Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003828.1 Corchorus capsularis cultivar CVL-1 contig03836, 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: 5597
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:579 original size:33 final size:33
Alignment explanation
Indices: 540--612 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
530 ATTTGGTTAC
*
540 ACATGTTATAGGTAACACCCTGTAACTGGTAAT
1 ACATGTTATAGATAACACCCTGTAACTGGTAAT
* * * * * *
573 GCATGTTGTTGATAATACCTTGTGACTGGTAAT
1 ACATGTTATAGATAACACCCTGTAACTGGTAAT
606 ACATGTT
1 ACATGTT
613 GTTGGTAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (33 bp):
ACATGTTATAGATAACACCCTGTAACTGGTAAT
Found at i:620 original size:16 final size:16
Alignment explanation
Indices: 566--622 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
556 ACCCTGTAAC
*
566 TGGTAATGCATGTTGT
1 TGGTAATACATGTTGT
* * *
582 TGATAATACCT-TGTGAC
1 TGGTAATACATGT-TG-T
599 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
615 TGGTAATA
1 TGGTAATA
623 TCCTATGAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
15 1 0.03
16 18 0.58
17 11 0.35
18 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (16 bp):
TGGTAATACATGTTGT
Found at i:1321 original size:41 final size:42
Alignment explanation
Indices: 1243--1322 Score: 128
Period size: 41 Copynumber: 1.9 Consensus size: 42
1233 TATATATTTA
1243 AGAGATAATTATGGTGATTATATAATTAACCATATTATCCAT
1 AGAGATAATTATGGTGATTATATAATTAACCATATTATCCAT
*
1285 AGAGATAATTAT-G-GATTATATTTATTAACCATATTATC
1 AGAGATAATTATGGTGATTATA-TAATTAACCATATTATC
1323 TACATAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 7 0.19
41 17 0.47
42 12 0.33
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (42 bp):
AGAGATAATTATGGTGATTATATAATTAACCATATTATCCAT
Found at i:1907 original size:13 final size:13
Alignment explanation
Indices: 1889--1918 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1879 ATTAGAAAGA
*
1889 TCAAGTTGGTGGG
1 TCAAGTTGGAGGG
1902 TCAAGTTGGAGGG
1 TCAAGTTGGAGGG
1915 TCAA
1 TCAA
1919 ATAGAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.27
Consensus pattern (13 bp):
TCAAGTTGGAGGG
Found at i:3308 original size:57 final size:57
Alignment explanation
Indices: 3241--3357 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
3231 CCGATTACAT
3241 GTTCATTGCATCTTGCATAATCAAAAGCTTGAAAAAGACATTAATGTATTTAATTTC
1 GTTCATTGCATCTTGCATAATCAAAAGCTTGAAAAAGACATTAATGTATTTAATTTC
3298 GTTCATTGCATCTTGCATAATCAAAAGCTTGAAAAAGACATTAATGTATTTAATTTC
1 GTTCATTGCATCTTGCATAATCAAAAGCTTGAAAAAGACATTAATGTATTTAATTTC
3355 GTT
1 GTT
3358 AATAATTACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (57 bp):
GTTCATTGCATCTTGCATAATCAAAAGCTTGAAAAAGACATTAATGTATTTAATTTC
Found at i:4058 original size:22 final size:22
Alignment explanation
Indices: 4016--4059 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4006 TATTCATATG
* *
4016 AAATTATTATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
4038 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
4060 TTTTATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:4099 original size:22 final size:22
Alignment explanation
Indices: 4074--4290 Score: 109
Period size: 22 Copynumber: 9.8 Consensus size: 22
4064 ATGATCCCAT
*
4074 TATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAACCTTCC
* * ** *
4096 TATGAAAATTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
4118 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
4140 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* *
4162 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
4184 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
4206 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* ***
4227 AAATGAAATTTTGATAACGAACAC
1 -TATGAAATTTTGATAACCTTC-C
* * *
4251 TATGAGATGTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* *
4273 TATGATATATTGATAACC
1 TATGAAATTTTGATAACC
4291 ACGTTATGAA
Statistics
Matches: 142, Mismatches: 44, Indels: 18
0.70 0.22 0.09
Matches are distributed among these distances:
21 5 0.04
22 116 0.82
23 20 0.14
24 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:4382 original size:22 final size:22
Alignment explanation
Indices: 4344--4403 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
4334 AAAAACTCCA
*
4344 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
4366 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
4388 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
4404 GCTCGCAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:4467 original size:22 final size:23
Alignment explanation
Indices: 4368--4663 Score: 104
Period size: 22 Copynumber: 13.7 Consensus size: 23
4358 AATCACACTC
*
4368 TGAAATTTTGATAA-TC-ACACTA
1 TGAAATTTTGATAACTCTTC-CTA
* * *
4390 TGAAATTGTGATAAGCTC--GCAA
1 TGAAATTTTGATAA-CTCTTCCTA
*
4412 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAACTCTTCCTA
* *
4435 TAAAATTTTGATAACT-TTCTTA
1 TGAAATTTTGATAACTCTTCCTA
*
4457 TGAAATCTTGATAA------CTA
1 TGAAATTTTGATAACTCTTCCTA
*
4474 -CAAATTTTGATAACCTC--CCTA
1 TGAAATTTTGATAA-CTCTTCCTA
** *
4495 TGATTTTTTGATAAC-C-TCATTA
1 TGAAATTTTGATAACTCTTC-CTA
* * *
4517 TTAAATTTTGTTAA-T-GTCCTTA
1 TGAAATTTTGATAACTCTTCC-TA
* *
4539 TGAAATTTTGAT--CTACATACTA
1 TGAAATTTTGATAACT-CTTCCTA
* *
4561 TGAAATTTTGATAAC-CCTCTTA
1 TGAAATTTTGATAACTCTTCCTA
* * ***
4583 TAAAATTTTGAAAACT-AAACTA
1 TGAAATTTTGATAACTCTTCCTA
*
4605 TGAAATTTTGATAAC-CTTCATA
1 TGAAATTTTGATAACTCTTCCTA
* *
4627 TGAAATTTTGAT-A-TCCTCC-C
1 TGAAATTTTGATAACTCTTCCTA
*
4647 TGAAATTTTGATTACTC
1 TGAAATTTTGATAACTC
4664 CATAATAAAA
Statistics
Matches: 203, Mismatches: 46, Indels: 50
0.68 0.15 0.17
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
20 13 0.06
21 13 0.06
22 143 0.70
23 18 0.09
24 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (23 bp):
TGAAATTTTGATAACTCTTCCTA
Found at i:4583 original size:44 final size:42
Alignment explanation
Indices: 4535--4638 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 42
4525 TGTTAATGTC
4535 CTTATGAAATTTTGATCTACATACTATGAAATTTTGATAACCCT
1 CTTATGAAATTTTGATCTA-A-ACTATGAAATTTTGATAACCCT
* * *
4579 CTTATAAAATTTTGAAAACTAAACTATGAAATTTTGATAACCTT
1 CTTATGAAATTTTG--ATCTAAACTATGAAATTTTGATAACCCT
*
4623 CATATGAAATTTTGAT
1 CTTATGAAATTTTGAT
4639 ATCCTCCCTG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
42 1 0.02
44 46 0.88
45 1 0.02
46 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (42 bp):
CTTATGAAATTTTGATCTAAACTATGAAATTTTGATAACCCT
Found at i:4790 original size:44 final size:44
Alignment explanation
Indices: 4740--4882 Score: 132
Period size: 44 Copynumber: 3.2 Consensus size: 44
4730 TAAATACCAC
*
4740 TATGAAATTTTTGTAATCACATTTTAAAATTTTGATAACCTTTT
1 TATGAAATTTTTGTAATCACATTTTAAAATTTTGATAACCTCTT
* * * * *
4784 TATGAAATTTTTATAA--ACTATTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTTGTAATCAC-ATTT-TAAAATTTTGATAACCTCTT
* * **
4828 TATGAAA-TTCTGATAATCACATTATGTAATTTTGATAACCTCGTT
1 TATGAAATTTTTG-TAATCACATTTTAAAATTTTGATAACCTC-TT
4873 T-TGAAATTTT
1 TATGAAATTTT
4883 GATACTAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 13
0.72 0.15 0.12
Matches are distributed among these distances:
42 2 0.03
43 7 0.09
44 58 0.76
45 7 0.09
46 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (44 bp):
TATGAAATTTTTGTAATCACATTTTAAAATTTTGATAACCTCTT
Found at i:4791 original size:22 final size:22
Alignment explanation
Indices: 4766--4886 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
4756 TCACATTTTA
*
4766 AAATTTTGATAACCTTTTTATG
1 AAATTTTGATAACCTCTTTATG
* * * *
4788 AAATTTTTATAAACTATTTATA
1 AAATTTTGATAACCTCTTTATG
* * * *
4810 AAATTTTGTTGACCCCTCTATG
1 AAATTTTGATAACCTCTTTATG
* * * *
4832 AAATTCTGATAATCACATTATG
1 AAATTTTGATAACCTCTTTATG
*
4854 TAATTTTGATAACCTCGTTT-TG
1 AAATTTTGATAACCTC-TTTATG
4876 AAATTTTGATA
1 AAATTTTGATA
4887 CTAAAATTTT
Statistics
Matches: 73, Mismatches: 25, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
22 71 0.97
23 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (22 bp):
AAATTTTGATAACCTCTTTATG
Found at i:5112 original size:22 final size:22
Alignment explanation
Indices: 5020--5143 Score: 94
Period size: 22 Copynumber: 5.6 Consensus size: 22
5010 ATAAACTTCA
5020 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* * *
5042 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * *
5064 CATCAAATATT-AGTAA-CATC-C
1 TATGAAATTTTGA-TAACCA-CAC
*
5085 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCACAC
* *
5108 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAC
*
5130 TATGACATTTTGAT
1 TATGAAATTTTGAT
5144 TATCTCTTTG
Statistics
Matches: 79, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
21 5 0.06
22 68 0.86
23 6 0.08
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:5241 original size:24 final size:22
Alignment explanation
Indices: 5180--5362 Score: 138
Period size: 22 Copynumber: 8.2 Consensus size: 22
5170 TTGTGATAAT
*
5180 TAACCATCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTAA
* *
5202 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTAA
**
5224 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTAA
* *
5248 TAACCA-CACTATAAAATTTTGA
1 TAACCATC-CTATGAAATTTTAA
*** * **
5270 TAATTTTCATATGAAATTTTGG
1 TAACCATCCTATGAAATTTTAA
* *
5292 TAACCA-CACTATGGAATTTTGA
1 TAACCATC-CTATGAAATTTTAA
5314 TAACC-TCCTCATGAAATTTTAA
1 TAACCATCCT-ATGAAATTTTAA
* * *
5336 TAACCATCTTATAAAATTTTGA
1 TAACCATCCTATGAAATTTTAA
5358 TAACC
1 TAACC
5363 TAATAGAGAT
Statistics
Matches: 127, Mismatches: 26, Indels: 16
0.75 0.15 0.09
Matches are distributed among these distances:
21 4 0.03
22 101 0.80
23 4 0.03
24 18 0.14
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTAA
Found at i:5291 original size:44 final size:43
Alignment explanation
Indices: 5235--5363 Score: 152
Period size: 44 Copynumber: 3.0 Consensus size: 43
5225 AACCTGATCC
**
5235 TATGAAATTTTGGTAACCACACTATAAAATTTTGATAATTTTCA
1 TATGAAATTTTGGTAACCACACTATAAAATTTTGATAA-CCTCA
** *
5279 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTCC
1 TATGAAATTTTGGTAACCACACTATAAAATTTTGATAACCTCA
** *
5322 TCATGAAATTTTAATAACCATC-TTATAAAATTTTGATAACCT
1 T-ATGAAATTTTGGTAACCA-CACTATAAAATTTTGATAACCT
5364 AATAGAGATA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 3 0.04
44 69 0.95
45 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGGTAACCACACTATAAAATTTTGATAACCTCA
Found at i:5574 original size:19 final size:19
Alignment explanation
Indices: 5531--5579 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
5521 ATTGACATTT
*
5531 AAATATTGAAATTAAAAGTA
1 AAATATT-AAATTAAAAGAA
5551 AAATATTAAATTAAAA-AA
1 AAATATTAAATTAAAAGAA
*
5569 ATAATAGTAAA
1 A-AATATTAAA
5580 GGAAATTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.65
20 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (19 bp):
AAATATTAAATTAAAAGAA
Done.