Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013525.1 Corchorus capsularis cultivar CVL-1 contig13546, 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: 33559
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:64 original size:32 final size:32
Alignment explanation
Indices: 28--110 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
18 AGCCCCCACC
*
28 GGGGCGGCCTGCCGTGGCGAAGATGCCCCAGT
1 GGGGCGGCCTGCCGTGGCGAAGACGCCCCAGT
* * *
60 GGGGCGGCCTGCCCATGGTGAAGCCGCCCCAGT
1 GGGGCGGCCTG-CCGTGGCGAAGACGCCCCAGT
* *
93 GGGGAGGCTCCGCCGTGG
1 GGGGCGGC-CTGCCGTGG
111 TTGAGCCGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 11 0.26
33 29 0.69
34 2 0.05
ACGTcount: A:0.11, C:0.33, G:0.45, T:0.12
Consensus pattern (32 bp):
GGGGCGGCCTGCCGTGGCGAAGACGCCCCAGT
Found at i:182 original size:15 final size:15
Alignment explanation
Indices: 141--182 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
131 GGCTCAGTGT
*
141 AAAAGTGTCAAAAGGGT
1 AAAAGTGT--AAAGGGC
158 AAAA-TGTAAAGGGC
1 AAAAGTGTAAAGGGC
172 AAAAGTGTAAA
1 AAAAGTGTAAA
183 AAGTGGTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.43
15 6 0.26
16 3 0.13
17 4 0.17
ACGTcount: A:0.52, C:0.05, G:0.26, T:0.17
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:3106 original size:31 final size:31
Alignment explanation
Indices: 3010--3106 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
3000 GGCTAAATGT
*
3010 TCAATTTGGTCCTAAACCTTTCACA-GTCTGC
1 TCAATTTGGTCCTAAACCTTTCA-ATCTCTGC
* * *
3041 TCGATTTGGTCCTAAACC-TTC--TGCCCAGC
1 TCAATTTGGTCCTAAACCTTTCAAT-CTCTGC
* *
3070 TCAATTTGATCCTAAACCTTTCAATTTCTGC
1 TCAATTTGGTCCTAAACCTTTCAATCTCTGC
3101 TCAATT
1 TCAATT
3107 CAGTCTTCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
29 19 0.37
30 6 0.12
31 26 0.50
32 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.37
Consensus pattern (31 bp):
TCAATTTGGTCCTAAACCTTTCAATCTCTGC
Found at i:5401 original size:2 final size:2
Alignment explanation
Indices: 5394--5424 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5384 AAGGAGAATG
5394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5425 ATGAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7932 original size:17 final size:17
Alignment explanation
Indices: 7910--7943 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7900 TTGGTACTAG
7910 GGAAAATACTAGGGAAA
1 GGAAAATACTAGGGAAA
**
7927 GGAAAATTTTAGGGAAA
1 GGAAAATACTAGGGAAA
7944 ATTGAAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.29, T:0.18
Consensus pattern (17 bp):
GGAAAATACTAGGGAAA
Found at i:8020 original size:12 final size:12
Alignment explanation
Indices: 8000--8034 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
7990 TGTTTGGTGT
8000 CAAGGAAAATAC
1 CAAGGAAAATAC
* *
8012 TATGGAAAATAC
1 CAAGGAAAATAC
8024 CAAGGAAAATA
1 CAAGGAAAATA
8035 TTTTCTCAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.14
Consensus pattern (12 bp):
CAAGGAAAATAC
Found at i:15045 original size:21 final size:20
Alignment explanation
Indices: 14983--15595 Score: 219
Period size: 22 Copynumber: 28.8 Consensus size: 20
14973 ATCACCTTTC
*
14983 ACTCTTTACGGATTACTATCTT
1 ACTC-TTACTGATTACTAT-TT
* * * *
15005 ACTCTTTCTAATAACCATTT
1 ACTCTTACTGATTACTATTT
15025 AGCTCTTACTGATTACTATTTT
1 A-CTCTTACTGATTACTA-TTT
15047 AC-CTTACACTGATTACTTTTTACTATTTT
1 ACTCTT--ACTG---A---TT-ACTA-TTT
*
15076 ACTCTTTACTGATAACCT-TCTT
1 ACTC-TTACTGATTA-CTAT-TT
*
15098 ACTTTTTACTGATTACTATTTT
1 AC-TCTTACTGATTACTA-TTT
*
15120 ACTCTTTACTGATTACCATTTT
1 ACTC-TTACTGATTACTA-TTT
*
15142 GCTCTTACTGATTACCT-TTT
1 ACTCTTACTGATTA-CTATTT
*
15162 ACTCTTTACTGATTACCATTTT
1 ACTC-TTACTGATTACTA-TTT
* *
15184 GCTCTTACTGATTACCATTTT
1 ACTCTTACTGATTACTA-TTT
* *
15205 ACCTTTTACTGATTA-TCA-TC
1 A-CTCTTACTGATTACT-ATTT
*
15225 ACT-TT--T--TTACTGTTTT
1 ACTCTTACTGATTACT-ATTT
15241 ACTCTTTACTGATTACCT-TCTT
1 ACTC-TTACTGATTA-CTAT-TT
* *
15263 AGTTTTTACTGATTACTATTTT
1 A-CTCTTACTGATTACTA-TTT
*
15285 ACTCTTTACTGACTACCT-TCTT
1 ACTC-TTACTGATTA-CTAT-TT
* *
15307 AGTTTTTACTGATTACTATTTT
1 A-CTCTTACTGATTACTA-TTT
*
15329 ACTCTTTACTGATTACCATTTT
1 ACTC-TTACTGATTACTA-TTT
*
15351 GCTCTTACTGATTAC-ATTTT
1 ACTCTTACTGATTACTA-TTT
* *
15371 ACTCTTTATTGATTACCATTTT
1 ACTC-TTACTGATTACTA-TTT
* *
15393 GCTCTTACTGATTACCATTTT
1 ACTCTTACTGATTACTA-TTT
* *
15414 ACCTTTTACTGATTA-TCA-TC
1 A-CTCTTACTGATTACT-ATTT
*
15434 ACT-TT--T--TTACTGTTTT
1 ACTCTTACTGATTACT-ATTT
15450 ACTCTTTACTGATTACCT-TCTT
1 ACTC-TTACTGATTA-CTAT-TT
*
15472 ACTTTTTACTGATTACTATTTT
1 AC-TCTTACTGATTACTA-TTT
15494 ACTCTTTACTGATTACCT-TCTT
1 ACTC-TTACTGATTA-CTAT-TT
*
15516 ACTTTTTACTGATTACTATTTT
1 AC-TCTTACTGATTACTA-TTT
*
15538 ACTCTTTACTGATTACCATTTT
1 ACTC-TTACTGATTACTA-TTT
*
15560 GCTCTTACTGATTACCT-TTT
1 ACTCTTACTGATTA-CTATTT
15580 ACTCTTTACTGATTAC
1 ACTC-TTACTGATTAC
15596 CATTACCTTG
Statistics
Matches: 463, Mismatches: 57, Indels: 144
0.70 0.09 0.22
Matches are distributed among these distances:
14 6 0.01
15 2 0.00
16 10 0.02
18 8 0.02
19 4 0.01
20 34 0.07
21 136 0.29
22 221 0.48
23 21 0.05
25 1 0.00
26 1 0.00
28 2 0.00
29 14 0.03
30 1 0.00
31 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (20 bp):
ACTCTTACTGATTACTATTT
Found at i:15084 original size:22 final size:22
Alignment explanation
Indices: 15066--15599 Score: 513
Period size: 22 Copynumber: 25.4 Consensus size: 22
15056 TGATTACTTT
*
15066 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
* *
15088 TAACC-TTCTTACTTTTTACTGA
1 TTACCATT-TTACTCTTTACTGA
*
15110 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
15132 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTACTGA
15153 TTACC-TTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
15174 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTACTGA
15195 TTACCATTTTAC-CTTTTACTGA
1 TTACCATTTTACTC-TTTACTGA
* * *
15217 TTATCA--TCACTTTTTTACTG-
1 TTACCATTTTAC-TCTTTACTGA
15237 ------TTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
* *
15253 TTACC-TTCTTAGTTTTTACTGA
1 TTACCATT-TTACTCTTTACTGA
*
15275 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
* * *
15297 CTACC-TTCTTAGTTTTTACTGA
1 TTACCATT-TTACTCTTTACTGA
*
15319 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
15341 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTACTGA
*
15362 TTA-CATTTTACTCTTTATTGA
1 TTACCATTTTACTCTTTACTGA
*
15383 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTACTGA
15404 TTACCATTTTAC-CTTTTACTGA
1 TTACCATTTTACTC-TTTACTGA
* * *
15426 TTATCA--TCACTTTTTTACTG-
1 TTACCATTTTAC-TCTTTACTGA
15446 ------TTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
15462 TTACC-TTCTTACTTTTTACTGA
1 TTACCATT-TTACTCTTTACTGA
*
15484 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
15506 TTACC-TTCTTACTTTTTACTGA
1 TTACCATT-TTACTCTTTACTGA
*
15528 TTACTATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
*
15550 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTACTGA
15571 TTACC-TTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
15592 TTACCATT
1 TTACCATT
15600 ACCTTGACTT
Statistics
Matches: 421, Mismatches: 51, Indels: 80
0.76 0.09 0.14
Matches are distributed among these distances:
15 16 0.04
16 6 0.01
20 31 0.07
21 126 0.30
22 232 0.55
23 10 0.02
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (22 bp):
TTACCATTTTACTCTTTACTGA
Found at i:15086 original size:29 final size:31
Alignment explanation
Indices: 15037--15107 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
15027 CTCTTACTGA
* *
15037 TTACTATTTTAC-CTTACACTGATTA-CTTT
1 TTACTATTTTACTCTTACACTGATAACCTTC
*
15066 TTACTATTTTACTCTT-TACTGATAACCTTC
1 TTACTATTTTACTCTTACACTGATAACCTTC
15096 TTACT-TTTTACT
1 TTACTATTTTACT
15108 GATTACTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 26 0.70
30 11 0.30
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.54
Consensus pattern (31 bp):
TTACTATTTTACTCTTACACTGATAACCTTC
Found at i:15305 original size:209 final size:208
Alignment explanation
Indices: 15066--15599 Score: 1005
Period size: 209 Copynumber: 2.6 Consensus size: 208
15056 TGATTACTTT
15066 TTACTATTTTACTCTTTACTGATAACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTG
1 TTACTATTTTACTCTTTACTGAT-ACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTG
15131 ATTACCATTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGAT
65 ATTACCATTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGAT
15196 TACCATTTTACCTTTTACTGATTATCATCACTTTTTTACTGTTTTACTCTTTACTGATTACCTTC
130 TACCATTTTACCTTTTACTGATTATCATCACTTTTTTACTGTTTTACTCTTTACTGATTACCTTC
*
15261 TTAGTTTTTACTGA
195 TTACTTTTTACTGA
*
15275 TTACTATTTTACTCTTTACTGACTACCTTCTTAGTTTTTACTGATTACTATTTTACTCTTTACTG
1 TTACTATTTTACTCTTTACTGA-TACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTG
* *
15340 ATTACCATTTTGCTCTTACTGATTACATTTTACTCTTTATTGATTACCATTTTGCTCTTACTGAT
65 ATTACCATTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGAT
15405 TACCATTTTACCTTTTACTGATTATCATCACTTTTTTACTGTTTTACTCTTTACTGATTACCTTC
130 TACCATTTTACCTTTTACTGATTATCATCACTTTTTTACTGTTTTACTCTTTACTGATTACCTTC
15470 TTACTTTTTACTGA
195 TTACTTTTTACTGA
15484 TTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTG
1 TTACTATTTTACTCTTTACTGA-TACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTG
15549 ATTACCATTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACCATT
65 ATTACCATTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACCATT
15600 ACCTTGACTT
Statistics
Matches: 316, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
209 315 1.00
210 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (208 bp):
TTACTATTTTACTCTTTACTGATACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTGA
TTACCATTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATT
ACCATTTTACCTTTTACTGATTATCATCACTTTTTTACTGTTTTACTCTTTACTGATTACCTTCT
TACTTTTTACTGA
Found at i:15459 original size:15 final size:15
Alignment explanation
Indices: 15439--15548 Score: 70
Period size: 15 Copynumber: 7.5 Consensus size: 15
15429 TCATCACTTT
15439 TTTACTGTTTTACTC
1 TTTACTGTTTTACTC
*
15454 TTTACTG-ATTAC-C
1 TTTACTGTTTTACTC
*
15467 TTCTTACT-TTTTACTG
1 -T-TTACTGTTTTACTC
* *
15483 ATTACTATTTTACTC
1 TTTACTGTTTTACTC
*
15498 TTTACTG-ATTAC-C
1 TTTACTGTTTTACTC
*
15511 TTCTTACT-TTTTACTG
1 -T-TTACTGTTTTACTC
* *
15527 ATTACTATTTTACTC
1 TTTACTGTTTTACTC
15542 TTTACTG
1 TTTACTG
15549 ATTACCATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
13 2 0.03
14 20 0.28
15 49 0.69
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.55
Consensus pattern (15 bp):
TTTACTGTTTTACTC
Found at i:16587 original size:20 final size:19
Alignment explanation
Indices: 16550--16591 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
16540 ATATTTATTA
*
16550 TTATTTTTTATTTATTTCAT
1 TTATTATTTATTTATTTC-T
16570 TTATTATTTA-TTATTTTCT
1 TTATTATTTATTTA-TTTCT
16589 TTA
1 TTA
16592 CCCAAGACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTATTTATTTATTTCT
Found at i:18791 original size:23 final size:23
Alignment explanation
Indices: 18721--18791 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
18711 TAATGCAAAC
*
18721 TGTATTATTATATTTATGTAATTCT
1 TGTATTATTAT-TTT-TGTAATTTT
** * *
18746 TGTATTATTATTACTATATTTTT
1 TGTATTATTATTTTTGTAATTTT
*
18769 TGTATTATTATTTTTGTACTTTT
1 TGTATTATTATTTTTGTAATTTT
18792 ATTTAAATCA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 25 0.68
24 1 0.03
25 11 0.30
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (23 bp):
TGTATTATTATTTTTGTAATTTT
Found at i:31831 original size:54 final size:54
Alignment explanation
Indices: 31746--31855 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
31736 GTCTCGAACC
*
31746 TTCTTCATAAGTCTCAAGCACGTGCGATATCTCTTCGCTCTCATTTCTGTGTAA
1 TTCTTCATAAGTCTCAAGCACGTGCGATATCTCTTCACTCTCATTTCTGTGTAA
*
31800 TTCTTCATAAGTCTCAAGCACGTGCGGTATCTCTTCACTCTCATTTCTGTGTAA
1 TTCTTCATAAGTCTCAAGCACGTGCGATATCTCTTCACTCTCATTTCTGTGTAA
31854 TT
1 TT
31856 TAATCAACAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (54 bp):
TTCTTCATAAGTCTCAAGCACGTGCGATATCTCTTCACTCTCATTTCTGTGTAA
Done.