCT-AAAATTACATTTTGACCCCT
1 AAACTTCTCCAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTT-AACCCT
* *
12158121 AAACTTCTCTAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCT
1 AAACTTCTCCAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCT
* * *
12158180 TAAGTGT-TCCAAAATTCTATTTT
1 AAACT-TCTCCAAAATTATATTTT
12158203 TGACCTTGAT
Statistics
Matches: 127, Mismatches: 10, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
58 9 0.07
59 103 0.81
60 15 0.12
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (59 bp):
AAACTTCTCCAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCT
Found at i:12158262 original size:29 final size:29
Alignment explanation
Indices: 12158186--12158320 Score: 93
Period size: 29 Copynumber: 4.6 Consensus size: 29
12158176 CCCTTAAGTG
* *
12158186 TTCCAAAATTCTATTTTTGA-CCTTG-ATT
1 TTCCAAAATTCCATTTTT-ACCCTCGAATT
*
12158214 TTACTAAAAATTACCA-TTTTACCCTCGAATT
1 TT-C-CAAAATT-CCATTTTTACCCTCGAATT
*
12158245 TTCCAAAATTTCATTTTTGACCC-CGAATT
1 TTCCAAAATTCCATTTTT-ACCCTCGAATT
* *
12158274 TTTCAAAATTCCATTTTGA-CCTCG-ATT
1 TTCCAAAATTCCATTTTTACCCTCGAATT
*
12158301 TCACCAAAAATTGCCATTTT
1 T-TCC-AAAATT-CCATTTT
12158321 ACCTTTAAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
27 6 0.07
28 8 0.09
29 39 0.45
30 26 0.30
31 7 0.08
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (29 bp):
TTCCAAAATTCCATTTTTACCCTCGAATT
Found at i:12158341 original size:87 final size:88
Alignment explanation
Indices: 12158189--12158353 Score: 208
Period size: 87 Copynumber: 1.9 Consensus size: 88
12158179 TTAAGTGTTC
* * * * * *
12158189 CAAAATTCTATTTTTGACCTTGATTTTACTAAAAATTACCATTTTACCCTCGAATTTTCCAAAAT
1 CAAAATTCCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAATTCTCCAAAAT
*
12158254 TTCATTTTTGACCCCGAATTTTT
66 TCCATTTTTGACCCCGAATTTTT
* * * *
12158277 CAAAATTCCA-TTTTGACCTCGATTTCACCAAAAATTGCCATTTTACCTTTAAACTTCT-CGAAA
1 CAAAATTCCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAA-TTCTCCAAAA
12158340 TTCCATTTTTGACC
65 TTCCATTTTTGACC
12158354 TCAATTCCAC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
87 53 0.82
88 12 0.18
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (88 bp):
CAAAATTCCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAATTCTCCAAAAT
TCCATTTTTGACCCCGAATTTTT
Found at i:12158368 original size:87 final size:87
Alignment explanation
Indices: 12158188--12158378 Score: 197
Period size: 87 Copynumber: 2.2 Consensus size: 87
12158178 CTTAAGTGTT
* * * * * *
12158188 CCAAAATTCTATTTTTGACCTTGATTTTACTAAAAATTACCATTTTACCCTCGAATTTTCCAAAA
1 CCAAAATTCCA-TTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAATTCTCCAAAA
* **
12158253 TTTCATTTTTGACCCCGAATTTT
65 TTCCATTTTTGACCCCGAATTCA
* * * * *
12158276 TCAAAATTCCATTTTGACCTCGATTTCACCAAAAATTGCCATTTTACCTTTAAACTTCT-CGAAA
1 CCAAAATTCCATTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAA-TTCTCCAAAA
*
12158340 TTCCATTTTTGACCTC-AATTCCA
65 TTCCATTTTTGACCCCGAATT-CA
12158363 CCAAAATTACCATTTT
1 CCAAAATT-CCATTTT
12158379 ACTCCGGATA
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
86 4 0.05
87 61 0.73
88 19 0.23
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.40
Consensus pattern (87 bp):
CCAAAATTCCATTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCTCAAATTCTCCAAAAT
TCCATTTTTGACCCCGAATTCA
Found at i:12160247 original size:16 final size:16
Alignment explanation
Indices: 12160226--12160256 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12160216 ATTAAGGATA
12160226 AAATATTAATCAAATG
1 AAATATTAATCAAATG
*
12160242 AAATATTTATCAAAT
1 AAATATTAATCAAAT
12160257 TCCCCCTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
AAATATTAATCAAATG
Found at i:12161753 original size:6 final size:6
Alignment explanation
Indices: 12161744--12161821 Score: 50
Period size: 6 Copynumber: 12.5 Consensus size: 6
12161734 TCTGAAAAAG
* * * * *
12161744 AAATAA AAATTTA AAATAA AAATAA AGATAA AAATAA ATAGAA ATATAA
1 AAATAA AAA-TAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
**
12161793 ATAATCG AAAT-A AAATAATA AAATAA AAA
1 A-AATAA AAATAA AAAT-A-A AAATAA AAA
12161822 AAATAATACG
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 4 0.07
6 38 0.68
7 9 0.16
8 5 0.09
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:12161774 original size:12 final size:11
Alignment explanation
Indices: 12161744--12161824 Score: 58
Period size: 13 Copynumber: 6.7 Consensus size: 11
12161734 TCTGAAAAAG
12161744 AAATAAAAATTTA
1 AAATAAAAA--TA
12161757 AAATAAAAATA
1 AAATAAAAATA
12161768 AAGATAAAAAT-
1 AA-ATAAAAATA
*
12161779 AAATAGAAATA
1 AAATAAAAATA
12161790 TAAATAATCGAAATA
1 -AAATAA---AAATA
12161805 AAATAATAAAATA
1 AAAT-A-AAAATA
12161818 AAA-AAAA
1 AAATAAAA
12161825 TAATACGGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
10 10 0.17
11 7 0.12
12 13 0.22
13 17 0.29
14 4 0.07
15 6 0.10
16 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:12161804 original size:15 final size:14
Alignment explanation
Indices: 12161774--12161820 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
12161764 AATAAAGATA
*
12161774 AAAATAAATAGAAAT
1 AAAAT-AATCGAAAT
12161789 ATAAATAATCGAAAT
1 A-AAATAATCGAAAT
*
12161804 AAAATAAT-AAAAT
1 AAAATAATCGAAAT
12161817 AAAA
1 AAAA
12161821 AAAATAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 8 0.28
14 7 0.24
15 10 0.34
16 4 0.14
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (14 bp):
AAAATAATCGAAAT
Found at i:12171431 original size:3 final size:3
Alignment explanation
Indices: 12171423--12171468 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
12171413 TTTAAACTTT
12171423 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12171469 AAGAGCATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12180633 original size:16 final size:16
Alignment explanation
Indices: 12180585--12180633 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
12180575 TATTATATTG
12180585 AATTATAAGTAAGAAA
1 AATTATAAGTAAGAAA
* *** *
12180601 AATTCTACCAAAAAAA
1 AATTATAAGTAAGAAA
12180617 AATTATAAGTAAGAAA
1 AATTATAAGTAAGAAA
12180633 A
1 A
12180634 TTTAACTTAT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.22
Consensus pattern (16 bp):
AATTATAAGTAAGAAA
Found at i:12188743 original size:22 final size:22
Alignment explanation
Indices: 12188713--12188758 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
12188703 AAAAGTTTGA
* *
12188713 AATTCTGCTTTCATTGTAATTG
1 AATTATGCTTTCATTGCAATTG
*
12188735 AATTATGCTTTTATTGCAATTG
1 AATTATGCTTTCATTGCAATTG
12188757 AA
1 AA
12188759 GATAGATGAG
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:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (22 bp):
AATTATGCTTTCATTGCAATTG
Found at i:12205821 original size:39 final size:40
Alignment explanation
Indices: 12205765--12205844 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
12205755 TATGCACTCA
*
12205765 ATGGACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGG
1 ATGGACACCTTTAGAAGAGTCACAACCCTTTTCAAATTGG
*
12205804 ATGGACACCTTTAGAAGAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTAGAAGAGTCACAACCCTTTTCAAATTGG
12205844 A
1 A
12205845 CATACCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (40 bp):
ATGGACACCTTTAGAAGAGTCACAACCCTTTTCAAATTGG
Found at i:12205860 original size:39 final size:38
Alignment explanation
Indices: 12205769--12205861 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
12205759 CACTCAATGG
* *
12205769 ACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATGG
1 ACACCTTTAGAAGAGTCACAACCCTTTCAAATTGGA-GC
*
12205808 ACACCTTTAGAAGAGTCACAACCCTTTTCATATTGGA-C
1 ACACCTTTAGAAGAGTCACAACCC-TTTCAAATTGGAGC
* *
12205846 ATACCTCTTGGAAGAG
1 ACACCT-TTAGAAGAG
12205862 ACTTGTCCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 5 0.11
39 31 0.66
40 11 0.23
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (38 bp):
ACACCTTTAGAAGAGTCACAACCCTTTCAAATTGGAGC
Found at i:12218651 original size:17 final size:17
Alignment explanation
Indices: 12218626--12218661 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12218616 TTAAATACAT
12218626 ATTAAATATTAAATTTA
1 ATTAAATATTAAATTTA
* *
12218643 ATTATATATTAATTTTA
1 ATTAAATATTAAATTTA
12218660 AT
1 AT
12218662 ATTATTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAATATTAAATTTA
Found at i:12219649 original size:24 final size:27
Alignment explanation
Indices: 12219598--12219650 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
12219588 ATTTCTGTCA
*
12219598 ATTTTTATTATTATTTCGCTTTATATT
1 ATTTCTATTATTATTTCGCTTTATATT
12219625 ATTTCTATTATT-TTT-GCTTTA-ATT
1 ATTTCTATTATTATTTCGCTTTATATT
12219649 AT
1 AT
12219651 ATTTAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 6 0.24
26 3 0.12
27 11 0.44
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.66
Consensus pattern (27 bp):
ATTTCTATTATTATTTCGCTTTATATT
Found at i:12223584 original size:34 final size:34
Alignment explanation
Indices: 12223541--12223609 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
12223531 AAATAGAAAC
*
12223541 TAAAAATACATGGTGGTTCACTATTTCACCTAAT
1 TAAAAATACATGGTGATTCACTATTTCACCTAAT
*
12223575 TAAAAATACATGGTGATTCACTATTTCACTTAAT
1 TAAAAATACATGGTGATTCACTATTTCACCTAAT
12223609 T
1 T
12223610 GATGATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (34 bp):
TAAAAATACATGGTGATTCACTATTTCACCTAAT
Found at i:12225181 original size:62 final size:63
Alignment explanation
Indices: 12225027--12225206 Score: 251
Period size: 62 Copynumber: 2.9 Consensus size: 63
12225017 AAAAATCCAA
* **
12225027 ATAACATGGTATGCTCTTTCTTGTGGTGTAATCTTAGCAT--A-ATAGATAATATTAATCTCC
1 ATAACATGGCATGCTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAATAAAAATCTCC
*
12225087 ATAACATAGCATGCTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAA-AAAAATCTCC
1 ATAACATGGCATGCTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAATAAAAATCTCC
* * * *
12225149 ATGACATGGCATGTTCTTTCTTGTGGTCTAATCTTAGCATAAACACAGATAGATAAAA
1 ATAACATGGCATGCTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATA-ATAAAA
12225207 CAATCTCATA
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
60 38 0.36
62 55 0.52
63 9 0.08
64 4 0.04
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (63 bp):
ATAACATGGCATGCTCTTTCTTGTGGTGTAATCTTAGCATAAACATAGATAATAAAAATCTCC
Found at i:12226825 original size:7 final size:7
Alignment explanation
Indices: 12226813--12226838 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12226803 AAATTTTAAA
12226813 AAAATTC
1 AAAATTC
12226820 AAAATTC
1 AAAATTC
12226827 AAAATTC
1 AAAATTC
12226834 AAAAT
1 AAAAT
12226839 AAATAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTC
Found at i:12227209 original size:15 final size:16
Alignment explanation
Indices: 12227183--12227223 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
12227173 TTATTATATA
12227183 AATTTATTTAATAAAA-
1 AATTT-TTTAATAAAAT
*
12227199 AGTTTTTTAATAAAAT
1 AATTTTTTAATAAAAT
12227215 AATTTTTTA
1 AATTTTTTA
12227224 CTTGTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
AATTTTTTAATAAAAT
Found at i:12227280 original size:17 final size:16
Alignment explanation
Indices: 12227258--12227300 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
12227248 ATCAAATAAA
12227258 TTTATTTAATTAAATAT
1 TTTATTTAATTAAA-AT
*
12227275 TTTATTAAAATTAAAAT
1 TTTATT-TAATTAAAAT
12227292 TTGTATTTA
1 TT-TATTTA
12227301 TAAATTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTATTTAATTAAAAT
Found at i:12235956 original size:2 final size:2
Alignment explanation
Indices: 12235949--12235974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12235939 GTTTTAAGTA
12235949 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12235975 GACAGCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12237301 original size:13 final size:13
Alignment explanation
Indices: 12237285--12237310 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12237275 TATAAAAAAA
12237285 ATTTATTTATTTT
1 ATTTATTTATTTT
12237298 ATTTATTTATTTT
1 ATTTATTTATTTT
12237311 TTTCTCTCTT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:12241717 original size:133 final size:133
Alignment explanation
Indices: 12241479--12241721 Score: 353
Period size: 133 Copynumber: 1.8 Consensus size: 133
12241469 AGAATGAATT
*
12241479 CGGGTGTTGTGATCGAGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGAATTCTCTGAA
1 CGGGTGTTATGATCGAGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGAATTCTCTGAA
*
12241544 GCTAATGTTAGCAACCCTAATCTGAAGCCAGTGTTAGCAGCCCGAATATGTTAACTTGTATAAAC
66 GCTAATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGAATATGTTAACTTGTATAAAC
12241609 AAA
131 AAA
* * * * * * *
12241612 CGGGTGTTATGATC-AGGGATTAATTCGATGGCTTGAGATTCAACATATGTTGTGGATTCTCTGA
1 CGGGTGTTATGATCGA-GGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGAATTCTCTGA
* * * *
12241676 AGCTAGTGTTAGCAATCCTGATCCGAAGCTAGTGTTAGCAGCCCGA
65 AGCTAATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGA
12241722 TAATGTCAAC
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
132 1 0.01
133 95 0.99
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (133 bp):
CGGGTGTTATGATCGAGGATTAATACAATGGCTTGAAATCCAAAATATGTTGCGAATTCTCTGAA
GCTAATGTTAGCAACCCTAATCCGAAGCCAGTGTTAGCAGCCCGAATATGTTAACTTGTATAAAC
AAA
Found at i:12245373 original size:20 final size:21
Alignment explanation
Indices: 12245336--12245374 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12245326 TCATGAAGTT
* *
12245336 AAGAAAATAACTCTTAATTTA
1 AAGAAAATAACACATAATTTA
12245357 AAGAAAATAA-ACATAATT
1 AAGAAAATAACACATAATT
12245375 ATCTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (21 bp):
AAGAAAATAACACATAATTTA
Found at i:12246311 original size:20 final size:20
Alignment explanation
Indices: 12246286--12246331 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
12246276 GTATTACCAC
12246286 ACTAATCGGAGCACTTTACA
1 ACTAATCGGAGCACTTTACA
12246306 ACTAATCGGAGCACTTTACA
1 ACTAATCGGAGCACTTTACA
12246326 ACTAAT
1 ACTAAT
12246332 AACGATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (20 bp):
ACTAATCGGAGCACTTTACA
Found at i:12247479 original size:34 final size:35
Alignment explanation
Indices: 12247441--12247526 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
12247431 TATAAATCGT
* *
12247441 TTCATCCAACACACCATGTACTCGTAAGAGTTA-C
1 TTCATCCAACACACCATATACTCGTAAGAGCTAGC
* *
12247475 TTCATCCACCACACCATATGCTCGTAAGAGCTAGC
1 TTCATCCAACACACCATATACTCGTAAGAGCTAGC
* *
12247510 -CCATCCAACACATCATA
1 TTCATCCAACACACCATA
12247527 ACATGTAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 43 0.98
35 1 0.02
ACGTcount: A:0.33, C:0.34, G:0.10, T:0.23
Consensus pattern (35 bp):
TTCATCCAACACACCATATACTCGTAAGAGCTAGC
Found at i:12249941 original size:31 final size:31
Alignment explanation
Indices: 12249868--12249941 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
12249858 AAAAAAGATT
* * * *
12249868 AAGTACTAAATTAGGAATAACTGTAAAGTTT
1 AAGTTCTAAATTAGGAAAAACTATAAAGTTC
* *
12249899 AGGTTCTAAATTAGGAAAAAGTATAAAGTTC
1 AAGTTCTAAATTAGGAAAAACTATAAAGTTC
12249930 AAGTATC-AAATT
1 AAGT-TCTAAATT
12249942 GAAAAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (31 bp):
AAGTTCTAAATTAGGAAAAACTATAAAGTTC
Found at i:12251526 original size:17 final size:17
Alignment explanation
Indices: 12251506--12251546 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
12251496 TCCATTGACT
*
12251506 TTTAACCTTTCATCTTC
1 TTTAACCTTTCATATTC
12251523 TTTAACCTTTCATATTC
1 TTTAACCTTTCATATTC
12251540 TTGTAAC
1 TT-TAAC
12251547 TATTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAACCTTTCATATTC
Found at i:12252441 original size:21 final size:21
Alignment explanation
Indices: 12252395--12252441 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12252385 TGATCTAAGG
* *
12252395 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAGAAATAGAACT
12252416 AAAAATAAAAGAAGATAGAACT
1 AAAAATAAAAGAA-ATAGAACT
12252438 AAAA
1 AAAA
12252442 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (21 bp):
AAAAATAAAAGAAATAGAACT
Found at i:12252450 original size:15 final size:16
Alignment explanation
Indices: 12252421--12252450 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12252411 GAATTAAAAA
12252421 TAAAAGAAGATAGAAC
1 TAAAAGAAGATAGAAC
12252437 TAAAAGAA-ATAGAA
1 TAAAAGAAGATAGAA
12252451 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.03, G:0.17, T:0.13
Consensus pattern (16 bp):
TAAAAGAAGATAGAAC
Found at i:12253277 original size:19 final size:19
Alignment explanation
Indices: 12253253--12253295 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12253243 AAACATAAAT
12253253 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
12253272 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
12253291 TAAAT
1 TAAAT
12253296 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:12269721 original size:42 final size:37
Alignment explanation
Indices: 12269641--12269715 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
12269631 TTTAATAACG
* * *
12269641 TAATCTAGTATTTGCTTTTTTTTTCCTTTTTTTTATA
1 TAATCTACTATTTACTTTCTTTTTCCTTTTTTTTATA
*
12269678 TAATCTACTATTTACTATTCTTTTTCC-TTTCTTTATA
1 TAATCTACTATTTACT-TTCTTTTTCCTTTTTTTTATA
12269715 T
1 T
12269716 TATATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.19, C:0.15, G:0.03, T:0.64
Consensus pattern (37 bp):
TAATCTACTATTTACTTTCTTTTTCCTTTTTTTTATA
Found at i:12273078 original size:74 final size:74
Alignment explanation
Indices: 12272989--12273147 Score: 228
Period size: 74 Copynumber: 2.1 Consensus size: 74
12272979 CAACGAATAT
* * * *
12272989 GTTTTGAGACAAGATAATCAAATTTAAATTGAGCATGCATTTTTGGGTATATGTCTCGGGACATG
1 GTTTTGAGACAAGATAATCAAATTTAAATCGAACATGCATTTTTGGGTACATGTCTCAGGACATG
*
12273054 AAGGGCAAA
66 AAGGGAAAA
* * * *
12273063 GTTTTGAGACAAGATAATCAAATTTGAATCGAACATGCATTTTTTGGTGCATGTCTCAGGATATG
1 GTTTTGAGACAAGATAATCAAATTTAAATCGAACATGCATTTTTGGGTACATGTCTCAGGACATG
12273128 AAGGGAAAA
66 AAGGGAAAA
*
12273137 GTCTTGAGACA
1 GTTTTGAGACA
12273148 TTCGAAGCCA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (74 bp):
GTTTTGAGACAAGATAATCAAATTTAAATCGAACATGCATTTTTGGGTACATGTCTCAGGACATG
AAGGGAAAA
Found at i:12277439 original size:17 final size:17
Alignment explanation
Indices: 12277417--12277449 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12277407 GAGTTATTTA
12277417 AATATTGAATT-AAGAAC
1 AATATT-AATTGAAGAAC
12277434 AATATTAATTGAAGAA
1 AATATTAATTGAAGAA
12277450 TTAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (17 bp):
AATATTAATTGAAGAAC
Found at i:12315820 original size:91 final size:91
Alignment explanation
Indices: 12315643--12315822 Score: 231
Period size: 90 Copynumber: 2.0 Consensus size: 91
12315633 AGGAAATTTT
** *
12315643 TACCTCATATTAAATTTTGAGGTTTTTTTTCCAATTCATCAAAAGTTAAGAAGAGATTTAGAGAT
1 TACCTCATATTAAATTTTGAGCCTTTTTTTCCAATTCATCAAAAGTGAAGAAGAGATTTAGAGAT
12315708 TAGAGTATTTTCTCAATTTTTTTCTC
66 TAGAGTATTTTCTCAATTTTTTTCTC
* * * * *
12315734 TACCTCATATTTAATTTTGAGCCTTTTTTT-CAATTCATCATACGTGAGGAAGCGATTTAG-GAA
1 TACCTCATATTAAATTTTGAGCCTTTTTTTCCAATTCATCAAAAGTGAAGAAGAGATTTAGAG-A
* *
12315797 TTA-AGGTATTTTCTTATTTTTTTTCT
65 TTAGA-GTATTTTCTCAATTTTTTTCT
12315823 TTTCTTCTCC
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
89 2 0.03
90 48 0.62
91 27 0.35
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (91 bp):
TACCTCATATTAAATTTTGAGCCTTTTTTTCCAATTCATCAAAAGTGAAGAAGAGATTTAGAGAT
TAGAGTATTTTCTCAATTTTTTTCTC
Found at i:12316310 original size:19 final size:20
Alignment explanation
Indices: 12316273--12316318 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
12316263 AAATATTTAT
* *
12316273 TAAAAATTATAAAGAAATAC
1 TAAAAATTAAAAAGAAATAA
12316293 TAAAAATTAAAAAG-AATAA
1 TAAAAATTAAAAAGAAATAA
12316312 TAAAAAT
1 TAAAAAT
12316319 ACTAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
TAAAAATTAAAAAGAAATAA
Found at i:12316985 original size:21 final size:20
Alignment explanation
Indices: 12316943--12316987 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
12316933 ATAAATACTT
**
12316943 ATCA-TTTTTAATATTTTTA
1 ATCATTTTTTAATATTTGGA
12316962 ATCATTTTTGTAATATTTGGA
1 ATCATTTTT-TAATATTTGGA
12316983 ATCAT
1 ATCAT
12316988 GTCTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 14 0.64
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (20 bp):
ATCATTTTTTAATATTTGGA
Found at i:12318273 original size:23 final size:23
Alignment explanation
Indices: 12318230--12318280 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
12318220 TAGCCAACAT
12318230 GAGCCAGAATGATTAGCTCTTAC
1 GAGCCAGAATGATTAGCTCTTAC
12318253 GAGCCAGAATGATTAGCTCTTAC
1 GAGCCAGAATGATTAGCTCTTAC
*
12318276 AAGCC
1 GAGCC
12318281 CAAACAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
GAGCCAGAATGATTAGCTCTTAC
Found at i:12321711 original size:11 final size:11
Alignment explanation
Indices: 12321688--12321721 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12321678 TGTCCGGCCT
*
12321688 AAAAAA-AATA
1 AAAAAACAAAA
12321698 AAAAAACAAAA
1 AAAAAACAAAA
12321709 AAAAAACAAAA
1 AAAAAACAAAA
12321720 AA
1 AA
12321722 GTCCAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:12321789 original size:13 final size:13
Alignment explanation
Indices: 12321770--12321804 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12321760 GCCCAAATTA
12321770 CCAAACCTAATAAC
1 CCAAACCTAAT-AC
12321784 CC-AACCTAATAC
1 CCAAACCTAATAC
12321796 CCAAACCTA
1 CCAAACCTA
12321805 GACCTAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 14 0.70
14 2 0.10
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (13 bp):
CCAAACCTAATAC
Found at i:12323081 original size:11 final size:10
Alignment explanation
Indices: 12323065--12323117 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 10
12323055 CTTTAGATCT
12323065 TTTATTTTATA
1 TTTATTTT-TA
12323076 TTTATTTTTTCA
1 TTTA-TTTTT-A
12323088 TTT-TTATTTA
1 TTTATT-TTTA
12323098 TTTATTATTTA
1 TTTATT-TTTA
12323109 TTTATTTTT
1 TTTATTTTT
12323118 TGTGTCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.24
11 21 0.55
12 8 0.21
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:12323094 original size:25 final size:25
Alignment explanation
Indices: 12323064--12323117 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12323054 GCTTTAGATC
12323064 TTTTATTT-TATATTTATTT-TTTCAT
1 TTTTATTTATATA-TTATTTATTT-AT
*
12323089 TTTTATTTATTTATTATTTATTTAT
1 TTTTATTTATATATTATTTATTTAT
12323114 TTTT
1 TTTT
12323118 TGTGTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTATTTATATATTATTTATTTAT
Found at i:12323213 original size:3 final size:3
Alignment explanation
Indices: 12323205--12323317 Score: 54
Period size: 3 Copynumber: 36.7 Consensus size: 3
12323195 TTGACTGTGG
* **
12323205 TTA TTA TTA TTA TTA TT- TGTCA TTG TTA ACA TTA TTAA TTAA TGT-
1 TTA TTA TTA TTA TTA TTA T-T-A TTA TTA TTA TTA TT-A TT-A T-TA
* * * *
12323250 TTA TTA TTA TTA TCA TCA -TA GTCA -TA TTA TTA TTT TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA
* *
12323295 TCA ATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
12323318 TATTTATGCT
Statistics
Matches: 84, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
2 4 0.05
3 67 0.80
4 11 0.13
5 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:12323330 original size:25 final size:27
Alignment explanation
Indices: 12323274--12323347 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 27
12323264 ATCATAGTCA
* *
12323274 TATTATTATTTTTATTTATTATCAATAT
1 TATTATTATTATTATTTATTAT-AATAC
*
12323302 TATTATTATTATTATTTATT-T-ATGC
1 TATTATTATTATTATTTATTATAATAC
*
12323327 TATTAATT-GTATTATTTATTA
1 TATT-ATTATTATTATTTATTA
12323348 GTGTTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 17 0.43
26 3 0.08
27 1 0.03
28 19 0.47
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (27 bp):
TATTATTATTATTATTTATTATAATAC
Found at i:12324495 original size:23 final size:23
Alignment explanation
Indices: 12324461--12324971 Score: 697
Period size: 23 Copynumber: 22.3 Consensus size: 23
12324451 CTTATATCTA
12324461 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12324484 TGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
12324507 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12324530 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
12324553 TGCTTAAACATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12324576 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
12324599 TGCTTAAGTATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12324622 TGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
12324645 TACTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
12324668 TGCTCAAATATTAGTGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
12324691 TGCTTAAATATTAAAGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
12324714 TGCTTAAATATTAAT-TGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
12324736 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12324759 TGCTTAAGTATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
12324782 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12324805 TGCTCAAATATT-A-GTGAGTTTA
1 TGCTTAAATATTAATGTGA-TTTG
12324827 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
12324850 TGCTTAAATATTAAT-TGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
12324872 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
12324895 TGCTTAAGTATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
12324918 TGCTTAAATATTAATATAATTTA
1 TGCTTAAATATTAATGTGATTTG
*
12324941 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
12324964 TGCTTAAA
1 TGCTTAAA
12324972 AATTTAAGAT
Statistics
Matches: 431, Mismatches: 52, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
21 3 0.01
22 57 0.13
23 367 0.85
24 4 0.01
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:12328208 original size:15 final size:16
Alignment explanation
Indices: 12328173--12328210 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
12328163 AAAAAATATA
* *
12328173 TTAATATTATATTATT
1 TTAATATTATAATAAT
12328189 TTAATATT-TAATAAT
1 TTAATATTATAATAAT
12328204 TTAATAT
1 TTAATAT
12328211 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATATTATAATAAT
Found at i:12328227 original size:24 final size:25
Alignment explanation
Indices: 12328171--12328229 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
12328161 TTAAAAAATA
12328171 TATTAATATTATATTATTTTAATATT
1 TATTAAT-TTATATTATTTTAATATT
* *
12328197 TAATAATTTA-ATATATTTT-TTATT
1 TATTAATTTATAT-TATTTTAATATT
12328221 TATTAATTT
1 TATTAATTT
12328230 TTTTTATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 14 0.48
25 9 0.31
26 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTAATTTATATTATTTTAATATT
Found at i:12330059 original size:66 final size:66
Alignment explanation
Indices: 12329963--12330091 Score: 204
Period size: 66 Copynumber: 2.0 Consensus size: 66
12329953 AGTTGAACCA
* *
12329963 AAACTGCTAGAAGAAAATGCCGTTGAGCTCGGTTGTGAAGCATTCTGAAAATCCCCAAATGCACT
1 AAACCGCTAGAAGAAAATGCAGTTGAGCTCGGTTGTGAAGCATTCTGAAAATCCCCAAATGCACT
12330028 G
66 G
* * * *
12330029 AAACCGCTAGAAGGAAATGCAGTTGTGCTCGGTTTTGAAGCATTCTGAAAATCCCCGAATGCA
1 AAACCGCTAGAAGAAAATGCAGTTGAGCTCGGTTGTGAAGCATTCTGAAAATCCCCAAATGCA
12330092 TCATTTGCAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (66 bp):
AAACCGCTAGAAGAAAATGCAGTTGAGCTCGGTTGTGAAGCATTCTGAAAATCCCCAAATGCACT
G
Found at i:12340192 original size:25 final size:23
Alignment explanation
Indices: 12340140--12340194 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
12340130 GCTGGGTAAT
*
12340140 AGAGGGCACACAAAGTGCTAATC
1 AGAGGGCACACAAAGTGCTAAAC
*
12340163 AGAGGGCACACGATACGTGCTAAAC
1 AGAGGGCACAC-A-AAGTGCTAAAC
*
12340188 GGAGGGC
1 AGAGGGC
12340195 GTGCTAGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 15 0.56
ACGTcount: A:0.35, C:0.22, G:0.33, T:0.11
Consensus pattern (23 bp):
AGAGGGCACACAAAGTGCTAAAC
Found at i:12347233 original size:23 final size:24
Alignment explanation
Indices: 12347203--12347248 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
12347193 TGCTGTGTAG
12347203 CAGAGGGCACAC-AAAGTGCTAAT
1 CAGAGGGCACACGAAAGTGCTAAT
*
12347226 CAGAGGGCACACGAACGTGCTAA
1 CAGAGGGCACACGAAAGTGCTAA
12347249 ATGGAGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.37, C:0.24, G:0.28, T:0.11
Consensus pattern (24 bp):
CAGAGGGCACACGAAAGTGCTAAT
Found at i:12347926 original size:18 final size:18
Alignment explanation
Indices: 12347880--12347915 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12347870 ACTTTTTCTT
12347880 TTAAAGTTTAAATTTAAA
1 TTAAAGTTTAAATTTAAA
*
12347898 TTAAAGATTAAATTTAAA
1 TTAAAGTTTAAATTTAAA
12347916 ATTGAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (18 bp):
TTAAAGTTTAAATTTAAA
Found at i:12348365 original size:26 final size:26
Alignment explanation
Indices: 12348325--12348374 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
12348315 AATGGGTACC
12348325 AACCCTTTTTGAAAAATCAATATACG
1 AACCCTTTTTGAAAAATCAATATACG
12348351 AACCCTTTTCT-AAAAATCAATATA
1 AACCCTTTT-TGAAAAATCAATATA
12348375 AATAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (26 bp):
AACCCTTTTTGAAAAATCAATATACG
Found at i:12349962 original size:30 final size:29
Alignment explanation
Indices: 12349898--12350121 Score: 176
Period size: 29 Copynumber: 7.7 Consensus size: 29
12349888 TGATTTTTCT
*
12349898 AAAAATTACA-TTTTACCCCTG-AAGTT-C
1 AAAAATTACATTTTTA-CCCTGAAACTTCC
* *
12349925 TAAAATTACATTTTTGACCCTAAAACTTCC
1 AAAAATTACATTTTT-ACCCTGAAACTTCC
*
12349955 AAAAATTACATTTTTACCCCT-AAACTTTC
1 AAAAATTACATTTTTA-CCCTGAAACTTCC
**
12349984 AAAAATTACATTTTTGACACC-GAAACTTTT
1 AAAAATTACATTTTT-AC-CCTGAAACTTCC
*
12350014 AAAAATTACATTTTTA-CCTCGAAACTTCT
1 AAAAATTACATTTTTACCCT-GAAACTTCC
* * * *
12350043 GAAAATCATATTTTTACCCCCG-AACTTCC
1 AAAAATTACATTTTTA-CCCTGAAACTTCC
* * * *
12350072 AAAAATTCCACTTTTGACCCCGAAACTTGC
1 AAAAATTACA-TTTTTACCCTGAAACTTCC
12350102 AAAAATTACCA-TTTTACCCT
1 AAAAATTA-CATTTTTACCCT
12350122 CGAATGTAAA
Statistics
Matches: 161, Mismatches: 21, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
27 11 0.07
28 8 0.05
29 75 0.47
30 63 0.39
31 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCTGAAACTTCC
Found at i:12349998 original size:59 final size:58
Alignment explanation
Indices: 12349898--12350116 Score: 205
Period size: 59 Copynumber: 3.7 Consensus size: 58
12349888 TGATTTTTCT
* *
12349898 AAAAATTACA-TTTTACCCCTG-AA-GTTCTAAAATTACATTTTTGACCCTAAAACTTCC
1 AAAAATTACATTTTTACCCC-GAAACTTTCAAAAATTACATTTTTGACCC-AAAACTTCC
* * **
12349955 AAAAATTACATTTTTACCCCTAAACTTTCAAAAATTACATTTTTGACACCGAAACTTTT
1 AAAAATTACATTTTTACCCCGAAACTTTCAAAAATTACATTTTTGAC-CCAAAACTTCC
* * * * **
12350014 AAAAATTACATTTTTACCTCGAAAC-TTCTGAAAATCATATTTTT-ACCCCCGAACTTCC
1 AAAAATTACATTTTTACCCCGAAACTTTC-AAAAATTACATTTTTGA-CCCAAAACTTCC
* * *
12350072 AAAAATTCCACTTTTGACCCCGAAACTTGCAAAAATTACCATTTT
1 AAAAATTACA-TTTTTACCCCGAAACTTTCAAAAATTA-CATTTT
12350117 ACCCTCGAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
57 10 0.08
58 31 0.24
59 81 0.62
60 9 0.07
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAAATTACATTTTTACCCCGAAACTTTCAAAAATTACATTTTTGACCCAAAACTTCC
Found at i:12350166 original size:59 final size:58
Alignment explanation
Indices: 12350094--12350245 Score: 162
Period size: 59 Copynumber: 2.6 Consensus size: 58
12350084 TTTGACCCCG
*
12350094 AAACTTGCAAAAATTACCATTTTACCCTCGAATGTAAAAAAACTCCATTTTTAA-CCTA
1 AAACTTTC-AAAATTACCATTTTACCCTCGAATGTAAAAAAACTCCATTTTTAACCCTA
* * * * * * * ** *
12350152 GAGACTTTTTAAAATCACTATTTTACCCCCAAAAGTCCAAATACTCCATTTTTAACCCTA
1 -AAAC-TTTCAAAATTACCATTTTACCCTCGAATGTAAAAAAACTCCATTTTTAACCCTA
*
12350212 AAACTTTCAAAATTACCATTTTACCCTTGAATGT
1 AAACTTTCAAAATTACCATTTTACCCTCGAATGT
12350246 CCAAAAATTT
Statistics
Matches: 72, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
58 23 0.32
59 43 0.60
60 6 0.08
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (58 bp):
AAACTTTCAAAATTACCATTTTACCCTCGAATGTAAAAAAACTCCATTTTTAACCCTA
Found at i:12354896 original size:180 final size:180
Alignment explanation
Indices: 12354588--12354949 Score: 616
Period size: 180 Copynumber: 2.0 Consensus size: 180
12354578 ATTTATAACG
* * *
12354588 TTTAATAGATTCATAAATTAGTCCCCAAGTTAGCTAGATTAAGCTAATACGAACTTAAAAACATA
1 TTTAACAGATTCACAAATTAGTCCCCAAGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATA
*
12354653 AAAATTACTAAAAACGGGCAAGATTTACATACCAAACGCATGGACTAAAGTTGGCCGAAGCTTCC
66 AAAATTACTAAAAACGGGCAAGATTTACATACCAAACCCATGGACTAAAGTTGGCCGAAGCTTCC
12354718 TCCCATGGTGTTTAGGGTTTACGATTCTAAAATAGGTGGAAGAAGGTGAT
131 TCCCATGGTGTTTAGGGTTTACGATTCTAAAATAGGTGGAAGAAGGTGAT
* ** *
12354768 TTTAACAGATTCACAAATTAGTCCTCGGGTTAGCTAGATTAAGCTAATGCGAACTCAAAAACATA
1 TTTAACAGATTCACAAATTAGTCCCCAAGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATA
*
12354833 AAAATTACTAAAAAGGGGCAAGATTTACATACCAAACCCATGGACTAAAGTTGGCCGAAGCTTCC
66 AAAATTACTAAAAACGGGCAAGATTTACATACCAAACCCATGGACTAAAGTTGGCCGAAGCTTCC
** *
12354898 TCCCATGGTGTTTAGGGTTTTTGGTTCTAAAATAGGTGGAAGAAGGTGAT
131 TCCCATGGTGTTTAGGGTTTACGATTCTAAAATAGGTGGAAGAAGGTGAT
12354948 TT
1 TT
12354950 CTTCCAATTT
Statistics
Matches: 170, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
180 170 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (180 bp):
TTTAACAGATTCACAAATTAGTCCCCAAGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATA
AAAATTACTAAAAACGGGCAAGATTTACATACCAAACCCATGGACTAAAGTTGGCCGAAGCTTCC
TCCCATGGTGTTTAGGGTTTACGATTCTAAAATAGGTGGAAGAAGGTGAT
Found at i:12364705 original size:3 final size:3
Alignment explanation
Indices: 12364697--12364737 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12364687 CAATAGGGGA
12364697 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12364738 AAGGATTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12371420 original size:19 final size:19
Alignment explanation
Indices: 12371370--12371421 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
12371360 CCCATATTGT
*
12371370 TCTTACGAGCCAATATCGC
1 TCTTACGAGCCAGTATCGC
* *
12371389 TTTTATGAGCCAGTATCGC
1 TCTTACGAGCCAGTATCGC
*
12371408 TCTTACGACCCAGT
1 TCTTACGAGCCAGT
12371422 TCAATAATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (19 bp):
TCTTACGAGCCAGTATCGC
Found at i:12377640 original size:30 final size:32
Alignment explanation
Indices: 12377576--12377640 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
12377566 CAATTAATTA
*
12377576 ATTAATATTCTTCATCAATTTCTTTTTTAAAAT
1 ATTAATATTCTTCATCAA-TTCTTTTTAAAAAT
12377609 ATTAATATTCTTCATCAA-TC-TTTTAAAAAT
1 ATTAATATTCTTCATCAATTCTTTTTAAAAAT
12377639 AT
1 AT
12377641 AACCTTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 11 0.35
31 2 0.06
33 18 0.58
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTAATATTCTTCATCAATTCTTTTTAAAAAT
Found at i:12381581 original size:28 final size:27
Alignment explanation
Indices: 12381541--12381604 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
12381531 AGTAATAATA
* *
12381541 AAATTATATTTTATTTTTTTAAAATGAT
1 AAATTATAATTTA-ATTTTTAAAATGAT
* *
12381569 AAATTTTAATTTAATTTTTAAAATTAT
1 AAATTATAATTTAATTTTTAAAATGAT
*
12381596 AAAATATAA
1 AAATTATAA
12381605 ATTATTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
AAATTATAATTTAATTTTTAAAATGAT
Found at i:12381600 original size:8 final size:8
Alignment explanation
Indices: 12381587--12381627 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
12381577 ATTTAATTTT
12381587 TAAAATTA
1 TAAAATTA
12381595 TAAAA-TA
1 TAAAATTA
12381602 T-AAATTA
1 TAAAATTA
*
12381609 TTAAAATAA
1 -TAAAATTA
12381618 TAAAATTA
1 TAAAATTA
12381626 TA
1 TA
12381628 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 3 0.11
7 5 0.18
8 15 0.54
9 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAAATTA
Found at i:12381612 original size:23 final size:23
Alignment explanation
Indices: 12381581--12381654 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
12381571 ATTTTAATTT
12381581 AATTTTTAAAATTATAAAATATA
1 AATTTTTAAAATTATAAAATATA
* *
12381604 AATTATTAAAATAATAAAAT-TA
1 AATTTTTAAAATTATAAAATATA
* **
12381626 TATTTTTATTATTATAAAATATA
1 AATTTTTAAAATTATAAAATATA
12381649 CAATTT
1 -AATTT
12381655 AATTTCGATT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.41
23 20 0.49
24 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTTTAAAATTATAAAATATA
Found at i:12381672 original size:29 final size:31
Alignment explanation
Indices: 12381605--12381672 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
12381595 TAAAATATAA
**
12381605 ATTATTAAAATAATAAAATTATATTTTTATT
1 ATTATTAAAATAATAAAATTATATTTCGATT
*
12381636 ATTA-TAAAAT-ATACAATT-TAATTTCGATT
1 ATTATTAAAATAATAAAATTAT-ATTTCGATT
12381665 -TTATTAAA
1 ATTATTAAA
12381673 TTCTTTTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 4 0.12
29 18 0.56
30 6 0.19
31 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTATTAAAATAATAAAATTATATTTCGATT
Found at i:12382061 original size:26 final size:29
Alignment explanation
Indices: 12382024--12382084 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 29
12382014 AATATTTATA
*
12382024 TTATAT-TATTTTAATAT-TTAATAA-TT
1 TTATATATATTTTAATATATTAAGAATTT
* *
12382050 TTATATAT-TTTTTATTTATTAAGAATTT
1 TTATATATATTTTAATATATTAAGAATTT
12382078 TTATATA
1 TTATATA
12382085 GTCCTCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 13 0.45
27 7 0.24
28 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTATATATATTTTAATATATTAAGAATTT
Found at i:12382069 original size:28 final size:28
Alignment explanation
Indices: 12382025--12382084 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
12382015 ATATTTATAT
*
12382025 TATATTATTTTAATATTTAATAA-TTTTA
1 TATATTATTTTAATA-TTAAGAATTTTTA
*
12382053 TATATT-TTTTATTTATTAAGAATTTTTA
1 TATATTATTTTA-ATATTAAGAATTTTTA
12382081 TATA
1 TATA
12382085 GTCCTCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TATATTATTTTAATATTAAGAATTTTTA
Found at i:12383165 original size:21 final size:20
Alignment explanation
Indices: 12383141--12383190 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
12383131 TTAAAGCTAT
* *
12383141 TTTTTATTTTTATTTTTTGAA
1 TTTTTATTTCTATTTTATG-A
*
12383162 TTTTTATATCTATTTTATGA
1 TTTTTATTTCTATTTTATGA
*
12383182 TTTATATTT
1 TTTTTATTT
12383191 GTGTTGGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTTTATTTCTATTTTATGA
Found at i:12384817 original size:25 final size:25
Alignment explanation
Indices: 12384789--12384844 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
12384779 TATATTTTAT
**
12384789 AATAAGATA-ATATTTTATAATAATA
1 AATAAGATATATAAATT-TAATAATA
**
12384814 AATATCATATATAAATTTAATAATA
1 AATAAGATATATAAATTTAATAATA
12384839 AATAAG
1 AATAAG
12384845 GTTTAATTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
AATAAGATATATAAATTTAATAATA
Found at i:12384827 original size:13 final size:12
Alignment explanation
Indices: 12384804--12384842 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12384794 GATAATATTT
12384804 TATAATAATAAA
1 TATAATAATAAA
*
12384816 TATCATATATAAA
1 TATAATA-ATAAA
*
12384829 TTTAATAATAAA
1 TATAATAATAAA
12384841 TA
1 TA
12384843 AGGTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TATAATAATAAA
Found at i:12390009 original size:22 final size:22
Alignment explanation
Indices: 12389984--12390046 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
12389974 GGGTGTTACC
12389984 AGACACCGAAGTGCAAATCAGT
1 AGACACCGAAGTGCAAATCAGT
* * * *
12390006 AGACACTGAAGTGTAGAGCAGT
1 AGACACCGAAGTGCAAATCAGT
*
12390028 AGGCACCGAAGTGCAAATC
1 AGACACCGAAGTGCAAATC
12390047 CTATACAAGC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.14
Consensus pattern (22 bp):
AGACACCGAAGTGCAAATCAGT
Found at i:12396987 original size:52 final size:52
Alignment explanation
Indices: 12396925--12397028 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
12396915 CCACACATGA
12396925 ATATATATATATATATCATAATATCATAGATCATATTTATCTCTCAATTCTT
1 ATATATATATATATATCATAATATCATAGATCATATTTATCTCTCAATTCTT
12396977 ATATATATATATATATCATAATATCATAGATCATATTTATCTCTCAATTCTT
1 ATATATATATATATATCATAATATCATAGATCATATTTATCTCTCAATTCTT
12397029 GTAAAAGCCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.46
Consensus pattern (52 bp):
ATATATATATATATATCATAATATCATAGATCATATTTATCTCTCAATTCTT
Found at i:12418485 original size:23 final size:21
Alignment explanation
Indices: 12418455--12418511 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
12418445 TAAGCATACA
12418455 AACTACCGATACATCAATACTAC
1 AACTACCGATACATCAAT--TAC
* * * *
12418478 AACTACCGAAACTTGAATTTC
1 AACTACCGATACATCAATTAC
12418499 AACTACCGATACA
1 AACTACCGATACA
12418512 ACTCAAGTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 13 0.46
23 15 0.54
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (21 bp):
AACTACCGATACATCAATTAC
Found at i:12421953 original size:13 final size:14
Alignment explanation
Indices: 12421917--12421945 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12421907 GTAGAGAATC
12421917 TCATACCTT-ATTT
1 TCATACCTTGATTT
12421930 TCATACCTTGATTT
1 TCATACCTTGATTT
12421944 TC
1 TC
12421946 CTACTTGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.52
Consensus pattern (14 bp):
TCATACCTTGATTT
Found at i:12432428 original size:17 final size:17
Alignment explanation
Indices: 12432371--12432428 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
12432361 AAACTTTTGA
12432371 TTAAATAATTACTATTATT
1 TTAAATAATTA--ATTATT
12432390 TAATAAA-AATTAA--ATT
1 T--TAAATAATTAATTATT
*
12432406 TAAAATAATTAATTATT
1 TTAAATAATTAATTATT
12432423 TTAAAT
1 TTAAAT
12432429 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 3 0.09
15 6 0.19
16 4 0.12
17 8 0.25
18 1 0.03
19 1 0.03
20 5 0.16
21 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATAATTAATTATT
Found at i:12432870 original size:6 final size:6
Alignment explanation
Indices: 12432859--12432938 Score: 76
Period size: 6 Copynumber: 13.3 Consensus size: 6
12432849 AATTGATTTT
12432859 ATTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* * * *
12432907 CTTTAA ATTTAA ATTAAA ATTAAA ATTAAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
12432939 ACTAAACATT
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
4 2 0.03
5 6 0.09
6 49 0.75
7 2 0.03
8 6 0.09
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTTAA
Found at i:12432919 original size:37 final size:37
Alignment explanation
Indices: 12432857--12432927 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
12432847 TAAATTGATT
*
12432857 TTATTTAAATTTAAATTTATCTTAAATTTAAATTTAA
1 TTATTTAAATTTAAATTTATCTTAAATTAAAATTTAA
*
12432894 TTATTTAAATTT-ACTTTAAAT-TTAAATTAAAATT
1 TTATTTAAATTTAAATTT--ATCTTAAATTAAAATT
12432928 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 4 0.13
37 24 0.80
38 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (37 bp):
TTATTTAAATTTAAATTTATCTTAAATTAAAATTTAA
Found at i:12432923 original size:11 final size:11
Alignment explanation
Indices: 12432859--12432936 Score: 61
Period size: 11 Copynumber: 7.1 Consensus size: 11
12432849 AATTGATTTT
12432859 ATTTAAATTTAA
1 ATTTAAA-TTAA
**
12432871 ATTTATCTTAA
1 ATTTAAATTAA
*
12432882 ATTTAAATTTA
1 ATTTAAATTAA
*
12432893 A-TT-ATTTAA
1 ATTTAAATTAA
**
12432902 ATTTACTTTAA
1 ATTTAAATTAA
12432913 ATTTAAATTAAA
1 ATTTAAATT-AA
*
12432925 ATTAAAATTAA
1 ATTTAAATTAA
12432936 A
1 A
12432937 ATACTAAACA
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 5 0.10
10 4 0.08
11 28 0.54
12 15 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTAAATTAA
Found at i:12432929 original size:17 final size:17
Alignment explanation
Indices: 12432861--12432936 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
12432851 TTGATTTTAT
**
12432861 TTAAATTTAAATTTATC
1 TTAAATTTAAATTTAAA
12432878 TTAAATTTAAATTT-AA
1 TTAAATTTAAATTTAAA
**
12432894 TT--ATTTAAATTTACT
1 TTAAATTTAAATTTAAA
*
12432909 TTAAATTTAAATTAAAA
1 TTAAATTTAAATTTAAA
*
12432926 TTAAAATTAAA
1 TTAAATTTAAA
12432937 ATACTAAACA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 10 0.21
15 2 0.04
16 2 0.04
17 34 0.71
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:12434741 original size:30 final size:30
Alignment explanation
Indices: 12434705--12434891 Score: 211
Period size: 30 Copynumber: 6.3 Consensus size: 30
12434695 TAAATTGTCC
* *
12434705 AAAAATTACATTTTGACCCTAAAACTTTCT
1 AAAAATTATATTTTGACCCCAAAACTTTCT
12434735 AAAAATTATATTTTGACCCCAAAACTTT-T
1 AAAAATTATATTTTGACCCCAAAACTTTCT
* *
12434764 CCAAAATTACATTTTGACCCCAAAACTTT-T
1 -AAAAATTATATTTTGACCCCAAAACTTTCT
* * *
12434794 CCAAAATTATATTTTGGCCCTAAAACTTTCT
1 -AAAAATTATATTTTGACCCCAAAACTTTCT
* *
12434825 AAAAATCATATTTTGACCCCAAAA-TTTCCA
1 AAAAATTATATTTTGACCCCAAAACTTT-CT
* * *
12434855 AAAAATTGTATTTTTACCCCGAAACTTTC-
1 AAAAATTATATTTTGACCCCAAAACTTTCT
12434884 AAAAATTA
1 AAAAATTA
12434892 CCATTTCACC
Statistics
Matches: 136, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.08
30 121 0.89
31 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAAATTATATTTTGACCCCAAAACTTTCT
Found at i:12434860 original size:90 final size:88
Alignment explanation
Indices: 12434704--12434897 Score: 264
Period size: 90 Copynumber: 2.2 Consensus size: 88
12434694 CTAAATTGTC
*
12434704 CAAAAATTACATTTTGACCCTAAAACTTTCTAAAAATTATATTTTGACCCCAAAACTTTTCCAAA
1 CAAAAATTACATTTTGACCCTAAAACTTTCTAAAAATCATATTTTGACCCCAAAAC-TTTCCAAA
12434769 ATTACATTTTGACCCCAAAACTTTT
65 ATTACATTTTGACCCCAAAAC-TTT
* * *
12434794 CCAAAATTATATTTTGGCCCTAAAACTTTCTAAAAATCATATTTTGACCCCAAAA-TTTCCAAAA
1 CAAAAATTACATTTTGACCCTAAAACTTTCTAAAAATCATATTTTGACCCCAAAACTTTCC--AA
** * *
12434858 AATTGTATTTTTACCCCGAAACTTT
64 AATTACATTTTGACCCCAAAACTTT
12434883 CAAAAATTACCATTT
1 CAAAAATTA-CATTT
12434898 CACCCCCAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
88 5 0.05
89 11 0.12
90 75 0.82
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.36
Consensus pattern (88 bp):
CAAAAATTACATTTTGACCCTAAAACTTTCTAAAAATCATATTTTGACCCCAAAACTTTCCAAAA
TTACATTTTGACCCCAAAACTTT
Done.