Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017668.1 Corchorus olitorius cultivar O-4 contig17701, 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: 60085
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4201 original size:26 final size:26
Alignment explanation
Indices: 4165--4220 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
4155 CTAAACCCTA
4165 TATT-TTATTATAATATTATTATAAC
1 TATTATTATTATAATATTATTATAAC
4190 TATTATTATTATAATATTATTATAAC
1 TATTATTATTATAATATTATTATAAC
4216 TATTA
1 TATTA
4221 CTTTCATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTATTATTATAATATTATTATAAC
Found at i:11448 original size:21 final size:20
Alignment explanation
Indices: 11397--11460 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
11387 TTGACACTGT
*
11397 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATTAGA
11418 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATTAGA
11437 TTAGCTACTGTACAG-TTAAGA
1 TTAGC-ACTGTACAGATT-AGA
11458 TTA
1 TTA
11461 TTAGAGCAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 17 0.44
20 4 0.10
21 18 0.46
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATTAGA
Found at i:15759 original size:31 final size:31
Alignment explanation
Indices: 15724--15807 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
15714 TTTGTGCACG
** *
15724 TGGCATGCCATGTGTCACTTTTTGAAACACA
1 TGGCATGCCACATGTCACTTTTGGAAACACA
*
15755 TGGCATGCCACATGTCACTTTTGGATACACA
1 TGGCATGCCACATGTCACTTTTGGAAACACA
* **
15786 TGGCGTGATACATGTCACTTTT
1 TGGCATGCCACATGTCACTTTT
15808 TGGTACACGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (31 bp):
TGGCATGCCACATGTCACTTTTGGAAACACA
Found at i:15815 original size:31 final size:31
Alignment explanation
Indices: 15736--15876 Score: 142
Period size: 31 Copynumber: 4.5 Consensus size: 31
15726 GCATGCCATG
** * *
15736 TGTCACTTTTTGAAACACATGGCATGCCACA
1 TGTCACTTTTTGGTACACATGGCGTGCTACA
*
15767 TGTCAC-TTTTGGATACACATGGCGTGATACA
1 TGTCACTTTTTGG-TACACATGGCGTGCTACA
* *
15798 TGTCACTTTTTGGTACACGTGACGTGCCT-CA
1 TGTCACTTTTTGGTACACATGGCGTG-CTACA
* * *
15829 TGTCGCTTTTTGGTACACGTGGCGTGTTACA
1 TGTCACTTTTTGGTACACATGGCGTGCTACA
**
15860 TGTTGCTTTTTGGTACA
1 TGTCACTTTTTGGTACA
15877 TGTGGCAAGC
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
30 6 0.06
31 81 0.86
32 7 0.07
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (31 bp):
TGTCACTTTTTGGTACACATGGCGTGCTACA
Found at i:15872 original size:62 final size:62
Alignment explanation
Indices: 15736--15876 Score: 167
Period size: 62 Copynumber: 2.3 Consensus size: 62
15726 GCATGCCATG
** * * *
15736 TGTCACTTTTTGAAACACATGGCATGCCACATGTCACTTTTGGATACACATGGCGTGATACA
1 TGTCACTTTTTGGTACACGTGACGTGCCACATGTCACTTTTGGATACACATGGCGTGATACA
* * * *
15798 TGTCACTTTTTGGTACACGTGACGTGCCTCATGTCGCTTTTTGG-TACACGTGGCGTGTTACA
1 TGTCACTTTTTGGTACACGTGACGTGCCACATGTCAC-TTTTGGATACACATGGCGTGATACA
**
15860 TGTTGCTTTTTGGTACA
1 TGTCACTTTTTGGTACA
15877 TGTGGCAAGC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
62 61 0.91
63 6 0.09
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (62 bp):
TGTCACTTTTTGGTACACGTGACGTGCCACATGTCACTTTTGGATACACATGGCGTGATACA
Found at i:16080 original size:16 final size:15
Alignment explanation
Indices: 16059--16092 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
16049 CTAAACAAGC
16059 TTTTCTTTTTTTTTCT
1 TTTTCTTTTTTTTT-T
16075 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
16090 TTT
1 TTT
16093 GGGTAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:24723 original size:26 final size:26
Alignment explanation
Indices: 24694--24770 Score: 145
Period size: 26 Copynumber: 3.0 Consensus size: 26
24684 CTTGTCTCGC
24694 CGGCTATTTTGAATCAGTAAAGTCAA
1 CGGCTATTTTGAATCAGTAAAGTCAA
24720 CGGCTATTTTGAATCAGTAAAGTCAA
1 CGGCTATTTTGAATCAGTAAAGTCAA
*
24746 CGGCTATTTTGAATCAGTAATGTCA
1 CGGCTATTTTGAATCAGTAAAGTCA
24771 GTTGCATGGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (26 bp):
CGGCTATTTTGAATCAGTAAAGTCAA
Found at i:26284 original size:6 final size:6
Alignment explanation
Indices: 26273--26297 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
26263 CAACAAAACT
26273 AACTTC AACTTC AACTTC AACTTC A
1 AACTTC AACTTC AACTTC AACTTC A
26298 GCTTGATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
AACTTC
Found at i:26970 original size:3 final size:3
Alignment explanation
Indices: 26964--26996 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
26954 TCCCCCTCCT
*
26964 CCA CCA CCA CCA ACA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
26997 AACCTAGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:31613 original size:55 final size:55
Alignment explanation
Indices: 31547--31664 Score: 227
Period size: 55 Copynumber: 2.1 Consensus size: 55
31537 TAACACAAGA
*
31547 CAAAACTAATGGCATTTTAAACAAAAGAAAAGGAAATGGGTTTAAGCCTTAGATT
1 CAAAACTAATGGCATTTTAAACAAAAGAAAAGAAAATGGGTTTAAGCCTTAGATT
31602 CAAAACTAATGGCATTTTAAACAAAAGAAAAGAAAATGGGTTTAAGCCTTAGATT
1 CAAAACTAATGGCATTTTAAACAAAAGAAAAGAAAATGGGTTTAAGCCTTAGATT
31657 CAAAACTA
1 CAAAACTA
31665 TGCCTCTCCC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (55 bp):
CAAAACTAATGGCATTTTAAACAAAAGAAAAGAAAATGGGTTTAAGCCTTAGATT
Found at i:43621 original size:15 final size:15
Alignment explanation
Indices: 43601--43631 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43591 TTTCTTTTCT
43601 TCAATTCAGGAGAAG
1 TCAATTCAGGAGAAG
43616 TCAATTCAGGAGAAG
1 TCAATTCAGGAGAAG
43631 T
1 T
43632 ATATCATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (15 bp):
TCAATTCAGGAGAAG
Found at i:44094 original size:22 final size:23
Alignment explanation
Indices: 44069--44118 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
44059 AATGCTATAA
* **
44069 ATAAATTCTTTATTTGTTTT-AT
1 ATAAATACTTTATTCATTTTAAT
*
44091 ATAACTACTTTATTCATTTTAAT
1 ATAAATACTTTATTCATTTTAAT
44114 ATAAA
1 ATAAA
44119 GTTTCTGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (23 bp):
ATAAATACTTTATTCATTTTAAT
Found at i:44281 original size:2 final size:2
Alignment explanation
Indices: 44274--44346 Score: 76
Period size: 2 Copynumber: 36.5 Consensus size: 2
44264 ATACATACAT
* * * * *
44274 TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA CA TA CA T- TA GTC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
44316 TA CA 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 TA TA T
44347 GTATGTATGT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
1 1 0.02
2 55 0.96
3 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:49582 original size:13 final size:13
Alignment explanation
Indices: 49564--49588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49554 AAAAATAAAA
49564 TAATTATTAAATT
1 TAATTATTAAATT
49577 TAATTATTAAAT
1 TAATTATTAAAT
49589 GAAAATAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTATTAAATT
Found at i:50398 original size:18 final size:18
Alignment explanation
Indices: 50377--50411 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50367 CTGAGACTAA
50377 AAAATAAACTGACTCAAT
1 AAAATAAACTGACTCAAT
**
50395 AAAATTGACTGACTCAA
1 AAAATAAACTGACTCAA
50412 AACAACTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (18 bp):
AAAATAAACTGACTCAAT
Found at i:50580 original size:27 final size:27
Alignment explanation
Indices: 50539--50593 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
50529 GTCGAAACAC
* *
50539 TAAAGAAGAATTAAAAAACTGTGAAGA
1 TAAAGAAGAACTAAAAAACTGCGAAGA
50566 TAAAGAAGAACTAAAAAACTGCGAAGA
1 TAAAGAAGAACTAAAAAACTGCGAAGA
50593 T
1 T
50594 GGAGGAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.58, C:0.07, G:0.18, T:0.16
Consensus pattern (27 bp):
TAAAGAAGAACTAAAAAACTGCGAAGA
Found at i:50932 original size:4 final size:4
Alignment explanation
Indices: 50923--50954 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
50913 GCTGATTTGT
50923 TTTC TTTC TTTC -TTC TTTC TTT- TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
50955 AGTTCTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.23
4 20 0.77
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:50960 original size:18 final size:18
Alignment explanation
Indices: 50927--50961 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50917 ATTTGTTTTC
**
50927 TTTCTTTCTTCTTTCTTT
1 TTTCTTTCTTAGTTCTTT
50945 TTTCTTTCTTAGTTCTT
1 TTTCTTTCTTAGTTCTT
50962 CCTCTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTCTTTCTTAGTTCTTT
Found at i:50960 original size:22 final size:23
Alignment explanation
Indices: 50922--50971 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
50912 TGCTGATTTG
*
50922 TTTTCTTTCTTTCTTCTT-TCTT
1 TTTTCTTTCTTACTTCTTCTCTT
*
50944 TTTTCTTTCTTAGTTCTTCCTCTT
1 TTTTCTTTCTTACTTCTT-CTCTT
50968 TTTT
1 TTTT
50972 ATCTCTCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
24 8 0.33
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTCTTTCTTACTTCTTCTCTT
Found at i:50961 original size:11 final size:11
Alignment explanation
Indices: 50924--50954 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
50914 CTGATTTGTT
50924 TTCTTTCTTTC
1 TTCTTTCTTTC
*
50935 TTCTTTCTTTT
1 TTCTTTCTTTC
50946 TTCTTTCTT
1 TTCTTTCTT
50955 AGTTCTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTCTTTCTTTC
Found at i:58417 original size:15 final size:15
Alignment explanation
Indices: 58397--58426 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58387 CATGCCTTTG
58397 TTTTAATTATATTTA
1 TTTTAATTATATTTA
58412 TTTTAATTATATTTA
1 TTTTAATTATATTTA
58427 CATTATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATTATATTTA
Found at i:58943 original size:28 final size:29
Alignment explanation
Indices: 58901--58973 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 29
58891 TTTTTTAGTG
*
58901 GATATGGTCTTTGTTCAAGTCCTCATTAA
1 GATATGGTGTTTGTTCAAGTCCTCATTAA
*
58930 GATAT-GTGTTTGTTCAGGTCCTCATTAA
1 GATATGGTGTTTGTTCAAGTCCTCATTAA
58958 GATATGGTGTTTGTTC
1 GATATGGTGTTTGTTC
58974 CTGGTCTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 26 0.63
29 15 0.37
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.44
Consensus pattern (29 bp):
GATATGGTGTTTGTTCAAGTCCTCATTAA
Done.