Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023572.1 Corchorus olitorius cultivar O-4 contig23605, 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: 7146
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:1347 original size:20 final size:20
Alignment explanation
Indices: 1318--1363 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1308 TTCTTTTTTC
*
1318 AAAAATGCAACCCAAAAATT
1 AAAAACGCAACCCAAAAATT
1338 AAAAACGCAACCCAAAAATT
1 AAAAACGCAACCCAAAAATT
1358 AAAAAC
1 AAAAAC
1364 ACAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.63, C:0.22, G:0.04, T:0.11
Consensus pattern (20 bp):
AAAAACGCAACCCAAAAATT
Found at i:4083 original size:22 final size:22
Alignment explanation
Indices: 4052--4106 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
4042 TAATTACACT
* *
4052 ATTTTGATAACCTTCTTATGAA
1 ATTTTAATAACCTTCCTATGAA
4074 ATTTTAATAACCTTCCTATGAA
1 ATTTTAATAACCTTCCTATGAA
*
4096 ACTTTAATAAC
1 ATTTTAATAAC
4107 GATATTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (22 bp):
ATTTTAATAACCTTCCTATGAA
Found at i:4172 original size:22 final size:21
Alignment explanation
Indices: 4147--4480 Score: 169
Period size: 22 Copynumber: 15.3 Consensus size: 21
4137 AAATTTTTTT
4147 TAACCTCCTTATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* *
4169 TAACCTCCCTAAGGAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
*
4191 AAACCTCACTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGA
* * *
4213 TAACTTCCGAACGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* * *
4235 TAACCAACACTATGAGATGTTGA
1 TAACC-TC-CTATGAAATTTTGA
* *
4258 TAACCTCCATATGACATATTGA
1 TAACCTCC-TATGAAATTTTGA
* * *
4280 TAACCACGCTATGAAAATTTAA
1 TAACCTC-CTATGAAATTTTGA
* *
4302 GAACCTCCATTTG-AATTGTT-A
1 TAACCTCC-TATGAAATT-TTGA
* * *
4323 GTAATCACACTCTGAAATTTTGA
1 -TAACCTC-CTATGAAATTTTGA
* * *
4346 TAATCACACTATGAAATTGTGA
1 TAACCTC-CTATGAAATTTTGA
* * *
4368 TAATCTTGCTATAAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
*
4390 TAAACCTCCTTATAAAATTTTTGA
1 T-AACCTCC-TATGAAA-TTTTGA
* *
4414 TAACATCCTTATGAAATCTTGA
1 TAACCTCC-TATGAAATTTTGA
*
4436 TAA----CTA-CAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
4452 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
4474 TAACCTC
1 TAACCTC
4481 ATTTACATAC
Statistics
Matches: 240, Mismatches: 49, Indels: 47
0.71 0.15 0.14
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
18 1 0.00
21 12 0.05
22 160 0.67
23 46 0.19
24 8 0.03
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Found at i:4416 original size:24 final size:23
Alignment explanation
Indices: 4377--4438 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
4367 ATAATCTTGC
*
4377 TATAAAATTTTGATAAACCTCCT
1 TATAAAATTTTGATAAACATCCT
4400 TATAAAATTTTTGAT-AACATCCT
1 TATAAAA-TTTTGATAAACATCCT
* *
4423 TATGAAATCTTGATAA
1 TATAAAATTTTGATAA
4439 CTACAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.18
23 21 0.62
24 7 0.21
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (23 bp):
TATAAAATTTTGATAAACATCCT
Found at i:4519 original size:22 final size:21
Alignment explanation
Indices: 4490--4590 Score: 96
Period size: 22 Copynumber: 4.7 Consensus size: 21
4480 CATTTACATA
*
4490 CTATGAAATTTTGATAACCCT
1 CTATGAAATTTTGATAACCAT
* * *
4511 CTTATGAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGATAAC-CAT
*
4534 CTATGAAATTTTGATAACCTT
1 CTATGAAATTTTGATAACCAT
*
4555 CATATGAAATTTTGATATCC-T
1 C-TATGAAATTTTGATAACCAT
**
4576 CCCTGAAATTTTGAT
1 CTATGAAATTTTGAT
4591 CACTCCATAG
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
20 12 0.18
21 4 0.06
22 49 0.74
23 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCAT
Found at i:4727 original size:22 final size:22
Alignment explanation
Indices: 4673--4941 Score: 104
Period size: 22 Copynumber: 12.3 Consensus size: 22
4663 AAATACACTG
* * *
4673 TGAAATTTTGGTAATCACATTT-
1 TGAAATTTTGATAACCTC-TTTA
*
4695 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
4717 TGGAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
4739 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
*** *
4761 TGAAATTTTGATATTTTCATTA
1 TGAAATTTTGATAACCTCTTTA
* * *
4783 TGTAATTTGGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
4805 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
* * *
4827 TGAAATTTCGATAAACATC-CTA
1 TGAAATTTTGAT-AACCTCTTTA
* *
4849 T-AAATTTTTATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
4873 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
4895 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
4915 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
4935 TGAAATT
1 TGAAATT
4942 AAGGCTTTTA
Statistics
Matches: 184, Mismatches: 52, Indels: 24
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.01
20 18 0.10
21 26 0.14
22 114 0.62
23 9 0.05
24 5 0.03
25 10 0.05
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:4990 original size:22 final size:23
Alignment explanation
Indices: 4965--5022 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
4955 CCTTCATACG
4965 AAATTTTGATAACCACACTA-AA
1 AAATTTTGATAACCACACTATAA
* * *
4987 AAATTTTAATAACCACATTATGA
1 AAATTTTGATAACCACACTATAA
5010 AAA-TTTGATAACC
1 AAATTTTGATAACC
5023 TCCTTACCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (23 bp):
AAATTTTGATAACCACACTATAA
Found at i:5073 original size:22 final size:22
Alignment explanation
Indices: 5035--5094 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
5025 CTTACCTCCT
*
5035 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
5057 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAC
*
5079 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
5095 TCTCTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:5270 original size:66 final size:65
Alignment explanation
Indices: 5127--5333 Score: 229
Period size: 66 Copynumber: 3.1 Consensus size: 65
5117 AAATTGTGAA
** * *
5127 AACCACACTATGAAATTTCAATAACCTTCCTA-AAAATTTTAATAACCTGATCCTATGAAATTTT
1 AACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTAATAA-CT-ATCC-ATGAAATTTT
5191 GGT
63 GGT
** * *
5194 AACCTTACTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAACTTTCACATGAAATTTTGG
1 AACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTAATAACTATC-CATGAAATTTTGG
5259 T
65 T
* * * *
5260 AACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCATCTTATGAAATTTTG
1 AACCACACTATGAAATTTTGATAACCTTCC-CATGAAATTTTAATAACTATC-CATGAAATTTTG
*
5324 AT
64 GT
5326 AACCACAC
1 AACCACAC
5334 AGAGACAAGA
Statistics
Matches: 119, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
65 3 0.03
66 75 0.63
67 30 0.25
68 11 0.09
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (65 bp):
AACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTTAATAACTATCCATGAAATTTTGGT
Found at i:5330 original size:22 final size:22
Alignment explanation
Indices: 5099--5330 Score: 177
Period size: 22 Copynumber: 10.5 Consensus size: 22
5089 TGATAATCTC
* * *
5099 TTTGATAACCTTTCTATAAAAT
1 TTTGATAACCATCCTATGAAAT
* *
5121 TGTGAAAACCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
** * *
5143 TTCAATAACCTTCCTA-AAAAT
1 TTTGATAACCATCCTATGAAAT
*
5164 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAACC--ATCCTATGAAAT
* * *
5188 TTTGGTAACCTTACTATGAAAT
1 TTTGATAACCATCCTATGAAAT
* *
5210 TTTGATAACCTTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
**
5232 TTTGATAACTTTCAC-ATGAAAT
1 TTTGATAACCATC-CTATGAAAT
* *
5254 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
5276 TTTGATAACC-TCCTCATGAAAT
1 TTTGATAACCATCCT-ATGAAAT
* * *
5298 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
5320 TTTGATAACCA
1 TTTGATAACCA
5331 CACAGAGACA
Statistics
Matches: 167, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
21 18 0.11
22 127 0.76
23 10 0.06
24 12 0.07
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:5527 original size:19 final size:20
Alignment explanation
Indices: 5496--5533 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5486 TATTGACATT
5496 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
5515 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
5534 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:6606 original size:22 final size:22
Alignment explanation
Indices: 6580--6681 Score: 98
Period size: 22 Copynumber: 4.7 Consensus size: 22
6570 ATATTTTTAG
* *
6580 GAAATTTTGATAACTACCCTAT
1 GAAATTTTGATAACCACCATAT
* *
6602 TAAATTTTGATGACCACCATAT
1 GAAATTTTGATAACCACCATAT
** *
6624 GAAATTTTGATAATTATC-TAT
1 GAAATTTTGATAACCACCATAT
* * *
6645 GAAATTATGATAAACGCCATAT
1 GAAATTTTGATAACCACCATAT
*
6667 GAAACTTTGATAACC
1 GAAATTTTGATAACC
6682 TGACTATAAA
Statistics
Matches: 62, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
21 16 0.26
22 46 0.74
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
GAAATTTTGATAACCACCATAT
Found at i:6647 original size:21 final size:21
Alignment explanation
Indices: 6580--6701 Score: 95
Period size: 22 Copynumber: 5.6 Consensus size: 21
6570 ATATTTTTAG
6580 GAAATTTTGATAACTACCCTAT
1 GAAATTTTGATAACTA-CCTAT
* * *
6602 TAAATTTTGATGACCACCATAT
1 GAAATTTTGATAACTACC-TAT
* *
6624 GAAATTTTGATAATTATCTAT
1 GAAATTTTGATAACTACCTAT
* *
6645 GAAATTATGATAAAC-GCCATAT
1 GAAATTTTGAT-AACTACC-TAT
*
6667 GAAACTTTGATAACCTGA-CTAT
1 GAAATTTTGATAA-CT-ACCTAT
*
6689 AAAATTTTGATAA
1 GAAATTTTGATAA
6702 GCTTTTCTAT
Statistics
Matches: 77, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
21 18 0.23
22 58 0.75
23 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (21 bp):
GAAATTTTGATAACTACCTAT
Found at i:6666 original size:43 final size:44
Alignment explanation
Indices: 6580--6680 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
6570 ATATTTTTAG
* * * *
6580 GAAATTTTGATAACTACCCTATTAAATTTTGATGACCACCATAT
1 GAAATTTTGATAACTACCCTATGAAATTATGATAAACACCATAT
* * *
6624 GAAATTTTGATAATTA-TCTATGAAATTATGATAAACGCCATAT
1 GAAATTTTGATAACTACCCTATGAAATTATGATAAACACCATAT
*
6667 GAAACTTTGATAAC
1 GAAATTTTGATAAC
6681 CTGACTATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
43 33 0.69
44 15 0.31
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (44 bp):
GAAATTTTGATAACTACCCTATGAAATTATGATAAACACCATAT
Found at i:6749 original size:37 final size:37
Alignment explanation
Indices: 6686--6758 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
6676 ATAACCTGAC
* * *
6686 TATAAAATTTTGATAAGCTTTTCTATAAATTTTGTAT
1 TATAAAATTTTAATAAACTTTCCTATAAATTTTGTAT
6723 TATAAAATTTTAATAAACTTTCCTATAAATTTTGTA
1 TATAAAATTTTAATAAACTTTCCTATAAATTTTGTA
6759 ATCTTCCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.49
Consensus pattern (37 bp):
TATAAAATTTTAATAAACTTTCCTATAAATTTTGTAT
Done.