Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014246.1 Corchorus capsularis cultivar CVL-1 contig14267, 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: 43606
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:4642 original size:11 final size:12
Alignment explanation
Indices: 4620--4644 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4610 AAAGAAACAG
4620 AAAAATGAAAAA
1 AAAAATGAAAAA
4632 AAAAATGAAAAA
1 AAAAATGAAAAA
4644 A
1 A
4645 TCAGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAATGAAAAA
Found at i:5857 original size:30 final size:32
Alignment explanation
Indices: 5778--5857 Score: 114
Period size: 30 Copynumber: 2.6 Consensus size: 32
5768 TGTATTAACT
5778 AAATCCTTACTTATGTG--TGTTGTCAAAAAA
1 AAATCCTTACTTATGTGATTGTTGTCAAAAAA
*
5808 AAATCCTTACTTATGTGATTGTTG-C-CAAAA
1 AAATCCTTACTTATGTGATTGTTGTCAAAAAA
*
5838 AAATCCTTAATTATGTGATT
1 AAATCCTTACTTATGTGATT
5858 AATGTGCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 40 0.87
31 1 0.02
32 5 0.11
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (32 bp):
AAATCCTTACTTATGTGATTGTTGTCAAAAAA
Found at i:6640 original size:167 final size:166
Alignment explanation
Indices: 6261--6702 Score: 557
Period size: 167 Copynumber: 2.7 Consensus size: 166
6251 GTCATTTGTC
* * * * * * *
6261 AATTAAGAAATGACCAAAAAAATTTAGTTATTTAATCCTTTCAAGAATAAAAAATTAGGATATTT
1 AATTAAGAAATAACCAAAAAGA-TTAATTATTTAATCCCTTCAAGAATCAAAAGTTAGGACATTT
* * * * ** *
6326 AAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTGAT
65 AAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAATCCTTGAT
* * * * *
6391 GGGGATCTTTTATTAATTCCACTACTCTATTCAAGTC
130 AGGGATCTTTTAGTAATTCCACTACTATATTAAAGTA
* * * *
6428 CATTAAGAAATTACCAAAAAGATTATTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTTA
1 AATTAAGAAATAACCAAAAAGATTAATTATTTAATCCCTTCAAGAATCAAAAGTTAGGACATTTA
*
6493 AGTAATCTGTCAAGTAGGAAAAGACGAAAAAAAATAAGTTCTCTAACTCTAAAAGCAAGT-CTTG
66 AGTAATCTGTCAAGTAGGAAAAGACG-AAAAAAATTAGTTCTCTAACTC-AAAAGCAA-TCCTTG
*
6557 GTAGGGAT-TTTTAGTAATTCCACTACTATATTAAAGTA
128 ATAGGGATCTTTTAGTAATTCCACTACTATATTAAAGTA
* * *
6595 AATTGAGAAATAACTAAAAAG-TCTAATTATTTAATCCCTTCAAGAATCAAAAGTTATGACATTT
1 AATTAAGAAATAACCAAAAAGAT-TAATTATTTAATCCCTTCAAGAATCAAAAGTTAGGACATTT
*
6659 AAGTAATCTGTCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCT
65 AAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT
6703 CGCTCCTCAT
Statistics
Matches: 239, Mismatches: 32, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
166 78 0.33
167 145 0.61
168 15 0.06
169 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (166 bp):
AATTAAGAAATAACCAAAAAGATTAATTATTTAATCCCTTCAAGAATCAAAAGTTAGGACATTTA
AGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAATCCTTGATA
GGGATCTTTTAGTAATTCCACTACTATATTAAAGTA
Found at i:6900 original size:45 final size:45
Alignment explanation
Indices: 6835--6924 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
6825 TATACTTCTC
*
6835 CAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACT
1 CAGCTCATCATTAATCCGGGGTAGGGATCTATTAGTAATTCCACT
*
6880 CAGCTCATCATTAATTCGGGGTAGGGATCTATTAGTAATTCCACT
1 CAGCTCATCATTAATCCGGGGTAGGGATCTATTAGTAATTCCACT
6925 ACTCTATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (45 bp):
CAGCTCATCATTAATCCGGGGTAGGGATCTATTAGTAATTCCACT
Found at i:9263 original size:22 final size:22
Alignment explanation
Indices: 9238--9314 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
9228 TCAGCCCCAT
9238 CTTTTACTTTTCATCACCCTTG
1 CTTTTACTTTTCATCACCCTTG
* * *
9260 CTTTTACAAGTTGTGATCAACCTTG
1 CTTTTAC---TTTTCATCACCCTTG
* *
9285 TCATTTACTTTTCATCACCATTG
1 -CTTTTACTTTTCATCACCCTTG
*
9308 TTTTTAC
1 CTTTTAC
9315 AAGGTGTAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
22 12 0.29
23 11 0.27
25 12 0.29
26 6 0.15
ACGTcount: A:0.19, C:0.25, G:0.08, T:0.48
Consensus pattern (22 bp):
CTTTTACTTTTCATCACCCTTG
Found at i:14850 original size:11 final size:11
Alignment explanation
Indices: 14834--14868 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
14824 CCAATTTAAT
*
14834 ATTTTAAACGG
1 ATTTTATACGG
14845 ATTTTATACGG
1 ATTTTATACGG
*
14856 TTTTTATACGG
1 ATTTTATACGG
14867 AT
1 AT
14869 ATCCGCTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.46
Consensus pattern (11 bp):
ATTTTATACGG
Found at i:17049 original size:16 final size:16
Alignment explanation
Indices: 17028--17062 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
17018 ACAATTCAGA
17028 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
17044 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
17060 AAG
1 AAG
17063 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:18150 original size:16 final size:16
Alignment explanation
Indices: 18131--18226 Score: 72
Period size: 16 Copynumber: 6.0 Consensus size: 16
18121 AACCCGCCTG
18131 AACCTGAACCCGAAAA
1 AACCTGAACCCGAAAA
*
18147 AACCCGAACCCG-AAA
1 AACCTGAACCCGAAAA
* * *
18162 AAGCTCAAATCCGAAAA
1 AACCT-GAACCCGAAAA
*
18179 AACAC-GAATCCG-AAA
1 AAC-CTGAACCCGAAAA
* *
18194 AAGCTCAAACCCGAAAA
1 AACCT-GAACCCGAAAA
*
18211 AACCTGAATCCGAAAA
1 AACCTGAACCCGAAAA
18227 TTTATGAAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
14 1 0.02
15 11 0.18
16 36 0.59
17 12 0.20
18 1 0.02
ACGTcount: A:0.51, C:0.29, G:0.12, T:0.07
Consensus pattern (16 bp):
AACCTGAACCCGAAAA
Found at i:18176 original size:32 final size:32
Alignment explanation
Indices: 18137--18226 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
18127 CCTGAACCTG
*
18137 AACCCGAAAAAACCCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAATCCGAAAAAGCTCA
* *
18169 AATCCGAAAAAACACGAATCCGAAAAAGCTCA
1 AACCCGAAAAAACCCGAATCCGAAAAAGCTCA
*
18201 AACCCGAAAAAACCTGAATCCGAAAA
1 AACCCGAAAAAACCCGAATCCGAAAA
18227 TTTATGAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.07
Consensus pattern (32 bp):
AACCCGAAAAAACCCGAATCCGAAAAAGCTCA
Found at i:18449 original size:31 final size:32
Alignment explanation
Indices: 18377--18479 Score: 181
Period size: 32 Copynumber: 3.2 Consensus size: 32
18367 CAAACAGAAT
18377 CCGAACCCGAATTAACCTGACCCAAATTCAAC
1 CCGAACCCGAATTAACCTGACCCAAATTCAAC
18409 CCGAACCCGAATTAACCTGACCCAAATT-AAC
1 CCGAACCCGAATTAACCTGACCCAAATTCAAC
* *
18440 CTGAACCCGAATTAACCTGACCCAAATCCAAC
1 CCGAACCCGAATTAACCTGACCCAAATTCAAC
18472 CCGAACCC
1 CCGAACCC
18480 AAAAATGACC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 29 0.43
32 38 0.57
ACGTcount: A:0.37, C:0.39, G:0.10, T:0.15
Consensus pattern (32 bp):
CCGAACCCGAATTAACCTGACCCAAATTCAAC
Found at i:24028 original size:16 final size:16
Alignment explanation
Indices: 24004--24034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23994 TGTTTGACTA
*
24004 TCATTCTTTACTTTTT
1 TCATACTTTACTTTTT
24020 TCATACTTTACTTTT
1 TCATACTTTACTTTT
24035 CTTTTTACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (16 bp):
TCATACTTTACTTTTT
Found at i:24132 original size:22 final size:22
Alignment explanation
Indices: 24092--24184 Score: 70
Period size: 22 Copynumber: 4.2 Consensus size: 22
24082 CTGATTATTC
24092 TTTACT-TTGTACTGATTACTAT
1 TTTACTCTTGTA-TGATTACTAT
24114 TTTACTCTTGT-TGATTTACCT-T
1 TTTACTCTTGTATGA-TTA-CTAT
* *
24136 CTTACT-TTTTACTGATTACTAT
1 TTTACTCTTGTA-TGATTACTAT
* *
24158 TTTACTCTT-TACTAATTACCAT
1 TTTACTCTTGTA-TGATTACTAT
24180 TTTAC
1 TTTAC
24185 CCTTTCAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
21 8 0.14
22 40 0.68
23 11 0.19
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTACTCTTGTATGATTACTAT
Found at i:24189 original size:22 final size:22
Alignment explanation
Indices: 24143--24189 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
24133 CTTCTTACTT
* * *
24143 TTTACTGATTACTATTTTACTC
1 TTTACTAATTACCATTTTACCC
24165 TTTACTAATTACCATTTTACCC
1 TTTACTAATTACCATTTTACCC
24187 TTT
1 TTT
24190 CAGATACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTACTAATTACCATTTTACCC
Found at i:24461 original size:16 final size:16
Alignment explanation
Indices: 24440--24501 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
24430 GGCTCTTTAA
24440 TTACTGATTACTCAAT
1 TTACTGATTACTCAAT
**
24456 TTACTGATTACTATCTTT
1 TTACTGATTAC--TCAAT
*
24474 TTACCTGATTACT-GAT
1 TTA-CTGATTACTCAAT
24490 TTACTGATTACT
1 TTACTGATTACT
24502 ATTACCTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.23
16 15 0.38
17 1 0.03
18 6 0.15
19 8 0.21
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (16 bp):
TTACTGATTACTCAAT
Found at i:24528 original size:55 final size:55
Alignment explanation
Indices: 24481--24986 Score: 852
Period size: 55 Copynumber: 9.2 Consensus size: 55
24471 TTTTTACCTG
* *
24481 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
* *
24536 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
* * * *
24591 ATTACTGATTTACTGATCACTACTACTCTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
*
24646 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATTTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
* * *
24701 ATTACTGATTTACTGATTACTATTACTTTGACTCTAATGAACCTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
24756 ATTACTGATTTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
1 ATTACTGA-TTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
24812 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
1 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
*
24867 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
* *
24922 ATTACTGATTTACTGATCT-CTACTACTCTGACTCTGATTAATCTCTTTTCACTTA
1 ATTACTGATTTACTGAT-TACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
24977 ATTACTGATT
1 ATTACTGATT
24987 GCCCCCTTTT
Statistics
Matches: 429, Mismatches: 20, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
55 376 0.88
56 53 0.12
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.48
Consensus pattern (55 bp):
ATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTA
Found at i:24982 original size:276 final size:275
Alignment explanation
Indices: 24481--24986 Score: 897
Period size: 276 Copynumber: 1.8 Consensus size: 275
24471 TTTTTACCTG
*
24481 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATT
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
*
24546 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATCAC
66 TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATCAC
* *
24611 TACTACTCTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTG
131 TACTACTCTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTACTACTCTG
*
24676 ACTCTGATTAATTTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTAATGA
196 ACTCTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTAATGA
24741 ACCTCTTTTCACTTA
261 ACCTCTTTTCACTTA
*
24756 ATTACTGATTTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTAATTACTGAT
1 ATTACTGA-TTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGAT
* *
24821 TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTA
65 TTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATCA
* *
24886 CTATTACTTTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATCT-CTACTACTC
130 CTACTACTCTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGAT-TACTACTACTC
24950 TGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
194 TGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
24987 GCCCCCTTTT
Statistics
Matches: 219, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
275 8 0.04
276 210 0.96
277 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.48
Consensus pattern (275 bp):
ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATT
TACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATCAC
TACTACTCTGACTCTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTACTACTCTG
ACTCTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTAATGA
ACCTCTTTTCACTTA
Found at i:30385 original size:6 final size:6
Alignment explanation
Indices: 30374--30404 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
30364 ATAATTGCTA
30374 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
30405 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:31006 original size:13 final size:14
Alignment explanation
Indices: 30983--31011 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
30973 ATTGTTCTCA
30983 TAAATATTTTTATT
1 TAAATATTTTTATT
30997 TAAA-ATTTTTATT
1 TAAATATTTTTATT
31010 TA
1 TA
31012 TTTATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAAATATTTTTATT
Found at i:35264 original size:1 final size:1
Alignment explanation
Indices: 35253--35282 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
35243 TACTAACTCC
*
35253 TTTTTTATTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35283 CCAGAGGGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:35704 original size:2 final size:2
Alignment explanation
Indices: 35697--35724 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35687 TAATCACTCG
35697 AT 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 AT
35725 GAAAAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37562 original size:22 final size:22
Alignment explanation
Indices: 37532--37575 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
37522 TTTTCATGCA
*
37532 ACAACTTCTGTCCCGAAGTTGT
1 ACAACTTCTGGCCCGAAGTTGT
* *
37554 ACAAGTTCTGGGCCGAAGTTGT
1 ACAACTTCTGGCCCGAAGTTGT
37576 CCTGCGCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
ACAACTTCTGGCCCGAAGTTGT
Found at i:37610 original size:52 final size:52
Alignment explanation
Indices: 37529--37631 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
37519 GGTTTTTCAT
* *
37529 GCAACAACTTCTGTCCCGAAGTTGTACAAGTTCTGGGCCGAAGTTGTCCTGC
1 GCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTAGGCCGAAGTTGTCCTGC
*
37581 GCAACAACTTTTGTCCCGAAGTTGAACAAGTTCTAGGCCGAAGTTGTCCTG
1 GCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTAGGCCGAAGTTGTCCTG
37632 AAATTCTTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.27
Consensus pattern (52 bp):
GCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTAGGCCGAAGTTGTCCTGC
Found at i:40178 original size:23 final size:23
Alignment explanation
Indices: 40148--40201 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
40138 GGAGTTGAGG
40148 ACCGGCCACCATCGCATGGAGCA
1 ACCGGCCACCATCGCATGGAGCA
40171 ACCGGCCACCATCGCATGGAGCA
1 ACCGGCCACCATCGCATGGAGCA
40194 ACCGGCCA
1 ACCGGCCA
40202 TGACCGGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.41, G:0.26, T:0.07
Consensus pattern (23 bp):
ACCGGCCACCATCGCATGGAGCA
Found at i:40283 original size:42 final size:42
Alignment explanation
Indices: 40222--40304 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
40212 ACGCATGGGA
*
40222 CATCGCACGGGACAACGCACGGGCCATCCGGCCACAACCGGT
1 CATCACACGGGACAACGCACGGGCCATCCGGCCACAACCGGT
* * *
40264 CATCACACGGGCCATCGCACGGGCCATCCGGCCATAACCGG
1 CATCACACGGGACAACGCACGGGCCATCCGGCCACAACCGG
40305 CCACTTGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.23, C:0.41, G:0.28, T:0.08
Consensus pattern (42 bp):
CATCACACGGGACAACGCACGGGCCATCCGGCCACAACCGGT
Found at i:41341 original size:11 final size:11
Alignment explanation
Indices: 41325--41361 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
41315 AGTTATATTG
41325 AAAAATATAAA
1 AAAAATATAAA
41336 AAAAATA-AAA
1 AAAAATATAAA
*
41346 AACAA-ATAAA
1 AAAAATATAAA
41356 AAAAAT
1 AAAAAT
41362 TTTCTACCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 1 0.05
10 14 0.64
11 7 0.32
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAATATAAA
Done.