Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014402.1 Corchorus olitorius cultivar O-4 contig14435, 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: 64362
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:2426 original size:93 final size:93
Alignment explanation
Indices: 2273--2457 Score: 262
Period size: 93 Copynumber: 2.0 Consensus size: 93
2263 TTGTTTAAAT
* * * * * *
2273 TTTTATAGTTTTAGTCAGCTAAAAACTCCATTTTTATTTAATTAAATATAATATTCTTATAACTA
1 TTTTATAGTCTTACTAAACTAAAAACTCCATTTATATTTAATTAAATATAATATCCTTATAACTA
* *
2338 TTTTATTTTTACCATTTTACTATTTTAC
66 TTTTATTTTTACCATATTACTAATTTAC
* * *
2366 TTTTATAGTCTTACTAAACTAAAAACTCTATTTATATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTCTTACTAAACTAAAAACTCCATTTATATTTAATTAAATATAATATCCTTATAACTA
*
2431 TTTTATTTTTACGATATTACTAATTTA
66 TTTTATTTTTACCATATTACTAATTTA
2458 ATTAAAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (93 bp):
TTTTATAGTCTTACTAAACTAAAAACTCCATTTATATTTAATTAAATATAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC
Found at i:4260 original size:10 final size:11
Alignment explanation
Indices: 4241--4265 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4231 CCTGACTATC
4241 TTTTCTTTTTT
1 TTTTCTTTTTT
4252 TTTTCTTTTTT
1 TTTTCTTTTTT
4263 TTT
1 TTT
4266 ATTTGTTTCA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:4867 original size:73 final size:72
Alignment explanation
Indices: 4727--4874 Score: 188
Period size: 73 Copynumber: 2.0 Consensus size: 72
4717 AAATACATAT
* * * *
4727 ATTTTTACGAATGTTTCATATGAGTCAATGAACACTTAACATAGTTTAATCCAATTGAGGTGTGC
1 ATTTTTACGAATGTTTCATATGAGCCAATAAACACTTAACATAGTTAAATCCAATTGAGGTGAGC
*
4792 ACTCCCA
66 ACTCACA
** * * * *
4799 ATTTTTATTAATGTTTCATATGGGCCCAATAAACACTTAACATGGTTAAATTCAATTGGGGTGAG
1 ATTTTTACGAATGTTTCATATGAG-CCAATAAACACTTAACATAGTTAAATCCAATTGAGGTGAG
4864 CACTCACA
65 CACTCACA
4872 ATT
1 ATT
4875 ATTTTGGATG
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
72 21 0.33
73 43 0.67
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (72 bp):
ATTTTTACGAATGTTTCATATGAGCCAATAAACACTTAACATAGTTAAATCCAATTGAGGTGAGC
ACTCACA
Found at i:12090 original size:30 final size:31
Alignment explanation
Indices: 12054--12124 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
12044 GGCGAAAATG
* *
12054 CAATTCAGGAAACACCGTTA-CGACTTGTGT
1 CAATTCAGGAAACAACATTATCGACTTGTGT
* * * *
12084 CAATTCAAGATATAACATTATCGAGTTGTGT
1 CAATTCAGGAAACAACATTATCGACTTGTGT
12115 CAATTCAGGA
1 CAATTCAGGA
12125 TAAATTGCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (31 bp):
CAATTCAGGAAACAACATTATCGACTTGTGT
Found at i:13534 original size:19 final size:19
Alignment explanation
Indices: 13494--13537 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
13484 AAAAGATAAC
* *
13494 TTTTTTATCTTTTTGTTTT
1 TTTTTTAACTTTTTGTTCT
13513 TTTTTTAACTTTTT-TTCCT
1 TTTTTTAACTTTTTGTT-CT
13532 TTTTTT
1 TTTTTT
13538 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (19 bp):
TTTTTTAACTTTTTGTTCT
Found at i:21351 original size:33 final size:33
Alignment explanation
Indices: 21307--21376 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
21297 CCAAATGAGT
* *
21307 TGATCTAAGATTACCACCCAAGATCACCATGGG
1 TGATCTAAGATTACCACCCAAAATCACCACGGG
* *
21340 TGATCTGAGATTACCACCTAAAATCACCACGGG
1 TGATCTAAGATTACCACCCAAAATCACCACGGG
21373 TGAT
1 TGAT
21377 TTGCAAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (33 bp):
TGATCTAAGATTACCACCCAAAATCACCACGGG
Found at i:28488 original size:16 final size:16
Alignment explanation
Indices: 28463--28536 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
28453 CGGGTTGATC
28463 GGGTTCGGGTCATTTT
1 GGGTTCGGGTCATTTT
*
28479 GGGTTTGGGTCATTTT
1 GGGTTCGGGTCATTTT
* * *
28495 CGGGATCGGATC-GTTT
1 -GGGTTCGGGTCATTTT
* * *
28511 GGATTCGGGTAATTTC
1 GGGTTCGGGTCATTTT
28527 GGGTTCGGGT
1 GGGTTCGGGT
28537 ACCCAAAATT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
15 7 0.16
16 29 0.66
17 8 0.18
ACGTcount: A:0.09, C:0.12, G:0.39, T:0.39
Consensus pattern (16 bp):
GGGTTCGGGTCATTTT
Found at i:31464 original size:2 final size:2
Alignment explanation
Indices: 31453--31497 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
31443 ATCTATATTT
* *
31453 TA TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TC TG TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31492 TA TA TA
1 TA TA TA
31498 AAAGTATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32750 original size:22 final size:22
Alignment explanation
Indices: 32722--32954 Score: 123
Period size: 22 Copynumber: 10.5 Consensus size: 22
32712 TCTCTTTGTG
*
32722 TGGTTATTAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
32744 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
32767 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * * *
32788 TGGTTACCAAAGTTTCATATGG
1 TGGTTATCAAAATTTCATAAGA
* *
32810 TAGTTATCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
32832 AGGTTATCAAAGTTGCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
32854 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
32876 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** *
32900 AGGTTATTGAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * *
32922 TGGTTATCACAATTTTATAAAA
1 TGGTTATCAAAATTTCATAAGA
*
32944 AGGTTATCAAA
1 TGGTTATCAAA
32955 TAGATTATCA
Statistics
Matches: 157, Mismatches: 44, Indels: 20
0.71 0.20 0.09
Matches are distributed among these distances:
20 1 0.01
21 2 0.01
22 130 0.83
23 6 0.04
24 18 0.11
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:32825 original size:66 final size:67
Alignment explanation
Indices: 32719--32936 Score: 221
Period size: 66 Copynumber: 3.3 Consensus size: 67
32709 TCTTCTCTTT
** * * *
32719 GTGTGGTTATTAAAATTTCATAAGAT--GGTTATTATAATTTCATGAGGAGGTTATCAAAATTCC
1 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATCAAAATTTCAT-AGGAGGTTATCAAAATTCC
32782 ATA
65 ATA
* * * *
32785 GTGTGGTTACCAAAGTTTCATATGG-T-A-GTTATCAAAATTTCATATGAAGGTTATCAAAGTTG
1 GTGTGGTTACCAAAATTTCATA-GGATCAGGTTATCAAAATTTCATA-GGAGGTTATCAAAATTC
32847 CATA
64 CATA
* * ** *
32851 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATCAAAATTTCATAGG-AGGTTATCAAAATTCC
32916 ATA
65 ATA
* *
32919 GTGTGGTTATCACAATTT
1 GTGTGGTTACCAAAATTT
32937 TATAAAAAGG
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
65 3 0.02
66 74 0.59
67 3 0.02
68 46 0.37
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (67 bp):
GTGTGGTTACCAAAATTTCATAGGATCAGGTTATCAAAATTTCATAGGAGGTTATCAAAATTCCA
TA
Found at i:33072 original size:22 final size:21
Alignment explanation
Indices: 32959--33285 Score: 101
Period size: 22 Copynumber: 14.7 Consensus size: 21
32949 ATCAAATAGA
* * *
32959 TTATCAAAATGTCGTAGTGAGG
1 TTATCAAAATTTCATAG-AAGG
**
32981 TTA-CAAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-AAGG
* * *
33003 TTAACAACATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGAAGG
* * *
33025 TTA-CTAACATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGAAGG
33047 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GAAGG
* *
33069 TTAT-AAAAGTCTCAATTTCATAAGG
1 TTATCAAAA-TTTC-A--T-AGAAGG
* * *
33094 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGAAGG
*
33116 TTATC-AAATCTCATAG-AGTG
1 TTATCAAAATTTCATAGAAG-G
* * * *
33136 ATTACCGAAATCTCATAGAGATCAGA
1 -TTATCAAAATTTCAT--AGA--AGG
* *
33162 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-AAGG
*
33184 TTATCAAAATTAT-ATA-ATGTG
1 TTATCAAAATT-TCATAGAAG-G
*
33205 ATTATCAAAATTTCATAGAGGGG
1 -TTATCAAAATTTCATAGA-AGG
* * *
33228 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
33250 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGA-AGG
*
33272 TTATCAAATTTTCA
1 TTATCAAAATTTCA
33286 AAATGTGATT
Statistics
Matches: 235, Mismatches: 42, Indels: 56
0.71 0.13 0.17
Matches are distributed among these distances:
19 2 0.01
20 11 0.05
21 17 0.07
22 161 0.69
23 13 0.06
24 3 0.01
25 17 0.07
26 5 0.02
27 6 0.03
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAGG
Found at i:33211 original size:44 final size:44
Alignment explanation
Indices: 33160--33305 Score: 154
Period size: 44 Copynumber: 3.3 Consensus size: 44
33150 ATAGAGATCA
* *
33160 GATTATCAAAATTTCAAAGCGAGGTTATCAAAATTATATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTTATAATGT
* * * * *
33204 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGA-GA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTTATA-ATGT
* *
33248 GGTTATCAAAATTTCATAA-AGAGGTTATC-AAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTT-ATAATGT
*
33292 GATTACCAAAATTT
1 GATTATCAAAATTT
33306 TATAGTGGTA
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
43 8 0.10
44 72 0.88
45 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTTATAATGT
Found at i:33631 original size:23 final size:22
Alignment explanation
Indices: 33391--33974 Score: 257
Period size: 22 Copynumber: 26.9 Consensus size: 22
33381 TTATGGAGTA
*
33391 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
33411 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
33433 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
33455 TTCAAATTTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * * *
33477 ATCAAAATTTTATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
33499 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
** * **
33521 AAAAAAAGTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* ** *
33543 CTCAAAAAATCATAGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
33565 ATCAAAATTT--T---TA-GTT
1 ATCAAAATTTCATAGGGAGGTT
** *
33581 ATCAGGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
33603 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
33626 ATCAAAATTTTATA-GAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
*
33648 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
33670 ATCACAATTTCACAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
** * * * *
33692 ATTTAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
33714 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * ** *
33736 TTTAAAATTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
33758 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
33780 ATCAACATCTCATAGTGTTA-GTT
1 ATCAAAATTTCATAG-G-GAGGTT
* * *
33803 ATCAAAATTTTATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
33825 ATCAAAATTTCATAGTGAAGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
33848 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
33869 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** ***
33891 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * * **
33912 CTCGAAATTCCATAGTGTCGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
33934 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
33956 ATCAGAATTTCATAAGGAG
1 ATCAAAATTTCATAGGGAG
33975 ATCATCAATA
Statistics
Matches: 415, Mismatches: 124, Indels: 48
0.71 0.21 0.08
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 1 0.00
20 13 0.03
21 22 0.05
22 325 0.78
23 41 0.10
24 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:33981 original size:22 final size:22
Alignment explanation
Indices: 33939--33981 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
33929 TCGTTATTAA
* *
33939 AATTTCATAGGAAGGTTATCAG
1 AATTTCATAGGAAGATCATCAG
33961 AATTTCATAAGG-AGATCATCA
1 AATTTCAT-AGGAAGATCATCA
33982 ATAATAGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (22 bp):
AATTTCATAGGAAGATCATCAG
Found at i:36532 original size:5 final size:5
Alignment explanation
Indices: 36511--36566 Score: 67
Period size: 5 Copynumber: 10.2 Consensus size: 5
36501 TTAAGATTAG
36511 TATATA TATATA TATAA TATAA TATAA TATAA TATAACA GTATAA TATAA
1 TATA-A TATA-A TATAA TATAA TATAA TATAA TAT-A-A -TATAA TATAA
36561 TATAA T
1 TATAA T
36567 TCCTTTAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
5 30 0.64
6 12 0.26
7 2 0.04
8 3 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:36980 original size:43 final size:43
Alignment explanation
Indices: 36932--37016 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
36922 ATGTTCTGGT
* *
36932 GATTTTAAAAATGGAGGAATAGCGCGTAAATTACACAAATAAA
1 GATTTTAAAAATAGAGGAATAGCGAGTAAATTACACAAATAAA
*
36975 GATTTTAAAGATAGAGGAATAGCGAGTAAATTACACAAATAA
1 GATTTTAAAAATAGAGGAATAGCGAGTAAATTACACAAATAA
37017 TCAAGGAGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (43 bp):
GATTTTAAAAATAGAGGAATAGCGAGTAAATTACACAAATAAA
Found at i:39636 original size:17 final size:16
Alignment explanation
Indices: 39612--39648 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
39602 GAAGTATAAA
39612 AGAAAAGAGAATATAG
1 AGAAAAGAGAATATAG
*
39628 AGAACAAGAGAATATGG
1 AGAA-AAGAGAATATAG
39645 AGAA
1 AGAA
39649 GGGGAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.59, C:0.03, G:0.27, T:0.11
Consensus pattern (16 bp):
AGAAAAGAGAATATAG
Found at i:42974 original size:2 final size:2
Alignment explanation
Indices: 42967--42993 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42957 GTTTCTTATG
42967 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 T
42994 CATTGAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46163 original size:1 final size:1
Alignment explanation
Indices: 46157--46188 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
46147 AGTACCTTCC
46157 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46189 CCTTTTCCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:56246 original size:27 final size:26
Alignment explanation
Indices: 56206--56309 Score: 93
Period size: 27 Copynumber: 3.8 Consensus size: 26
56196 AATGGAGTAG
* *
56206 AAATGACCACAATGCGCCCTGAAGCAC
1 AAATGACCAAAATGC-CCCTGGAGCAC
* * * *
56233 AAATGACTAAAATGCCCCCTAGGTGTAA
1 AAATGACCAAAATG-CCCCT-GGAGCAC
56261 AAATGACCAAAATGCCCCTGGA-CATGC
1 AAATGACCAAAATGCCCCTGGAGCA--C
*
56288 AAATGACTAAAATGCCCCTGGA
1 AAATGACCAAAATGCCCCTGGA
56310 TTTTGAAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
25 1 0.02
26 2 0.03
27 42 0.68
28 17 0.27
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.16
Consensus pattern (26 bp):
AAATGACCAAAATGCCCCTGGAGCAC
Found at i:57684 original size:16 final size:15
Alignment explanation
Indices: 57646--57687 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
57636 ACAGAGGTTG
57646 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
57661 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
57676 ACTAGAAAACAA
1 AC-AGAAAACAA
57688 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.