Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010184.1 Corchorus capsularis cultivar CVL-1 contig10205, 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: 19789
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Found at i:60 original size:27 final size:25
Alignment explanation
Indices: 30--90 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
20 AATTTTTGTT
*
30 TTTTTTAATAAAAAAATCAATTTTCTG
1 TTTTTTAA-AAAAAAA-CAATTTTCTC
* * *
57 TTTTTCAAAAAAAAACCATTTTTTC
1 TTTTTTAAAAAAAAACAATTTTCTC
82 TTTTTTAAA
1 TTTTTTAAA
91 GAAGAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 15 0.52
26 7 0.24
27 7 0.24
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTTTAAAAAAAAACAATTTTCTC
Found at i:98 original size:27 final size:25
Alignment explanation
Indices: 21--119 Score: 76
Period size: 26 Copynumber: 3.8 Consensus size: 25
11 TTTGACCCTA
* *
21 ATTTTTGTTTTTTTTAATAAAAAAATC
1 ATTTTT-TCTTTTTTAA-AAAAAAACC
*
48 A-ATTTTCTGTTTTTCAAAAAAAAACC
1 ATTTTTTCT-TTTTT-AAAAAAAAACC
**
74 ATTTTTTCTTTTTTAAAGAAGAAAATG
1 ATTTTTTCTTTTTTAAA-AA-AAAACC
*
101 ATTTTTT-TTTTATAAAAAA
1 ATTTTTTCTTTTTTAAAAAA
120 TTTTGATACT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
24 1 0.02
25 7 0.12
26 32 0.53
27 20 0.33
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.49
Consensus pattern (25 bp):
ATTTTTTCTTTTTTAAAAAAAAACC
Found at i:739 original size:16 final size:16
Alignment explanation
Indices: 709--753 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
699 TTCATTTTTA
*
709 TTTTAAAATATATATTT
1 TTTTAAAA-AAATATTT
726 TTTTAAAAAAATATTT
1 TTTTAAAAAAATATTT
742 TTTTAATAAAAA
1 TTTTAA-AAAAA
754 AGTATGACGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAAAAAAATATTT
Found at i:3111 original size:26 final size:26
Alignment explanation
Indices: 3078--3144 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
3068 AAACTCATTG
***
3078 CTTCTTCTTTTCATTCCCTTCATTTT
1 CTTCTTCTTTTCATTCCAAACATTTT
* *
3104 CTTCTTCTTTTCTTTCCAAACTTTTT
1 CTTCTTCTTTTCATTCCAAACATTTT
3130 CTTCTTC-TTTCATTC
1 CTTCTTCTTTTCATTC
3145 TCTTTCCTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 7 0.20
26 28 0.80
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (26 bp):
CTTCTTCTTTTCATTCCAAACATTTT
Found at i:4158 original size:2 final size:2
Alignment explanation
Indices: 4153--4184 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4143 ATAGATAGGG
4153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4185 ATCCACCGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4836 original size:26 final size:26
Alignment explanation
Indices: 4798--4864 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
4788 TAGAAACTGT
* * *
4798 TTTGGT-ATGTTTTT-TTTAGCTATA
1 TTTGGTGATGTTTTTGTTGACCTAAA
4822 TTTGGTGATGTTTTTGTTGACCTAAA
1 TTTGGTGATGTTTTTGTTGACCTAAA
* *
4848 TTTGGTGTTGTTGTTGT
1 TTTGGTGATGTTTTTGT
4865 GTTTTGGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 6 0.17
25 8 0.22
26 22 0.61
ACGTcount: A:0.13, C:0.04, G:0.24, T:0.58
Consensus pattern (26 bp):
TTTGGTGATGTTTTTGTTGACCTAAA
Found at i:10428 original size:22 final size:22
Alignment explanation
Indices: 10402--10467 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 22
10392 CTAACTACTT
10402 TTCTGCTAATTGTGTTACATAA
1 TTCTGCTAATTGTGTTACATAA
*
10424 TTCTG-TAATT-TCGACTA-ACTAA
1 TTCTGCTAATTGT-G-TTACA-TAA
10446 TT-TGC-AATTGTGTTACATAA
1 TTCTGCTAATTGTGTTACATAA
10466 TT
1 TT
10468 ATGTTATCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
20 8 0.22
21 15 0.42
22 13 0.36
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (22 bp):
TTCTGCTAATTGTGTTACATAA
Found at i:10466 original size:42 final size:45
Alignment explanation
Indices: 10382--10467 Score: 124
Period size: 42 Copynumber: 2.0 Consensus size: 45
10372 GAGCTGGTAA
* *
10382 GTAATTTGGACTAACTACTTTTCTGCTAATTGTGTTACATAATTCT
1 GTAATTTCGACTAACTAC-ATTCTGCTAATTGTGTTACATAATTCT
10428 GTAATTTCGACTAACTA-ATT-TGC-AATTGTGTTACATAATT
1 GTAATTTCGACTAACTACATTCTGCTAATTGTGTTACATAATT
10468 ATGTTATCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 17 0.45
43 3 0.08
44 2 0.05
46 16 0.42
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (45 bp):
GTAATTTCGACTAACTACATTCTGCTAATTGTGTTACATAATTCT
Found at i:12206 original size:32 final size:32
Alignment explanation
Indices: 12165--12263 Score: 137
Period size: 32 Copynumber: 3.1 Consensus size: 32
12155 AATTATAACA
*
12165 AAATAGTGGCGTTTTAAGAACAAAACGCCACC
1 AAATGGTGGCGTTTTAAGAACAAAACGCCACC
* * *
12197 ATATGGTGGCGTTTTAAGAACAAAATGCCACA
1 AAATGGTGGCGTTTTAAGAACAAAACGCCACC
*
12229 AAATGGTGGCG-TTTAATGAAAAAAACGCCACC
1 AAATGGTGGCGTTTTAA-GAACAAAACGCCACC
12261 AAA
1 AAA
12264 CGCTCCAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 5 0.09
32 53 0.91
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (32 bp):
AAATGGTGGCGTTTTAAGAACAAAACGCCACC
Found at i:13406 original size:20 final size:20
Alignment explanation
Indices: 13381--13418 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13371 TGGTCATGGT
13381 TTTTTTAAAAAATTAATTAA
1 TTTTTTAAAAAATTAATTAA
**
13401 TTTTTTAATTAATTAATT
1 TTTTTTAAAAAATTAATT
13419 TTAATTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTTAAAAAATTAATTAA
Found at i:13477 original size:26 final size:24
Alignment explanation
Indices: 13393--13477 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 24
13383 TTTTAAAAAA
* * *
13393 TTAATTAATTTTTTAATTAATTAATT
1 TTAATTAGTTTATTAA--AATTAGTT
13419 TTAATTAGTTTATTAAAATTAGTTT
1 TTAATTAGTTTATTAAAATTAG-TT
* *
13444 GTTTATTAGTTTATGTTAAATTAGTT
1 -TTAATTAGTTTAT-TAAAATTAGTT
13470 TATAATTA
1 T-TAATTA
13478 ATTAGTTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
24 5 0.10
25 3 0.06
26 33 0.67
27 8 0.16
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (24 bp):
TTAATTAGTTTATTAAAATTAGTT
Found at i:13480 original size:15 final size:14
Alignment explanation
Indices: 13392--13484 Score: 61
Period size: 14 Copynumber: 6.8 Consensus size: 14
13382 TTTTTAAAAA
*
13392 ATTAATTAATTT-T
1 ATTAATTAGTTTAT
* *
13405 -TTAATTAATTAAT
1 ATTAATTAGTTTAT
*
13418 TTTAATTAGTTTAT
1 ATTAATTAGTTTAT
* *
13432 -TAAAATTAGTTTGT
1 AT-TAATTAGTTTAT
13446 -TT-ATTAGTTTAT
1 ATTAATTAGTTTAT
*
13458 GTTAAATTAGTTTAT
1 ATT-AATTAGTTTAT
13473 AATTAATTAGTT
1 -ATTAATTAGTT
13485 CATTATTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
12 19 0.29
13 4 0.06
14 22 0.34
15 18 0.28
16 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (14 bp):
ATTAATTAGTTTAT
Found at i:13604 original size:18 final size:18
Alignment explanation
Indices: 13571--13772 Score: 76
Period size: 18 Copynumber: 11.8 Consensus size: 18
13561 AATTAATCTA
*
13571 AATTTTGATT-GTTTATT
1 AATTTTAATTAGTTTATT
*
13588 AGTTTTAATTAGTTTA-T
1 AATTTTAATTAGTTTATT
* *
13605 -ACTTTAATT--TTAATT
1 AATTTTAATTAGTTTATT
** * * *
13620 AATACTAATTTTGATGATT
1 AATTTTAA-TTAGTTTATT
13639 AATTTTAATTAGTTTATT
1 AATTTTAATTAGTTTATT
*
13657 AA----AATTAGTTTGTT
1 AATTTTAATTAGTTTATT
*
13671 TATTTGT--TTATGTTTAATT
1 AATTT-TAATTA-GTTT-ATT
*
13690 AGTATTTAATTAGTTTA-T
1 AAT-TTTAATTAGTTTATT
*
13708 AA--TTAATTAGTTCATT
1 AATTTTAATTAGTTTATT
** *
13724 -ATTTTTGTT-TTTTATT
1 AATTTTAATTAGTTTATT
*
13740 AATTATTACTTAGTTTATT
1 AATT-TTAATTAGTTTATT
*
13759 AGTTTTAATTAGTT
1 AATTTTAATTAGTT
13773 AATTTATGAT
Statistics
Matches: 132, Mismatches: 31, Indels: 43
0.64 0.15 0.21
Matches are distributed among these distances:
14 15 0.11
15 13 0.10
16 17 0.13
17 21 0.16
18 33 0.25
19 24 0.18
20 6 0.05
21 3 0.02
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (18 bp):
AATTTTAATTAGTTTATT
Found at i:13705 original size:26 final size:25
Alignment explanation
Indices: 13642--13718 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
13632 GATGATTAAT
** *
13642 TTTAATTAGTTTATTAAAATTAGTT
1 TTTAATTAGTTTATTTTAATTAGTA
* *
13667 TGTTTATTTGTTTATGTTTAATTAGTA
1 T-TTAATTAGTTTAT-TTTAATTAGTA
*
13694 TTTAATTAGTTTATAATTAATTAGT
1 TTTAATTAGTTTAT-TTTAATTAGT
13719 TCATTATTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 1 0.02
26 31 0.76
27 9 0.22
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.58
Consensus pattern (25 bp):
TTTAATTAGTTTATTTTAATTAGTA
Found at i:14225 original size:23 final size:24
Alignment explanation
Indices: 14180--14225 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
14170 GAGTAGGCTG
14180 AATTTAGTTATTAAATTTGATAAA
1 AATTTAGTTATTAAATTTGATAAA
*
14204 AATTTAGTTATT-AATTTTATAA
1 AATTTAGTTATTAAATTTGATAA
14226 TATTAGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
AATTTAGTTATTAAATTTGATAAA
Found at i:19642 original size:15 final size:15
Alignment explanation
Indices: 19624--19671 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
19614 TATCATTAAT
19624 TAATTAATCATAAAC
1 TAATTAATCATAAAC
19639 TAATTAA--AT--AC
1 TAATTAATCATAAAC
19650 TAATTAATCATAAAC
1 TAATTAATCATAAAC
19665 TAATTAA
1 TAATTAA
19672 ATATTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.31
13 4 0.14
15 16 0.55
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATTAATCATAAAC
Found at i:19654 original size:26 final size:26
Alignment explanation
Indices: 19624--19744 Score: 126
Period size: 26 Copynumber: 4.8 Consensus size: 26
19614 TATCATTAAT
19624 TAATTAATCATAAACTAATTAAATAC
1 TAATTAATCATAAACTAATTAAATAC
*
19650 TAATTAATCATAAACTAATTAAATAT
1 TAATTAATCATAAACTAATTAAATAC
*
19676 TAATTAAACATAAACTAA-T-AA-AC
1 TAATTAATCATAAACTAATTAAATAC
* * * * * *
19699 TAAGTAAT-TTTAATTAACTAATTA-
1 TAATTAATCATAAACTAATTAAATAC
*
19723 AAATTAATCATAAACTAATTAA
1 TAATTAATCATAAACTAATTAA
19745 TATTAAAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
22 6 0.08
23 8 0.11
24 9 0.12
25 11 0.14
26 42 0.55
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.36
Consensus pattern (26 bp):
TAATTAATCATAAACTAATTAAATAC
Found at i:19729 original size:18 final size:18
Alignment explanation
Indices: 19662--19750 Score: 51
Period size: 18 Copynumber: 4.9 Consensus size: 18
19652 ATTAATCATA
19662 AACTAATTAAATATTAATT
1 AACTAATTAAA-ATTAATT
* *
19681 AA--ACA-T-AAACTAATA
1 AACTA-ATTAAAATTAATT
* **
19696 AACTAAGTAATTTTAATT
1 AACTAATTAAAATTAATT
19714 AACTAATTAAAATTAATCAT
1 AACTAATTAAAATTAAT--T
*
19734 AAACTAATTAATATTAA
1 -AACTAATTAAAATTAA
19751 AAAATTTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
15 7 0.13
16 3 0.06
17 4 0.08
18 20 0.38
19 2 0.04
20 1 0.02
21 15 0.29
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.36
Consensus pattern (18 bp):
AACTAATTAAAATTAATT
Found at i:19786 original size:25 final size:26
Alignment explanation
Indices: 19734--19787 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
19724 AATTAATCAT
* *
19734 AAACTAATTAATATTAAAAAATTTAA
1 AAACTAATTAATATAAAAAAATTCAA
*
19760 AAACTAATTAGTA-AAAAAAATTCAA
1 AAACTAATTAATATAAAAAAATTCAA
19785 AAA
1 AAA
19788 AT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.28
Consensus pattern (26 bp):
AAACTAATTAATATAAAAAAATTCAA
Found at i:19788 original size:26 final size:26
Alignment explanation
Indices: 19734--19788 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
19724 AATTAATCAT
* *
19734 AAACTAATTAATATTAAAAAATTTAA
1 AAACTAATTAATATAAAAAAATTAAA
*
19760 AAACTAATTAGTA-AAAAAAATTCAAA
1 AAACTAATTAATATAAAAAAATT-AAA
19786 AAA
1 AAA
19789 T
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (26 bp):
AAACTAATTAATATAAAAAAATTAAA
Done.