Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014279.1 Corchorus capsularis cultivar CVL-1 contig14300, 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: 63098
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:770 original size:25 final size:25
Alignment explanation
Indices: 731--785 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
721 GACCGATCAT
*
731 GCAAGCACAGCCTCGTTTGCTAAAC
1 GCAAGCACAGCCTCGTTTGCCAAAC
756 GCAAGCACAAG-CTCGTTTGCCAAAC
1 GCAAGCAC-AGCCTCGTTTGCCAAAC
781 GCAAG
1 GCAAG
786 AACATGAGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (25 bp):
GCAAGCACAGCCTCGTTTGCCAAAC
Found at i:797 original size:25 final size:25
Alignment explanation
Indices: 744--798 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
734 AGCACAGCCT
* * **
744 CGTTTGCTAAACGCAAGCACAAGCT
1 CGTTTGCCAAACGCAAGAACAAGAG
*
769 CGTTTGCCAAACGCAAGAACATGAG
1 CGTTTGCCAAACGCAAGAACAAGAG
794 CGTTT
1 CGTTT
799 ACCCAGTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (25 bp):
CGTTTGCCAAACGCAAGAACAAGAG
Found at i:3500 original size:18 final size:17
Alignment explanation
Indices: 3477--3512 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
3467 CTCAACCTAA
3477 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
3495 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
3512 A
1 A
3513 TGAAAAGAAA
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:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:3990 original size:10 final size:10
Alignment explanation
Indices: 3975--3999 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3965 TAACTCCAAT
3975 TATGGACTTA
1 TATGGACTTA
3985 TATGGACTTA
1 TATGGACTTA
3995 TATGG
1 TATGG
4000 GCTGAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (10 bp):
TATGGACTTA
Found at i:8527 original size:19 final size:18
Alignment explanation
Indices: 8503--8538 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8493 TGAAGATTTC
8503 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
8522 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
8539 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:12247 original size:6 final size:6
Alignment explanation
Indices: 12236--12272 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
12226 ATAATTGTTA
12236 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
12273 CTTTGCTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:12614 original size:27 final size:28
Alignment explanation
Indices: 12565--12620 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
12555 CCGTTTTTTC
*
12565 TAAAAAAAAATTTGCGTCGAAAA-AAAT
1 TAAAAAAAAATTTGCGTCAAAAATAAAT
*
12592 TAAAAAAAAATTT-TGTCAAAAAATAAAT
1 TAAAAAAAAATTTGCGTC-AAAAATAAAT
12620 T
1 T
12621 TAGGTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.12
27 17 0.68
28 5 0.20
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (28 bp):
TAAAAAAAAATTTGCGTCAAAAATAAAT
Found at i:19800 original size:25 final size:25
Alignment explanation
Indices: 19766--19819 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
19756 TAAGTTAACT
19766 TGGTAAGAATATTCTGAGTCTATGA
1 TGGTAAGAATATTCTGAGTCTATGA
19791 TGGTAAGAATATTCTGAGTCTATGA
1 TGGTAAGAATATTCTGAGTCTATGA
19816 TGGT
1 TGGT
19820 TGAAGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (25 bp):
TGGTAAGAATATTCTGAGTCTATGA
Found at i:21161 original size:25 final size:25
Alignment explanation
Indices: 21133--21199 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
21123 GCAGCCTATG
21133 CGTTTGCTAAACGCAAGCACAACCT
1 CGTTTGCTAAACGCAAGCACAACCT
**
21158 CGTTTGCTAAACGCAAGCACAGGCT
1 CGTTTGCTAAACGCAAGCACAACCT
21183 CGTTTG-TCAAACGCAAG
1 CGTTTGCT-AAACGCAAG
21200 AACATGAGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (25 bp):
CGTTTGCTAAACGCAAGCACAACCT
Found at i:25474 original size:53 final size:53
Alignment explanation
Indices: 25394--25500 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
25384 CGGCTGTTTT
* *
25394 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTATGA
* *
25447 ATTTTATAAATTCTCTTATGAAAATTCAGTTAAGAAATCAAATTTTGTTATGA
1 ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTATGA
25500 A
1 A
25501 ATGATAACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (53 bp):
ATTTTATAAATTCTCTTAAGAAAATTCAGTTAAAAAATCAAATTTTGTTATGA
Found at i:26023 original size:3 final size:3
Alignment explanation
Indices: 26015--26082 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
26005 TATATATATT
* * * *
26015 ATA ATA ATA ATA ATA ATA AT- ATA GTA TATA ATA AT- ATT ATT ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
26059 ATG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
26083 TTATTATTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 52 0.90
4 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:26044 original size:38 final size:41
Alignment explanation
Indices: 25991--26098 Score: 127
Period size: 41 Copynumber: 2.7 Consensus size: 41
25981 ATAGTAGGTT
25991 TAAT-ATATAGTATAT-AT-ATA-TATTATAATAATAATAA
1 TAATAATATAGTATATAATAATATTATTATAATAATAATAA
* *
26028 TAATAATATAGTATATAATAATATTATTATTATGATAATAA
1 TAATAATATAGTATATAATAATATTATTATAATAATAATAA
* * *
26069 TAATAATAATAATAT-TATTATTATTATTAT
1 TAATAAT-ATAGTATATAATAATATTATTAT
26099 TATTATTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 4 0.07
38 11 0.18
39 2 0.03
40 3 0.05
41 35 0.57
42 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (41 bp):
TAATAATATAGTATATAATAATATTATTATAATAATAATAA
Found at i:26066 original size:32 final size:32
Alignment explanation
Indices: 26027--26092 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
26017 AATAATAATA
26027 ATAATAATATAGTATATAATAATATTATTATTATG
1 ATAATAATA-A-TA-ATAATAATATTATTATTATG
26062 ATAATAATAATAATAATAATATTATTATTAT
1 ATAATAATAATAATAATAATATTATTATTAT
26093 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 19 0.61
33 2 0.06
34 1 0.03
35 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
ATAATAATAATAATAATAATATTATTATTATG
Found at i:26087 original size:3 final size:3
Alignment explanation
Indices: 26081--26110 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
26071 ATAATAATAA
26081 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26111 CTTTTCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31631 original size:14 final size:14
Alignment explanation
Indices: 31612--31651 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
31602 GTCGGGTTGG
*
31612 ATTTGGGTTCGGTT
1 ATTTGGGTTAGGTT
31626 ATTTGGGTTAGGTT
1 ATTTGGGTTAGGTT
31640 AGTTTCGGGTTA
1 A-TTT-GGGTTA
31652 AGGAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.12, C:0.05, G:0.35, T:0.47
Consensus pattern (14 bp):
ATTTGGGTTAGGTT
Found at i:42158 original size:2 final size:2
Alignment explanation
Indices: 42153--42185 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
42143 TATAAAATGC
*
42153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42186 ATTTGCTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46461 original size:29 final size:29
Alignment explanation
Indices: 46429--46497 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
46419 CCATCAGGAC
46429 CAATTTGAAGGTCCAGATGATCTGAATGA
1 CAATTTGAAGGTCCAGATGATCTGAATGA
*
46458 CAATTTGAAGATCCAGATGATCTGAATGA
1 CAATTTGAAGGTCCAGATGATCTGAATGA
* *
46487 TAAATTGAAGG
1 CAATTTGAAGG
46498 CAACACCATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (29 bp):
CAATTTGAAGGTCCAGATGATCTGAATGA
Found at i:48052 original size:12 final size:12
Alignment explanation
Indices: 48035--48060 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48025 TCGTTTTTAC
48035 AGTAGAAGAAAT
1 AGTAGAAGAAAT
48047 AGTAGAAGAAAT
1 AGTAGAAGAAAT
48059 AG
1 AG
48061 CATTCAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (12 bp):
AGTAGAAGAAAT
Found at i:48909 original size:29 final size:30
Alignment explanation
Indices: 48866--48923 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
48856 AAATATTAAG
* *
48866 AATTAATTTTAAAAG-TACAATGGTTTGGA
1 AATTAATTTTAAAAGCAACAAGGGTTTGGA
* *
48895 AATTATTTTTTAAAGCAACAAGGGTTTGG
1 AATTAATTTTAAAAGCAACAAGGGTTTGG
48924 TCAAAAATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (30 bp):
AATTAATTTTAAAAGCAACAAGGGTTTGGA
Found at i:56254 original size:22 final size:21
Alignment explanation
Indices: 56209--56253 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
56199 TTTTTAGGGG
56209 TTTGCTAAACACCGCCCCCCT
1 TTTGCTAAACACCGCCCCCCT
*
56230 TTTGCTAAACACTGCCCCCCT
1 TTTGCTAAACACCGCCCCCCT
56251 TTT
1 TTT
56254 TATAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.42, G:0.09, T:0.31
Consensus pattern (21 bp):
TTTGCTAAACACCGCCCCCCT
Found at i:56565 original size:15 final size:15
Alignment explanation
Indices: 56541--56612 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 15
56531 AAATTACTTA
56541 GTTT-ATTAGTTTAT
1 GTTTAATTAGTTTAT
56555 GTTTAATTAG--TA-
1 GTTTAATTAGTTTAT
*
56567 -TCTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
56581 GATTAATTAG--TA-
1 GTTTAATTAGTTTAT
56593 -TTTAATTAGTTTAT
1 GTTTAATTAGTTTAT
*
56607 GATTAA
1 GTTTAA
56613 AATGAAGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
11 16 0.36
13 8 0.18
14 4 0.09
15 16 0.36
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (15 bp):
GTTTAATTAGTTTAT
Found at i:56574 original size:26 final size:26
Alignment explanation
Indices: 56545--56612 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
56535 TACTTAGTTT
*
56545 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
56571 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
56597 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
56613 AATGAAGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:56656 original size:24 final size:25
Alignment explanation
Indices: 56622--56680 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
56612 AAATGAAGGA
*
56622 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
56645 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
56670 AAATAAAGTTT
1 AAATGAAGTTT
56681 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:56780 original size:22 final size:21
Alignment explanation
Indices: 56751--56794 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
56741 CAAAAGTGTA
56751 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGGGGGCGGTATTTAGC
*
56772 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGGCGGTATTTAGC
56793 AA
1 AA
56795 TCCAGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.43, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGGCGGTATTTAGC
Found at i:61913 original size:20 final size:20
Alignment explanation
Indices: 61890--61931 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
61880 CATTTTGATT
*
61890 AAAAAAATATTTTTTTAAAA
1 AAAAAAATATATTTTTAAAA
*
61910 AAAAATATATATTTTTAAAA
1 AAAAAAATATATTTTTAAAA
61930 AA
1 AA
61932 CTTGGGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAAAATATATTTTTAAAA
Done.