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 23 of 163
Found at i:6262415 original size:60 final size:60
Alignment explanation
Indices: 6262288--6262428 Score: 191
Period size: 60 Copynumber: 2.4 Consensus size: 60
6262278 CCCTAAACTA
* * *
6262288 TCCAAAAATTATATTTTGACCCAAAACTTTTTGAAAATTACACTTTGACCCTCTAACTTC
1 TCCAAAAATTATATTTTGACCCAAAACTTTTTAAAAATTACACTTTAACCCTCTAAATTC
*
6262348 TCC-AAAATTATATTTTGACCTCAAAACTTTTTAAAAATTACATTTTAACCCTC-AAATT-
1 TCCAAAAATTATATTTTGACC-CAAAACTTTTTAAAAATTACACTTTAACCCTCTAAATTC
6262406 TCCTAAAAATTACTATTTT-ACCC
1 TCC-AAAAATTA-TATTTTGACCC
6262429 CCGAACTTTC
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
58 3 0.04
59 22 0.30
60 42 0.58
61 6 0.08
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (60 bp):
TCCAAAAATTATATTTTGACCCAAAACTTTTTAAAAATTACACTTTAACCCTCTAAATTC
Found at i:6262554 original size:59 final size:57
Alignment explanation
Indices: 6262410--6262576 Score: 190
Period size: 59 Copynumber: 2.8 Consensus size: 57
6262400 CAAATTTCCT
* * *
6262410 AAAAATTACTATTTTACCCCCGAACTTTCTAAAATTATGTTTTTCACCTCGATTTCACC
1 AAAAATT-CTATTTTACCCCCGAACTTTCTAAAATT-TATTTTTAACCCCGATTTCACC
* * * **
6262469 AAAAATTATATTTTTGCGCCTAAACTTTCTAAAATTCTATTTTTAACCCCGATTTCACC
1 AAAAATTCTA-TTTTACCCCCGAACTTTCTAAAATT-TATTTTTAACCCCGATTTCACC
* *
6262528 AAAAATTGCCATTTTACCCCCGAACTTTCCAAAATTTCATTTTTAACCC
1 AAAAATT-CTATTTTACCCCCGAACTTTCTAAAATTT-ATTTTTAACCC
6262577 AAATTTTCCC
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
58 3 0.03
59 85 0.96
60 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (57 bp):
AAAAATTCTATTTTACCCCCGAACTTTCTAAAATTTATTTTTAACCCCGATTTCACC
Found at i:6262571 original size:29 final size:30
Alignment explanation
Indices: 6262381--6262608 Score: 95
Period size: 29 Copynumber: 7.7 Consensus size: 30
6262371 AAACTTTTTA
* * * *
6262381 AAAATTACATTTTAACCCTC-AAATTTCCTA
1 AAAATTACATTTTTACCCCCGAACTTTCC-C
*
6262411 AAAATTAC-TATTTTACCCCCGAACTTT-CT
1 AAAATTACAT-TTTTACCCCCGAACTTTCCC
** *
6262440 AAAATTATGTTTTT-CACCTCG-A-TTTCACC
1 AAAATTACATTTTTAC-CCCCGAACTTTC-CC
* * * ** *
6262469 AAAAATTATATTTTTGCGCCTAAACTTT-CT
1 -AAAATTACATTTTTACCCCCGAACTTTCCC
*
6262499 AAAATT-CTATTTTTAACCCCG-A-TTTCACC
1 AAAATTAC-ATTTTTACCCCCGAACTTTC-CC
*
6262528 AAAAATTGCCA-TTTTACCCCCGAACTTT-CC
1 -AAAATT-ACATTTTTACCCCCGAACTTTCCC
* * * *
6262558 AAAATTTCATTTTTA-ACCCAAATTTTCCC
1 AAAATTACATTTTTACCCCCGAACTTTCCC
*
6262587 AAAATTACATTTTTGCCCCCGA
1 AAAATTACATTTTTACCCCCGA
6262609 GAGTCAAAAA
Statistics
Matches: 148, Mismatches: 29, Indels: 42
0.68 0.13 0.19
Matches are distributed among these distances:
27 6 0.04
28 13 0.09
29 58 0.39
30 55 0.37
31 9 0.06
32 7 0.05
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTTACCCCCGAACTTTCCC
Found at i:6263319 original size:157 final size:157
Alignment explanation
Indices: 6263148--6263432 Score: 360
Period size: 157 Copynumber: 1.8 Consensus size: 157
6263138 ATTTTAAAAT
* * * * **
6263148 AAAACGAGGCAATGTCCTTTCGT-GTGAAAACCTCGAAAAATCGCGCTTTAACGTGTTGAGTGTG
1 AAAAAGAGACAATGTCCTTTC-TCGTGAAAACCTCGAAAAACCACGCCCTAACGTGTTGAGTGTG
* * * * *
6263212 ATTTTCG-TAATTTATGCAAATCGGATA-TCCTCTTTAAAATTTCTCGAAACATCCTTCAATTTT
65 ATTTTCGATAATTCACGC-AATAGAATACT-CTCTTCAAAATTTCTCGAAACATCCTTCAATTTT
6263275 ATATATCTATATACAAAGGATTTTAAGACA
128 ATATATCTATATACAAAGGATTTTAAGACA
* * * *
6263305 AAAAAGAGACAATGTCCTTTCTCGTGAAGACCTCGAAACACCATGCCCTAACGTGTTGGGTGTGA
1 AAAAAGAGACAATGTCCTTTCTCGTGAAAACCTCGAAAAACCACGCCCTAACGTGTTGAGTGTGA
* *
6263370 TTTTCGTATAATTCACGCGATAGAATACTCTCTTCAAAATTTCTCGAAACGTCCTTCAATTTT
66 TTTTCG-ATAATTCACGCAATAGAATACTCTCTTCAAAATTTCTCGAAACATCCTTCAATTTT
6263433 GAAACTCCGA
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
156 1 0.01
157 59 0.55
158 38 0.36
159 9 0.08
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (157 bp):
AAAAAGAGACAATGTCCTTTCTCGTGAAAACCTCGAAAAACCACGCCCTAACGTGTTGAGTGTGA
TTTTCGATAATTCACGCAATAGAATACTCTCTTCAAAATTTCTCGAAACATCCTTCAATTTTATA
TATCTATATACAAAGGATTTTAAGACA
Found at i:6268561 original size:2 final size:2
Alignment explanation
Indices: 6268554--6268587 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6268544 CCTAAAAAGG
6268554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6268588 AGTAATGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6269653 original size:17 final size:16
Alignment explanation
Indices: 6269624--6269676 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
6269614 AACTATATAA
*
6269624 TTTTTATTTAAATGTTT
1 TTTTTA-TTAAATATTT
6269641 TATTTTATTAAATATTAT
1 T-TTTTATTAAATATT-T
*
6269659 TTATTATTAAATATTT
1 TTTTTATTAAATATTT
6269675 TT
1 TT
6269677 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.09
17 22 0.69
18 7 0.22
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTTATTAAATATTT
Found at i:6270260 original size:18 final size:18
Alignment explanation
Indices: 6270239--6270278 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
6270229 AGCTCGAATT
6270239 ATTTAATTAAAAATTTAA
1 ATTTAATTAAAAATTTAA
* *
6270257 ATTTTTATTAAAATTTTAA
1 A-TTTAATTAAAAATTTAA
6270276 ATT
1 ATT
6270279 AAATCAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAATTAAAAATTTAA
Found at i:6273318 original size:21 final size:23
Alignment explanation
Indices: 6273292--6273339 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
6273282 TAAAAATATT
*
6273292 AAAAAATCA-CAAAAA-TATAAA
1 AAAAAATCAGAAAAAATTATAAA
6273313 AAAAAATCAGAAAAAATTATAAA
1 AAAAAATCAGAAAAAATTATAAA
6273336 AAAA
1 AAAA
6273340 TATAAGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 5 0.21
23 10 0.42
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (23 bp):
AAAAAATCAGAAAAAATTATAAA
Found at i:6273340 original size:21 final size:20
Alignment explanation
Indices: 6273283--6273340 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
6273273 ATTTTTTTAT
* *
6273283 AAAAA-TATTAAAAAATCAC
1 AAAAATTATAAAAAAATCAA
*
6273302 AAAAATATAAAAAAAAATCAGA
1 AAAAAT-TATAAAAAAATCA-A
6273324 AAAAATTATAAAAAAAT
1 AAAAATTATAAAAAAAT
6273341 ATAAGTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.16
21 21 0.66
22 6 0.19
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAATTATAAAAAAATCAA
Found at i:6273343 original size:10 final size:10
Alignment explanation
Indices: 6273283--6273344 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
6273273 ATTTTTTTAT
*
6273283 AAAAATATTA
1 AAAAATATAA
* *
6273293 AAAAAT-CAC
1 AAAAATATAA
6273302 AAAAATATAA
1 AAAAATATAA
*
6273312 AAAAAAATCAGA
1 AAAAATAT-A-A
6273324 AAAAATTATAA
1 AAAAA-TATAA
6273335 AAAAATATAA
1 AAAAATATAA
6273345 GTATTATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 6 0.15
10 19 0.46
11 7 0.17
12 7 0.17
13 2 0.05
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (10 bp):
AAAAATATAA
Found at i:6273403 original size:29 final size:29
Alignment explanation
Indices: 6273352--6273480 Score: 97
Period size: 29 Copynumber: 4.4 Consensus size: 29
6273342 TAAGTATTAT
*
6273352 TAAATATTA-AAAATATATGAAAATTGATA
1 TAAATATTATAAAATATAT-AAAATTAATA
* **
6273381 TAAACT-TTATAAAATTTATAAAAAAAATA
1 TAAA-TATTATAAAATATATAAAATTAATA
*
6273410 TAAATATTATAAAAGATATAAAATTCTAATA
1 TAAATATTATAAAATATATAAAA-T-TAATA
* * *
6273441 -AATTATAAAAAAAT-TATAAAATTAATA
1 TAAATATTATAAAATATATAAAATTAATA
*
6273468 AAACATATT-TAAA
1 TAA-ATATTATAAA
6273481 TTTTTATAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
27 5 0.06
28 7 0.09
29 43 0.55
30 19 0.24
31 4 0.05
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAATATTATAAAATATATAAAATTAATA
Found at i:6273537 original size:37 final size:37
Alignment explanation
Indices: 6273495--6273569 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
6273485 TATAAAACCT
6273495 TATTAAAA-TACTATAAATTCATA-AAACATCATAAAAA
1 TATTAAAAGTACTA-AAATTCATATAAAC-TCATAAAAA
* * *
6273532 TATTAAAAGTATTAAAATTGATATAAACTTATAAAAA
1 TATTAAAAGTACTAAAATTCATATAAACTCATAAAAA
6273569 T
1 T
6273570 TATAAAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 25 0.76
38 8 0.24
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (37 bp):
TATTAAAAGTACTAAAATTCATATAAACTCATAAAAA
Found at i:6273574 original size:9 final size:9
Alignment explanation
Indices: 6273324--6273577 Score: 72
Period size: 9 Copynumber: 26.6 Consensus size: 9
6273314 AAAAATCAGA
6273324 AAAAATTAT
1 AAAAATTAT
*
6273333 AAAAAAATAT
1 -AAAAATTAT
**
6273343 AAGTATTAT
1 AAAAATTAT
*
6273352 -TAAA-TATT
1 AAAAATTA-T
6273360 AAAAATATAT
1 AAAAAT-TAT
*
6273370 GAAAATTGAT
1 AAAAATT-AT
*
6273380 ATAAACTTTAT
1 A-AAA-ATTAT
*
6273391 AAAATTTAT
1 AAAAATTAT
*
6273400 AAAAAAAATAT
1 --AAAAATTAT
*
6273411 AAATATTAT
1 AAAAATTAT
6273420 AAAAGA-TAT
1 AAAA-ATTAT
*
6273429 -AAAATTCT
1 AAAAATTAT
6273437 AATAAATTAT
1 AA-AAATTAT
6273447 AAAAAAATTAT
1 --AAAAATTAT
6273458 -AAAATTAAT
1 AAAAATT-AT
*
6273467 AAAACATATTT
1 AAAA-AT-TAT
**
6273478 AAATTTTTAT
1 AAA-AATTAT
*
6273488 AAAACCTTAT
1 AAAA-ATTAT
*
6273498 TAAAA-TACT
1 AAAAATTA-T
*
6273507 ATAAATTCAT
1 AAAAATT-AT
*
6273517 AAAACATCAT
1 AAAA-ATTAT
6273527 AAAAA-TAT
1 AAAAATTAT
* *
6273535 TAAAAGTAT
1 AAAAATTAT
*
6273544 TAAAATTGAT
1 AAAAATT-AT
*
6273554 ATAAACTTAT
1 A-AAAATTAT
6273564 AAAAATTAT
1 AAAAATTAT
6273573 AAAAA
1 AAAAA
6273578 CTTAAACTGG
Statistics
Matches: 180, Mismatches: 36, Indels: 57
0.66 0.13 0.21
Matches are distributed among these distances:
7 3 0.02
8 21 0.12
9 57 0.32
10 57 0.32
11 37 0.21
12 5 0.03
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6280990 original size:9 final size:9
Alignment explanation
Indices: 6280783--6281000 Score: 88
Period size: 9 Copynumber: 22.9 Consensus size: 9
6280773 ATTTATTAAA
6280783 TATAAAAA-
1 TATAAAAAT
*
6280791 TATGAAAAT
1 TATAAAAAT
*
6280800 TGATATAAACT
1 T-ATA-AAAAT
*
6280811 TATAAATAT
1 TATAAAAAT
*
6280820 TATAAATAT
1 TATAAAAAT
6280829 TATAAAAGA-
1 TATAAAA-AT
6280838 TATAAAAAT
1 TATAAAAAT
*
6280847 TCTAATAAAT
1 TATAA-AAAT
6280857 TATAAAAAAAT
1 TAT--AAAAAT
6280868 TAT-AAAAT
1 TATAAAAAT
6280876 TAATTAAACATAT
1 T-A-TAAA-A-AT
6280889 T-TAAAAATT
1 TATAAAAA-T
6280898 TATAAAAATGT
1 TATAAAAA--T
* *
6280909 TTTAAAATAC
1 TATAAAA-AT
*
6280919 TATAAAAAA
1 TATAAAAAT
* *
6280928 CAT-AACAT
1 TATAAAAAT
6280936 CT-TAAAAAT
1 -TATAAAAAT
* *
6280945 TATTAAAAG
1 TATAAAAAT
*
6280954 TATTAAAAT
1 TATAAAAAT
*
6280963 TAATATAAACT
1 T-ATA-AAAAT
*
6280974 TCTAAAAAT
1 TATAAAAAT
6280983 TATAAAAAAT
1 TAT-AAAAAT
*
6280993 CATAAAAA
1 TATAAAAA
6281001 CTTAAACTAG
Statistics
Matches: 160, Mismatches: 27, Indels: 45
0.69 0.12 0.19
Matches are distributed among these distances:
8 20 0.12
9 66 0.41
10 41 0.26
11 26 0.16
12 4 0.03
13 3 0.02
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (9 bp):
TATAAAAAT
Found at i:6281469 original size:22 final size:21
Alignment explanation
Indices: 6281444--6281484 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6281434 TCAATTTTAA
*
6281444 TATTTTTTTCTATAATTTTTCT
1 TATTTTTTT-TACAATTTTTCT
6281466 TATTTTTTTTACAATTTTT
1 TATTTTTTTTACAATTTTT
6281485 AAGGGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTTTTTTTACAATTTTTCT
Found at i:6285529 original size:40 final size:40
Alignment explanation
Indices: 6285465--6285541 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
6285455 AGGGCAACGG
* *
6285465 AGAGCACACACAGTGCTAAACAGTGAGTACACAAAGTACT
1 AGAGCACACAAAGTGCTAAACAGTGAGCACACAAAGTACT
* * * *
6285505 AGAGCACATAAAGTGTTAATCAGTGAGCACACGAAGT
1 AGAGCACACAAAGTGCTAAACAGTGAGCACACAAAGT
6285542 GCTAATAACG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (40 bp):
AGAGCACACAAAGTGCTAAACAGTGAGCACACAAAGTACT
Found at i:6289306 original size:17 final size:17
Alignment explanation
Indices: 6289286--6289334 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
6289276 TGTTCATATT
6289286 AAATAATAGTTCATACC
1 AAATAATAGTTCATACC
* * *
6289303 AAATGATAGTTTATTCC
1 AAATAATAGTTCATACC
* *
6289320 AATTAACAGTTCATA
1 AAATAATAGTTCATA
6289335 ACACATAACA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (17 bp):
AAATAATAGTTCATACC
Found at i:6290071 original size:11 final size:10
Alignment explanation
Indices: 6290054--6290095 Score: 57
Period size: 11 Copynumber: 3.9 Consensus size: 10
6290044 GCCCAACAAA
6290054 ATTTAAATTT
1 ATTTAAATTT
6290064 ATTTTAAATTT
1 A-TTTAAATTT
6290075 AAGTTTAAATTT
1 -A-TTTAAATTT
6290087 ATTTAAATT
1 ATTTAAATT
6290096 AAAAAGTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.31
11 10 0.34
12 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:6292114 original size:30 final size:30
Alignment explanation
Indices: 6292024--6292121 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
6292014 CCTAAATTTT
* * * *
6292024 CAAAAATGCCATTTTTGTCCCCAAACTTTC
1 CAAAAATTCCATTTTTGACCCCGAACCTTC
* *
6292054 CCAAAATTACCA-TTTTCACCCTCGAA-CTTC
1 CAAAAATT-CCATTTTTGACCC-CGAACCTTC
6292084 CAAAAATTCCATTTTTGACCCCGAACCTTC
1 CAAAAATTCCATTTTTGACCCCGAACCTTC
6292114 CAAAAATT
1 CAAAAATT
6292122 ACCGTTTTGC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 7 0.12
30 43 0.77
31 6 0.11
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.31
Consensus pattern (30 bp):
CAAAAATTCCATTTTTGACCCCGAACCTTC
Found at i:6292120 original size:60 final size:58
Alignment explanation
Indices: 6291989--6292129 Score: 167
Period size: 60 Copynumber: 2.4 Consensus size: 58
6291979 CCCAAAACCT
* * * *
6291989 GAACTTTCCAAAAATTA-CATTTTTCCCTAAATTTTCAAAAATGCCATTTTTGTCCCC
1 GAACTTTCCAAAAATTACCATTTTACCCTAAACTTCCAAAAATGCCATTTTTGACCCC
* * * *
6292046 AAACTTTCCCAAAATTACCATTTTCACCCTCGAACTTCCAAAAATTCCATTTTTGACCCC
1 GAACTTTCCAAAAATTACCATTTT-ACCCT-AAACTTCCAAAAATGCCATTTTTGACCCC
* *
6292106 GAACCTTCCAAAAATTACCGTTTT
1 GAACTTTCCAAAAATTACCATTTT
6292130 GCCCCCAAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
57 15 0.22
58 6 0.09
59 4 0.06
60 44 0.64
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (58 bp):
GAACTTTCCAAAAATTACCATTTTACCCTAAACTTCCAAAAATGCCATTTTTGACCCC
Found at i:6292134 original size:29 final size:30
Alignment explanation
Indices: 6292036--6292135 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
6292026 AAAATGCCAT
* * * *
6292036 TTTTGTCCCCAAACTTTCCCAAAATTACCA
1 TTTTGACCCCGAACCTTCCAAAAATTACCA
*
6292066 TTTTCACCCTCGAA-CTTCCAAAAATT-CCA
1 TTTTGACCC-CGAACCTTCCAAAAATTACCA
*
6292095 TTTTTGACCCCGAACCTTCCAAAAATTACCG
1 -TTTTGACCCCGAACCTTCCAAAAATTACCA
*
6292126 TTTTGCCCCC
1 TTTTGACCCC
6292136 AAAGTATCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 7 0.12
30 46 0.79
31 5 0.09
ACGTcount: A:0.27, C:0.35, G:0.06, T:0.32
Consensus pattern (30 bp):
TTTTGACCCCGAACCTTCCAAAAATTACCA
Found at i:6293800 original size:35 final size:35
Alignment explanation
Indices: 6293726--6293803 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
6293716 CACTCATGCC
* * *
6293726 TATATATATTATATATAATCCAACCCCTATATACG
1 TATATATATTATATAGAATCAAACCCCTATAAACG
*
6293761 TATATATATTATAT-GAATCAATACCCCT-TGAAACT
1 TATATATATTATATAGAATCAA-ACCCCTAT-AAACG
6293796 TATATATA
1 TATATATA
6293804 ATCATAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.16
35 31 0.84
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (35 bp):
TATATATATTATATAGAATCAAACCCCTATAAACG
Found at i:6296536 original size:11 final size:10
Alignment explanation
Indices: 6296511--6296544 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
6296501 GGTTTATTCA
6296511 ATTTAATTTT
1 ATTTAATTTT
6296521 ATTTAATTTCT
1 ATTTAATTT-T
*
6296532 ATTTATTTTT
1 ATTTAATTTT
6296542 ATT
1 ATT
6296545 GTTATTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTAATTTT
Found at i:6298273 original size:26 final size:26
Alignment explanation
Indices: 6298244--6298294 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
6298234 GACAAATCCT
*
6298244 ATTTTTGC-AATCGAATTCAATTTGAA
1 ATTTTTGCGAATCGAA-TCAAATTGAA
*
6298270 ATTTTTTCGAATCGAATCAAATTGA
1 ATTTTTGCGAATCGAATCAAATTGA
6298295 GACGAATCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (26 bp):
ATTTTTGCGAATCGAATCAAATTGAA
Found at i:6299152 original size:24 final size:24
Alignment explanation
Indices: 6299120--6299167 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
6299110 TAATGGACTA
*
6299120 ACAACGAAGGCGACATGGAAGATT
1 ACAACGAAGGCCACATGGAAGATT
*
6299144 ACAAGGAAGGCCACATGGAAGATT
1 ACAACGAAGGCCACATGGAAGATT
6299168 GAAGTGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.29, T:0.12
Consensus pattern (24 bp):
ACAACGAAGGCCACATGGAAGATT
Found at i:6308923 original size:6 final size:6
Alignment explanation
Indices: 6308912--6308968 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
6308902 TGATCAAAAT
* * * * * *
6308912 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGAAAT TGGAAT
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
6308960 TGAAAG TGA
1 TGAAAG TGA
6308969 TATGAATTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.25
Consensus pattern (6 bp):
TGAAAG
Found at i:6308945 original size:18 final size:18
Alignment explanation
Indices: 6308924--6308968 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
6308914 AAAGTGAAAG
6308924 TGAAAGTGAAATTGGAAT
1 TGAAAGTGAAATTGGAAT
6308942 TGAAAGTGAAATTGGAAT
1 TGAAAGTGAAATTGGAAT
6308960 TGAAAGTGA
1 TGAAAGTGA
6308969 TATGAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (18 bp):
TGAAAGTGAAATTGGAAT
Found at i:6314149 original size:19 final size:19
Alignment explanation
Indices: 6314125--6314165 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
6314115 TTAGGGAAAT
6314125 TAAATGTTAGATATAATTC
1 TAAATGTTAGATATAATTC
6314144 TAAATGTTAGATATAATTC
1 TAAATGTTAGATATAATTC
6314163 TAA
1 TAA
6314166 TTATCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (19 bp):
TAAATGTTAGATATAATTC
Found at i:6317712 original size:7 final size:6
Alignment explanation
Indices: 6317683--6317708 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6317673 GGCAACCCAA
6317683 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
6317709 TATTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:6317730 original size:22 final size:21
Alignment explanation
Indices: 6317700--6317750 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
6317690 TATTTTTATT
*
6317700 TTTATTTTTTATTATTT-TTCTA
1 TTTATTTTGT-TTATTTATT-TA
6317722 TCTTATTTTGTTTATTTATTTA
1 T-TTATTTTGTTTATTTATTTA
6317744 TTTATTT
1 TTTATTT
6317751 CTGTCTAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.23
22 10 0.38
23 10 0.38
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTATTTTGTTTATTTATTTA
Found at i:6317739 original size:29 final size:28
Alignment explanation
Indices: 6317682--6317746 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
6317672 AGGCAACCCA
* *
6317682 ATTATTTTTATTTTTATTTTTATTTTTT
1 ATTATTTTTATTCTTATTTTTATTATTT
*
6317710 ATTATTTTTCTATCTTATTTTGT-TTATTT
1 ATTATTTTTAT-TCTTATTTT-TATTATTT
6317739 ATTTATTT
1 A-TTATTT
6317747 ATTTCTGTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 10 0.32
29 14 0.45
30 7 0.23
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (28 bp):
ATTATTTTTATTCTTATTTTTATTATTT
Found at i:6317740 original size:13 final size:12
Alignment explanation
Indices: 6317688--6317750 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
6317678 CCCAATTATT
6317688 TTTATTTTTATT-
1 TTTATTTTT-TTA
6317700 TTTA-TTTTTTA
1 TTTATTTTTTTA
*
6317711 -TTATTTTTCTA
1 TTTATTTTTTTA
6317722 TCTTATTTTGTTTA
1 T-TTATTTT-TTTA
*
6317736 TTTATTTATTTA
1 TTTATTTTTTTA
6317748 TTT
1 TTT
6317751 CTGTCTAGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
10 5 0.12
11 10 0.23
12 11 0.26
13 13 0.30
14 4 0.09
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:6318123 original size:21 final size:25
Alignment explanation
Indices: 6318076--6318123 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 25
6318066 CCTATCAGTA
*
6318076 TGATTCTTGTTTACTGAGTTAATTT
1 TGATTCTTGTTTACTGAGTTAAATT
6318101 TGATT-TTG-TTA-TGA-TTAAATT
1 TGATTCTTGTTTACTGAGTTAAATT
6318122 TG
1 TG
6318124 TCTCCACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 8 0.36
22 3 0.14
23 3 0.14
24 3 0.14
25 5 0.23
ACGTcount: A:0.23, C:0.04, G:0.17, T:0.56
Consensus pattern (25 bp):
TGATTCTTGTTTACTGAGTTAAATT
Found at i:6318617 original size:104 final size:105
Alignment explanation
Indices: 6318490--6318683 Score: 259
Period size: 104 Copynumber: 1.9 Consensus size: 105
6318480 ACTCGAATAA
* * * **
6318490 AAAAAAGAAAATAATAAATAAATTCG-GAATGTGTTAGACTGAGTAACC-GGAGTGGAGTGCTTG
1 AAAAAAGAAAAGAAGAAAAAAATT-GAGAACATGTTAGACTGAGTAACCGGGA-TGGAGTGCTTG
*
6318553 GTTGTCATTTCACTTCGCGTCAAAAGGGCTAATGCATTGTAC
64 GGTGTCATTTCACTTCGCGTCAAAAGGGCTAATGCATTGTAC
* * *
6318595 AAAAAA-AAAAGAAGAAAAAAATTGAGAGCATGTTGGGCTGAGTAACCGGGATGGAGTGCTTGGG
1 AAAAAAGAAAAGAAGAAAAAAATTGAGAACATGTTAGACTGAGTAACCGGGATGGAGTGCTTGGG
*
6318659 TGTCATTTCATTTCGCGTCAAAAGG
66 TGTCATTTCACTTCGCGTCAAAAGG
6318684 TCCAATGTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
103 1 0.01
104 67 0.87
105 9 0.12
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.25
Consensus pattern (105 bp):
AAAAAAGAAAAGAAGAAAAAAATTGAGAACATGTTAGACTGAGTAACCGGGATGGAGTGCTTGGG
TGTCATTTCACTTCGCGTCAAAAGGGCTAATGCATTGTAC
Found at i:6318707 original size:104 final size:104
Alignment explanation
Indices: 6318528--6318721 Score: 266
Period size: 104 Copynumber: 1.9 Consensus size: 104
6318518 ATGTGTTAGA
* *
6318528 CTGAGTAACCGGAGTGGAGTGCTTGGTTGTCATTTCACTTCGCGTCAAAAGGGCTAATGCATTGT
1 CTGAGTAACCGGAGTGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTGT
*
6318593 ACAAAAAAAAAAGAAGAAAAAAATTGAGAGCATGTTGGG
66 ACAAAAAAAAAAAAAGAAAAAAATTGAGAGCATGTTGGG
* * *
6318632 CTGAGTAACCGG-GATGGAGTGCTTGGGTGTCATTTCATTTCGCGTCAAAAGGTCCAATGTATTC
1 CTGAGTAACCGGAG-TGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATT-
* ** *
6318696 TTA-AAGGAAAAAAAAAGGAAAAAATT
64 GTACAAAAAAAAAAAAAGAAAAAAATT
6318722 CACAAAATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
103 1 0.01
104 75 0.96
105 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (104 bp):
CTGAGTAACCGGAGTGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAATGCATTGT
ACAAAAAAAAAAAAAGAAAAAAATTGAGAGCATGTTGGG
Found at i:6319304 original size:19 final size:19
Alignment explanation
Indices: 6319282--6319326 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
6319272 TTATATTAGG
6319282 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
6319301 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
6319320 ATTTAAT
1 ATTTAAT
6319327 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:6320174 original size:21 final size:22
Alignment explanation
Indices: 6320138--6320184 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
6320128 TTTCTATTTC
*
6320138 TTTTAATTCTATTTTCTTTAAT
1 TTTTAAATCTATTTTCTTTAAT
*
6320160 TTTTAAATCTA-TTTCTTTTAT
1 TTTTAAATCTATTTTCTTTAAT
6320181 TTTT
1 TTTT
6320185 CCTTAGATCG
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:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAAATCTATTTTCTTTAAT
Found at i:6328909 original size:11 final size:11
Alignment explanation
Indices: 6328893--6328917 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6328883 TTTTATTATT
6328893 TTATTTATTTA
1 TTATTTATTTA
6328904 TTATTTATTTA
1 TTATTTATTTA
6328915 TTA
1 TTA
6328918 AATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:6329799 original size:33 final size:33
Alignment explanation
Indices: 6329762--6329827 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
6329752 AATAGAAAGA
*
6329762 ATGGATTTTTTTAAATGGAAATAATCATATTGT
1 ATGGATTTTTTTAAATGGAAATAATCAAATTGT
6329795 ATGGATTTTTTTAAATGGAAATAATCAAATTGT
1 ATGGATTTTTTTAAATGGAAATAATCAAATTGT
6329828 CTTTTATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (33 bp):
ATGGATTTTTTTAAATGGAAATAATCAAATTGT
Found at i:6330147 original size:30 final size:30
Alignment explanation
Indices: 6330112--6330285 Score: 199
Period size: 30 Copynumber: 5.8 Consensus size: 30
6330102 ACCGTCAAAG
*
6330112 TTTTT-AAAAATTTAAATTTAACCCCTAAA
1 TTTTTCAAAAATTCAAATTTAACCCCTAAA
* * * *
6330141 TTTTTTAAAAATTGAAATTTCACCCCCAAA
1 TTTTTCAAAAATTCAAATTTAACCCCTAAA
*
6330171 TTTTCCAAAAATTCAAATTTAATCCCC-AAA
1 TTTTTCAAAAATTCAAATTTAA-CCCCTAAA
* *
6330201 GTTTTCAAAAATTCAAATTTAACCTCTTAAA
1 TTTTTCAAAAATTCAAATTTAACC-CCTAAA
* *
6330232 TTTTCCAAAAATTCAAATTTAACCCTTAAA
1 TTTTTCAAAAATTCAAATTTAACCCCTAAA
* * *
6330262 GTTTTAAAAAATTAAAATTTAACC
1 TTTTTCAAAAATTCAAATTTAACC
6330286 TGTTTTAATG
Statistics
Matches: 125, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.06
30 89 0.71
31 29 0.23
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (30 bp):
TTTTTCAAAAATTCAAATTTAACCCCTAAA
Found at i:6330249 original size:61 final size:60
Alignment explanation
Indices: 6330117--6330286 Score: 216
Period size: 61 Copynumber: 2.8 Consensus size: 60
6330107 CAAAGTTTTT
* * * * *
6330117 AAAAATTTAAATTTAACCCCTAAATTTTTTAAAAATTGAAATTTCACC-CCCAAATTTTCC
1 AAAAATTCAAATTTAACCCC-AAAGTTTTAAAAAATTAAAATTTAACCTCCCAAATTTTCC
* * **
6330177 AAAAATTCAAATTTAATCCCCAAAGTTTTCAAAAATTCAAATTTAACCTCTTAAATTTTCC
1 AAAAATTCAAATTTAA-CCCCAAAGTTTTAAAAAATTAAAATTTAACCTCCCAAATTTTCC
*
6330238 AAAAATTCAAATTTAACCCTTAAAGTTTTAAAAAATTAAAATTTAACCT
1 AAAAATTCAAATTTAACCC-CAAAGTTTTAAAAAATTAAAATTTAACCT
6330287 GTTTTAATGT
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
60 41 0.42
61 56 0.58
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.36
Consensus pattern (60 bp):
AAAAATTCAAATTTAACCCCAAAGTTTTAAAAAATTAAAATTTAACCTCCCAAATTTTCC
Found at i:6342042 original size:50 final size:50
Alignment explanation
Indices: 6341978--6342204 Score: 294
Period size: 50 Copynumber: 4.5 Consensus size: 50
6341968 ATCTTTTACC
* * *
6341978 CCTAAAGTTGTAGAGGTGCATATTGAAACCGCAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
* * * *
6342028 CCTAAAGCTATAGAGGGGCAGAATGAAACCGCAATA-TCAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAA-AGGCAAATCTCATACA
* * *
6342078 CCTAAAGCTATAAAGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
* * * * *
6342128 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGCAATGACAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
*
6342178 CCTAAAGCTGTAAAGGGGCAGATTGAA
1 CCTAAAGCTGTAGAGGGGCAGATTGAA
6342205 GTCACAAGGA
Statistics
Matches: 153, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
49 1 0.01
50 151 0.99
51 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAAAGGCAAATCTCATACA
Found at i:6342142 original size:100 final size:100
Alignment explanation
Indices: 6341991--6342204 Score: 367
Period size: 100 Copynumber: 2.1 Consensus size: 100
6341981 AAAGTTGTAG
*
6341991 AGGTGCATATTGAAACCGCAAAGGCAAATCTCATACACCTAAAGCTATAGAGGGGCAGAATGAAA
1 AGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACACCTAAAGCTATAGAGGGGCAGAATGAAA
6342056 CCGCAAT-ATCAAATCTCATTCACCTAAAGCTATAA
66 CCGCAATGA-CAAATCTCATTCACCTAAAGCTATAA
* *
6342091 AGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACACCTAAAGCTGTAGAGGGGCAGAATGAAG
1 AGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACACCTAAAGCTATAGAGGGGCAGAATGAAA
*
6342156 CCGCAATGACAAATCTCATTCACCTAAAGCTGTAA
66 CCGCAATGACAAATCTCATTCACCTAAAGCTATAA
*
6342191 AGGGGCAGATTGAA
1 AGGTGCAGATTGAA
6342205 GTCACAAGGA
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
100 107 0.99
101 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (100 bp):
AGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACACCTAAAGCTATAGAGGGGCAGAATGAAA
CCGCAATGACAAATCTCATTCACCTAAAGCTATAA
Found at i:6342237 original size:50 final size:50
Alignment explanation
Indices: 6341978--6342237 Score: 256
Period size: 50 Copynumber: 5.2 Consensus size: 50
6341968 ATCTTTTACC
* * * * *
6341978 CCTAAAGTTGTAGAGGTGCATATTGAAACCGCAAAGG-CAAATCTCATACA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGC-AAGGACAAATCTCATACA
* * * * * *
6342028 CCTAAAGCTATAGAGGGGCAGAATGAAACCGCAA-TATCAAATCTCATTCA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGCAAGGA-CAAATCTCATACA
* * *
6342078 CCTAAAGCTATAAAGGTGCAGATTGAAACCGCAAAGG-CAAATCTCATACA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGC-AAGGACAAATCTCATACA
* * * *
6342128 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGCAATGACAAATCTCATTCA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGCAAGGACAAATCTCATACA
* * * * *
6342178 CCTAAAGCTGTAAAGGGGCAGATTGAAGTCACAAGGACGAATCTTATACT
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGCAAGGACAAATCTCATACA
*
6342228 CCTGAAGCTG
1 CCTAAAGCTG
6342238 AAATGAAGTG
Statistics
Matches: 176, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
49 5 0.03
50 169 0.96
51 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGCAAGGACAAATCTCATACA
Found at i:6342325 original size:39 final size:41
Alignment explanation
Indices: 6342278--6342549 Score: 305
Period size: 40 Copynumber: 6.9 Consensus size: 41
6342268 TTACCTCGAT
6342278 CATG-GGGCAGATTGAAGA-AATCCAATCTTTTACCCTAAC
1 CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAAC
** * * *
6342317 CA-GAGGGCAAGATTGAAGACCGTCCGATCTTTTACCCTGAT
1 CATGAGGGC-AGATTGAAGACAATCCAATCTTTTACCCTAAC
*
6342358 CATG-GGGCAGATTGAAGA-AATCCAATCTTTTACCCTGAC
1 CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAAC
* * *
6342397 TATGA-GGTAGATTGAAG-CAATCCAATCTTTTACCCTAAT
1 CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAAC
* * *
6342436 CA-GAGGGCAGATTGAAGATAATCCAATCTCTTACCCCAAC
1 CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAAC
* **
6342476 CATG-GGGCAGATTGAAGACAATCCAATCTCTTACCCCGAC
1 CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAAC
* *
6342516 CAT-AGGACAGGTTGAA-ACAATCCAATCTTTTACC
1 CATGAGGGCAGATTGAAGACAATCCAATCTTTTACC
6342550 TTTAAAGTTA
Statistics
Matches: 199, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.02
39 85 0.43
40 87 0.44
41 23 0.12
42 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
CATGAGGGCAGATTGAAGACAATCCAATCTTTTACCCTAAC
Found at i:6342370 original size:40 final size:40
Alignment explanation
Indices: 6342259--6342549 Score: 292
Period size: 39 Copynumber: 7.3 Consensus size: 40
6342249 AGTAACAACC
* *
6342259 TCCAATTTTTTA-CCTCGATCATGGGGCAGATTGAAGA-AA
1 TCCAATCTTTTACCCT-AATCATGGGGCAGATTGAAGACAA
* **
6342298 TCCAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCG
1 TCCAATCTTTTACCCTAATCATG-GGGC-AGATTGAAGACAA
* *
6342339 TCCGATCTTTTACCCTGATCATGGGGCAGATTGAAGA-AA
1 TCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGACAA
* * *
6342378 TCCAATCTTTTACCCTGA-CTATGAGGTAGATTGAAG-CAA
1 TCCAATCTTTTACCCTAATC-ATGGGGCAGATTGAAGACAA
*
6342417 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGATAA
1 TCCAATCTTTTACCCTAATCATG-GGGCAGATTGAAGACAA
* * *
6342457 TCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGACAA
* ** * * * *
6342497 TCCAATCTCTTACCCCGACCATAGGACAGGTTGAA-ACAA
1 TCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGACAA
6342536 TCCAATCTTTTACC
1 TCCAATCTTTTACC
6342550 TTTAAAGTTA
Statistics
Matches: 215, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.01
39 97 0.45
40 91 0.42
41 23 0.11
42 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAATCATGGGGCAGATTGAAGACAA
Found at i:6342499 original size:119 final size:119
Alignment explanation
Indices: 6342285--6342549 Score: 354
Period size: 119 Copynumber: 2.2 Consensus size: 119
6342275 GATCATGGGG
* ** * *
6342285 CAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCGTCCGATCTTTT
1 CAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCCAATCTCTT
** * * * *
6342350 ACCCTGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTGACTATGAGG-
66 ACCCCAACCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCCGACCAT-AGGA
* * *
6342404 TAGATTGAAGCAATCCAATCTTTTACCCTAATCAGAGGGC-AGATTGAAGATAATCCAATCTCTT
1 CAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCCAATCTCTT
6342468 ACCCCAACCATGGGGCAGATTGAAGACAATCCAATCTCTTACCCCGACCATAGGA
66 ACCCCAACCATGGGGCAGATTGAAGA-AATCCAATCTCTTACCCCGACCATAGGA
* *
6342523 CAGGTTGAAACAATCCAATCTTTTACC
1 CAGATTGAAGCAATCCAATCTTTTACC
6342550 TTTAAAGTTA
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
118 45 0.35
119 82 0.65
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (119 bp):
CAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACAATCCAATCTCTT
ACCCCAACCATGGGGCAGATTGAAGAAATCCAATCTCTTACCCCGACCATAGGA
Found at i:6342606 original size:50 final size:50
Alignment explanation
Indices: 6342552--6342674 Score: 160
Period size: 50 Copynumber: 2.5 Consensus size: 50
6342542 CTTTTACCTT
*
6342552 TAAAGTTACAGAGGGACAGATTAAAGCTACAAAAGCAAATCTTATACCCC
1 TAAAGTTACAGAGGGACAGATTAAAGCTACAAAAACAAATCTTATACCCC
* * *
6342602 TAAAGTTACAGA-TGAGCAGATTGAAGCTACAAAAATAAATCTTATACCCC
1 TAAAGTTACAGAGGGA-CAGATTAAAGCTACAAAAACAAATCTTATACCCC
* *
6342652 TAAAGTAATAGAGAGG-CAGATTA
1 TAAAGTTACAGAG-GGACAGATTA
6342675 TCAATCTTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
49 2 0.03
50 59 0.95
52 1 0.02
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (50 bp):
TAAAGTTACAGAGGGACAGATTAAAGCTACAAAAACAAATCTTATACCCC
Found at i:6343958 original size:22 final size:22
Alignment explanation
Indices: 6343920--6343975 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
6343910 ATAAAGGGAA
* * *
6343920 TTTTAAAAATAAA-AATGGTTT
1 TTTTAAATAGAAAGAATGGGTT
*
6343941 TTTTTAATAGAAAGAATGGGTT
1 TTTTAAATAGAAAGAATGGGTT
*
6343963 TTTTAAATGGAAA
1 TTTTAAATAGAAA
6343976 TAATCAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (22 bp):
TTTTAAATAGAAAGAATGGGTT
Found at i:6344301 original size:30 final size:30
Alignment explanation
Indices: 6344265--6344415 Score: 178
Period size: 30 Copynumber: 5.0 Consensus size: 30
6344255 TCATTTTTTG
6344265 ACCCCCAAAGTTTTTAAAAATTCAAATTTA
1 ACCCCCAAAGTTTTTAAAAATTCAAATTTA
* * * *
6344295 ACCCCCATATTTTTTAAAAATTGAAATTTC
1 ACCCCCAAAGTTTTTAAAAATTCAAATTTA
*
6344325 ACCCCCAAA-TTTTTCAAAAAGTCAAATTTA
1 ACCCCCAAAGTTTTT-AAAAATTCAAATTTA
* * *
6344355 ATCTCCAAAGTTTTCAAAAATTCAAATTTA
1 ACCCCCAAAGTTTTTAAAAATTCAAATTTA
** * *
6344385 ACCCTTAAAGTTTTCAAAAATTAAAATTTA
1 ACCCCCAAAGTTTTTAAAAATTCAAATTTA
6344415 A
1 A
6344416 TCGGTTTTAA
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
29 5 0.05
30 93 0.91
31 4 0.04
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (30 bp):
ACCCCCAAAGTTTTTAAAAATTCAAATTTA
Found at i:6344517 original size:21 final size:23
Alignment explanation
Indices: 6344482--6344523 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
6344472 ATATTACTTC
6344482 ATTTTATTATATTTTATGTATGT
1 ATTTTATTATATTTTATGTATGT
6344505 ATTTT-TT-TATTTTATGTAT
1 ATTTTATTATATTTTATGTAT
6344524 ACTTGTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (23 bp):
ATTTTATTATATTTTATGTATGT
Found at i:6345615 original size:96 final size:97
Alignment explanation
Indices: 6345451--6345710 Score: 396
Period size: 96 Copynumber: 2.6 Consensus size: 97
6345441 TCAATAATTG
6345451 ATCAAAGAAGGAGAGGAGAAGAAACCGTGAATCTTCCTAGATAGCATCTTCTACCTCCACAGTAT
1 ATCAAAGAAGGAGAGGAGAAGAAACCGTGAATCTTCCTAGATAGCATCTTCTACCTCCACAGTAT
6345516 CTCATCATGGGAGG-TATAGCTTATATATCTA
66 CTCATCATGGGAGGTTATAGCTTATATATCTA
*
6345547 ATCAAAGAAGGAGAGGAGAAGAAACCGTGAATCTTCCTAGATAGCATCTTCTACCTCCACATTAT
1 ATCAAAGAAGGAGAGGAGAAGAAACCGTGAATCTTCCTAGATAGCATCTTCTACCTCCACAGTAT
6345612 CTCATCATGGGAGGTTTTACTATATATATAGCTTATATATCTA
66 CTCATCATGGGAGG----------T-TATAGCTTATATATCTA
*
6345655 ATCAAAGAAGGAGAGGAGAAGAAACCTTGAATCTTCCTAGATAGCATCTTCTACCT
1 ATCAAAGAAGGAGAGGAGAAGAAACCGTGAATCTTCCTAGATAGCATCTTCTACCT
6345711 TAATGTATCT
Statistics
Matches: 150, Mismatches: 2, Indels: 12
0.91 0.01 0.07
Matches are distributed among these distances:
96 78 0.52
108 72 0.48
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (97 bp):
ATCAAAGAAGGAGAGGAGAAGAAACCGTGAATCTTCCTAGATAGCATCTTCTACCTCCACAGTAT
CTCATCATGGGAGGTTATAGCTTATATATCTA
Found at i:6351406 original size:22 final size:22
Alignment explanation
Indices: 6351374--6351417 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6351364 AATTTTTTTA
6351374 TTTTTACTTTCAATTTATATAT
1 TTTTTACTTTCAATTTATATAT
*
6351396 TTTTTATTTTCAATTTATATAT
1 TTTTTACTTTCAATTTATATAT
6351418 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTTACTTTCAATTTATATAT
Found at i:6351416 original size:2 final size:2
Alignment explanation
Indices: 6351411--6351441 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6351401 ATTTTCAATT
6351411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6351442 TAAGTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6351420 original size:28 final size:28
Alignment explanation
Indices: 6351367--6351423 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
6351357 TTTAACTAAT
* * *
6351367 TTTTTTATTTTTACTTTCAATTTATATA
1 TTTTTTATTTTCAATTTCAATATATATA
6351395 TTTTTTATTTTCAATTT-ATATATATATA
1 TTTTTTATTTTCAATTTCA-ATATATATA
6351423 T
1 T
6351424 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTTTATTTTCAATTTCAATATATATA
Found at i:6351478 original size:33 final size:33
Alignment explanation
Indices: 6351441--6351508 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
6351431 TATATATATA
*
6351441 TTAAGTTTTATAATTTATACATTTCTTATTTTT
1 TTAAGTTTTATAATTTATACATTTCTAATTTTT
*
6351474 TTAAGTTTTATAATTTATGCATTTCTAATTTTT
1 TTAAGTTTTATAATTTATACATTTCTAATTTTT
6351507 TT
1 TT
6351509 TAAAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.63
Consensus pattern (33 bp):
TTAAGTTTTATAATTTATACATTTCTAATTTTT
Found at i:6351517 original size:20 final size:21
Alignment explanation
Indices: 6351494--6351534 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
6351484 TAATTTATGC
6351494 ATTTCTAATTTTT-TTTAAAA
1 ATTTCTAATTTTTGTTTAAAA
*
6351514 ATTTTTAATTTTTGTTTAAAA
1 ATTTCTAATTTTTGTTTAAAA
6351535 TTTTAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTCTAATTTTTGTTTAAAA
Found at i:6351986 original size:9 final size:9
Alignment explanation
Indices: 6351969--6352028 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
6351959 TTAATTAATT
6351969 AATTT-AAA
1 AATTTAAAA
*
6351977 ATTTTAAAAA
1 AATTT-AAAA
*
6351987 AATATAAAA
1 AATTTAAAA
*
6351996 AATCTAAAA
1 AATTTAAAA
6352005 AATTTATAAA
1 AATTTA-AAA
6352015 AATTACTAAAA
1 AATT--TAAAA
6352026 AAT
1 AAT
6352029 AATAAAAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
8 4 0.10
9 17 0.40
10 13 0.31
11 6 0.14
12 2 0.05
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATTTAAAA
Found at i:6352033 original size:20 final size:18
Alignment explanation
Indices: 6351983--6352035 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 18
6351973 TAAAATTTTA
6351983 AAAAAATATAAAAAATCT
1 AAAAAATATAAAAAATCT
*
6352001 AAAAAATTTATAAAAATTACT
1 AAAAAA--TATAAAAAAT-CT
6352022 AAAAAATAATAAAA
1 AAAAAAT-ATAAAA
6352036 GTATAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.20
19 1 0.03
20 15 0.50
21 8 0.27
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAAATATAAAAAATCT
Found at i:6352885 original size:3 final size:3
Alignment explanation
Indices: 6352877--6352917 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
6352867 TTTTCCTACA
6352877 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6352918 CAAATTAATA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6354078 original size:19 final size:18
Alignment explanation
Indices: 6354054--6354089 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6354044 ATATTTGAAA
6354054 TTAATAAAATATAATATAT
1 TTAATAAAATA-AATATAT
*
6354073 TTAATACAATAAATATA
1 TTAATAAAATAAATATA
6354090 AAATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATAAAATAAATATAT
Found at i:6355853 original size:27 final size:27
Alignment explanation
Indices: 6355761--6355855 Score: 127
Period size: 27 Copynumber: 3.4 Consensus size: 27
6355751 TGTTTCCTCT
**
6355761 GAAGAAGATGAAGAGGTGACTTCTTCTGAG
1 GAAGAAGATGAAG-GGT--CTTCAACTGAG
* *
6355791 GAAGAAGAAGAAGGGTCTTCAGCTGAG
1 GAAGAAGATGAAGGGTCTTCAACTGAG
6355818 GAAGAAGATGAAGGGTCTTCAACTGAG
1 GAAGAAGATGAAGGGTCTTCAACTGAG
6355845 GAAGAAGATGA
1 GAAGAAGATGA
6355856 GGAAGACCCC
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
27 45 0.75
29 3 0.05
30 12 0.20
ACGTcount: A:0.38, C:0.09, G:0.35, T:0.18
Consensus pattern (27 bp):
GAAGAAGATGAAGGGTCTTCAACTGAG
Found at i:6358011 original size:23 final size:23
Alignment explanation
Indices: 6357981--6358024 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
6357971 ATAGTATCAC
6357981 TATATATATTTTCAAATAAACAG
1 TATATATATTTTCAAATAAACAG
6358004 TATATATATTTTCAAATAAAC
1 TATATATATTTTCAAATAAAC
6358025 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (23 bp):
TATATATATTTTCAAATAAACAG
Found at i:6358035 original size:23 final size:23
Alignment explanation
Indices: 6357986--6358035 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6357976 ATCACTATAT
* *
6357986 ATATTTTCAAATAAACAGTATAT
1 ATATTTTCAAATAAACAGTAAAA
**
6358009 ATATTTTCAAATAAACTTTAAAA
1 ATATTTTCAAATAAACAGTAAAA
6358032 ATAT
1 ATAT
6358036 GAGATTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (23 bp):
ATATTTTCAAATAAACAGTAAAA
Found at i:6359525 original size:62 final size:60
Alignment explanation
Indices: 6359208--6359597 Score: 399
Period size: 61 Copynumber: 6.5 Consensus size: 60
6359198 CTTGTTTCAA
** *
6359208 AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACAACCCATT-TTCTCGAG
1 AAAAAAATTTTAATTTTTTTGGTGTTGGCCATCAAATGGCCGAC-ACCCCTTATTCTCGAG
* ** *** * * *
6359268 AAAAAAAATTGCA--TTTTTGGATGTTGGCCATTGTATAGCCGATACCCCTTGTT-TC-AG
1 AAAAAAATTTTAATTTTTTTGG-TGTTGGCCATCAAATGGCCGACACCCCTTATTCTCGAG
*
6359325 AAAAAAAATTTTAAATTTTTTTCGTGTTGGCCATCAAATGGCCGACACCACC-TATTCTC-A-
1 -AAAAAAATTTT-AATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC-CCTTATTCTCGAG
* * *
6359385 AAAAAAA--TTACA-TTTTTGGGTGTTAGCCATCAAATGGCCGACACCCCCTATTCTCGAG
1 AAAAAAATTTTA-ATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTATTCTCGAG
* *
6359443 AAAAAAGTTTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTATTCTCGAG
1 AAAAAAATTT-TAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTATTCTCGAG
* * *
6359504 AAAAAATTTTTAATTTTTTTTTGTGTTGGCTATCAAATGGCCGACATCCCCCTT-TTCTCGAG
1 AAAAAAATTTTAA-TTTTTTTGGTGTTGGCCATCAAATGGCCGACA--CCCCTTATTCTCGAG
* *
6359566 AAAAAAATTCTAAATTTTTTGGTGTTGGCCAT
1 AAAAAAATTTTAATTTTTTTGGTGTTGGCCAT
6359598 TTCTCGAATA
Statistics
Matches: 274, Mismatches: 37, Indels: 37
0.79 0.11 0.11
Matches are distributed among these distances:
55 2 0.01
56 38 0.14
57 6 0.02
58 30 0.11
59 27 0.10
60 36 0.13
61 110 0.40
62 19 0.07
63 6 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (60 bp):
AAAAAAATTTTAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCTTATTCTCGAG
Found at i:6359621 original size:41 final size:41
Alignment explanation
Indices: 6359557--6359637 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 41
6359547 ACATCCCCCT
6359557 TTTCTCGAGAAAAAAATTCTAAA-TTTTTTGGTGTTGGCCA
1 TTTCTCGAGAAAAAAATTCTAAATTTTTTTGGTGTTGGCCA
* *
6359597 TTTCTCGAATAAAAAAATTTTAAATTTTTTTGGTGTTGGCC
1 TTTCTCG-AGAAAAAAATTCTAAATTTTTTTGGTGTTGGCC
6359638 GTCAAATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 7 0.19
41 14 0.38
42 16 0.43
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (41 bp):
TTTCTCGAGAAAAAAATTCTAAATTTTTTTGGTGTTGGCCA
Found at i:6363390 original size:12 final size:12
Alignment explanation
Indices: 6363373--6363399 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6363363 CATATTTGTG
6363373 TAAAAATTAATT
1 TAAAAATTAATT
6363385 TAAAAATTAATT
1 TAAAAATTAATT
6363397 TAA
1 TAA
6363400 GCTGAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAAATTAATT
Found at i:6363698 original size:45 final size:45
Alignment explanation
Indices: 6363640--6363781 Score: 128
Period size: 45 Copynumber: 3.4 Consensus size: 45
6363630 ACAAATTATT
6363640 ATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATAC
1 ATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATAC
* * ***
6363685 ATTAT-TTATTAATTTTATATC-TTTAA-AT-AAAATTT-----T--
1 ATTATATTA-TAATTTT-TATCATATAATGTGTTGATTTGACAATAC
6363721 ATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATAC
1 ATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATAC
6363766 ATTAT-TTATTAATTTT
1 ATTATATTA-TAATTTT
6363782 ATATTTTTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
35 4 0.05
36 16 0.22
37 4 0.05
38 5 0.07
43 5 0.07
44 7 0.10
45 28 0.38
46 4 0.05
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.54
Consensus pattern (45 bp):
ATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATAC
Found at i:6363804 original size:30 final size:29
Alignment explanation
Indices: 6363761--6363819 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
6363751 TTGATTTGAC
* * *
6363761 AATACATTATTTATTAATTTTATATTTTTA
1 AATAAATTATTTATT-ATATTATAATTTTA
*
6363791 AATAAATTTTTTATTATATTATAATTTTA
1 AATAAATTATTTATTATATTATAATTTTA
6363820 TCATATAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
AATAAATTATTTATTATATTATAATTTTA
Found at i:6363878 original size:86 final size:83
Alignment explanation
Indices: 6363554--6363997 Score: 557
Period size: 81 Copynumber: 5.3 Consensus size: 83
6363544 AAAAAGATAG
* * * * * * * * *
6363554 TTATTATATTACAATTTATATCAAATATTGTATTAATTTGATAATACGTTATTTATCAAATTTTC
1 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT-TAATTTT-
*
6363619 ATA--TTTAAAGTACAAA-TTA
64 ATATCTTTAAA-TA-AAATTTT
6363638 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
6363703 ATCTTTAAATAAAA--TT
66 ATCTTTAAATAAAATTTT
6363719 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
1 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
*
6363784 ATTTTTAAAT-AAATTTT
66 ATCTTTAAATAAAATTTT
* *
6363801 TTATTATATTATAA-TTTTATCATATAATGTGTTGACTTGACTTGATAATATATTATTTATTAAT
1 TTATTATATTATAATTTTTATCATATAATGTGTTGA--T---TTGACAATACATTATTTATTAAT
6363865 TTTATATCTTTAAATAAAATTTT
61 TTTATATCTTTAAATAAAATTTT
* * *
6363888 TTATTATATTACAACTTTTATTATATAATGTGTTGATTTGACAATACA--A-TTATTAATTTTAT
1 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
6363950 ATCTTTAAATAAAAATTATT
66 ATCTTTAAAT-AAAATT-TT
*
6363970 ATTATTATATTACAATTTTTATCATATA
1 -TTATTATATTATAATTTTTATCATATA
6363998 TTAAATTTAT
Statistics
Matches: 326, Mismatches: 20, Indels: 29
0.87 0.05 0.08
Matches are distributed among these distances:
80 26 0.08
81 103 0.32
82 24 0.07
83 43 0.13
84 54 0.17
86 36 0.11
87 20 0.06
88 20 0.06
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (83 bp):
TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTTAT
ATCTTTAAATAAAATTTT
Found at i:6364175 original size:10 final size:10
Alignment explanation
Indices: 6364157--6364191 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6364147 AATGTCCCTA
6364157 GACCGCCGTT
1 GACCGCCGTT
*
6364167 GACCACCGTT
1 GACCGCCGTT
*
6364177 AACCGCCGTT
1 GACCGCCGTT
6364187 GACCG
1 GACCG
6364192 ACTTTGTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (10 bp):
GACCGCCGTT
Found at i:6366486 original size:30 final size:30
Alignment explanation
Indices: 6366435--6366526 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
6366425 TCCCTTTACT
** *
6366435 TTTTAAATTTAATTTGTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCAAATTTC-TTGTATA
6366465 TTTTAAATTTAATTTCAAATTTCTTGTATA
1 TTTTAAATTTAATTTCAAATTTCTTGTATA
* ** * *
6366495 TTTTAATTTTTCTTTCTAATTTCATGTATA
1 TTTTAAATTTAATTTCAAATTTCTTGTATA
6366525 TT
1 TT
6366527 CTAATTATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 2 0.04
30 51 0.96
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCAAATTTCTTGTATA
Found at i:6367562 original size:58 final size:58
Alignment explanation
Indices: 6367486--6367608 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 58
6367476 AAAAATGCAA
*
6367486 TTTTTTTGAGAAAAA-GGGGTGTC-AGCCATTTGATTGCCAACACCAAAAAAATTTAAAT
1 TTTTTTTGAGAAAAAGGGGGTGTCGA-CCATTTGATGGCCAACACC-AAAAAATTTAAAT
* *
6367544 TTTTTTTCGAG-AAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAATTTTGAAT
1 TTTTTTT-GAGAAAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAATTTAAAT
6367602 TTTTTTT
1 TTTTTTT
6367609 TTGAAACAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
58 29 0.49
59 29 0.49
60 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (58 bp):
TTTTTTTGAGAAAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAATTTAAAT
Found at i:6367609 original size:59 final size:58
Alignment explanation
Indices: 6367486--6367608 Score: 178
Period size: 59 Copynumber: 2.1 Consensus size: 58
6367476 AAAAATGCAA
*
6367486 TTTTTTTGAGAAAAAGGGGTGTCAGCCATTTGATTGCCAACACCAAAAAAATTTAAAT
1 TTTTTTTGAGAAAAAGGGGTGTCAGCCATTTGATGGCCAACACCAAAAAAATTTAAAT
* * *
6367544 TTTTTTTCGAGAAAAGGGGGTGTC-GACCATTTGATGGCCAACACC-AAAAATTTTGAAT
1 TTTTTTT-GAGAAAAAGGGGTGTCAG-CCATTTGATGGCCAACACCAAAAAAATTTAAAT
6367602 TTTTTTT
1 TTTTTTT
6367609 TTGAAACAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 26 0.44
59 33 0.56
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (58 bp):
TTTTTTTGAGAAAAAGGGGTGTCAGCCATTTGATGGCCAACACCAAAAAAATTTAAAT
Found at i:6371327 original size:37 final size:37
Alignment explanation
Indices: 6371267--6371411 Score: 220
Period size: 37 Copynumber: 3.9 Consensus size: 37
6371257 GTTCTTGAGT
*
6371267 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAAAA
1 CACCGGCACGAAGCCTACTAGGCACAAAGCCTGAAAA
*
6371304 -ACCCGACACGAAGCCTACTAGGCACAAAGCCTGAAAA
1 CA-CCGGCACGAAGCCTACTAGGCACAAAGCCTGAAAA
* * *
6371341 CACCGGTACGAAGCTTACTAGGGACAAAGCCTGAAAA
1 CACCGGCACGAAGCCTACTAGGCACAAAGCCTGAAAA
*
6371378 CACCGGCACGAAGCCTATTAGGCACAAAGCCTGA
1 CACCGGCACGAAGCCTACTAGGCACAAAGCCTGA
6371412 TTAATTAAAT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
36 1 0.01
37 94 0.98
38 1 0.01
ACGTcount: A:0.38, C:0.30, G:0.21, T:0.10
Consensus pattern (37 bp):
CACCGGCACGAAGCCTACTAGGCACAAAGCCTGAAAA
Found at i:6371407 original size:16 final size:17
Alignment explanation
Indices: 6371382--6371414 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6371372 TGAAAACACC
*
6371382 GGCACGAAGCCT-ATTA
1 GGCACAAAGCCTGATTA
6371398 GGCACAAAGCCTGATTA
1 GGCACAAAGCCTGATTA
6371415 ATTAAATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.18
Consensus pattern (17 bp):
GGCACAAAGCCTGATTA
Found at i:6372349 original size:23 final size:23
Alignment explanation
Indices: 6372202--6372351 Score: 119
Period size: 23 Copynumber: 6.4 Consensus size: 23
6372192 CGAAGTACTT
6372202 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
6372228 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * *
6372250 ATCCAGTAGGCACACACAGTG-TA
1 A-ACAGTAAGCACACAAAGTGCGA
* * * *
6372273 ATCAGTAGGCGCACATAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
6372295 AATCAGTAGGCACACAAGGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
6372319 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
6372342 AACAGTAAGC
1 AACAGTAAGC
6372352 GCGCTAGCGT
Statistics
Matches: 106, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
22 20 0.19
23 64 0.60
24 3 0.03
26 14 0.13
27 5 0.05
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.13
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:6381289 original size:13 final size:13
Alignment explanation
Indices: 6381271--6381298 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6381261 AATCAAAGAC
6381271 TTCATCTCTTCCA
1 TTCATCTCTTCCA
6381284 TTCATCTCTTCCA
1 TTCATCTCTTCCA
6381297 TT
1 TT
6381299 AAATGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (13 bp):
TTCATCTCTTCCA
Found at i:6382932 original size:15 final size:15
Alignment explanation
Indices: 6382880--6382944 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
6382870 TCAAGTCGAA
*
6382880 AAAAATATCAAAATT
1 AAAAATATAAAAATT
* *
6382895 -AAAATTTCAAAATTT
1 AAAAATAT-AAAAATT
6382910 GGAAAAATATAAAAATT
1 --AAAAATATAAAAATT
*
6382927 AAAAATGTAAAAATT
1 AAAAATATAAAAATT
6382942 AAA
1 AAA
6382945 GTATAAGGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 6 0.15
15 22 0.55
17 6 0.15
18 6 0.15
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATATAAAAATT
Found at i:6386688 original size:18 final size:19
Alignment explanation
Indices: 6386643--6386688 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
6386633 AGTTTGTATG
6386643 AATGAAAAAAGAAAAAGAAA
1 AATGAAAAAAG-AAAAGAAA
*
6386663 AATAAAAAAAG-AAAGAAA
1 AATGAAAAAAGAAAAGAAA
*
6386681 GATGAAAA
1 AATGAAAA
6386689 TAAATAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 13 0.57
20 10 0.43
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (19 bp):
AATGAAAAAAGAAAAGAAA
Found at i:6387323 original size:17 final size:18
Alignment explanation
Indices: 6387288--6387323 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6387278 TATAATATGG
6387288 TCATATTTTTATAACTTA
1 TCATATTTTTATAACTTA
6387306 TCATATTTTTATAA-TTA
1 TCATATTTTTATAACTTA
6387323 T
1 T
6387324 ATTTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATATTTTTATAACTTA
Found at i:6390363 original size:48 final size:48
Alignment explanation
Indices: 6390308--6390405 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
6390298 CTTTTAACGT
6390308 AGTTTTTCTATGTTTTACGTTAAGAAAGATGGAGAAGGAAGAGAAATA
1 AGTTTTTCTATGTTTTACGTTAAGAAAGATGGAGAAGGAAGAGAAATA
6390356 AGTTTTTCTATGTTTTACGTTAAGAAAGATGGAGAAGGAAGAGAAATA
1 AGTTTTTCTATGTTTTACGTTAAGAAAGATGGAGAAGGAAGAGAAATA
6390404 AG
1 AG
6390406 GGAGAAGCAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.31
Consensus pattern (48 bp):
AGTTTTTCTATGTTTTACGTTAAGAAAGATGGAGAAGGAAGAGAAATA
Found at i:6396326 original size:2 final size:2
Alignment explanation
Indices: 6396319--6396344 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6396309 AATGTATTAA
6396319 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
6396345 TTATTTATTT
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:6404319 original size:28 final size:27
Alignment explanation
Indices: 6404267--6404324 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
6404257 TTTGATCAAA
*
6404267 TATATAATGTTATACGTAAAATTTAATT
1 TATATAATGTTATACATAAAATTT-ATT
* * *
6404295 TATATAATTTTATACATATATTTTATT
1 TATATAATGTTATACATAAAATTTATT
6404322 TAT
1 TAT
6404325 CTAGTGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (27 bp):
TATATAATGTTATACATAAAATTTATT
Found at i:6418597 original size:7 final size:7
Alignment explanation
Indices: 6418574--6418671 Score: 78
Period size: 7 Copynumber: 14.6 Consensus size: 7
6418564 GAAAAAAAGA
6418574 GTCAACG
1 GTCAACG
*
6418581 GTCAA-A
1 GTCAACG
6418587 GTCAACG
1 GTCAACG
*
6418594 GTCAA-A
1 GTCAACG
*
6418600 ATCAACG
1 GTCAACG
6418607 GTCAACG
1 GTCAACG
*
6418614 GTCAA-A
1 GTCAACG
6418620 GTCAACG
1 GTCAACG
***
6418627 GTCAGTT
1 GTCAACG
6418634 GTCAACG
1 GTCAACG
6418641 GTCAACG
1 GTCAACG
* *
6418648 ATCAACA
1 GTCAACG
*
6418655 GTCAA-A
1 GTCAACG
6418661 GTCAACG
1 GTCAACG
6418668 GTCA
1 GTCA
6418672 GTCAACGGTT
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
6 20 0.29
7 49 0.71
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:6418610 original size:20 final size:20
Alignment explanation
Indices: 6418587--6418671 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
6418577 AACGGTCAAA
*
6418587 GTCAACGGTCAAAATCAACG
1 GTCAACGGTCAAAGTCAACG
6418607 GTCAACGGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
*** *
6418627 GTCAGTTGTCAACGGTCAACG
1 GTCAACGGTCAA-AGTCAACG
* *
6418648 ATCAACAGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
6418668 GTCA
1 GTCA
6418672 GTCAACGGTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 38 0.72
21 15 0.28
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
GTCAACGGTCAAAGTCAACG
Found at i:6418637 original size:14 final size:13
Alignment explanation
Indices: 6418573--6418680 Score: 97
Period size: 13 Copynumber: 8.8 Consensus size: 13
6418563 CGAAAAAAAG
6418573 AGTCAACGGTCAA
1 AGTCAACGGTCAA
6418586 AGTCAACGGTCAA
1 AGTCAACGGTCAA
*
6418599 AATCAAC-G----
1 AGTCAACGGTCAA
6418607 -GTCAACGGTCAA
1 AGTCAACGGTCAA
*
6418619 AGTCAACGGTCAGT
1 AGTCAACGGTCA-A
*
6418633 TGTCAACGGTCAA
1 AGTCAACGGTCAA
* *
6418646 CGATCAACAGTCAA
1 AG-TCAACGGTCAA
6418660 AGTCAACGGTC--
1 AGTCAACGGTCAA
6418671 AGTCAACGGT
1 AGTCAACGGT
6418681 TGGTCAACGC
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
11 10 0.13
12 1 0.01
13 39 0.50
14 22 0.28
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (13 bp):
AGTCAACGGTCAA
Found at i:6418637 original size:27 final size:26
Alignment explanation
Indices: 6418573--6418680 Score: 97
Period size: 27 Copynumber: 4.4 Consensus size: 26
6418563 CGAAAAAAAG
6418573 AGTCAACGGTCAAAGTCAACGGTCAA
1 AGTCAACGGTCAAAGTCAACGGTCAA
*
6418599 AATCAAC-G-----GTCAACGGTCAA
1 AGTCAACGGTCAAAGTCAACGGTCAA
**
6418619 AGTCAACGGTCAGTTGTCAACGGTCAA
1 AGTCAACGGTCA-AAGTCAACGGTCAA
* *
6418646 CGATCAACAGTCAAAGTCAACGGTC--
1 AG-TCAACGGTCAAAGTCAACGGTCAA
6418671 AGTCAACGGT
1 AGTCAACGGT
6418681 TGGTCAACGC
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
20 18 0.27
21 1 0.02
24 7 0.11
25 2 0.03
26 6 0.09
27 23 0.35
28 9 0.14
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (26 bp):
AGTCAACGGTCAAAGTCAACGGTCAA
Found at i:6418752 original size:14 final size:15
Alignment explanation
Indices: 6418733--6418767 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6418723 TGGGTTGGAC
*
6418733 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
6418747 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
6418762 TTGGTT
1 TTGGTT
6418768 AGGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:6418765 original size:20 final size:20
Alignment explanation
Indices: 6418742--6418788 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
6418732 CTTGGTTCAA
6418742 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
* *
6418762 TTGGTTAGGTTTAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
6418782 TTGGTTT
1 TTGGTTT
6418789 AAATGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.02, G:0.34, T:0.49
Consensus pattern (20 bp):
TTGGTTTGGTTCAAATGGGT
Found at i:6418782 original size:15 final size:15
Alignment explanation
Indices: 6418764--6418793 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6418754 AAATGGGTTT
6418764 GGTTAGGTTTAAATG
1 GGTTAGGTTTAAATG
*
6418779 GGTTTGGTTTAAATG
1 GGTTAGGTTTAAATG
6418794 AATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTAGGTTTAAATG
Found at i:6425677 original size:13 final size:13
Alignment explanation
Indices: 6425659--6425766 Score: 88
Period size: 13 Copynumber: 8.8 Consensus size: 13
6425649 CGAAAAAAAG
6425659 AGTCAACGGTCAA
1 AGTCAACGGTCAA
6425672 AGTCAACGGTCAA
1 AGTCAACGGTCAA
*
6425685 AATCAAC-G----
1 AGTCAACGGTCAA
6425693 -GTCAACGGTCAA
1 AGTCAACGGTCAA
*
6425705 AGTCAACGGTCAGT
1 AGTCAACGGTCA-A
* *
6425719 TGTCAATGGTCAA
1 AGTCAACGGTCAA
* *
6425732 CGATCAACAGTCAA
1 AG-TCAACGGTCAA
6425746 AGTCAACGGTC-A
1 AGTCAACGGTCAA
6425758 A-TCAACGGT
1 AGTCAACGGT
6425767 TGGTCAACGC
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
7 5 0.07
8 1 0.01
11 8 0.11
12 3 0.04
13 39 0.51
14 20 0.26
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (13 bp):
AGTCAACGGTCAA
Found at i:6425683 original size:7 final size:7
Alignment explanation
Indices: 6425660--6425758 Score: 71
Period size: 7 Copynumber: 14.7 Consensus size: 7
6425650 GAAAAAAAGA
6425660 GTCAACG
1 GTCAACG
*
6425667 GTCAA-A
1 GTCAACG
6425673 GTCAACG
1 GTCAACG
*
6425680 GTCAA-A
1 GTCAACG
*
6425686 ATCAACG
1 GTCAACG
6425693 GTCAACG
1 GTCAACG
*
6425700 GTCAA-A
1 GTCAACG
6425706 GTCAACG
1 GTCAACG
***
6425713 GTCAGTT
1 GTCAACG
*
6425720 GTCAATG
1 GTCAACG
6425727 GTCAACG
1 GTCAACG
* *
6425734 ATCAACA
1 GTCAACG
*
6425741 GTCAA-A
1 GTCAACG
6425747 GTCAACG
1 GTCAACG
6425754 GTCAA
1 GTCAA
6425759 TCAACGGTTG
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
6 20 0.29
7 50 0.71
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:6425696 original size:20 final size:20
Alignment explanation
Indices: 6425673--6425758 Score: 100
Period size: 20 Copynumber: 4.2 Consensus size: 20
6425663 AACGGTCAAA
*
6425673 GTCAACGGTCAAAATCAACG
1 GTCAACGGTCAAAGTCAACG
6425693 GTCAACGGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
*** *
6425713 GTCAGTTGTCAATGGTCAACG
1 GTCAACGGTCAA-AGTCAACG
* *
6425734 ATCAACAGTCAAAGTCAACG
1 GTCAACGGTCAAAGTCAACG
6425754 GTCAA
1 GTCAA
6425759 TCAACGGTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (20 bp):
GTCAACGGTCAAAGTCAACG
Found at i:6425723 original size:27 final size:26
Alignment explanation
Indices: 6425659--6425766 Score: 88
Period size: 27 Copynumber: 4.4 Consensus size: 26
6425649 CGAAAAAAAG
6425659 AGTCAACGGTCAAAGTCAACGGTCAA
1 AGTCAACGGTCAAAGTCAACGGTCAA
*
6425685 AATCAAC-G-----GTCAACGGTCAA
1 AGTCAACGGTCAAAGTCAACGGTCAA
** *
6425705 AGTCAACGGTCAGTTGTCAATGGTCAA
1 AGTCAACGGTCA-AAGTCAACGGTCAA
* *
6425732 CGATCAACAGTCAAAGTCAACGGTC-A
1 AG-TCAACGGTCAAAGTCAACGGTCAA
6425758 A-TCAACGGT
1 AGTCAACGGT
6425767 TGGTCAACGC
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
20 18 0.28
21 1 0.02
24 7 0.11
25 1 0.02
26 7 0.11
27 21 0.33
28 9 0.14
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (26 bp):
AGTCAACGGTCAAAGTCAACGGTCAA
Found at i:6425838 original size:14 final size:15
Alignment explanation
Indices: 6425819--6425853 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6425809 TGGGTGGGAC
*
6425819 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
6425833 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
6425848 TTGGTT
1 TTGGTT
6425854 AGGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:6425853 original size:20 final size:20
Alignment explanation
Indices: 6425828--6425874 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
6425818 CTTGGTTCAA
6425828 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
* *
6425848 TTGGTTAGGTTTAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
6425868 TTGGTTT
1 TTGGTTT
6425875 AAATGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.02, G:0.34, T:0.49
Consensus pattern (20 bp):
TTGGTTTGGTTCAAATGGGT
Found at i:6425868 original size:15 final size:15
Alignment explanation
Indices: 6425850--6425879 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6425840 AAATGGGTTT
6425850 GGTTAGGTTTAAATG
1 GGTTAGGTTTAAATG
*
6425865 GGTTTGGTTTAAATG
1 GGTTAGGTTTAAATG
6425880 AATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTAGGTTTAAATG
Found at i:6431828 original size:15 final size:16
Alignment explanation
Indices: 6431808--6431841 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
6431798 ATTTTTTTAA
6431808 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
6431823 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
6431839 AAA
1 AAA
6431842 ATTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:6432533 original size:31 final size:31
Alignment explanation
Indices: 6432495--6432624 Score: 132
Period size: 28 Copynumber: 4.4 Consensus size: 31
6432485 TTAATATAAC
* *
6432495 ATTTGGTACTTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
6432526 ATTTGGTACCTAAACTTGACAC---TTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* *
6432554 ATTTGGTACCTAAACTT----TTTTTTACCCA
1 ATTTGGTACCTAAACTTGACACTTTTT-CCTA
* * *
6432582 ATTTGGTACTTGAACTTGGCA-TTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
6432612 ATTTGGTACCTAA
1 ATTTGGTACCTAA
6432625 GATTTTTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
27 2 0.02
28 41 0.50
30 14 0.17
31 25 0.30
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:6432889 original size:57 final size:60
Alignment explanation
Indices: 6432809--6432954 Score: 169
Period size: 58 Copynumber: 2.5 Consensus size: 60
6432799 AAATTAGGTT
* * * * *
6432809 CCAAATT-AGAAAAAGGGTTAAGTTCAAGTACCAAATTGGATCC-CAAA-AAATTTAAGA-A
1 CCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAATTGGA-CCAAAAACAAATTTAA-ATA
* *
6432867 CCAACTT-AAAAAAA-TGTCAAGTTTGAGTACCAAATTGGACCAAAAACAAATTTAAATA
1 CCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAATTGGACCAAAAACAAATTTAAATA
6432925 CCAAATTAAAAAAAAGTGTCAAGTTTAAGT
1 CCAAATTAAAAAAAAGTGTCAAGTTTAAGT
6432955 GTCAAATGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
56 2 0.03
57 25 0.34
58 27 0.36
59 7 0.09
60 13 0.18
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (60 bp):
CCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAATTGGACCAAAAACAAATTTAAATA
Found at i:6433830 original size:22 final size:22
Alignment explanation
Indices: 6433779--6433836 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
6433769 AATTGAATAG
6433779 TTAATAA-ATTTATATTTTGAA
1 TTAATAACATTTATATTTTGAA
*
6433800 TAAATTAACATTTA-ATTTTGAA
1 TTAA-TAACATTTATATTTTGAA
*
6433822 TTTAATAACTTTTAT
1 -TTAATAACATTTAT
6433837 CAATTTAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 3 0.10
22 19 0.63
23 8 0.27
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
TTAATAACATTTATATTTTGAA
Found at i:6436061 original size:21 final size:21
Alignment explanation
Indices: 6436037--6436076 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6436027 ATTCATACTT
*
6436037 TATTTTTTGAAATTATAAAAA
1 TATTTTTTAAAATTATAAAAA
6436058 TATTTTTTAAAATTATAAA
1 TATTTTTTAAAATTATAAA
6436077 TATACGAAAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TATTTTTTAAAATTATAAAAA
Found at i:6437650 original size:23 final size:23
Alignment explanation
Indices: 6437624--6437691 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
6437614 TTTTTTATAC
6437624 AAGATGAGCTTTAAGATGAACCA
1 AAGATGAGCTTTAAGATGAACCA
* *
6437647 AAGATCCATC-TT--GA--AA-C-
1 AAGAT-GAGCTTTAAGATGAACCA
6437664 AAGATGAGCTTTAAGATGAACCA
1 AAGATGAGCTTTAAGATGAACCA
6437687 AAGAT
1 AAGAT
6437692 CCATCAGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 16
0.62 0.08 0.30
Matches are distributed among these distances:
16 2 0.06
17 7 0.21
18 1 0.03
19 4 0.12
21 4 0.12
22 1 0.03
23 12 0.36
24 2 0.06
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (23 bp):
AAGATGAGCTTTAAGATGAACCA
Found at i:6445714 original size:6 final size:6
Alignment explanation
Indices: 6445694--6445752 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
6445684 TAAAAGGGGT
* * *
6445694 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTCA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
6445742 TTTAAG TTTAA
1 TTTAAA TTTAA
6445753 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:6445729 original size:14 final size:14
Alignment explanation
Indices: 6445710--6445736 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6445700 TTTATTTTAA
6445710 ATTTAAATTTACTC
1 ATTTAAATTTACTC
6445724 ATTTAAATTTACT
1 ATTTAAATTTACT
6445737 TTAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATTTACTC
Found at i:6445808 original size:14 final size:14
Alignment explanation
Indices: 6445789--6445833 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
6445779 AATTAAAACT
6445789 AAAGTCCATTTACA
1 AAAGTCCATTTACA
*
6445803 AAAGTCCAATTACA
1 AAAGTCCATTTACA
* *
6445817 AATGTTCATTTACA
1 AAAGTCCATTTACA
6445831 AAA
1 AAA
6445834 AAGAAAGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAGTCCATTTACA
Found at i:6446226 original size:24 final size:23
Alignment explanation
Indices: 6446180--6446227 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
6446170 GTAAGGGGTT
* *
6446180 ACAAAAAAAAACCCTGTTCTGAA
1 ACAAAAAAAAACCCAGTGCTGAA
*
6446203 ACAAAAGAAAACCCAGTGCTTGAA
1 ACAAAAAAAAACCCAGTGC-TGAA
6446227 A
1 A
6446228 TCTGGTTACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.52, C:0.21, G:0.12, T:0.15
Consensus pattern (23 bp):
ACAAAAAAAAACCCAGTGCTGAA
Found at i:6446610 original size:19 final size:18
Alignment explanation
Indices: 6446586--6446621 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6446576 TAGTAATAAT
*
6446586 AATAATAAATATATTTTTA
1 AATAAT-AATAAATTTTTA
6446605 AATAATAATAAATTTTT
1 AATAATAATAAATTTTT
6446622 GGCCTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAATAATAAATTTTTA
Found at i:6446993 original size:17 final size:17
Alignment explanation
Indices: 6446967--6447001 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6446957 AAGTTTCGAA
6446967 TCTTTGCCAGATCTGGG
1 TCTTTGCCAGATCTGGG
*
6446984 TCTTTTCCAGATCTGGG
1 TCTTTGCCAGATCTGGG
6447001 T
1 T
6447002 TTGGTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (17 bp):
TCTTTGCCAGATCTGGG
Found at i:6447681 original size:9 final size:10
Alignment explanation
Indices: 6447657--6447682 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6447647 TGACCTAAGA
6447657 ATTTTTCGAG
1 ATTTTTCGAG
6447667 ATTTTTCGAG
1 ATTTTTCGAG
6447677 ATTTTT
1 ATTTTT
6447683 AAATTAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (10 bp):
ATTTTTCGAG
Found at i:6447715 original size:75 final size:75
Alignment explanation
Indices: 6447604--6447787 Score: 359
Period size: 75 Copynumber: 2.5 Consensus size: 75
6447594 TTTTAATTTG
*
6447604 TTTTAATTTAATCCTCAAATCAACTTTTGCTTAATTACAAGATTGACCTAAGAATTTTTCGAGAT
1 TTTTAAATTAATCCTCAAATCAACTTTTGCTTAATTACAAGATTGACCTAAGAATTTTTCGAGAT
6447669 TTTTCGAGAT
66 TTTTCGAGAT
6447679 TTTTAAATTAATCCTCAAATCAACTTTTGCTTAATTACAAGATTGACCTAAGAATTTTTCGAGAT
1 TTTTAAATTAATCCTCAAATCAACTTTTGCTTAATTACAAGATTGACCTAAGAATTTTTCGAGAT
6447744 TTTTCGAGAT
66 TTTTCGAGAT
6447754 TTTTAAATTAATCCTCAAATCAACTTTTGCTTAA
1 TTTTAAATTAATCCTCAAATCAACTTTTGCTTAA
6447788 GTCCTTTTTA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 108 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (75 bp):
TTTTAAATTAATCCTCAAATCAACTTTTGCTTAATTACAAGATTGACCTAAGAATTTTTCGAGAT
TTTTCGAGAT
Found at i:6447756 original size:9 final size:10
Alignment explanation
Indices: 6447732--6447757 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6447722 TGACCTAAGA
6447732 ATTTTTCGAG
1 ATTTTTCGAG
6447742 ATTTTTCGAG
1 ATTTTTCGAG
6447752 ATTTTT
1 ATTTTT
6447758 AAATTAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (10 bp):
ATTTTTCGAG
Found at i:6448045 original size:118 final size:117
Alignment explanation
Indices: 6447837--6448206 Score: 530
Period size: 118 Copynumber: 3.1 Consensus size: 117
6447827 CTTTGACTAT
* *
6447837 CAAAAATTACTATTTTA-CTCCTAAA-TTTCCCAAAATTCCATTTTTAACCCCGGTTTCACCAAA
1 CAAAAATTACCATTTTATC-CCTAAACTTT-CCAAAATTCCATTTTTAACCCCGATTTCACCAAA
* * * *
6447900 AATTACTATTTTACACCTAAACTTTCTAAAATTCGATTTTTGACATCGATTTCAC
64 AATTAC-ATTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCTCGATTTCAC
* *
6447955 CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCTATTTTTAACTCCGATTTCACCAAAAA
1 CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
* * *
6448020 TTATCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTGCCCTCGATTTTAC
66 TTA-CATTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCTCGATTTCAC
6448073 CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCAAAAA
1 CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
* * *
6448137 TTACCTTTTTATCCCCCAAACTTCCCAAAATTCCATTTTTGACCTCGATTTCAC
66 TTA-CATTTTA-CCCCCAAACTTTCTAAAATTCCATTTTTGACCTCGATTTCAC
*
6448191 CAAAAATTATCATTTT
1 CAAAAATTACCATTTT
6448207 GCCCCCAGGT
Statistics
Matches: 227, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
117 32 0.14
118 190 0.84
119 5 0.02
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (117 bp):
CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
TTACATTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCTCGATTTCAC
Found at i:6448057 original size:28 final size:28
Alignment explanation
Indices: 6448014--6448175 Score: 87
Period size: 29 Copynumber: 5.5 Consensus size: 28
6448004 CCGATTTCAC
*
6448014 CAAAAATTATCATTTTACCCCCGAACTTT
1 CAAAAATT-CCATTTTACCCCCGAACTTT
* * * *
6448043 CTAAAATTCCATTTTTGCCCTCG-ATTTT
1 CAAAAATTCCA-TTTTACCCCCGAACTTT
* **
6448071 ACCAAAAATTACCATTTTATCCCTAAACTTT
1 --CAAAAATT-CCATTTTACCCCCGAACTTT
* *
6448102 CCAAAATTCCATTTTAACCCCG-A-TTT
1 CAAAAATTCCATTTTACCCCCGAACTTT
* * *
6448128 CACCAAAAATTACCTTTTTATCCCCCAAACTTC
1 ---CAAAAATT-CCATTTTA-CCCCCGAACTTT
*
6448161 CCAAAATTCCATTTT
1 CAAAAATTCCATTTT
6448176 TGACCTCGAT
Statistics
Matches: 98, Mismatches: 23, Indels: 24
0.68 0.16 0.17
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 17 0.17
29 36 0.37
30 27 0.28
31 11 0.11
32 1 0.01
33 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.36
Consensus pattern (28 bp):
CAAAAATTCCATTTTACCCCCGAACTTT
Found at i:6448197 original size:30 final size:29
Alignment explanation
Indices: 6447927--6448198 Score: 111
Period size: 30 Copynumber: 9.2 Consensus size: 29
6447917 TAAACTTTCT
* *
6447927 AAAATTCGATTTTTGACATCGATTTCACCA
1 AAAATTCCATTTTT-ACCTCGATTTCACCA
* **
6447957 AAAATTACCATTTTATCCCTAAACTTT--CC-
1 AAAATT-CCATTTT-TACCTCGA-TTTCACCA
* *
6447986 AAAATTCTATTTTTAACTCCGATTTCACCA
1 AAAATTCCATTTTTACCT-CGATTTCACCA
* * *
6448016 AAAATTATCA-TTTTACCCCCGAACTTT---CT
1 AAAATT-CCATTTTTA-CCTCG-A-TTTCACCA
* *
6448045 AAAATTCCATTTTTGCCCTCGATTTTACCA
1 AAAATTCCATTTTT-ACCTCGATTTCACCA
* **
6448075 AAAATTACCATTTTATCCCTAAACTTT--CC-
1 AAAATT-CCATTTT-TACCTCGA-TTTCACCA
* *
6448104 AAAATTCCATTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTACCTCGATTTCACCA
* * *
6448133 AAAATTACC-TTTTTATCCCCCAAACTTC-CC-
1 AAAATT-CCATTTTTA--CCTC-GATTTCACCA
6448163 AAAATTCCATTTTTGACCTCGATTTCACCA
1 AAAATTCCATTTTT-ACCTCGATTTCACCA
6448193 AAAATT
1 AAAATT
6448199 ATCATTTTGC
Statistics
Matches: 180, Mismatches: 32, Indels: 60
0.66 0.12 0.22
Matches are distributed among these distances:
26 3 0.02
27 12 0.07
28 23 0.13
29 47 0.26
30 49 0.27
31 31 0.17
32 15 0.08
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAATTCCATTTTTACCTCGATTTCACCA
Found at i:6448213 original size:59 final size:59
Alignment explanation
Indices: 6447837--6448211 Score: 459
Period size: 59 Copynumber: 6.4 Consensus size: 59
6447827 CTTTGACTAT
* * * * *
6447837 CAAAAATTACTATTTTACTCCTAAA-TTTCCCAAAATTCCATTTTTAACCCCGGTTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTT-CCAAAATTCCATTTTTGACCTCGATTTCAC
* * * * *
6447896 CAAAAATTACTATTTTACACCTAAACTTTCTAAAATTCGATTTTTGACATCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
* * *
6447955 CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCTATTTTT-AACTCCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCT-CGATTTCAC
* ** * * *
6448014 CAAAAATTATCATTTTACCCCCGAACTTTCTAAAATTCCATTTTTGCCCTCGATTTTAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
* * *
6448073 CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
* * *
6448131 CAAAAATTACCTTTTTATCCCCCAAACTTCCCAAAATTCCATTTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTA-CCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
* *
6448191 CAAAAATTATCATTTTGCCCC
1 CAAAAATTACCATTTTACCCC
6448212 CAGGTACCCA
Statistics
Matches: 270, Mismatches: 41, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
58 32 0.12
59 203 0.75
60 35 0.13
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
Found at i:6460286 original size:92 final size:92
Alignment explanation
Indices: 6460167--6460798 Score: 1015
Period size: 92 Copynumber: 6.9 Consensus size: 92
6460157 ATCACGTCAA
*
6460167 ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTTA
1 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTTA
6460232 GAAATTGAAGTAAGAGTAAAATGAAGC
66 GAAATTGAAGTAAGAGTAAAATGAAGC
* *
6460259 ACCAACATCATTTTCCTATCCTTTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
1 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTTA
*
6460324 GAAATTGAAGTAAGAGTAAAACGAAGC
66 GAAATTGAAGTAAGAGTAAAATGAAGC
*
6460351 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGATAACAAGCCTTCGTCCCTCT
1 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCT-T
* *
6460416 -GAAATTGAAGTAAGAGTGAGAA-GAAGG
65 AGAAATTGAAGTAAGAGT-AAAATGAAGC
* * *
6460443 ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTAGATAACAAGCCTTCGTCCCTCA
1 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTTA
6460508 GAAATTGAAGTAAGAGTAAAATGAAGC
66 GAAATTGAAGTAAGAGTAAAATGAAGC
*
6460535 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
1 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTTA
6460600 GAAATTGAAGTAAGAGTAAAATGAAGC
66 GAAATTGAAGTAAGAGTAAAATGAAGC
*
6460627 ACCAACATCATTTTCCTATCCTCTTGAAATTGAATTAAAG-TGGATAACAAGCCTTCGTCCCTCT
1 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCT-T
** * *
6460691 -GAAATCAAAATAAGAGTAAGAA-GAAGG
65 AGAAATTGAAGTAAGAGTAA-AATGAAGC
*
6460718 ACCAACATCATTCTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
1 ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCT-T
*
6460783 -GAAATTGAAGTGAGAG
65 AGAAATTGAAGTAAGAG
6460799 GGATTGGAAT
Statistics
Matches: 504, Mismatches: 29, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
91 83 0.16
92 418 0.83
93 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (92 bp):
ACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTTA
GAAATTGAAGTAAGAGTAAAATGAAGC
Found at i:6460660 original size:276 final size:275
Alignment explanation
Indices: 6460167--6460798 Score: 1129
Period size: 276 Copynumber: 2.3 Consensus size: 275
6460157 ATCACGTCAA
*
6460167 ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTTA
1 ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
*
6460232 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTTCCTATCCTTTTGAAATTGAAGTAA
66 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAA
6460297 AGCTGGATAACAAGCCTTCGTCCCTCAGAAATTGAAGTAAGAGTAAAACGAAGCACCAACATCAT
131 AGCTGGATAACAAGCCTTCGTCCCTCAGAAATTGAAGTAAGAGTAAAACGAAGCACCAACATCAT
* ** *
6460362 TTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGATAACAAGCCTTCGTCCCTCTGAAATTGAAGT
196 TTTCCTATCCTCTTGAAATTGAAGTAAAG-TGGATAACAAGCCTTCGTCCCTCTGAAATCAAAAT
*
6460427 AAGAGTGAGAAGAAGG
260 AAGAGTAAGAAGAAGG
*
6460443 ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTAGATAACAAGCCTTCGTCCCTCA
1 ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
6460508 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAA
66 GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAA
*
6460573 AGCTGGATAACAAGCCTTCGTCCCTCAGAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCAT
131 AGCTGGATAACAAGCCTTCGTCCCTCAGAAATTGAAGTAAGAGTAAAACGAAGCACCAACATCAT
*
6460638 TTTCCTATCCTCTTGAAATTGAATTAAAGTGGATAACAAGCCTTCGTCCCTCTGAAATCAAAATA
196 TTTCCTATCCTCTTGAAATTGAAGTAAAGTGGATAACAAGCCTTCGTCCCTCTGAAATCAAAATA
6460703 AGAGTAAGAAGAAGG
261 AGAGTAAGAAGAAGG
* * *
6460718 ACCAACATCATTCTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCT
1 ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
*
6460783 GAAATTGAAGTGAGAG
66 GAAATTGAAGTAAGAG
6460799 GGATTGGAAT
Statistics
Matches: 341, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
275 123 0.36
276 218 0.64
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (275 bp):
ACCAACATTATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTCA
GAAATTGAAGTAAGAGTAAAATGAAGCACCAACATCATTTTCCTATCCTCTTGAAATTGAAGTAA
AGCTGGATAACAAGCCTTCGTCCCTCAGAAATTGAAGTAAGAGTAAAACGAAGCACCAACATCAT
TTTCCTATCCTCTTGAAATTGAAGTAAAGTGGATAACAAGCCTTCGTCCCTCTGAAATCAAAATA
AGAGTAAGAAGAAGG
Found at i:6461026 original size:6 final size:6
Alignment explanation
Indices: 6461006--6461064 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
6460996 TAAAAGGGGT
* * *
6461006 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTCA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
6461054 TTTAAG TTTAA
1 TTTAAA TTTAA
6461065 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Done.