Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014072.1 Corchorus capsularis cultivar CVL-1 contig14093, 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: 52699
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1003 original size:29 final size:29
Alignment explanation
Indices: 931--1037 Score: 117
Period size: 31 Copynumber: 3.6 Consensus size: 29
921 TATGGCTAAA
* *
931 TGCTCAATTTGGTCCTAAATCTTTCACGGTC
1 TGCTCAATTTGGTCCTAAA-CCTTCA-GATC
* *
962 TGCTCGATTTGGTCCTAAACCTTCAGACC
1 TGCTCAATTTGGTCCTAAACCTTCAGATC
*
991 TGCTCAATTTGGTCCTAAGCCTTCCA-ATTTC
1 TGCTCAATTTGGTCCTAAACCTT-CAGA--TC
1022 TGCTCAATTTGGTCCT
1 TGCTCAATTTGGTCCT
1038 TTTTCAGACA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
29 24 0.36
30 7 0.11
31 35 0.53
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (29 bp):
TGCTCAATTTGGTCCTAAACCTTCAGATC
Found at i:1134 original size:18 final size:18
Alignment explanation
Indices: 1107--1145 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1097 TGATGTGGCA
*
1107 TTTTTGTAT-TTTTA-AT
1 TTTTTTTATATTTTATAT
1123 TTTTTTTATATTTTATAT
1 TTTTTTTATATTTTATAT
1141 TTTTT
1 TTTTT
1146 CCATTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 5 0.25
18 7 0.35
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTTATATTTTATAT
Found at i:1233 original size:3 final size:3
Alignment explanation
Indices: 1225--1254 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1215 TCCAAATCTT
1225 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1255 ATTCTTCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2367 original size:4 final size:4
Alignment explanation
Indices: 2360--2388 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2350 CATGCCAACT
2360 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
2389 CGTATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:3599 original size:31 final size:30
Alignment explanation
Indices: 3564--3663 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 30
3554 AACAGGACTG
*
3564 AATTGAGCAGAAACTGGAAGGTTTAGGATCA
1 AATTGAGCAG-AACTGGAAGGTTTAGGACCA
* * **
3595 AATTGACCCGGTCT-GAAGGTTTAGGACCA
1 AATTGAGCAGAACTGGAAGGTTTAGGACCA
* * *
3624 AATCGAGCAGACCGTGAAAGGTTTAGGACCA
1 AATTGAGCAGAAC-TGGAAGGTTTAGGACCA
*
3655 AATTAAGCA
1 AATTGAGCA
3664 TTTAGCCCTG
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 22 0.41
30 3 0.06
31 29 0.54
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (30 bp):
AATTGAGCAGAACTGGAAGGTTTAGGACCA
Found at i:4398 original size:24 final size:24
Alignment explanation
Indices: 4371--4420 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4361 TACATTTAAT
4371 AGAAACAGAGCATGCCTAAAACTC
1 AGAAACAGAGCATGCCTAAAACTC
*
4395 AGAAACATAGCATGCCTAAAACTC
1 AGAAACAGAGCATGCCTAAAACTC
4419 AG
1 AG
4421 GGCAATGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (24 bp):
AGAAACAGAGCATGCCTAAAACTC
Found at i:4596 original size:24 final size:24
Alignment explanation
Indices: 4569--4618 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
4559 TACATTTAAT
4569 AGAAACAGAGCATGCCTAAAACTC
1 AGAAACAGAGCATGCCTAAAACTC
*
4593 AGAAACATAGCATGCCTAAAACTC
1 AGAAACAGAGCATGCCTAAAACTC
4617 AG
1 AG
4619 GGCAATGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (24 bp):
AGAAACAGAGCATGCCTAAAACTC
Found at i:4657 original size:198 final size:198
Alignment explanation
Indices: 4319--4714 Score: 792
Period size: 198 Copynumber: 2.0 Consensus size: 198
4309 GTTGTCATTT
4319 GCATTTTCAACACACTATTTCATTACATTTTTCACACAGGGATACATTTAATAGAAACAGAGCAT
1 GCATTTTCAACACACTATTTCATTACATTTTTCACACAGGGATACATTTAATAGAAACAGAGCAT
4384 GCCTAAAACTCAGAAACATAGCATGCCTAAAACTCAGGGCAATGCCTTGTTGGAGCTCATGTTTC
66 GCCTAAAACTCAGAAACATAGCATGCCTAAAACTCAGGGCAATGCCTTGTTGGAGCTCATGTTTC
4449 TCTTACCAATTACATTTTTAATAATGACACAACATACTAAAACAAACGAAACTACAAATAATATC
131 TCTTACCAATTACATTTTTAATAATGACACAACATACTAAAACAAACGAAACTACAAATAATATC
4514 TTC
196 TTC
4517 GCATTTTCAACACACTATTTCATTACATTTTTCACACAGGGATACATTTAATAGAAACAGAGCAT
1 GCATTTTCAACACACTATTTCATTACATTTTTCACACAGGGATACATTTAATAGAAACAGAGCAT
4582 GCCTAAAACTCAGAAACATAGCATGCCTAAAACTCAGGGCAATGCCTTGTTGGAGCTCATGTTTC
66 GCCTAAAACTCAGAAACATAGCATGCCTAAAACTCAGGGCAATGCCTTGTTGGAGCTCATGTTTC
4647 TCTTACCAATTACATTTTTAATAATGACACAACATACTAAAACAAACGAAACTACAAATAATATC
131 TCTTACCAATTACATTTTTAATAATGACACAACATACTAAAACAAACGAAACTACAAATAATATC
4712 TTC
196 TTC
4715 CTCCATTTCC
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 198 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (198 bp):
GCATTTTCAACACACTATTTCATTACATTTTTCACACAGGGATACATTTAATAGAAACAGAGCAT
GCCTAAAACTCAGAAACATAGCATGCCTAAAACTCAGGGCAATGCCTTGTTGGAGCTCATGTTTC
TCTTACCAATTACATTTTTAATAATGACACAACATACTAAAACAAACGAAACTACAAATAATATC
TTC
Found at i:5487 original size:68 final size:68
Alignment explanation
Indices: 5378--5513 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
5368 GCATGCTCAG
5378 GGCGCGTTTTGTACACGCACTGCTGATGTGGGTAATTTTGACCTGTTTTAACCCAACACGATAAC
1 GGCGCGTTTTGTACACGCACTGCTGATGTGGGTAATTTTGACCTGTTTTAACCCAACACGATAAC
5443 GTT
66 GTT
5446 GGCGCGTTTTGTACACGCACTGCTGATGTGGGTAATTTTGACCTGTTTTAACCCAACACGATAAC
1 GGCGCGTTTTGTACACGCACTGCTGATGTGGGTAATTTTGACCTGTTTTAACCCAACACGATAAC
5511 GTT
66 GTT
5514 AGCACCTAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (68 bp):
GGCGCGTTTTGTACACGCACTGCTGATGTGGGTAATTTTGACCTGTTTTAACCCAACACGATAAC
GTT
Found at i:6522 original size:6 final size:6
Alignment explanation
Indices: 6511--6536 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6501 AACAAATGAG
6511 TGAGTT TGAGTT TGAGTT TGAGTT TG
1 TGAGTT TGAGTT TGAGTT TGAGTT TG
6537 TGCCTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGAGTT
Found at i:16972 original size:33 final size:33
Alignment explanation
Indices: 16930--17061 Score: 246
Period size: 33 Copynumber: 4.0 Consensus size: 33
16920 GGAGAACAAA
16930 TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
1 TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
* *
16963 TTGTTCAGAAACACAACCTGTATCGACCTTAGG
1 TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
16996 TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
1 TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
17029 TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
1 TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
17062 CGTTAAAGAT
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 95 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (33 bp):
TTGTTCAGAAGCACAACCTGTATCGGCCTTAGG
Found at i:22330 original size:1 final size:1
Alignment explanation
Indices: 22326--22353 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
22316 TTTTTGCTTC
22326 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
22354 GAAAATTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24573 original size:65 final size:65
Alignment explanation
Indices: 24497--24623 Score: 245
Period size: 65 Copynumber: 2.0 Consensus size: 65
24487 CTTTTCATGC
24497 ACTCACATATTTAGAAATGTAAAATGAGGAATATCATGCATACATACCTTCAAAAACTTCATCGT
1 ACTCACATATTTAGAAATGTAAAATGAGGAATATCATGCATACATACCTTCAAAAACTTCATCGT
*
24562 ACTCACATATTTAGAAATGTGAAATGAGGAATATCATGCATACATACCTTCAAAAACTTCAT
1 ACTCACATATTTAGAAATGTAAAATGAGGAATATCATGCATACATACCTTCAAAAACTTCAT
24624 TGTAGACAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (65 bp):
ACTCACATATTTAGAAATGTAAAATGAGGAATATCATGCATACATACCTTCAAAAACTTCATCGT
Found at i:29212 original size:132 final size:132
Alignment explanation
Indices: 28983--29238 Score: 370
Period size: 132 Copynumber: 1.9 Consensus size: 132
28973 AAGTAGACCA
* * * * *
28983 AGCATTGAAGCTCTGAGCAGCACCATTGATGACATTACCACCATCTTTACCTTTTTGAGACCAAT
1 AGCATTGAAGCTCTGAGCAGCACCATTGATCAAATTACCACCACCTTTACCTTTTTGAGAACAAC
** * * * *
29048 CTCTATCTGTAAGATCTTGGGGCATTGCACTATCAGCCATAGGCATTGAAGATGTAGAAGTGGAA
66 CTCTATCTACAACATCTTGGGGCATTGCACTATCAGCCACAGACACTGAAGATGTAGAAGTGGAA
29113 CT
131 CT
*
29115 AGCATTGAAGCTCTGCGCAGCACCATTGATCAAATTACCACCACCTTTA-CTTTTTGGAGAACAA
1 AGCATTGAAGCTCTGAGCAGCACCATTGATCAAATTACCACCACCTTTACCTTTTT-GAGAACAA
* *
29179 CCTCTATCTACAACATCTTGGGGCATTGGACTATCAGCTACAGACACTGAAGATGTAGAA
65 CCTCTATCTACAACATCTTGGGGCATTGCACTATCAGCCACAGACACTGAAGATGTAGAA
29239 ATGCACCTTC
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
131 6 0.06
132 103 0.94
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (132 bp):
AGCATTGAAGCTCTGAGCAGCACCATTGATCAAATTACCACCACCTTTACCTTTTTGAGAACAAC
CTCTATCTACAACATCTTGGGGCATTGCACTATCAGCCACAGACACTGAAGATGTAGAAGTGGAA
CT
Found at i:36011 original size:29 final size:31
Alignment explanation
Indices: 35978--36041 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
35968 TTTATGAGGT
*
35978 AAAATGTCCAAA-ATTA-AAGTTCAGGTGGC
1 AAAATGTCCAAACATTATAAGTTCAGGGGGC
* *
36007 AAAATGTCTAAACATTATAAGTTGAGGGGGC
1 AAAATGTCCAAACATTATAAGTTCAGGGGGC
36038 AAAA
1 AAAA
36042 AGGTATTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 4 0.13
31 15 0.50
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAATGTCCAAACATTATAAGTTCAGGGGGC
Found at i:37393 original size:17 final size:17
Alignment explanation
Indices: 37342--37394 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
37332 TTCTACCCAT
*
37342 ATCACTAGTGATCAAAG
1 ATCACCAGTGATCAAAG
* **
37359 ATCACCAGTTATGTAAG
1 ATCACCAGTGATCAAAG
* *
37376 ATCATCGGTGATCAAAG
1 ATCACCAGTGATCAAAG
37393 AT
1 AT
37395 TACATGGGTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (17 bp):
ATCACCAGTGATCAAAG
Found at i:46703 original size:18 final size:18
Alignment explanation
Indices: 46666--46702 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
46656 ACCTTCAAAG
46666 TAATCAAAATTATTATAA
1 TAATCAAAATTATTATAA
46684 TAAT-AAAATT-TT-TAA
1 TAATCAAAATTATTATAA
46699 TAAT
1 TAAT
46703 ATTAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 2 0.11
17 6 0.32
18 4 0.21
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATCAAAATTATTATAA
Found at i:46710 original size:24 final size:24
Alignment explanation
Indices: 46681--46768 Score: 94
Period size: 24 Copynumber: 3.7 Consensus size: 24
46671 AAAATTATTA
46681 TAATAATAAAATTTTTAATAATAT
1 TAATAATAAAATTTTTAATAATAT
*
46705 TAATAATAAGATTTTTAGCATAA-A-
1 TAATAATAAAATTTTTA--ATAATAT
*
46729 -AATAATAAGAA-GTTTAATAATAT
1 TAATAATAA-AATTTTTAATAATAT
*
46752 TAATAATAAGATTTTTA
1 TAATAATAAAATTTTTA
46769 CCGTAAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
21 4 0.08
22 1 0.02
23 13 0.25
24 29 0.56
25 1 0.02
26 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (24 bp):
TAATAATAAAATTTTTAATAATAT
Found at i:46732 original size:23 final size:22
Alignment explanation
Indices: 46682--46781 Score: 78
Period size: 24 Copynumber: 4.3 Consensus size: 22
46672 AAATTATTAT
*
46682 AATAATAAAATTTTTA-ATAATA
1 AATAATAAGATTTTTACATAA-A
46704 TTAATAATAAGATTTTTAGCATAAA
1 --AATAATAAGATTTTTA-CATAAA
**
46729 AATAATAAGAAGTTTA-ATAATA
1 AATAATAAGATTTTTACATAA-A
*
46751 TTAATAATAAGATTTTTACCGTAAA
1 --AATAATAAGATTTTTA-CATAAA
46776 AATAAT
1 AATAAT
46782 TGTTATTATT
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.06
22 1 0.02
23 20 0.32
24 29 0.46
25 2 0.03
26 7 0.11
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (22 bp):
AATAATAAGATTTTTACATAAA
Found at i:46971 original size:6 final size:6
Alignment explanation
Indices: 46962--46994 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
46952 TTTATATAAT
46962 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATA
1 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATA
46995 TTCCTTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (6 bp):
ATAAAG
Found at i:47223 original size:29 final size:29
Alignment explanation
Indices: 47186--47245 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
47176 AAATAAAAAC
* *
47186 TACCCATTTTAGATAAAAACTACCCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
*
47215 TACCAATTTTAGAAAAAAACTACTCATTA
1 TACCAATTTTAGAAAAAAACTACCCATTA
47244 TA
1 TA
47246 AGATAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (29 bp):
TACCAATTTTAGAAAAAAACTACCCATTA
Done.