Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014893.1 Corchorus capsularis cultivar CVL-1 contig14914, 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: 70173
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2076 original size:20 final size:20
Alignment explanation
Indices: 2040--2078 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2030 ATGAAACTCA
**
2040 TTAAAGGAAAATTAAAAACT
1 TTAAAGGAAAAAAAAAAACT
2060 TTAAAGGAAAAAAAAAAAC
1 TTAAAGGAAAAAAAAAAAC
2079 ATGCAATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (20 bp):
TTAAAGGAAAAAAAAAAACT
Found at i:7144 original size:12 final size:12
Alignment explanation
Indices: 7127--7152 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7117 GACTTGGGTG
7127 TGCGGGACTTTC
1 TGCGGGACTTTC
7139 TGCGGGACTTTC
1 TGCGGGACTTTC
7151 TG
1 TG
7153 GAAACTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.35, T:0.35
Consensus pattern (12 bp):
TGCGGGACTTTC
Found at i:23369 original size:20 final size:20
Alignment explanation
Indices: 23334--23371 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23324 AAACCATTTA
**
23334 AAATTATTTTTCAAATATAC
1 AAATTATTTTGAAAATATAC
23354 AAATTATTTTGAAAATAT
1 AAATTATTTTGAAAATAT
23372 GTTTTATAGT
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:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (20 bp):
AAATTATTTTGAAAATATAC
Found at i:27056 original size:6 final size:6
Alignment explanation
Indices: 27045--27085 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
27035 AATAAATTAA
27045 ATCTAT ATCTAT ATCTAT ATC--T ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
27086 ATAAAAGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.12
5 5 0.16
6 23 0.72
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (6 bp):
ATCTAT
Found at i:27071 original size:10 final size:10
Alignment explanation
Indices: 27045--27085 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
27035 AATAAATTAA
27045 ATCTATATCTAT
1 ATCTATATC--T
27057 ATCTATATCT
1 ATCTATATCT
27067 ATCTATATCT
1 ATCTATATCT
27077 ATACTATAT
1 AT-CTATAT
27086 ATAAAAGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 13 0.46
11 6 0.21
12 9 0.32
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (10 bp):
ATCTATATCT
Found at i:27071 original size:16 final size:15
Alignment explanation
Indices: 27050--27088 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
27040 ATTAAATCTA
27050 TATCTATATCTATATC
1 TATCTATATCTATA-C
27066 TATCTATATCTATAC
1 TATCTATATCTATAC
*
27081 TATATATA
1 TATCTATA
27089 AAAGTACGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (15 bp):
TATCTATATCTATAC
Found at i:27368 original size:18 final size:17
Alignment explanation
Indices: 27347--27380 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
27337 AATTAAATTC
27347 AATATTTTATAATTTTAA
1 AATATTTTAT-ATTTTAA
27365 AATATTTTATATTTTA
1 AATATTTTATATTTTA
27381 TCATTTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATATTTTATATTTTAA
Found at i:27666 original size:14 final size:14
Alignment explanation
Indices: 27647--27686 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
27637 GTCGGGTTGG
*
27647 ATTTGGGTTCGGTT
1 ATTTGGGTTAGGTT
27661 ATTTGGGTTAGGTT
1 ATTTGGGTTAGGTT
27675 AGTTTCGGGTTA
1 A-TTT-GGGTTA
27687 AGGAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.12, C:0.05, G:0.35, T:0.47
Consensus pattern (14 bp):
ATTTGGGTTAGGTT
Found at i:29564 original size:17 final size:20
Alignment explanation
Indices: 29542--29585 Score: 67
Period size: 17 Copynumber: 2.4 Consensus size: 20
29532 ACCCCTTTTC
29542 TCTTCTTT-TCT-TTTCT-T
1 TCTTCTTTCTCTCTTTCTCT
29559 TCTTCTTTCTCTCTTTCTCT
1 TCTTCTTTCTCTCTTTCTCT
29579 TCTTCTT
1 TCTTCTT
29586 CTCCTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 3 0.12
19 5 0.21
20 8 0.33
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (20 bp):
TCTTCTTTCTCTCTTTCTCT
Found at i:29565 original size:20 final size:21
Alignment explanation
Indices: 29538--29587 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
29528 ACCGACCCCT
*
29538 TTTC-TCTTCTTTTCT-TTTC
1 TTTCTTCTTCTTCTCTCTTTC
29557 TTTCTTC-T-TTCTCTCTTTC
1 TTTCTTCTTCTTCTCTCTTTC
29576 TCTTCTTCTTCT
1 T-TTCTTCTTCT
29588 CCTTCTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 5 0.20
19 10 0.40
20 8 0.32
21 1 0.04
22 1 0.04
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTTCTTCTTCTCTCTTTC
Found at i:29588 original size:17 final size:17
Alignment explanation
Indices: 29538--29593 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
29528 ACCGACCCCT
29538 TTTCTCTTCTT-TTCT-
1 TTTCTCTTCTTCTTCTC
29553 TTTCT-TTCTTCTTTCTCTC
1 TTTCTCTTCTTC--T-TCTC
29572 TTTCTCTTCTTCTTCTC
1 TTTCTCTTCTTCTTCTC
*
29589 CTTCT
1 TTTCT
29594 TCCTTCTCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 5 0.15
15 5 0.15
17 9 0.26
18 4 0.12
19 5 0.15
20 6 0.18
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCTCTTCTTCTTCTC
Found at i:29594 original size:32 final size:33
Alignment explanation
Indices: 29538--29604 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
29528 ACCGACCCCT
* * *
29538 TTTCTCTTCTTTTCTTTTCTTTCTTCTTTCTCTC
1 TTTCTCTTC-TTTCTTCTCCTTCTTCCTTCTCTC
29572 TTTCTCTTC-TTCTTCTCCTTCTTCCTTCTCTC
1 TTTCTCTTCTTTCTTCTCCTTCTTCCTTCTCTC
29604 T
1 T
29605 CCCCGACCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 21 0.70
34 9 0.30
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTCTCTTCTTTCTTCTCCTTCTTCCTTCTCTC
Found at i:31954 original size:29 final size:29
Alignment explanation
Indices: 31921--31991 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
31911 ACTTGTAGTG
31921 TTTGGACGTTTTATTCCT-TAAACT-TCAAT
1 TTTGGAC-TTTT-TTCCTATAAACTCTCAAT
*
31950 TTTGGACATTTTTCCTCATAAACTCTCAAT
1 TTTGGACTTTTTTCCT-ATAAACTCTCAAT
*
31980 TTTGGACATTTT
1 TTTGGACTTTTT
31992 GCCCTTTCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 5 0.13
28 3 0.08
29 13 0.34
30 17 0.45
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (29 bp):
TTTGGACTTTTTTCCTATAAACTCTCAAT
Found at i:32285 original size:29 final size:30
Alignment explanation
Indices: 32219--32293 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
32209 ATTTGAGAGT
* * *
32219 GGGTAAAATATCCAAAATTGAGAGTTTATG
1 GGGTAAAATGTCCAAAATTGAGAGTTCAAG
*
32249 GGGCAAAATGTCCAAAATTGA-AGTTCAAG
1 GGGTAAAATGTCCAAAATTGAGAGTTCAAG
*
32278 GGGTAAAACGTCCAAA
1 GGGTAAAATGTCCAAA
32294 CACAACAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (30 bp):
GGGTAAAATGTCCAAAATTGAGAGTTCAAG
Found at i:33314 original size:14 final size:16
Alignment explanation
Indices: 33280--33318 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
33270 AATTATGATT
33280 TTATAATTTTATGATAA
1 TTATAATTTTA-GATAA
33297 TTATAATTTTA-A-AA
1 TTATAATTTTAGATAA
33311 TTATAATT
1 TTATAATT
33319 ATCCTTGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
17 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTATAATTTTAGATAA
Found at i:44056 original size:56 final size:58
Alignment explanation
Indices: 43951--44073 Score: 196
Period size: 56 Copynumber: 2.2 Consensus size: 58
43941 TCCAAAAAAA
*
43951 AATCCTAATTGATGTAGGATTATATATTATGTCTTTTAAAATTCACAATTGGTCTCAT
1 AATCCTAATTGATGTAGGATTATATATTATGTCTTTTAAAATTCACAATTGGTCTCAG
* * *
44009 AATCCTAATTGATGTAGGA-T-TATATTATGTCTTTTAGAATTCCCAATTGGTCTTAG
1 AATCCTAATTGATGTAGGATTATATATTATGTCTTTTAAAATTCACAATTGGTCTCAG
44065 AATCCTAAT
1 AATCCTAAT
44074 CCTAATTGAT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 41 0.67
57 1 0.02
58 19 0.31
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (58 bp):
AATCCTAATTGATGTAGGATTATATATTATGTCTTTTAAAATTCACAATTGGTCTCAG
Found at i:46069 original size:17 final size:18
Alignment explanation
Indices: 46038--46072 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
46028 ACAATATTGA
46038 CCCATGTCTTTAAGGGTT
1 CCCATGTCTTTAAGGGTT
46056 CCCATGTC-TTAAGGGTT
1 CCCATGTCTTTAAGGGTT
46073 AGAAATCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (18 bp):
CCCATGTCTTTAAGGGTT
Found at i:56406 original size:31 final size:31
Alignment explanation
Indices: 56352--56511 Score: 140
Period size: 31 Copynumber: 5.5 Consensus size: 31
56342 TTCTGTGCAC
* * **
56352 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
56383 GTGGCATGCCACGTGTCGCTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
56414 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
56445 GTGG---G--ACG-G---CTTTTTAGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
56467 GTGGCGTGCCACATGTCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
56498 GTGGCGTGCCACGT
1 GTGGCATGCCACGT
56512 CGGACACCGT
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
22 16 0.15
25 2 0.02
26 2 0.02
27 2 0.02
28 2 0.02
31 81 0.77
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAT
Found at i:56484 original size:53 final size:53
Alignment explanation
Indices: 56400--56501 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
56390 GCCACGTGTC
* ** *
56400 GCTTTTTGGTACATGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGGACG
1 GCTTTTTAGTACATGTGGCGTGACACATGTCACTTTTTGGTACACGTGGGACG
*
56453 GCTTTTTAGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGG
1 GCTTTTTAGTACATGTGGCGTGACACATGTCACTTTTTGGTACACGTGG
56502 CGTGCCACGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (53 bp):
GCTTTTTAGTACATGTGGCGTGACACATGTCACTTTTTGGTACACGTGGGACG
Found at i:56830 original size:34 final size:34
Alignment explanation
Indices: 56770--56835 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
56760 TTGGGGGTAA
*
56770 TTATGGAGTAATGACTAATGAGAAGGACAAAGCT
1 TTATGGAGTAATGACTAAGGAGAAGGACAAAGCT
*
56804 TTATGGA-TAATTACTAAGGAGTAAGGACAAAG
1 TTATGGAGTAATGACTAAGGAG-AAGGACAAAG
56836 TTTTTCTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (34 bp):
TTATGGAGTAATGACTAAGGAGAAGGACAAAGCT
Found at i:57934 original size:19 final size:19
Alignment explanation
Indices: 57907--57951 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
57897 TTAAGGTAGA
* *
57907 TTTTCTTTTTTCTTTTTCC
1 TTTTTTTTTTTCGTTTTCC
*
57926 TTTTTTTTTTTGGTTTTCC
1 TTTTTTTTTTTCGTTTTCC
57945 TTCTTTT
1 TT-TTTT
57952 GATTTGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTTTCGTTTTCC
Found at i:58679 original size:13 final size:13
Alignment explanation
Indices: 58663--58688 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58653 AAGAAGGAAA
58663 AACAATGCAAAGG
1 AACAATGCAAAGG
58676 AACAATGCAAAGG
1 AACAATGCAAAGG
58689 GCCCATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (13 bp):
AACAATGCAAAGG
Found at i:69395 original size:29 final size:30
Alignment explanation
Indices: 69360--69435 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
69350 CGTTTAGATG
*
69360 TTTTGTCCCAC-GAACTTTAATCTT-GGACA
1 TTTTGTCCC-CTGAACTTCAATCTTGGGACA
* *
69389 TTTTGTCCCCTGAACTTCAATTTTGGGACG
1 TTTTGTCCCCTGAACTTCAATCTTGGGACA
* *
69419 TTTTGCCCCCTCAACTT
1 TTTTGTCCCCTGAACTT
69436 AACAGATTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 1 0.03
29 20 0.50
30 19 0.47
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.39
Consensus pattern (30 bp):
TTTTGTCCCCTGAACTTCAATCTTGGGACA
Found at i:69429 original size:30 final size:29
Alignment explanation
Indices: 69327--69435 Score: 76
Period size: 29 Copynumber: 3.7 Consensus size: 29
69317 ACTAATCTAC
* * *
69327 CATTTTGCCCCCTGAACTTCTAGCGTTTAGA
1 CATTTTGCCCCCTGAACTTCAATC--TTGGA
** * *
69358 TGTTTTGTCCCAC-GAACTTTAATCTTGGA
1 CATTTTG-CCCCCTGAACTTCAATCTTGGA
* *
69387 CATTTTGTCCCCTGAACTTCAATTTTGGGA
1 CATTTTGCCCCCTGAACTTCAATCTT-GGA
* *
69417 CGTTTTGCCCCCTCAACTT
1 CATTTTGCCCCCTGAACTT
69436 AACAGATTCG
Statistics
Matches: 59, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
28 3 0.05
29 20 0.34
30 19 0.32
31 13 0.22
32 4 0.07
ACGTcount: A:0.18, C:0.28, G:0.16, T:0.39
Consensus pattern (29 bp):
CATTTTGCCCCCTGAACTTCAATCTTGGA
Found at i:69553 original size:29 final size:30
Alignment explanation
Indices: 69495--69558 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
69485 CGGATCCGTT
*
69495 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
* *
69525 AAGTTCAGGGGGCAAAATGT-CCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
69554 AAGTT
1 AAGTT
69559 GGGCAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTG
Done.