Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013346.1 Corchorus olitorius cultivar O-4 contig13379, 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: 65454
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2031 original size:51 final size:52
Alignment explanation
Indices: 1976--2074 Score: 182
Period size: 51 Copynumber: 1.9 Consensus size: 52
1966 TGTTAATCTA
*
1976 TTATACTTCTAATTATGGTAATTATATCATTATTATTATTA-TTATTGACCT
1 TTATACTTCTAATTATGGTAATTATATAATTATTATTATTATTTATTGACCT
2027 TTATACTTCTAATTATGGTAATTATATAATTATTATTATTATTTATTG
1 TTATACTTCTAATTATGGTAATTATATAATTATTATTATTATTTATTG
2075 GCCTAGGGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 40 0.87
52 6 0.13
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.55
Consensus pattern (52 bp):
TTATACTTCTAATTATGGTAATTATATAATTATTATTATTATTTATTGACCT
Found at i:2482 original size:16 final size:16
Alignment explanation
Indices: 2458--2488 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2448 TGAACCCTAG
*
2458 TTCTTAATGTCCAAAA
1 TTCTCAATGTCCAAAA
2474 TTCTCAATGTCCAAA
1 TTCTCAATGTCCAAA
2489 GGAAATTTCG
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:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (16 bp):
TTCTCAATGTCCAAAA
Found at i:7697 original size:55 final size:55
Alignment explanation
Indices: 7634--7744 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
7624 CATTCCTTTT
**
7634 AAATCATCGAGATCAAGCTGTCAAGTCCTCGAAAACTTTTCCAGGAGATCGAATC
1 AAATCATCGAGATCAAGCTGTCAAGTCCTCGAAAACGATTCCAGGAGATCGAATC
* *
7689 AAATCATCGAGATCAAGCTGTCAAGTTCTCGAAAACGATTCTAGGAGATCGAATC
1 AAATCATCGAGATCAAGCTGTCAAGTCCTCGAAAACGATTCCAGGAGATCGAATC
7744 A
1 A
7745 GAGGATTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (55 bp):
AAATCATCGAGATCAAGCTGTCAAGTCCTCGAAAACGATTCCAGGAGATCGAATC
Found at i:8028 original size:22 final size:22
Alignment explanation
Indices: 8003--8044 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7993 AGACTTAGGG
*
8003 TTTATAGTTTTAGGATTTAGTA
1 TTTAGAGTTTTAGGATTTAGTA
* *
8025 TTTAGGGTTTTAGGGTTTAG
1 TTTAGAGTTTTAGGATTTAG
8045 CTAGGAACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.52
Consensus pattern (22 bp):
TTTAGAGTTTTAGGATTTAGTA
Found at i:8506 original size:42 final size:42
Alignment explanation
Indices: 8460--8543 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
8450 TCAATTCCAA
8460 TTTTTGTTTTTTATTTATTTATTCAATAACCACATTGGATCCT
1 TTTTTGTTTTTT-TTTATTTATTCAATAACCACATTGGATCCT
*
8503 TTTTTGTTTTTTTTTATTTATTCAATAACCATATTGGATCC
1 TTTTTGTTTTTTTTTATTTATTCAATAACCACATTGGATCC
8544 CGATTAGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 28 0.70
43 12 0.30
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (42 bp):
TTTTTGTTTTTTTTTATTTATTCAATAACCACATTGGATCCT
Found at i:10301 original size:2 final size:2
Alignment explanation
Indices: 10294--10318 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10284 TTAATGGTCA
10294 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
10319 ACCATAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12245 original size:20 final size:21
Alignment explanation
Indices: 12220--12259 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12210 AGAATTGTTA
12220 ACAGA-GAAAAATTGTTTCTT
1 ACAGAGGAAAAATTGTTTCTT
**
12240 ACAGAGGAAGTATTGTTTCT
1 ACAGAGGAAAAATTGTTTCT
12260 CCCACTATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
ACAGAGGAAAAATTGTTTCTT
Found at i:12665 original size:15 final size:15
Alignment explanation
Indices: 12641--12673 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
12631 AGGTTACATC
12641 TTTTATTTTTTATTAT
1 TTTTATTTTTTATT-T
12657 TTTTA-TTTTTATTT
1 TTTTATTTTTTATTT
12671 TTT
1 TTT
12674 ATATAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTATTTTTTATTT
Found at i:22981 original size:16 final size:16
Alignment explanation
Indices: 22946--23003 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
22936 ACCTGAACAT
*
22946 GAACCCAAAAAAACC-
1 GAACCCGAAAAAACCA
*
22961 GAACCCGAAAAAGCTCA
1 GAACCCGAAAAAAC-CA
22978 -AACCCGAAAAAACCA
1 GAACCCGAAAAAACCA
22993 GAACCCGAAAA
1 GAACCCGAAAA
23004 TTCTGAAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 14 0.38
16 23 0.62
ACGTcount: A:0.55, C:0.31, G:0.12, T:0.02
Consensus pattern (16 bp):
GAACCCGAAAAAACCA
Found at i:22997 original size:32 final size:31
Alignment explanation
Indices: 22947--23029 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 31
22937 CCTGAACATG
*
22947 AACCCAAAAAAACCGAACCCGAAAAAGCTCA
1 AACCCGAAAAAACCGAACCCGAAAAAGCTCA
** *
22978 AACCCGAAAAAACCAGAACCCGAAAATTCTGA
1 AACCCGAAAAAACC-GAACCCGAAAAAGCTCA
*
23010 AACCCGATAAAATCCGAACC
1 AACCCGA-AAAAACCGAACC
23030 TGAACCTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.29
32 26 0.58
33 6 0.13
ACGTcount: A:0.51, C:0.31, G:0.11, T:0.07
Consensus pattern (31 bp):
AACCCGAAAAAACCGAACCCGAAAAAGCTCA
Found at i:23283 original size:32 final size:32
Alignment explanation
Indices: 23242--23333 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 32
23232 ACCTGAACCT
* * *
23242 GAATTAACCTTACCCAAAATTGACCCGAACTC
1 GAATCAACCTAACCCAAAATTAACCCGAACTC
*
23274 GAATCAACCTAACCCAAATTTAACCCGAACTC
1 GAATCAACCTAACCCAAAATTAACCCGAACTC
23306 GAATCAACCTAACCC-AAATCTAACCCGA
1 GAATCAACCTAACCCAAAAT-TAACCCGA
23334 TCTGACTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 3 0.06
32 51 0.94
ACGTcount: A:0.40, C:0.34, G:0.08, T:0.18
Consensus pattern (32 bp):
GAATCAACCTAACCCAAAATTAACCCGAACTC
Found at i:23314 original size:16 final size:16
Alignment explanation
Indices: 23264--23314 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
23254 CCCAAAATTG
23264 ACCCGAACTCGAATCA
1 ACCCGAACTCGAATCA
* * * *
23280 A-CCTAACCCAAATTTA
1 ACCCGAACTCGAA-TCA
23296 ACCCGAACTCGAATCA
1 ACCCGAACTCGAATCA
23312 ACC
1 ACC
23315 TAACCCAAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 8 0.32
16 9 0.36
17 8 0.32
ACGTcount: A:0.39, C:0.37, G:0.08, T:0.16
Consensus pattern (16 bp):
ACCCGAACTCGAATCA
Found at i:24724 original size:6 final size:6
Alignment explanation
Indices: 24713--24772 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
24703 TTGACAGCGC
*
24713 AACAAA AAC-AA AACGAA AAC-AA AACAAA AACAAA AACGAAA AACAGAAA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AAC-AAA AAC--AAA
*
24762 AACGAA AACAA
1 AACAAA AACAA
24773 TGCCAAACGT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
5 10 0.21
6 25 0.52
7 6 0.12
8 7 0.15
ACGTcount: A:0.77, C:0.17, G:0.07, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:24764 original size:15 final size:13
Alignment explanation
Indices: 24716--24769 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 13
24706 ACAGCGCAAC
24716 AAAAAC-AAAACG
1 AAAAACAAAAACG
24728 -AAAAC-AAAAC-
1 AAAAACAAAAACG
24738 AAAAACAAAAACG
1 AAAAACAAAAACG
24751 AAAAACAGAAAAACG
1 AAAAAC--AAAAACG
24766 AAAA
1 AAAA
24770 CAATGCCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 15 0.41
12 5 0.14
13 6 0.16
15 11 0.30
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAACG
Found at i:24856 original size:11 final size:11
Alignment explanation
Indices: 24840--24873 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
24830 TGCTTTACAC
24840 GTGAAAGTGAG
1 GTGAAAGTGAG
24851 GTGAAAGTGAG
1 GTGAAAGTGAG
24862 GTGAAAGTGAG
1 GTGAAAGTGAG
24873 G
1 G
24874 ATAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (11 bp):
GTGAAAGTGAG
Found at i:26406 original size:21 final size:25
Alignment explanation
Indices: 26362--26409 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 25
26352 AATCAAGGCC
26362 TGCTTGTACAAATGTTGTTGCAGCT
1 TGCTTGTACAAATGTTGTTGCAGCT
26387 TGCTT-TA-AAATGTT-TT-CAGCT
1 TGCTTGTACAAATGTTGTTGCAGCT
26408 TG
1 TG
26410 GCCTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 7 0.30
24 2 0.09
25 5 0.22
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (25 bp):
TGCTTGTACAAATGTTGTTGCAGCT
Found at i:27606 original size:31 final size:29
Alignment explanation
Indices: 27568--27703 Score: 94
Period size: 31 Copynumber: 4.4 Consensus size: 29
27558 TTATTAGCCT
***
27568 TTTTGCCCACTGAACTATTGCATCAAGGACG
1 TTTTGCCCACTGAACT-TCAAATC-AGGACG
*
27599 TTTTGCCCCCTGAACTTCAAATCAGGACG
1 TTTTGCCCACTGAACTTCAAATCAGGACG
* *
27628 TTTTGCCC-CTTGAATTTTCAAATTCAGGACA
1 TTTTGCCCAC-TGAA-CTTCAAA-TCAGGACG
* * *
27659 TTTTGCCCCCTAAACTTCCCAAATTCAGGACA
1 TTTTGCCCACTGAACTT--CAAA-TCAGGACG
* *
27691 TTTTACCCCCTGA
1 TTTTGCCCACTGA
27704 CGGAGGGGGC
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.01
29 18 0.20
30 12 0.13
31 33 0.37
32 25 0.28
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (29 bp):
TTTTGCCCACTGAACTTCAAATCAGGACG
Found at i:27682 original size:32 final size:30
Alignment explanation
Indices: 27593--27703 Score: 134
Period size: 32 Copynumber: 3.6 Consensus size: 30
27583 TATTGCATCA
*
27593 AGGACGTTTTGCCCCCTGAACTTCAAA-TC
1 AGGACATTTTGCCCCCTGAACTTCAAATTC
* * *
27622 AGGACGTTTTGCCCCTTGAATTTTCAAATTC
1 AGGACATTTTGCCCCCTGAA-CTTCAAATTC
*
27653 AGGACATTTTGCCCCCTAAACTTCCCAAATTC
1 AGGACATTTTGCCCCCTGAACTT--CAAATTC
*
27685 AGGACATTTTACCCCCTGA
1 AGGACATTTTGCCCCCTGA
27704 CGGAGGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
29 19 0.27
30 8 0.11
31 19 0.27
32 24 0.34
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (30 bp):
AGGACATTTTGCCCCCTGAACTTCAAATTC
Found at i:31013 original size:20 final size:20
Alignment explanation
Indices: 30988--31025 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
30978 GTGTGAGTTT
30988 ACACAAGCATACACTTGCGC
1 ACACAAGCATACACTTGCGC
31008 ACACAAGCATACACTTGC
1 ACACAAGCATACACTTGC
31026 TCACTCCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.34, G:0.13, T:0.16
Consensus pattern (20 bp):
ACACAAGCATACACTTGCGC
Found at i:38611 original size:36 final size:35
Alignment explanation
Indices: 38571--38640 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
38561 CAACCAAATC
* * * *
38571 GATGCAAGGACAAGATTAAACCGGATGGATATAAGA
1 GATGCAAAGAAAAGAGTAAACCGGACGGAT-TAAGA
38607 GATGCAAAGAAAAGAGTAAACCGGACGGATTAAG
1 GATGCAAAGAAAAGAGTAAACCGGACGGATTAAG
38641 TAGGGATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.46, C:0.11, G:0.29, T:0.14
Consensus pattern (35 bp):
GATGCAAAGAAAAGAGTAAACCGGACGGATTAAGA
Found at i:50062 original size:15 final size:15
Alignment explanation
Indices: 50042--50070 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
50032 CTTTGGTGTT
50042 TATTATTTCTATTAA
1 TATTATTTCTATTAA
50057 TATTATTTCTATTA
1 TATTATTTCTATTA
50071 GACATATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTTCTATTAA
Found at i:54023 original size:349 final size:351
Alignment explanation
Indices: 53604--54285 Score: 1147
Period size: 351 Copynumber: 1.9 Consensus size: 351
53594 TCCGAAAGAC
* *
53604 ATTTGCACGACAAAAAAGAAAAAGATCATCCAAAAAAAAAAAACAGAGATGAGACAACCCATGAC
1 ATTTGCACGAAAAAAAAGAAAAAGATCATCC-AAAAAAAAAAACAGAAATGAGACAACCCATGAC
*
53669 TATTTCTCCCTACTTTGATCGGCTTCCATTGCCCCTCTTCCACTCTTTTGGTAATTAGATGACCA
65 TATTTCTCCCTACTTTGATCGGCTTCCATTGCCCCTCTTCCACTCTTTTGGTAATGAGATGACCA
*
53734 AACGGCTCCATGCATAGGAC-AAAAAATACGGTGATAAAGGATCACCTTGTCTAAAACCTTGTTG
130 AACGGCTCCATGCATAGGACAAAAAAATACAGTGATAAAGGATCACCTTGTCTAAAACCTTGTTG
*
53798 AGGATGGAAAGCTTCAAGTTGTTCACTAGGGCTACTAAAAAA-CTGACCGAACCGATTGAACCGA
195 AGGATGGAAAGCCTCAAGTTGTTCACTAGGGCTACTAAAAAATC-GACCGAACCGATTGAACCGA
* * *
53862 CCACACCGACTTGAAAATGGTGCAAACGATGCGGTTTAAATGGTGTAGTCGGTTTTAGCCGGTGT
259 CCACACCGACTTGAAAATGGTGCAAACGATGCGGTTTAAACGGTGCAGTCGGATTTAGCCGGTGT
53927 AAGGTGGCAGTCAAGCTAAACACTTTAG
324 AAGGTGGCAGTCAAGCTAAACACTTTAG
* * *
53955 ATTTGCATGAAAAAAAAGAAAAAAGATCATCC-GAAAAAAAAA-AGAAATGAGACAACCTATGAC
1 ATTTGCACGAAAAAAAAG-AAAAAGATCATCCAAAAAAAAAAACAGAAATGAGACAACCCATGAC
54018 TATTTCTCCCTACTTTGATCGGCTTCCATTGCCCCTCTTCCACTCTTTTGGTAATGAGATGACCA
65 TATTTCTCCCTACTTTGATCGGCTTCCATTGCCCCTCTTCCACTCTTTTGGTAATGAGATGACCA
*
54083 AGCGGCTCCATGCATAGGACAGAAAAAATACAGTGATAAAGGATCACCTTGTCTAAAACCTTGTT
130 AACGGCTCCATGCATAGGACA-AAAAAATACAGTGATAAAGGATCACCTTGTCTAAAACCTTGTT
* *
54148 GAGGATGGAAAGCCTCAAGTTGTTCACTAGGGTTGCTAAAAAATCGACCGAACCGATTGAACCGA
194 GAGGATGGAAAGCCTCAAGTTGTTCACTAGGGCTACTAAAAAATCGACCGAACCGATTGAACCGA
* * *
54213 CCGCACCGACTTGAAAATGGTGCAAACGGTGCGGTTTAAACGGTGCAGTCGGATTTAGTCGGTGT
259 CCACACCGACTTGAAAATGGTGCAAACGATGCGGTTTAAACGGTGCAGTCGGATTTAGCCGGTGT
54278 AAGGTGGC
324 AAGGTGGC
54286 GGTTCAAACC
Statistics
Matches: 310, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
349 102 0.33
350 9 0.03
351 185 0.60
352 14 0.05
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (351 bp):
ATTTGCACGAAAAAAAAGAAAAAGATCATCCAAAAAAAAAAACAGAAATGAGACAACCCATGACT
ATTTCTCCCTACTTTGATCGGCTTCCATTGCCCCTCTTCCACTCTTTTGGTAATGAGATGACCAA
ACGGCTCCATGCATAGGACAAAAAAATACAGTGATAAAGGATCACCTTGTCTAAAACCTTGTTGA
GGATGGAAAGCCTCAAGTTGTTCACTAGGGCTACTAAAAAATCGACCGAACCGATTGAACCGACC
ACACCGACTTGAAAATGGTGCAAACGATGCGGTTTAAACGGTGCAGTCGGATTTAGCCGGTGTAA
GGTGGCAGTCAAGCTAAACACTTTAG
Found at i:54215 original size:18 final size:19
Alignment explanation
Indices: 54192--54227 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
54182 GCTAAAAAAT
54192 CGACCGAACCGA-TTGAAC
1 CGACCGAACCGACTTGAAC
*
54210 CGACCGCACCGACTTGAA
1 CGACCGAACCGACTTGAA
54228 AATGGTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.36, G:0.22, T:0.11
Consensus pattern (19 bp):
CGACCGAACCGACTTGAAC
Found at i:55110 original size:35 final size:35
Alignment explanation
Indices: 55064--55141 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
55054 TATTACCAAT
*
55064 TTGTAATCTTATTGCAAGGATTTGATGATGATTGA
1 TTGTATTCTTATTGCAAGGATTTGATGATGATTGA
55099 TTGTATTCTTATTGCAAGGATTTGATGATGATTGA
1 TTGTATTCTTATTGCAAGGATTTGATGATGATTGA
55134 TTGGTATT
1 TT-GTATT
55142 TGTATTCTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 36 0.88
36 5 0.12
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (35 bp):
TTGTATTCTTATTGCAAGGATTTGATGATGATTGA
Found at i:56573 original size:32 final size:32
Alignment explanation
Indices: 56490--56575 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
56480 CCAAAATAGT
* * ** *
56490 GGCGCTTTATTCAGTAAACAACCCTACTTTGG
1 GGCGTTTTATTCAGAAAACGCCCCTACTCTGG
* * *
56522 GGAGTTTTCTCCA-ATAAACGCCCCTACTCTGG
1 GGCGTTTTATTCAGA-AAACGCCCCTACTCTGG
56554 GGCGTTTTATTCAGAAAACGCC
1 GGCGTTTTATTCAGAAAACGCC
56576 ACTATTTTGG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (32 bp):
GGCGTTTTATTCAGAAAACGCCCCTACTCTGG
Found at i:61597 original size:54 final size:54
Alignment explanation
Indices: 61508--61630 Score: 201
Period size: 54 Copynumber: 2.3 Consensus size: 54
61498 TGTATGCATG
* *
61508 TGAGCTATAAATGCAGATATAATTGCTTGTAAAAGGTTATGTGATTGAAGCAAT
1 TGAGCTATAAATGCAGATATAATTGCATGTAAAAGGTTATGTAATTGAAGCAAT
* *
61562 TGAGCTATAGATGCAGATATAATTGCATGTTAAAGGTTATGTAATTGAAGCAAT
1 TGAGCTATAAATGCAGATATAATTGCATGTAAAAGGTTATGTAATTGAAGCAAT
*
61616 TGAGCTATTAATGCA
1 TGAGCTATAAATGCA
61631 CAAAATTAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (54 bp):
TGAGCTATAAATGCAGATATAATTGCATGTAAAAGGTTATGTAATTGAAGCAAT
Done.