Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012045.1 Kokia drynarioides strain JFW-HI SEQ_127043, whole genome shotgun sequence
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: 46137
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:570 original size:6 final size:6
Alignment explanation
Indices: 559--637 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
549 AATTGGACAT
559 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* **
605 TTTTAAA --TAAA CTT-AA TTTAAA AATAAA TTTAA
1 -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
638 TTTCTAGTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
4 9 0.16
5 7 0.12
6 31 0.53
7 11 0.19
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:640 original size:17 final size:17
Alignment explanation
Indices: 561--637 Score: 102
Period size: 17 Copynumber: 4.5 Consensus size: 17
551 TTGGACATTT
*
561 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
578 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
595 TAAATTTAAATTTTAAA
1 TAAATTTAAATTTAAAA
*
612 TAAACTT-AATTTAAAAA
1 TAAATTTAAATTT-AAAA
629 TAAATTTAA
1 TAAATTTAA
638 TTTCTAGTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
16 5 0.10
17 46 0.88
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1254 original size:159 final size:158
Alignment explanation
Indices: 1014--1302 Score: 463
Period size: 159 Copynumber: 1.8 Consensus size: 158
1004 ATTTATCGCG
* *
1014 CGTGGGTTTGATTGGTCATCTTATCAGTATTTCATCAGGAAGATGACCGCGTCGTGTTTTTCAAT
1 CGTGGGTTTGATTGGTCATCTTATCAGTATCTCATCAGGAAGATGACCACGTCGTGTTTTTCAAT
* * * *
1079 ATGCTTTTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCT
66 ACGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAGCT
1144 GGGGTTCGAAGATTTTGCTCACTTTGAA
131 GGGGTTCGAAGATTTTGCTCACTTTGAA
* * *
1172 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCACGTCGT-TTGTTTCA
1 CGTGGGTTTGA-TTGGTCATCTTATCAGTATCTCATCAGGAAGATGACCACGTCGTGTT-TTTCA
*
1236 ATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAG
64 ATACGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAG
1301 CT
129 CT
1303 ATTTGTTTTA
Statistics
Matches: 119, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
158 13 0.11
159 106 0.89
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (158 bp):
CGTGGGTTTGATTGGTCATCTTATCAGTATCTCATCAGGAAGATGACCACGTCGTGTTTTTCAAT
ACGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAGCT
GGGGTTCGAAGATTTTGCTCACTTTGAA
Found at i:1477 original size:207 final size:207
Alignment explanation
Indices: 1122--1645 Score: 931
Period size: 207 Copynumber: 2.5 Consensus size: 207
1112 TGGTTCACTC
*
1122 CTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAACGTGGGTTTGATTTG
1 CTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAACGTGGGTTTGATTTG
1187 GTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCACGTCGTTTGTTTCAATCCGCTTCTCTGTAT
66 GTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCACGTCGTTTGTTTCAATCCGCTTCTCTGTAT
**
1252 CTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAGCTATTTGTTTTATTAC
131 CTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAGCTATCCGTTTTATTAC
*
1317 TTCGACCTGCTT
196 TTCGACCTACTT
* *
1329 CTCAGTATCTCACCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAACGTGGGTTAGATTTG
1 CTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAACGTGGGTTTGATTTG
1394 GTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCACGTCGTTTGTTTCAATCCGCTTCTCTGTAT
66 GTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCACGTCGTTTGTTTCAATCCGCTTCTCTGTAT
*
1459 CTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAAGAAGCTATCCGTTTTATTAC
131 CTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAGCTATCCGTTTTATTAC
*
1524 TTTGACCTACTT
196 TTCGACCTACTT
* *
1536 CTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTTGCTTTGAGCGTGGGTTTGATTTG
1 CTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAACGTGGGTTTGATTTG
* * *
1601 GTCTTCTTCTCAGTATCTTATCAGGAAGCTAACCGCGTCGTTTGT
66 GTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCACGTCGTTTGT
1646 GGGTATCGCA
Statistics
Matches: 302, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
207 302 1.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (207 bp):
CTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGCTTTGAACGTGGGTTTGATTTG
GTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCACGTCGTTTGTTTCAATCCGCTTCTCTGTAT
CTCATCAGGAAGACGAATTTGGTTCACTCCTCAATATCTCATCAAGAAGCTATCCGTTTTATTAC
TTCGACCTACTT
Found at i:2145 original size:29 final size:29
Alignment explanation
Indices: 2104--2160 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2094 GTCGTTTTCC
*
2104 AAAAAAAAGGATCAAAGGAAACGATCATA
1 AAAAAAAAGGATCAAAGGAAACAATCATA
2133 AAAAAAAAGGATCAAAGGAAACAATCAT
1 AAAAAAAAGGATCAAAGGAAACAATCAT
2161 TAGTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.11
Consensus pattern (29 bp):
AAAAAAAAGGATCAAAGGAAACAATCATA
Found at i:13461 original size:30 final size:29
Alignment explanation
Indices: 13380--13767 Score: 345
Period size: 30 Copynumber: 13.2 Consensus size: 29
13370 AGACATTCGG
* *
13380 GGGTAAAAA-GGTAATTTTTGGAAGTTCGA
1 GGGTAAAAATGG-GATTTTTGGAAGTTTGA
* *
13409 -GGTAAAAA-GGGAATTTTGGGAAGTTTTA
1 GGGTAAAAATGGG-ATTTTTGGAAGTTTGA
* * *
13437 GGGTCAAAATTGGGATTTTTGGAAGTTCGG
1 GGGT-AAAAATGGGATTTTTGGAAGTTTGA
* *
13467 GGGT-AAAATGGAATTTTTGGAAGTTTCA
1 GGGTAAAAATGGGATTTTTGGAAGTTTGA
*
13495 GGGTCAAAAATGGGATTTTTTGGAAGTTTGG
1 GGGT-AAAAATGGGA-TTTTTGGAAGTTTGA
**** * *
13526 GGGTAAAAACAAAATTTTGGGAAGTTTTA
1 GGGTAAAAATGGGATTTTTGGAAGTTTGA
* *
13555 GGGTCAAAAATGGGATTTTTGGATGTTTGG
1 GGGT-AAAAATGGGATTTTTGGAAGTTTGA
* * *
13585 GGGTAAAATTGGAATTTTTGGAAGTTTTA
1 GGGTAAAAATGGGATTTTTGGAAGTTTGA
* * *
13614 AGGTCAAAAATGGGATTTTTGGAAGTTCGG
1 GGGT-AAAAATGGGATTTTTGGAAGTTTGA
* * * *
13644 GGGTAAAAATGGAATTTTGGGAAATTTTA
1 GGGTAAAAATGGGATTTTTGGAAGTTTGA
*
13673 GGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 GGG-TAAAAATGGGATTTTTGGAAGTTTGA
* *
13703 GGGTAAAAATGGAATTTTTTGATAGTTT-A
1 GGGTAAAAATGGGATTTTTGGA-AGTTTGA
* *
13732 GGGGTCAAAATTGGGATTTTTGGAAGTTCGA
1 -GGGT-AAAAATGGGATTTTTGGAAGTTTGA
13763 GGGTA
1 GGGTA
13768 GAAACATAAT
Statistics
Matches: 283, Mismatches: 62, Indels: 28
0.76 0.17 0.08
Matches are distributed among these distances:
28 46 0.16
29 83 0.29
30 118 0.42
31 36 0.13
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGGGATTTTTGGAAGTTTGA
Found at i:13515 original size:59 final size:59
Alignment explanation
Indices: 13393--13790 Score: 518
Period size: 59 Copynumber: 6.7 Consensus size: 59
13383 TAAAAAGGTA
* * * *
13393 ATTTTTGGAAGTTC-GAGGTAAAAAGGGAATTTTGGGAAGTTTTAGGGTCAAAATTGGG
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGG
*
13451 ATTTTTGGAAGTTCGGGGGT-AAAATGGAATTTTTGGAAGTTTCAGGGTCAAAAATGGG
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGG
* *** *
13509 ATTTTTTGGAAGTTTGGGGGTAAAAACAAAATTTTGGGAAGTTTTAGGGTCAAAAATGGG
1 A-TTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGG
* * * *
13569 ATTTTTGGATGTTTGGGGGTAAAATTGGAATTTTTGGAAGTTTTAAGGTCAAAAATGGG
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGG
* * *
13628 ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTGGGAAATTTTAGGGTTAAAAATGGG
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGG
* * *
13687 ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTGATAG-TTTAGGGGTCAAAATTGGG
1 ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGA-AGTTTTA-GGGTCAAAAATGGG
*
13747 ATTTTTGGAAGTTCGAGGGTAGAAACAT--AATTTTTGGACAGTTT
1 ATTTTTGGAAGTTCGGGGGTA-AAA-ATGGAATTTTTGGA-AGTTT
13791 ATGGACCTCC
Statistics
Matches: 299, Mismatches: 33, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
58 49 0.16
59 164 0.55
60 79 0.26
61 5 0.02
62 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.35
Consensus pattern (59 bp):
ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGG
Found at i:15640 original size:17 final size:17
Alignment explanation
Indices: 15618--15703 Score: 115
Period size: 17 Copynumber: 5.1 Consensus size: 17
15608 TTGGACATTT
15618 TAAATTTAAATTT-ATAA
1 TAAATTTAAATTTCA-AA
15635 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
15652 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
* *
15669 TAAACTT-AATTTAAAAA
1 TAAATTTAAATTT-CAAA
15686 TAAATTT-AATTTCAAA
1 TAAATTTAAATTTCAAA
15702 TA
1 TA
15704 GTCCCAGACA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
16 10 0.16
17 52 0.83
18 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:15669 original size:7 final size:6
Alignment explanation
Indices: 15616--15694 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
15606 AATTGGACAT
15616 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* **
15662 TTTCAAA --TAAA CTT-AA TTTAAA AATAAA TTTAA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
15695 TTTCAAATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
4 8 0.14
5 8 0.14
6 34 0.59
7 8 0.14
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:18137 original size:29 final size:28
Alignment explanation
Indices: 18044--18323 Score: 249
Period size: 29 Copynumber: 9.5 Consensus size: 28
18034 CAAAATTATA
*
18044 CAAAATTACATTTTAACCACTAAACTTTTC
1 CAAAATCACATTTTAACC-CTAAAC-TTTC
* * * *
18074 CAAAATTATATTTTTACCCCTAAACTATTA
1 CAAAATCACA-TTTTAACCCTAAACT-TTC
* *
18104 TAAAATCACATTTTGACCCTTAAAC-TTC
1 CAAAATCACATTTTAACCC-TAAACTTTC
* *
18132 CAAAAATCATATTTTGACCCTTAAACTTTCC
1 C-AAAATCACATTTTAACCC-TAAACTTT-C
* * *
18163 CAAAATAACATTTTAACCCAAAATTTATC
1 CAAAATCACATTTTAACCCTAAACTT-TC
* *
18192 CAAAATTACATTTTAACCCCAAACTTATC
1 CAAAATCACATTTTAACCCTAAACTT-TC
*
18221 CAAAATCACATTTTAACCCCTAAACATTC
1 CAAAATCACATTTTAA-CCCTAAACTTTC
18250 TCAAAATCACATTTTAACCCTAAACTTCTC
1 -CAAAATCACATTTTAACCCTAAACTT-TC
*
18280 TAAAATCACATTTTAACCC-AAATCTTTCC
1 CAAAATCACATTTTAACCCTAAA-CTTT-C
*
18309 CAAAAATTACATTTT
1 C-AAAATCACATTTT
18324 TACCATTAAA
Statistics
Matches: 211, Mismatches: 26, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.03
29 111 0.53
30 85 0.40
31 9 0.04
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (28 bp):
CAAAATCACATTTTAACCCTAAACTTTC
Found at i:18168 original size:59 final size:56
Alignment explanation
Indices: 18044--18323 Score: 249
Period size: 59 Copynumber: 4.8 Consensus size: 56
18034 CAAAATTATA
* * * * *
18044 CAAAATTACATTTTAACCACTAAACTTTTCCAAAATTATATTTTTACCCCTAAACTATTA
1 CAAAATCACATTTTAACC-CTAAAC-TTTCCAAAATCACA-TTTTAACCCTAAACT-TTC
* * * *
18104 TAAAATCACATTTTGACCCTTAAAC-TTCCAAAAATCATATTTTGACCCTTAAACTTTCC
1 CAAAATCACATTTTAACCC-TAAACTTTCC-AAAATCACATTTTAACCC-TAAACTTT-C
* * * * *
18163 CAAAATAACATTTTAACCCAAAATTTATCCAAAATTACATTTTAACCCCAAACTTATC
1 CAAAATCACATTTTAACCCTAAACTT-TCCAAAATCACATTTTAACCCTAAACTT-TC
*
18221 CAAAATCACATTTTAACCCCTAAACATTCTCAAAATCACATTTTAACCCTAAACTTCTC
1 CAAAATCACATTTTAA-CCCTAAACTTTC-CAAAATCACATTTTAACCCTAAACTT-TC
* *
18280 TAAAATCACATTTTAACCC-AAATCTTTCCCAAAAATTACATTTT
1 CAAAATCACATTTTAACCCTAAA-CTTT-CC-AAAATCACATTTT
18324 TACCATTAAA
Statistics
Matches: 182, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
57 3 0.02
58 47 0.26
59 109 0.60
60 23 0.13
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (56 bp):
CAAAATCACATTTTAACCCTAAACTTTCCAAAATCACATTTTAACCCTAAACTTTC
Found at i:21779 original size:337 final size:333
Alignment explanation
Indices: 21139--21805 Score: 996
Period size: 337 Copynumber: 2.0 Consensus size: 333
21129 CTGAATTCTG
*
21139 CATTTTCATGGGTTAGAAATATGTAAAGGAAGTGTTTTGTTCTATATTAGTGGCTAAGCCACCAA
1 CATTTTCATGGGTTAGAAAGATGTAAAGGAAGTGTTTTGTTCTATATTAGTGGCTAAGCCACCAA
** ** ** * *
21204 TATTTGTAATCTAATTTGGCTTCTAGACTACAATTAATGAACTGTGTCATACCGACACTATGTGA
66 TATCCGTAATCTAATTTGGCAGCTAGACTACAATTAATGAACCATCTCATACCGACACTATGCGA
* *
21269 TGTGTAAGGTTGGACGGGTATCAAATACCTAAATGGTGTGTTGGTATGGACGGAGATGGTGTGTA
131 TGTGTAAGGTTGGACAGGTATCAAATACCTAAATGGTGTGTTGGTATGGACGAAGATGGTGTGTA
* * * *
21334 GCGGATGGGGGTAAGAAAATTGCATTTGTATCTATATCTGTTATGTTCTGTATCTAATCTACTTT
196 GCGGATGGGGGTAAGAAAATTGCATTTGTATCTATATCTGATATATTCTGTATCTAATATACTCT
*
21399 GTATTTGGAATTTAAATGATTCACCATATCTGGACTATTAAATTTGAATAAGTGATATCTAAAAA
261 GTATTTGGAATTTAAATGATTCACCATATCTGGACTATTAAATTTGAATAAGTGAAATCTAAAAA
21464 TGATACTA
326 TGATACTA
* * *
21472 CATTTTCATGGGGTTAGAAGGATGTAAAGAAGGAAGTGTTTTGTTCTGTATTAGTGGTTAAGCCA
1 CATTTTCAT-GGGTTAGAAAGATGT--A-AAGGAAGTGTTTTGTTCTATATTAGTGGCTAAGCCA
* *
21537 CCAATATCCGTAATCTAGTTTGGCAGCTAGACTACAATTACTGAACCATCTCATACCGACACTAT
62 CCAATATCCGTAATCTAATTTGGCAGCTAGACTACAATTAATGAACCATCTCATACCGACACTAT
* * *
21602 GCGATGTGTAGGGTTGGATAGGTATCAAATACCTATATGGTGTGTTGGTATGGACGAAGATGGTG
127 GCGATGTGTAAGGTTGGACAGGTATCAAATACCTAAATGGTGTGTTGGTATGGACGAAGATGGTG
* *
21667 TGTAGCGGATGGGGGTAAGAAAATTGCAGTTT-TATTTATATCTGATCTATTCTGTATCTAATAT
192 TGTAGCGGATGGGGGTAAGAAAATTGCA-TTTGTATCTATATCTGATATATTCTGTATCTAATAT
* * *
21731 TCTCTGTATTTGGAATTTAAATGATTCACCATATCT-GATTTGTTAAATTTGAATAAGTGAAATC
256 ACTCTGTATTTGGAATTTAAATGATTCACCATATCTGGA-CTATTAAATTTGAATAAGTGAAATC
*
21795 TGAAAATGATA
320 TAAAAATGATA
21806 TTAAATCTGA
Statistics
Matches: 298, Mismatches: 30, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
333 9 0.03
334 13 0.04
336 3 0.01
337 270 0.91
338 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (333 bp):
CATTTTCATGGGTTAGAAAGATGTAAAGGAAGTGTTTTGTTCTATATTAGTGGCTAAGCCACCAA
TATCCGTAATCTAATTTGGCAGCTAGACTACAATTAATGAACCATCTCATACCGACACTATGCGA
TGTGTAAGGTTGGACAGGTATCAAATACCTAAATGGTGTGTTGGTATGGACGAAGATGGTGTGTA
GCGGATGGGGGTAAGAAAATTGCATTTGTATCTATATCTGATATATTCTGTATCTAATATACTCT
GTATTTGGAATTTAAATGATTCACCATATCTGGACTATTAAATTTGAATAAGTGAAATCTAAAAA
TGATACTA
Found at i:28687 original size:790 final size:783
Alignment explanation
Indices: 27268--29154 Score: 2101
Period size: 790 Copynumber: 2.4 Consensus size: 783
27258 TTTCAGAAGA
* * *
27268 AAAAAAATTATTCATTAAAGTGTCATTTGACGTGATGA-TGTTGGGGACAGGGGATTGATGGAAT
1 AAAAAAA-T-TTCATTAAAGTGTCATGTGACGTGAT-ATTGTTGGGGACAAGGGTTTGATGGAAT
* *
27332 GAAGGGAGTAGATTAGATAAAAAAATTTAAAATTTGAAAATTTTTTGCACAATGATGCTTCAATT
63 GAAGGGAGTAGA-TAGAT-AAAAAATTTAAAATTTTAAAATTTTTTGCACAATGATGTTTCAATT
* * * * * *
27397 TATAGCTAGGT-AGTGGTCTGATCGCCCCCTAGCACAGTTGTTGTAGAAAAA-A-A-A---TTAT
126 GATAGCTAGGTAAG-GGTCTGACCGCCCCCTAAC-CAGCTATTTTAGAAAAATATATATTTTTAT
* * * * *
27455 TAATTTGAAATCGCGATATAAGGGGGCACTTTTAGATATAATTTTTTTTTGTATATTTTGATATC
189 TAATTTGAAA---C--TATAAAGGGGCACTTTTAGAAATAA-CTTTTTTTGTATATCTTGA-AAC
* * * * * *
27520 GCCATGTAAAGAGACTTTCAAAATAAAAAATTATTTTATATTTTGAAAATGCCACGTGTCAGAAT
247 ACCACGTAAAGACACATTCAAAATAAAAAATTATTTTATATTTTGAAAACGACACGTGTCAGAAT
*
27585 CGAGTGAAACAAATATTATCTTAAGTTAAATTCTAAGAATAGTCCTCGTACTTATTGATTTGCAT
312 CGAGTGAAACAAATATCATCTTAAGTTAAATTCTAAGAATAGTCCTCGTACTTATTGATTTGCAT
* * * * *** * *
27650 AGATTTGGTCCCTCTATTTTTATTTACTGGTTGTATTCAAATTGGTGTCTTTGATATAGTGAGTT
377 AGATTTAGTCCCTCCACTTTTATTTA-TGCTACCATTAAAATTGGTGTCTTTGATATAGTGAATT
* * * * *
27715 TGTCCATTGTAATGGGTCACAACATCAAATTTACTATTCATCTTATCTTAACAACCTACACATTA
441 TGTCCATTGTAATGGGTCAAAACATCAAATTTACGATCCATCTTATCCTAACAACATACACATTA
27780 AAAAATAATAAAAAAAATATAACAATTGCAAACAAATAACATTATCCCCATTGATAGTGAAACTT
506 AAAAATAATAAAAAAAATATAACAATTGCAAACAAATAACATTATCCCCATTGATAGTGAAACTT
* *
27845 AACTAAATTAAGAAAATAATTAAAAAAAACTAAGAAGAGCAAACTTACTTCAACAAAACGGAGAG
571 AACTAAATTAAAAAAATAATTAAAAAAAACTAAGAAAAGCAAACTTACTTCAACAAAACGGAGAG
* * * * *
27910 CCGTTTAAATAGAGAAGAAATTGTTAGAATATTTTTCTGGGA-AAAAGGAGGTGACAGTCATATA
636 CAGTTTAAATAGAGAAGAAATTGTGAGAATATTTTTCTAGGAGAAAAGAAGGTGACAATCATATA
* * *
27974 GA-TTACATTGGGTA-TTTTCGTAATTTTATTTTCAATTTT-AGAATCTCAAAATTTGTAATTGC
701 GATTTACATTGGATACTTTT-GTAATTTTATTTTCAATTTTGA-AATCTCAAAATTTGAAACTGC
*
28036 CTCCTGACATGTCAA-TT-TC
764 CACCTGACA-GTCAATTTATC
* * *
28055 -AAAAAATTTCATTAAAATGTCATGTGACGTGCTATTGTTGGGGACAAGGGTTTGAT-GAAAGAA
1 AAAAAAATTTCATTAAAGTGTCATGTGACGTGATATTGTTGGGGACAAGGGTTTGATGGAATGAA
*
28118 GGGAGTAGATAGGATAAAAAAGTTTAAAATTTTAAAATTTTTTGCCCAATGGATGTTTCAATTGA
66 GGGAGTAGATA-GATAAAAAA-TTTAAAATTTTAAAATTTTTTGCACAAT-GATGTTTCAATTGA
* * * **
28183 AAGCTAGGTAAGGGTTTGACCACCCCCTAACCGAGCTATTTTAGAAAAATATATATTTTTATTCT
128 TAGCTAGGTAAGGGTCTGACCGCCCCCTAACC-AGCTATTTTAGAAAAATATATATTTTTATTAA
* * *
28248 TTTGAAACTATAAAGGGGCACTTTTAAAAATAACTTTTTTTATATATCTTGAAACAACCGCGTAA
192 TTTGAAACTATAAAGGGGCACTTTTAGAAATAACTTTTTTTGTATATCTTGAAAC-ACCACGTAA
* * * * *
28313 CATGACAGATTCAAAATAAAAGAATTATTATTATATTATATTAAGAACGACGCGTGTTAGAGTCG
256 -A-GACACATTCAAAATAAAA-AATTATT-TTATATT-T-TGAA-AACGACACGTGTCAGAATCG
* ** * * * * *
28378 AGTGAAACAAATATCATTTTTTGTTAAATTTTGAGAATAGTCCTTGTACTTATTGATTTGTATGG
314 AGTGAAACAAATATCATCTTAAGTTAAATTCTAAGAATAGTCCTCGTACTTATTGATTTGCATAG
*
28443 ATTTAGTCCCTCCACTTTTATTT-T-CTACCATTAAAATTGGTTTCTTTGATATAGTGAATTTGT
379 ATTTAGTCCCTCCACTTTTATTTATGCTACCATTAAAATTGGTGTCTTTGATATAGTGAATTTGT
** * * *
28506 CCATTGTAATGGGTCAAAACATTGAATTTACGATCCATCTTCTCCTACCAACATGCACATTCAAA
444 CCATTGTAATGGGTCAAAACATCAAATTTACGATCCATCTTATCCTAACAACATACACATT-AAA
* ** * * ** *
28571 GAAA-ACTAACAAAAAATATAACAATTGCATTCAAATAATATTGTTGCCTTTGATAGTGCAAA-T
508 -AAATAATAA-AAAAAATATAACAATTGCAAACAAATAACATTATCCCCATTGATAGTG-AAACT
* * * *
28634 TAACTAAATTAAAAAAATATTTAAAAAAAGCTATGAAAAGCAAACTTACTTCAACAAAATGGAGA
570 TAACTAAATTAAAAAAATAATTAAAAAAAACTAAGAAAAGCAAACTTACTTCAACAAAACGGAGA
* * *
28699 GTAGTTTAAATAGAGAAGAAATTGTGAGAATATTTTTGTAGGAGAAATGAAGGTGACAATCATAT
635 GCAGTTTAAATAGAGAAGAAATTGTGAGAATATTTTTCTAGGAGAAAAGAAGGTGACAATCATAT
* * *
28764 AGATTTACATTGGATACTTTTGTAATTTTATTTTCAATTTTGAAATCTCGAAGTTTGAAACTGTC
700 AGATTTACATTGGATACTTTTGTAATTTTATTTTCAATTTTGAAATCTCAAAATTTGAAACTGCC
* *
28829 ACTTGAGAGTCAATTTCAATC
765 ACCTGACAGTCAATTT--ATC
* * * *
28850 AAAAAGAATTT-ATTAAAGTGTCATGTGACGTGATGTTGTTGGGGAC-TGGATTTGATGGACTGA
1 AAAAA-AATTTCATTAAAGTGTCATGTGACGTGATATTGTTGGGGACAAGGGTTTGATGGAATGA
* * *
28913 AGGGAGAAGATCAGATAAAAGAATATTAAAA-TTTGAATTCTTTTTGCACAATTGATGTTTCAAT
65 AGGGAGTAGAT-AGATAAAA-AAT-TTAAAATTTTAAAAT-TTTTTGCACAA-TGATGTTTCAAT
* *
28977 TGATAGCTAAGTAAGGGTCTGACCGCCCCGTAACCCAGCTATTTTAGAAAAAATATATATTTTTA
125 TGATAGCTAGGTAAGGGTCTGACCGCCCCCTAA-CCAGCTATTTTAG-AAAAATATATATTTTTA
* * *
29042 TTAATTTGAAACTGCGGTATAAGGGGACACTTTTAGAAATAGCCTTTTTTGTATATCTTGAAATC
188 TTAATTTGAAACT---ATA-AAGGGG-CACTTTTAGAAATAACTTTTTTTGTATATCTTGAAA-C
* * * * ** *
29107 GCCATGTAAAGAAACTTTCAAAATAAAATTTTATTTTATATCTTGAAA
247 ACCACGTAAAGACACATTCAAAATAAAAAATTATTTTATATTTTGAAA
29155 CAACCATGCA
Statistics
Matches: 920, Mismatches: 132, Indels: 87
0.81 0.12 0.08
Matches are distributed among these distances:
782 8 0.01
783 48 0.05
784 112 0.12
785 27 0.03
786 22 0.02
787 9 0.01
788 90 0.10
789 9 0.01
790 157 0.17
791 120 0.13
792 55 0.06
793 5 0.01
795 10 0.01
796 65 0.07
797 77 0.08
798 32 0.03
799 6 0.01
800 5 0.01
801 17 0.02
802 7 0.01
803 38 0.04
804 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (783 bp):
AAAAAAATTTCATTAAAGTGTCATGTGACGTGATATTGTTGGGGACAAGGGTTTGATGGAATGAA
GGGAGTAGATAGATAAAAAATTTAAAATTTTAAAATTTTTTGCACAATGATGTTTCAATTGATAG
CTAGGTAAGGGTCTGACCGCCCCCTAACCAGCTATTTTAGAAAAATATATATTTTTATTAATTTG
AAACTATAAAGGGGCACTTTTAGAAATAACTTTTTTTGTATATCTTGAAACACCACGTAAAGACA
CATTCAAAATAAAAAATTATTTTATATTTTGAAAACGACACGTGTCAGAATCGAGTGAAACAAAT
ATCATCTTAAGTTAAATTCTAAGAATAGTCCTCGTACTTATTGATTTGCATAGATTTAGTCCCTC
CACTTTTATTTATGCTACCATTAAAATTGGTGTCTTTGATATAGTGAATTTGTCCATTGTAATGG
GTCAAAACATCAAATTTACGATCCATCTTATCCTAACAACATACACATTAAAAAATAATAAAAAA
AATATAACAATTGCAAACAAATAACATTATCCCCATTGATAGTGAAACTTAACTAAATTAAAAAA
ATAATTAAAAAAAACTAAGAAAAGCAAACTTACTTCAACAAAACGGAGAGCAGTTTAAATAGAGA
AGAAATTGTGAGAATATTTTTCTAGGAGAAAAGAAGGTGACAATCATATAGATTTACATTGGATA
CTTTTGTAATTTTATTTTCAATTTTGAAATCTCAAAATTTGAAACTGCCACCTGACAGTCAATTT
ATC
Found at i:32814 original size:20 final size:21
Alignment explanation
Indices: 32789--32830 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
32779 TTTGATAGTT
*
32789 ATAATTAAATAAATTAA-AAA
1 ATAATTAAAGAAATTAAGAAA
*
32809 ATAATTTAAGAAATTAAGAAA
1 ATAATTAAAGAAATTAAGAAA
32830 A
1 A
32831 GCAAACTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
ATAATTAAAGAAATTAAGAAA
Found at i:34792 original size:21 final size:21
Alignment explanation
Indices: 34768--34807 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34758 ACCTTTCTAA
*
34768 AATTAAAAAAAAATCATTTTC
1 AATTAAAAAAAAATAATTTTC
*
34789 AATTCAAAAAAAATAATTT
1 AATTAAAAAAAAATAATTT
34808 ATTAAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTAAAAAAAAATAATTTTC
Found at i:35042 original size:305 final size:306
Alignment explanation
Indices: 34489--35096 Score: 972
Period size: 305 Copynumber: 2.0 Consensus size: 306
34479 TTAATTTCAG
* *
34489 AAAAAAAATAATTTATTAAAGTGTCATGTGACATGATTTTGTTGGGGACTGGATTTGATGGACTG
1 AAAAAAAATAATTTATTAAAGTATCATGTGACATGATTTTGTTGGGAACTGGATTTGATGGACTG
*
34554 AAGGAAGTAAGTCGAATAAAAACTTTTAAAATTTGAATTTTTTTGCATAATGAATGTTTCAATTA
66 AAGGAAGTAAGTCGAATAAAAACTTTTAAAATTTGAATTTTTTTGCACAATGAATGTTTCAATTA
*
34619 ACAATGGGGTAAGGGTCTGACCGCCCCTAACCCAGTTATTTTAGAAAAAAATATATTTTTATTAA
131 ACAATGGGGTAAGGGTCTGACCGCCCCTAACCCAGCTATTTTAGAAAAAAATATATTTTTATTAA
* * * *
34684 TTTGAAACCGCAGTATAATGGGGCATTTTTAGGATTAACTTTTTCTGTATATCTTGAAACCAACA
196 TTTGAAACCACAGTATAATGGGGCACTTTTAGGAATAACTTTTTCTATATATCTTGAAACCAACA
*
34749 TATAAAGAGACCTTT-CTAAAATTAAA-AAAAAATCATTTTCAATTC
261 TATAAAGAGACCTTTAC-AAAATAAAATAAAAAATCATTTTCAATTC
** *
34794 AAAAAAAATAATTTATTAAAGTATCATGTGATGTGATTTTGTTGGGAACTGGGTTTGATGGACTG
1 AAAAAAAATAATTTATTAAAGTATCATGTGACATGATTTTGTTGGGAACTGGATTTGATGGACTG
* * *
34859 AAGGAAGTAGGTCGAATAAAAACTTTTAAAATTTGAATTTTTTTGCGCAATGGATGTTTCAATTA
66 AAGGAAGTAAGTCGAATAAAAACTTTTAAAATTTGAATTTTTTTGCACAATGAATGTTTCAATTA
* *
34924 ACAATTGGGTAAGGGTTTGACCGCCCCCTAA-CCAGCTATTTTAGAAAAAAATATATTTTTTATT
131 ACAATGGGGTAAGGGTCTGACCG-CCCCTAACCCAGCTATTTTAGAAAAAAATATA-TTTTTATT
* * * *
34988 AATTTGAAACCATAGTATAA-GGGGTACTTTTAGGAATAATTTTTTCTATATATCTTGAAACCGA
194 AATTTGAAACCACAGTATAATGGGGCACTTTTAGGAATAACTTTTTCTATATATCTTGAAACCAA
35052 CATATAAAGAGACCTTTACAAAATAAAATAAAAAATCATTTTCAA
259 CATATAAAGAGACCTTTACAAAATAAAATAAAAAATCATTTTCAA
35097 AATAAAAGGA
Statistics
Matches: 278, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
305 228 0.82
306 50 0.18
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (306 bp):
AAAAAAAATAATTTATTAAAGTATCATGTGACATGATTTTGTTGGGAACTGGATTTGATGGACTG
AAGGAAGTAAGTCGAATAAAAACTTTTAAAATTTGAATTTTTTTGCACAATGAATGTTTCAATTA
ACAATGGGGTAAGGGTCTGACCGCCCCTAACCCAGCTATTTTAGAAAAAAATATATTTTTATTAA
TTTGAAACCACAGTATAATGGGGCACTTTTAGGAATAACTTTTTCTATATATCTTGAAACCAACA
TATAAAGAGACCTTTACAAAATAAAATAAAAAATCATTTTCAATTC
Found at i:35100 original size:19 final size:19
Alignment explanation
Indices: 35075--35118 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
35065 CTTTACAAAA
35075 TAAAATAAAA-AATCATTT
1 TAAAATAAAAGAATCATTT
35093 TCAAAATAAAAGGAATCATTT
1 T-AAAATAAAA-GAATCATTT
35114 TAAAA
1 TAAAA
35119 AAATAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 4 0.17
21 9 0.39
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAATAAAAGAATCATTT
Found at i:35111 original size:21 final size:19
Alignment explanation
Indices: 35076--35119 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
35066 TTTACAAAAT
*
35076 AAAATAAAAAATCATTTTC
1 AAAATAAAAAATCATTTTA
35095 AAAATAAAAGGAATCATTTTA
1 AAAATAAAA--AATCATTTTA
35116 AAAA
1 AAAA
35120 AATAAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATAAAAAATCATTTTA
Found at i:39399 original size:438 final size:435
Alignment explanation
Indices: 38751--39613 Score: 1284
Period size: 438 Copynumber: 2.0 Consensus size: 435
38741 AACCGTCGTG
* * *
38751 TAAGATGGCAGTTTTAAAAATAAAAAATTTATTATTATTTTATATAAAAAACCGCGTGACAGAGT
1 TAAGATGGCAGTTTTAAAAATAAAAAATTTATTATTATCTTATATAAAAAACCACGTGACAAAGT
38816 TGAGTGAAACAAATATTATTTTTGTTTAATTTCTAAGAAGAGTCCTTGTACTTTTTGATTTGCGC
66 TGAGTGAAACAAATATTATTTTTGTTTAATTTCTAAGAAGAGTCCTTGTACTTTTTGATTTGCGC
* * * *
38881 TTTTGGTCTCTCCACTTTTATTTACTGCCATTCAAATTGGTGTCTTTGATATAGTGAGTTTGTCC
131 ATTTGATCCCTCCACTTTTATTTACTACCATTCAAATTGGTGTCTTTGATATAGTGAGTTTGTCC
* * * * *
38946 CTTGTAATTGGCCACAATATTGAATTTACTATCCATCTTCTCTTACCAACTTGCACATTAAAAAA
196 CTTGTAATGGGCCACAACATTGAATTTACAATCCATCTTCTCCTACCAACCTGCACATT-AAAAA
*
39011 AAAATAACAAAAAATATAACAGTTGCATACAAATAACATTA-TAGATAATAGAAATTAACTAAAT
260 AAAATAACAAAAAATATAACAGTTGCATACAAATAACATTAGTAGATAATAAAAATTAACTAAAT
* *
39075 T-AAAAAATATTTAAAAAACCTAAAAAATAAATTACTTCAACAAAATGGAGAGTAGTTTAAATAG
325 TAAAAAAATATTAAAAAAAACTAAAAAATAAATTACTTCAACAAAATGGAGAGTAGTTTAAATA-
* *
39139 AGAAGAAATTGTGAGAATGTTTTTGTGGGAAAAATAACATTACGCCATA
389 A-AA-AAATTATGAGAATATTTTTGTGGGAAAAATAACATTACGCCATA
* **
39188 TAAGATGGTAGTTTT-AAAAT-AAAAATTTATTATTATCTTATATAAAAAAACCATTTGACAAAG
1 TAAGATGGCAGTTTTAAAAATAAAAAATTTATTATTATCTTATAT-AAAAAACCACGTGACAAAG
* * * * * * *
39251 TTGTGTGAAATAAATATTTTTTTTGTTTAATTTTTAAGAATAGTCTTTGTACTTTTTGATTTGTG
65 TTGAGTGAAACAAATATTATTTTTGTTTAATTTCTAAGAAGAGTCCTTGTACTTTTTGATTTGCG
*
39316 CAGATTTGATCCCTCCACTTTTATTTACTACCATTCGAATTGGTGTCTTTGATATAGTGAGTTTG
130 C--ATTTGATCCCTCCACTTTTATTTACTACCATTCAAATTGGTGTCTTTGATATAGTGAGTTTG
* * *
39381 TCCCTTGTAATGGGCCACAACATTGAATTTACAATTCATCTTCTCCTACCAACCTGCACATTCAG
193 TCCCTTGTAATGGGCCACAACATTGAATTTACAATCCATCTTCTCCTACCAACCTGCACATTAAA
** *
39446 AAAAAATAACAAAAAATATAGTAGTTGCATACAAATAACATTATGCGTTAGATAGTAAAAATTAA
258 AAAAAATAACAAAAAATATAACAGTTGCATACAAATAACATTA---G-TAGATAATAAAAATTAA
39511 CTAAATTAAAAAAATATTAAAAAAAACTAAAAAATAAATTACTTCAACAAAATGGAGAGTAGTTT
319 CTAAATTAAAAAAATATTAAAAAAAACTAAAAAATAAATTACTTCAACAAAATGGAGAGTAGTTT
*
39576 AAATAAAAAAATTATGAGAATATTTTTGTGGGAGAAAT
384 AAATAAAAAAATTATGAGAATATTTTTGTGGGAAAAAT
39614 GGAGGTGGCA
Statistics
Matches: 382, Mismatches: 35, Indels: 15
0.88 0.08 0.03
Matches are distributed among these distances:
435 22 0.06
436 79 0.21
437 56 0.15
438 113 0.30
440 27 0.07
441 2 0.01
442 23 0.06
443 60 0.16
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (435 bp):
TAAGATGGCAGTTTTAAAAATAAAAAATTTATTATTATCTTATATAAAAAACCACGTGACAAAGT
TGAGTGAAACAAATATTATTTTTGTTTAATTTCTAAGAAGAGTCCTTGTACTTTTTGATTTGCGC
ATTTGATCCCTCCACTTTTATTTACTACCATTCAAATTGGTGTCTTTGATATAGTGAGTTTGTCC
CTTGTAATGGGCCACAACATTGAATTTACAATCCATCTTCTCCTACCAACCTGCACATTAAAAAA
AAATAACAAAAAATATAACAGTTGCATACAAATAACATTAGTAGATAATAAAAATTAACTAAATT
AAAAAAATATTAAAAAAAACTAAAAAATAAATTACTTCAACAAAATGGAGAGTAGTTTAAATAAA
AAAATTATGAGAATATTTTTGTGGGAAAAATAACATTACGCCATA
Found at i:40863 original size:92 final size:92
Alignment explanation
Indices: 40682--40869 Score: 236
Period size: 92 Copynumber: 2.0 Consensus size: 92
40672 AGCTGTCACG
* * * *
40682 TGATACGACGGTTTTACCCATTGTGTCGTCTTGTTATAAAACTAATATTATTATCATGAAATTGC
1 TGATACGACGGTTTCACCCATTATATCATCTTGTTATAAAACTAATATTATTATCATGAAATTGC
40747 TATAGAAGCAATTTTAACAAAAAAAAT
66 TATAGAAGCAATTTTAACAAAAAAAAT
* * * *
40774 TGATACGACGGTTTCACTCATTATATCATCTTGTTATAAAA-TATTATTTTTTTTTCATGAAATT
1 TGATACGACGGTTTCACCCATTATATCATCTTGTTATAAAACTA--ATATTATTATCATGAAATT
*
40838 GCTGT-GAAAGCAATTTTAACCAAAAAATAAT
64 GCTATAG-AAGCAATTTTAA-CAAAAAA-AAT
40869 T
1 T
40870 ATATCAGAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
91 2 0.02
92 37 0.45
93 32 0.39
94 7 0.09
95 4 0.05
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (92 bp):
TGATACGACGGTTTCACCCATTATATCATCTTGTTATAAAACTAATATTATTATCATGAAATTGC
TATAGAAGCAATTTTAACAAAAAAAAT
Found at i:42772 original size:132 final size:132
Alignment explanation
Indices: 42535--42800 Score: 498
Period size: 132 Copynumber: 2.0 Consensus size: 132
42525 TTGTGGAAGT
*
42535 AATTTTTATTTAATTGTTAATGTAATTTAAATTGTACCTTTAAATTTGAAAGAGTTCAACTATAA
1 AATTTTTATTTAATTGTTAATGTAATTTAAATTGTACCTTTAAATCTGAAAGAGTTCAACTATAA
*
42600 ATAAATATATTTATCTCATTTGTAATCATTTCAATCATTTTATTTTTGAGTAATAGAATACTTTT
66 ATAAATACATTTATCTCATTTGTAATCATTTCAATCATTTTATTTTTGAGTAATAGAATACTTTT
42665 GA
131 GA
42667 AATTTTTATTTAATTGTTAATGTAATTTAAATTGTACCTTTAAATCTGAAAGAGTTCAACTATAA
1 AATTTTTATTTAATTGTTAATGTAATTTAAATTGTACCTTTAAATCTGAAAGAGTTCAACTATAA
42732 ATAAAGT-CATTTATCTCATTTGTAATCATTTCAATCATTTTATTTTTGAGTAATAGAATACTTT
66 ATAAA-TACATTTATCTCATTTGTAATCATTTCAATCATTTTATTTTTGAGTAATAGAATACTTT
42796 TGA
130 TGA
42799 AA
1 AA
42801 CCATTTACTC
Statistics
Matches: 131, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
132 130 0.99
133 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (132 bp):
AATTTTTATTTAATTGTTAATGTAATTTAAATTGTACCTTTAAATCTGAAAGAGTTCAACTATAA
ATAAATACATTTATCTCATTTGTAATCATTTCAATCATTTTATTTTTGAGTAATAGAATACTTTT
GA
Found at i:45355 original size:336 final size:335
Alignment explanation
Indices: 44562--45364 Score: 1279
Period size: 336 Copynumber: 2.4 Consensus size: 335
44552 TATCAGAATT
*
44562 CTGCATTTGCATGGGGTTAGAAGTATGTAAAGAAGGAACTGTTCTGTTCTGTATTAGTGGCTAAG
1 CTGCATTTGCATGGGGTTAGAAGTATGTAAAGAAGGAAGTGTTCTGTTCTGTATTAGTGGCTAAG
*
44627 CCACCAATATTTGTAATCTAATTTGGCAGCTAGACTACAATTACTGAACCGTGTCATACCGACAC
66 CCACCAATATATGTAATCTAATTTGGCAGCTAGACTACAATTACTGAACCGTGTCATACCGACAC
* * * *
44692 TATGTGATATGTAAGTTTGGATGGGTATCAAATACCTATATGGTGTGTTAGTATGGACGTAGATA
131 TATGTGATATATAAGGTTGAATGGGTATCAAATACCTATATGGTGTGTTAGTATGGACGGAGATA
*
44757 GTGTATAGCGGATGGGGGTAAGAAAATTGCATTTGTATTTATATCTGATCTGTTTGTATCTGATA
196 GTGTATAGCGGATGGGGGTAAGAAAATTGCATTTGTATCTATATCTGATCTGTTTGTATCTGATA
* * *
44822 TGCTCTGTATCTGGAATTTAAATGATTCACCATATCTGATCCATTAAATTTGAATATGTGATATC
261 TACTCTGTATCTAGAATTTAAATGATTCACCATATCTGA-CCATTAAATTTGAATAAGTGATATC
44887 TAAAAATGATA
325 TAAAAATGATA
* * *
44898 CTGCATTTGTATGTGGTTAGAAGTATGTAAAGAAGGAAGTGTTTTGTTCTGTATTAGTGGCTAAG
1 CTGCATTTGCATGGGGTTAGAAGTATGTAAAGAAGGAAGTGTTCTGTTCTGTATTAGTGGCTAAG
*
44963 CTACCAATATATGTAATCTAATTTGGCAGCTAGACTACAATTACTGAACCGTGTCATACCGACAC
66 CCACCAATATATGTAATCTAATTTGGCAGCTAGACTACAATTACTGAACCGTGTCATACCGACAC
* * *
45028 TATGTGATGTATAAGGTTGAATGGGTATCAAATACCTATATGGTGTGTTGGTATGGACGGAGATG
131 TATGTGATATATAAGGTTGAATGGGTATCAAATACCTATATGGTGTGTTAGTATGGACGGAGATA
* *
45093 GTGTGTAGCGGATGGGGGTAAGAAAATTGCATTTGTATCTATATCTGATCTGTTTTGTATTTGAT
196 GTGTATAGCGGATGGGGGTAAGAAAATTGCATTTGTATCTATATCTGATCTG-TTTGTATCTGAT
* * *
45158 CTACTTTGTATCTAGAATTTAAATTATTCACCACT-TCTTG-CCTATTAAATTTGAATAAGTGAT
260 ATACTCTGTATCTAGAATTTAAATGATTCACCA-TATC-TGACC-ATTAAATTTGAATAAGTGAT
45221 ATCTAAAAATGATA
322 ATCTAAAAATGATA
*
45235 CTGCATTTGCATGGGGTTAGAAGTATGTAAAGAAGGAAGTGTTCTGTTCTGTATTAGTGGTTAAG
1 CTGCATTTGCATGGGGTTAGAAGTATGTAAAGAAGGAAGTGTTCTGTTCTGTATTAGTGGCTAAG
** * ** *
45300 CCACCAATATCCGTAATCTAATTTGGCAACTAGACTACAATT-CTGAATTGTGTCATACCAACAC
66 CCACCAATATATGTAATCTAATTTGGCAGCTAGACTACAATTACTGAACCGTGTCATACCGACAC
45364 T
131 T
45365 GTTGAAGCTC
Statistics
Matches: 430, Mismatches: 33, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
336 254 0.59
337 173 0.40
338 3 0.01
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (335 bp):
CTGCATTTGCATGGGGTTAGAAGTATGTAAAGAAGGAAGTGTTCTGTTCTGTATTAGTGGCTAAG
CCACCAATATATGTAATCTAATTTGGCAGCTAGACTACAATTACTGAACCGTGTCATACCGACAC
TATGTGATATATAAGGTTGAATGGGTATCAAATACCTATATGGTGTGTTAGTATGGACGGAGATA
GTGTATAGCGGATGGGGGTAAGAAAATTGCATTTGTATCTATATCTGATCTGTTTGTATCTGATA
TACTCTGTATCTAGAATTTAAATGATTCACCATATCTGACCATTAAATTTGAATAAGTGATATCT
AAAAATGATA
Found at i:45443 original size:6 final size:6
Alignment explanation
Indices: 45432--45495 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
45422 ATTTGTGTAG
* *
45432 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
* *
45478 -AATTG AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
45496 TTTTCCAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.09
5 8 0.17
6 30 0.65
7 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:45454 original size:17 final size:18
Alignment explanation
Indices: 45432--45527 Score: 94
Period size: 17 Copynumber: 5.5 Consensus size: 18
45422 ATTTGTGTAG
45432 AAATTTAAATTTATATT-
1 AAATTTAAATTTATATTC
45449 AAATTTAAATTTAT-TTC
1 AAATTTAAATTTATATTC
* *
45466 GAATTTAAATTTA-ATTG
1 AAATTTAAATTTATATTC
* *
45483 AAGTTTAAATTTATTTTCC
1 AAATTTAAATTTATATT-C
*
45502 AAATTTAAGA-TTAT-TTT
1 AAATTTAA-ATTTATATTC
45519 AAATTTAAA
1 AAATTTAAA
45528 ATAAATAAGG
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
16 3 0.05
17 47 0.71
18 4 0.06
19 11 0.17
20 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (18 bp):
AAATTTAAATTTATATTC
Found at i:45458 original size:35 final size:34
Alignment explanation
Indices: 45400--45496 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 34
45390 CGAAACTCCC
* * *
45400 TTTAAATTTATTTTAAGA-ATAAATTTGTGTAGAAA
1 TTTAAATTTATATTAA-ATTTAAATTTATGTAG-AA
* *
45435 TTTAAATTTATATTAAATTTAAATTTATTTCGAA
1 TTTAAATTTATATTAAATTTAAATTTATGTAGAA
*
45469 TTTAAATTTA-ATTGAAGTTTAAATTTAT
1 TTTAAATTTATATT-AAATTTAAATTTAT
45497 TTTCCAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
33 3 0.06
34 26 0.48
35 25 0.46
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (34 bp):
TTTAAATTTATATTAAATTTAAATTTATGTAGAA
Done.