Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014387.1 Corchorus capsularis cultivar CVL-1 contig14408, 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: 25316
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1212 original size:29 final size:29
Alignment explanation
Indices: 1170--1240 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
1160 CTTGTAGCTG
**
1170 TTTGGACGTTTTGCCCTCTGGACTTCAAT
1 TTTGGACGTTTTGCCCTCTCAACTTCAAT
*
1199 TTTGGACATTTTGCCCTCTCAACTTCAAT
1 TTTGGACGTTTTGCCCTCTCAACTTCAAT
1228 TTTGAGACGTTTT
1 TTTG-GACGTTTT
1241 ACCCCCTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCTCTCAACTTCAAT
Found at i:1473 original size:31 final size:30
Alignment explanation
Indices: 1432--1489 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1422 GTTAGCATAA
*
1432 GGGGTCAAAATGTCCCAAAAATTGAAGTTAAG
1 GGGGTCAAAATAT-CC-AAAATTGAAGTTAAG
1464 GGGGT-AAAATATCCAAAATTGAAGTT
1 GGGGTCAAAATATCCAAAATTGAAGTT
1490 CATGGGGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 2 0.08
31 6 0.24
32 5 0.20
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (30 bp):
GGGGTCAAAATATCCAAAATTGAAGTTAAG
Found at i:1507 original size:29 final size:29
Alignment explanation
Indices: 1449--1509 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1439 AAATGTCCCA
* *
1449 AAAATTGAAGTTAAGGGGGTAAAATATCC
1 AAAATTGAAGTTAAGGGGGCAAAACATCC
* * *
1478 AAAATTGAAGTTCATGGGGCAAAACGTCC
1 AAAATTGAAGTTAAGGGGGCAAAACATCC
1507 AAA
1 AAA
1510 CGCTACAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (29 bp):
AAAATTGAAGTTAAGGGGGCAAAACATCC
Found at i:5579 original size:13 final size:13
Alignment explanation
Indices: 5561--5590 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5551 TTGTTTCGTA
5561 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
5574 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
5587 TTTT
1 TTTT
5591 TGTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTTGTTTTTGTT
Found at i:10707 original size:267 final size:267
Alignment explanation
Indices: 10232--10764 Score: 1057
Period size: 267 Copynumber: 2.0 Consensus size: 267
10222 TGCATATGCA
10232 TTTGTTTGCTTGTCTTTAGTTTTCTTTAAGTTGTTAGTTTTTGTTTTGTTTTTCTAGGTTGCTAG
1 TTTGTTTGCTTGTCTTTAGTTTTCTTTAAGTTGTTAGTTTTTGTTTTGTTTTTCTAGGTTGCTAG
10297 GGACTAGCAAGATCTAAGTGTGTGGGAATTTGTTAGGCACATATTTTTCTATATTTTATATGTTA
66 GGACTAGCAAGATCTAAGTGTGTGGGAATTTGTTAGGCACATATTTTTCTATATTTTATATGTTA
10362 ATTCTATTTGATCATGTGCCTATTTCTATGTACTTGACGCTTGATTTATTCATATTTATGTTTTA
131 ATTCTATTTGATCATGTGCCTATTTCTATGTACTTGACGCTTGATTTATTCATATTTATGTTTTA
10427 GGTACATATTGGAGTGTTTCAAGGCAAAAGGAGCTAAATTGGAGCTATTTAGAACAAGTTGGAAA
196 GGTACATATTGGAGTGTTTCAAGGCAAAAGGAGCTAAATTGGAGCTATTTAGAACAAGTTGGAAA
10492 AATTCTG
261 AATTCTG
10499 TTTGTTTGCTTGTCTTTAGTTTTCTTTAAGTTGTTAGTTTTTGTTTTGTTTTTCTAGGTTGCTAG
1 TTTGTTTGCTTGTCTTTAGTTTTCTTTAAGTTGTTAGTTTTTGTTTTGTTTTTCTAGGTTGCTAG
10564 GGACTAGCAAGATCTAAGTGTGTGGGAATTTGTTAGGCACATATTTTTCTATATTTTATATGTTA
66 GGACTAGCAAGATCTAAGTGTGTGGGAATTTGTTAGGCACATATTTTTCTATATTTTATATGTTA
*
10629 ATTCTATTTGATTATGTGCCTATTTCTATGTACTTGACGCTTGATTTATTCATATTTATGTTTTA
131 ATTCTATTTGATCATGTGCCTATTTCTATGTACTTGACGCTTGATTTATTCATATTTATGTTTTA
10694 GGTACATATTGGAGTGTTTCAAGGCAAAAGGAGCTAAATTGGAGCTATTTAGAACAAGTTGGAAA
196 GGTACATATTGGAGTGTTTCAAGGCAAAAGGAGCTAAATTGGAGCTATTTAGAACAAGTTGGAAA
10759 AATTCT
261 AATTCT
10765 ATTTCAACCT
Statistics
Matches: 265, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
267 265 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (267 bp):
TTTGTTTGCTTGTCTTTAGTTTTCTTTAAGTTGTTAGTTTTTGTTTTGTTTTTCTAGGTTGCTAG
GGACTAGCAAGATCTAAGTGTGTGGGAATTTGTTAGGCACATATTTTTCTATATTTTATATGTTA
ATTCTATTTGATCATGTGCCTATTTCTATGTACTTGACGCTTGATTTATTCATATTTATGTTTTA
GGTACATATTGGAGTGTTTCAAGGCAAAAGGAGCTAAATTGGAGCTATTTAGAACAAGTTGGAAA
AATTCTG
Found at i:13677 original size:15 final size:16
Alignment explanation
Indices: 13657--13687 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13647 AGTATCTAGG
13657 AATGAGTCAAA-TAAA
1 AATGAGTCAAACTAAA
13672 AATGAGTCAAACTAAA
1 AATGAGTCAAACTAAA
13688 TCAAAATCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (16 bp):
AATGAGTCAAACTAAA
Found at i:13750 original size:2 final size:2
Alignment explanation
Indices: 13743--13767 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13733 TCTCTATAGT
13743 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 T
13768 CTTTATACTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18308 original size:2 final size:2
Alignment explanation
Indices: 18301--18329 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18291 CCTTTACAAG
18301 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18330 AAGGACACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19473 original size:2 final size:2
Alignment explanation
Indices: 19466--19494 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19456 CCTATACTAG
19466 TA 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 T
19495 GTTCTCCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19598 original size:21 final size:23
Alignment explanation
Indices: 19563--19606 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
19553 TATCATATAA
19563 ATATTCTATTCTTCTTA-TTACT
1 ATATTCTATTCTTCTTAGTTACT
*
19585 ATATT-TATTTTTCTTAGTTACT
1 ATATTCTATTCTTCTTAGTTACT
19607 TTAAATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.23, C:0.14, G:0.02, T:0.61
Consensus pattern (23 bp):
ATATTCTATTCTTCTTAGTTACT
Found at i:20201 original size:24 final size:24
Alignment explanation
Indices: 20170--20226 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
20160 TTCATCCGGC
*
20170 GATGATGCACCGGCACCACCAGCT
1 GATGATGCACCGGCACCACCAACT
*
20194 GATGATGCACCGGCACCGCCAACT
1 GATGATGCACCGGCACCACCAACT
20218 GATGATGCA
1 GATGATGCA
20227 GTACCGGCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.14
Consensus pattern (24 bp):
GATGATGCACCGGCACCACCAACT
Found at i:20223 original size:27 final size:24
Alignment explanation
Indices: 20170--20240 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 24
20160 TTCATCCGGC
* *
20170 GATGATGCACCGGCACCACCAGCT
1 GATGATGCACCGGCACCGCCAGAT
20194 GATGATGCACCGGCACCGCCA-ACT
1 GATGATGCACCGGCACCGCCAGA-T
20218 GATGATGCAGTACCGGCACCGCC
1 GATGATGC---ACCGGCACCGCC
20241 CGCTAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
24 29 0.71
27 12 0.29
ACGTcount: A:0.24, C:0.37, G:0.27, T:0.13
Consensus pattern (24 bp):
GATGATGCACCGGCACCGCCAGAT
Found at i:20249 original size:27 final size:27
Alignment explanation
Indices: 20178--20268 Score: 116
Period size: 27 Copynumber: 3.5 Consensus size: 27
20168 GCGATGATGC
*
20178 ACCGGCACCACCAGCTGATGATGC---
1 ACCGGCACCGCCAGCTGATGATGCAGT
*
20202 ACCGGCACCGCCAACTGATGATGCAGT
1 ACCGGCACCGCCAGCTGATGATGCAGT
* * *
20229 ACCGGCACCGCCCGCTAATGAAGCAGT
1 ACCGGCACCGCCAGCTGATGATGCAGT
20256 ACCGGCACCGCCA
1 ACCGGCACCGCCA
20269 ACCAAGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
24 22 0.39
27 35 0.61
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.11
Consensus pattern (27 bp):
ACCGGCACCGCCAGCTGATGATGCAGT
Found at i:22605 original size:6 final size:6
Alignment explanation
Indices: 22589--22618 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
22579 ACAATTCCTT
*
22589 CAAAAA AAAAAA CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
22619 AGGAAAGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:25231 original size:59 final size:60
Alignment explanation
Indices: 25139--25255 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 60
25129 CGTTAGGTAC
* * * *
25139 TTATTTGACCAAATTAAAAGATCGGATCCTTATTTGAGCATTTTTA-TAACATTAGACTG
1 TTATTTGACCAAATTAAAAGATCAGATCCTTATTTAAGCATTTTGACAAACATTAGACTG
** *
25198 TTATTTGGTCAAATTAAAAGATCAGATTCTTATTTAAGCATTTTGACAAACATTAGAC
1 TTATTTGACCAAATTAAAAGATCAGATCCTTATTTAAGCATTTTGACAAACATTAGAC
25256 CCTTATTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 40 0.80
60 10 0.20
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (60 bp):
TTATTTGACCAAATTAAAAGATCAGATCCTTATTTAAGCATTTTGACAAACATTAGACTG
Done.