Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012745.1 Corchorus capsularis cultivar CVL-1 contig12766, 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: 36304
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2879 original size:21 final size:23
Alignment explanation
Indices: 2837--2881 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2827 TTAAAAATAC
2837 TAGGCTCTTTGAAATTTTTGTCAT
1 TAGGCTCTTTGAAA-TTTTGTCAT
2861 TAGGCTCTTT-AAA-TTTGTCAT
1 TAGGCTCTTTGAAATTTTGTCAT
2882 GAACCTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (23 bp):
TAGGCTCTTTGAAATTTTGTCAT
Found at i:12038 original size:19 final size:19
Alignment explanation
Indices: 12014--12051 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12004 TTACGCCGAA
* *
12014 AATGAAACATTTTGTCCTT
1 AATGAAACAATTAGTCCTT
12033 AATGAAACAATTAGTCCTT
1 AATGAAACAATTAGTCCTT
12052 TAGTAATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
AATGAAACAATTAGTCCTT
Found at i:20067 original size:27 final size:27
Alignment explanation
Indices: 20025--20078 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
20015 TCGTGATCCC
*
20025 TTTACTTAGTTGTGATATGGTCCTCGG
1 TTTACTTAGTTATGATATGGTCCTCGG
20052 TTTACTTAGTTATGATATGGTCCTCGG
1 TTTACTTAGTTATGATATGGTCCTCGG
20079 CGTGTGTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44
Consensus pattern (27 bp):
TTTACTTAGTTATGATATGGTCCTCGG
Found at i:20526 original size:24 final size:25
Alignment explanation
Indices: 20488--20534 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
20478 ATCCTCTTCT
20488 TACTTATTACCATTTTTACTTTTGC
1 TACTTATTACCATTTTTACTTTTGC
*
20513 TACTT-TTATCATTTTTACTTTT
1 TACTTATTACCATTTTTACTTTT
20535 ACCATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.19, C:0.17, G:0.02, T:0.62
Consensus pattern (25 bp):
TACTTATTACCATTTTTACTTTTGC
Found at i:20531 original size:15 final size:15
Alignment explanation
Indices: 20513--20543 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20503 TTACTTTTGC
*
20513 TACTTTTATCATTTT
1 TACTTTTACCATTTT
20528 TACTTTTACCATTTT
1 TACTTTTACCATTTT
20543 T
1 T
20544 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:20543 original size:24 final size:24
Alignment explanation
Indices: 20498--20570 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
20488 TACTTATTAC
* * *
20498 CATTTTTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCATTTTTAT
*
20522 CATTTTTACTTTTACCATTTTTCT
1 CATTTTTACTTTTACCATTTTTAT
* *
20546 TACTCTTTTACTTAATACCATTTTT
1 CA-T-TTTTACTT-TTACCATTTTT
20571 TTACTTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 21 0.52
25 1 0.03
26 8 0.20
27 10 0.25
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (24 bp):
CATTTTTACTTTTACCATTTTTAT
Found at i:20558 original size:26 final size:26
Alignment explanation
Indices: 20525--20575 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
20515 CTTTTATCAT
*
20525 TTTTACTT-TTACCATTTTTCTTACTC
1 TTTTACTTAATACCATTTTT-TTACTC
20551 TTTTACTTAATACCATTTTTTTACT
1 TTTTACTTAATACCATTTTTTTACT
20576 TAATACCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTACTTAATACCATTTTTTTACTC
Found at i:20569 original size:42 final size:43
Alignment explanation
Indices: 20525--20675 Score: 172
Period size: 42 Copynumber: 3.6 Consensus size: 43
20515 CTTTTATCAT
* *
20525 TTTTACTT-TTACCATTTTTCTTACTCTTTTACTTAATACCATTT
1 TTTTACTTAATACCA-TTTTCTTACTCTTTTACTTAATACCA-TA
*
20569 TTTTACTTAATACCATTCT-TTACTCTTTTACTTAATACCATA
1 TTTTACTTAATACCATTTTCTTACTCTTTTACTTAATACCATA
* *
20611 TTTCACTTGATACCA--TTCTTGAC-CTTCTTACTTAATACCATA
1 TTTTACTTAATACCATTTTCTT-ACTCTT-TTACTTAATACCATA
20653 TTTTACTTAATACC-TTTT-TTACT
1 TTTTACTTAATACCATTTTCTTACT
20676 TAATACCATT
Statistics
Matches: 92, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
40 1 0.01
41 7 0.08
42 45 0.49
43 23 0.25
44 11 0.12
45 5 0.05
ACGTcount: A:0.25, C:0.22, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTTACTTAATACCATTTTCTTACTCTTTTACTTAATACCATA
Found at i:20590 original size:17 final size:18
Alignment explanation
Indices: 20552--20686 Score: 71
Period size: 17 Copynumber: 6.9 Consensus size: 18
20542 TTCTTACTCT
*
20552 TTTACTTAATACCATTTT
1 TTTACTTAATACCATTTC
20570 TTTACTTAATACCATTCTTTACTC
1 TTTACTTAATACCA----TT--TC
*
20594 TTTTACTTAATACCATAT-
1 -TTTACTTAATACCATTTC
* *
20612 TTCACTTGATACCATTCTTGACC
1 TTTACTTAATACCA-T-TT---C
*
20635 TTCTTACTTAATACCATAT-
1 -T-TTACTTAATACCATTTC
20654 TTTACTTAATACC-TTT-
1 TTTACTTAATACCATTTC
20670 TTTACTTAATACCATTT
1 TTTACTTAATACCATTT
20687 TTACTCTTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 33
0.69 0.07 0.25
Matches are distributed among these distances:
16 15 0.16
17 27 0.29
18 16 0.17
19 2 0.02
21 1 0.01
22 2 0.02
23 1 0.01
24 3 0.03
25 25 0.27
ACGTcount: A:0.27, C:0.21, G:0.01, T:0.50
Consensus pattern (18 bp):
TTTACTTAATACCATTTC
Found at i:20674 original size:16 final size:16
Alignment explanation
Indices: 20638--20691 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
20628 CTTGACCTTC
*
20638 TTACTTAATACCATATT
1 TTACTTAATACC-TTTT
20655 TTACTTAATACCTTTT
1 TTACTTAATACCTTTT
*
20671 TTACTTAATACCATTT
1 TTACTTAATACCTTTT
20687 TTACT
1 TTACT
20692 CTTTTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (16 bp):
TTACTTAATACCTTTT
Found at i:21325 original size:81 final size:80
Alignment explanation
Indices: 21193--21421 Score: 222
Period size: 81 Copynumber: 2.9 Consensus size: 80
21183 CACTCAACTC
* ** * *
21193 TTAATTACTGATTTGCTGATTACCA-TC--ACTTTGACTCTTAATTATCGATTTACTGATTACTA
1 TTAATTACTGATTTACTGATTAATACTCTTAC-TTGACCCTTAATTATCAATTTACTGATTACTA
* *
21255 TTTTTACCTTGACTCT
65 TTTTTACCTTAACTAT
* *
21271 TTAATTACTGACTTTACTTATTAAT-CTCTTACCTTGACCCTTAATTATCAATTTACCGATTACT
1 TTAATTACTGA-TTTACTGATTAATACTCTTA-CTTGACCCTTAATTATCAATTTACTGATTACT
*
21335 ATCTTTTTA-CTTAATTAT
64 A--TTTTTACCTTAACTAT
* * * *
21353 TTAATTACTGATTTACTGATTACTACTTTTAC-T--CCCTTAATTATCAATTTACTTGATTAATC
1 TTAATTACTGATTTACTGATTAATACTCTTACTTGACCCTTAATTATCAATTTAC-TGATTACTA
21415 TTTTTAC
65 TTTTTAC
21422 TTTATTACTG
Statistics
Matches: 125, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
77 6 0.05
78 30 0.24
79 17 0.14
80 1 0.01
81 42 0.34
82 23 0.18
83 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.49
Consensus pattern (80 bp):
TTAATTACTGATTTACTGATTAATACTCTTACTTGACCCTTAATTATCAATTTACTGATTACTAT
TTTTACCTTAACTAT
Found at i:21395 original size:36 final size:34
Alignment explanation
Indices: 21352--21446 Score: 99
Period size: 36 Copynumber: 2.8 Consensus size: 34
21342 TACTTAATTA
21352 TTTAATTACTGATTTACTGATTACTAC-TTTTAC
1 TTTAATTACTGATTTACTGATTACTACTTTTTAC
* *
21385 TCCCTTAATTA-TCAATTTACTTGATTAAT-CTTTTTAC
1 T---TTAATTACT-GATTTAC-TGATTACTACTTTTTAC
21422 TTT-ATTACTGATTTACTGATTACTA
1 TTTAATTACTGATTTACTGATTACTA
21447 TTACCTTGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
32 7 0.14
33 11 0.22
34 3 0.06
35 1 0.02
36 14 0.28
37 14 0.28
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (34 bp):
TTTAATTACTGATTTACTGATTACTACTTTTTAC
Found at i:21440 original size:77 final size:75
Alignment explanation
Indices: 21308--21450 Score: 198
Period size: 77 Copynumber: 1.9 Consensus size: 75
21298 CTTACCTTGA
* *
21308 CCCTTAATTATCAATTTACCGATTACTATCTTTTTACTTAATTATTTAATTACTGATTTACTGAT
1 CCCTTAATTATCAATTTACCGATTAC-ATCTTTTTACTTAATTACTGAATTACTGA-TTACT-AT
21373 TACTACTTTTACT
63 TACTACTTTTACT
* * *
21386 CCCTTAATTATCAATTTACTTGATTA-ATCTTTTTACTTTATTACTGATTTACTGATTACTATTA
1 CCCTTAATTATCAATTTAC-CGATTACATCTTTTTACTTAATTACTGAATTACTGATTACTATTA
21450 C
65 C
21451 CTTGACTCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
75 5 0.08
76 5 0.08
77 25 0.42
78 19 0.32
79 5 0.08
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (75 bp):
CCCTTAATTATCAATTTACCGATTACATCTTTTTACTTAATTACTGAATTACTGATTACTATTAC
TACTTTTACT
Found at i:21484 original size:55 final size:53
Alignment explanation
Indices: 21406--21514 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 53
21396 TCAATTTACT
* *
21406 TGATTAATCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTC
1 TGATTAATCTTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTC
*
21459 TGATTAATCTCTTTTTACTTAATTACTTATTTACTGATTACTATCACCTTGACTC
1 TGATTAA--TCTTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTC
21514 T
1 T
21515 TAATTATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 7 0.14
55 44 0.86
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.50
Consensus pattern (53 bp):
TGATTAATCTTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTC
Found at i:28435 original size:16 final size:16
Alignment explanation
Indices: 28397--28435 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
28387 CAAAGTGCAA
28397 TTTTTTTATTTCACTT
1 TTTTTTTATTTCACTT
28413 TCTTTTTT-TTTCACTT
1 T-TTTTTTATTTCACTT
28429 TTTTTTT
1 TTTTTTT
28436 CAAAGGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTATTTCACTT
Found at i:31762 original size:2 final size:2
Alignment explanation
Indices: 31757--31781 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31747 TTAAGTTGAA
31757 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 A
31782 ACGTGGGTAG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32259 original size:28 final size:31
Alignment explanation
Indices: 32227--32289 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
32217 AATTTGGGAT
* *
32227 TATAACGTTTCA-G-AACG-CCAATTCAAGA
1 TATAACGTTACATGAAACGACCAAATCAAGA
32255 TATAACGTTACATGAAACGACCAAATCAAGA
1 TATAACGTTACATGAAACGACCAAATCAAGA
32286 TATA
1 TATA
32290 TTTAGACGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 11 0.37
29 1 0.03
30 4 0.13
31 14 0.47
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (31 bp):
TATAACGTTACATGAAACGACCAAATCAAGA
Found at i:34565 original size:8 final size:8
Alignment explanation
Indices: 34552--34585 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
34542 CACCTTCTTG
34552 AAAAATTC
1 AAAAATTC
34560 AAAAATTC
1 AAAAATTC
*
34568 AGAAACTTC
1 A-AAAATTC
34577 AAAAATTC
1 AAAAATTC
34585 A
1 A
34586 TAGCCAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:35186 original size:26 final size:26
Alignment explanation
Indices: 35130--35194 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
35120 GGCATTAGGG
35130 TCACA-TAGGGGCACTTCGGTCATTC
1 TCACATTAGGGGCACTTCGGTCATTC
* *
35155 TAACATTAGGGGCACTTTGGTCATT-
1 TCACATTAGGGGCACTTCGGTCATTC
35180 TGCACATTCAGGGGC
1 T-CACATT-AGGGGC
35195 GTTTTAGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.15
26 23 0.68
27 6 0.18
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (26 bp):
TCACATTAGGGGCACTTCGGTCATTC
Found at i:35204 original size:27 final size:26
Alignment explanation
Indices: 35131--35207 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
35121 GCATTAGGGT
**
35131 CACA-TAGGGGCACTTCGGTCATTCT-
1 CACATTAGGGGCACTTTAGTCATT-TG
* *
35156 AACATTAGGGGCACTTTGGTCATTTG
1 CACATTAGGGGCACTTTAGTCATTTG
**
35182 CACATTCAGGGGCGTTTTAGTCATTT
1 CACATT-AGGGGCACTTTAGTCATTT
35208 CCATGATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.09
26 23 0.53
27 16 0.37
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (26 bp):
CACATTAGGGGCACTTTAGTCATTTG
Found at i:35384 original size:51 final size:52
Alignment explanation
Indices: 35310--35407 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 52
35300 ATAAAAATTC
35310 AAAATACAAAAATGGGAATTGAAAAAG-TTTAAAAAAAAAAAGAGAAATACA
1 AAAATACAAAAATGGGAATTGAAAAAGTTTTAAAAAAAAAAAGAGAAATACA
*
35361 AAAATACAAAAATGGGAATTGAAAAAGTTTTTAAAAAAAAAAGAGAA
1 AAAATACAAAAATGGGAATTGAAAAAGTTTTAAAAAAAAAAAGAGAA
35408 GAGAAAGAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 27 0.60
52 18 0.40
ACGTcount: A:0.65, C:0.03, G:0.14, T:0.17
Consensus pattern (52 bp):
AAAATACAAAAATGGGAATTGAAAAAGTTTTAAAAAAAAAAAGAGAAATACA
Done.