Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014644.1 Corchorus capsularis cultivar CVL-1 contig14665, 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: 27256
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4532 original size:22 final size:22
Alignment explanation
Indices: 4476--4767 Score: 140
Period size: 22 Copynumber: 13.7 Consensus size: 22
4466 GTATACAAAA
* *
4476 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCTCACTAT
*
4498 G-AATTTGTAATAACCTCACTAT
1 GAAATTT-TGATAACCTCACTAT
*
4520 GAAATTTTGATAAACCTCCCTAT
1 GAAATTTTGAT-AACCTCACTAT
* *
4543 AAAAATTTGATAACCTC-CTAT
1 GAAATTTTGATAACCTCACTAT
*
4564 -AAGATTTTGGTAA--TCAC---
1 GAA-ATTTTGATAACCTCACTAT
4581 -AAATTTTGATAACCTC-CATAT
1 GAAATTTTGATAACCTCAC-TAT
** * *
4602 GATTTTTTCCATAACCTCATTAT
1 GAAATTTT-GATAACCTCACTAT
* *
4625 GAAATTTT-ATTAACCTCCCAAT
1 GAAATTTTGA-TAACCTCACTAT
*
4647 GAAATTTTGATAATCCCCA-TAT
1 GAAATTTTGATAA-CCTCACTAT
* * *
4669 GAAATTTTGA-AAACTAAAGTAT
1 GAAATTTTGATAACCT-CACTAT
*
4691 GAAATTTTAATAA---C-CT-T
1 GAAATTTTGATAACCTCACTAT
4708 GAAAATTTTGATAACAC-C-CTAT
1 G-AAATTTTGATAAC-CTCACTAT
* *
4730 GAAATTTTGATTACACT-ACAAT
1 GAAATTTTGATAAC-CTCACTAT
* *
4752 AAAATTTTAATAACCT
1 GAAATTTTGATAACCT
4768 TCATATTCTA
Statistics
Matches: 209, Mismatches: 34, Indels: 55
0.70 0.11 0.18
Matches are distributed among these distances:
16 9 0.04
17 5 0.02
18 14 0.07
19 2 0.01
20 4 0.02
21 40 0.19
22 88 0.42
23 47 0.22
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
GAAATTTTGATAACCTCACTAT
Found at i:4739 original size:61 final size:61
Alignment explanation
Indices: 4648--4768 Score: 160
Period size: 61 Copynumber: 2.0 Consensus size: 61
4638 CCTCCCAATG
4648 AAATTTTGATAATCCCCATATGAAATTTTGA-AAACTA-AAGTATGAAATTTTAATAACCTTGA
1 AAATTTTGATAATCCCCATATGAAATTTTGATAAACTACAA-TA--AAATTTTAATAACCTTGA
*
4710 AAATTTTGATAA-CACCC-TATGAAATTTTGATTACACTACAATAAAATTTTAATAACCTT
1 AAATTTTGATAATC-CCCATATGAAATTTTGA-TAAACTACAATAAAATTTTAATAACCTT
4769 CATATTCTAG
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
61 30 0.56
62 15 0.28
63 7 0.13
64 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (61 bp):
AAATTTTGATAATCCCCATATGAAATTTTGATAAACTACAATAAAATTTTAATAACCTTGA
Found at i:4874 original size:22 final size:22
Alignment explanation
Indices: 4849--5704 Score: 224
Period size: 22 Copynumber: 38.6 Consensus size: 22
4839 TCACACTATA
4849 AAATTTTGATAACCTCTTTATG
1 AAATTTTGATAACCTCTTTATG
* * *
4871 AAATTTTAAT-ACCTCTCTATT
1 AAATTTTGATAACCTCTTTATG
* * * **
4892 AAAGTTTGTTAACGTCTCAATG
1 AAATTTTGATAACCTCTTTATG
* **
4914 AAATTTTGATAACCACGGTATG
1 AAATTTTGATAACCTCTTTATG
* * *
4936 AAATTTCGATAACCTCGTTATA
1 AAATTTTGATAACCTCTTTATG
*
4958 AAATTTTGATAACCTCATTT-TA
1 AAATTTTGATAACCTC-TTTATG
* *
4980 AAATTTTGATAACCTCATTGTG
1 AAATTTTGATAACCTCTTTATG
* *
5002 AAATTTTAATAACCT-TCATATG
1 AAATTTTGATAACCTCT-TTATG
*
5024 AAATTTTGATAA-CTGCATTATG
1 AAATTTTGATAACCT-CTTTATG
* * *
5046 AAAATTTGATAACAT-TCCTATG
1 AAATTTTGATAACCTCT-TTATG
*
5068 AAATTTTGATAA-CTACATTATG
1 AAATTTTGATAACCT-CTTTATG
* *
5090 AAAATTTGATAA--TATTCCTATG
1 AAATTTTGATAACCTCTT--TATG
*
5112 AAATTTTGGTAACCT-TCTTATG
1 AAATTTTGATAACCTCT-TTATG
** *
5134 AAATTTTGATAATTTGACCTCTATG
1 AAATTTTGATAACCT---CTTTATG
** * * *
5159 AAAAATTAATAACCACTCTATG
1 AAATTTTGATAACCTCTTTATG
* * * **
5181 AGATATTGATAATCTCCGTATG
1 AAATTTTGATAACCTCTTTATG
* * * ** *
5203 AATTTTTTTATAACCACACTATA
1 AA-ATTTTGATAACCTCTTTATG
* * *
5226 AAATTTTGATAACTTAC-CTATT
1 AAATTTTGATAACCT-CTTTATG
* *
5248 AAATTTTGATAA-CT-TTACAATT
1 AAATTTTGATAACCTCTT--TATG
* *
5270 AAATTTTGACAACTTACTTATGAAATTG
1 AAATTTTGATAACCT-CTT-T---A-TG
* * *
5298 AGATTTTTATAACCT-TACTATG
1 AAATTTTGATAACCTCT-TTATG
* * ** * ** *
5320 AAACTTTGGTAGTCACACTATA
1 AAATTTTGATAACCTCTTTATG
* ** *
5342 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCTCTTTATG
**
5364 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCTTTATG
*
5386 AAATTTTGACT--CC-C--AATG
1 AAATTTTGA-TAACCTCTTTATG
* * **
5404 TAATTTT-AGTAATCTCCATATG
1 AAATTTTGA-TAACCTCTTTATG
*
5426 AAATTTCGATAACCATAC-TT-TG
1 AAATTTTGATAACC-T-CTTTATG
***
5448 AAATTTTG-TAACCTGGCTATG
1 AAATTTTGATAACCTCTTTATG
*
5469 AAATTTTTATAACCTTCTTT-TG
1 AAATTTTGATAACC-TCTTTATG
5491 AAATTTTGATAACCT-TTTGATG
1 AAATTTTGATAACCTCTTT-ATG
* ** * *
5513 AAATTTTAATAATTTGATCCTATGG
1 AAATTTTGATAACCT-CT-TTAT-G
* *
5538 AATTTTTGATAA-CTATTCTATG
1 AAATTTTGATAACCTCTT-TATG
*
5560 AAATCTTGATAA--TCTTCCTATG
1 AAATTTTGATAACCTCTT--TATG
* *****
5582 AAATTTTGGTAACCAAACAATG
1 AAATTTTGATAACCTCTTTATG
** * *
5604 AAATTTTGATAACCTCCATGTA
1 AAATTTTGATAACCTCTTTATG
* *
5626 AAATTTT-AGTAACCACATTATG
1 AAATTTTGA-TAACCTCTTTATG
* *
5648 AAAATTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCTTTATG
* * *
5670 AAATTATAAT-TCCT-TCTTATG
1 AAATTTTGATAACCTCT-TTATG
*
5691 ATATTTTGATAACC
1 AAATTTTGATAACC
5705 ACACAGAGAC
Statistics
Matches: 610, Mismatches: 164, Indels: 120
0.68 0.18 0.13
Matches are distributed among these distances:
17 2 0.00
18 9 0.01
19 1 0.00
20 8 0.01
21 59 0.10
22 448 0.73
23 33 0.05
24 7 0.01
25 27 0.04
26 3 0.00
27 1 0.00
28 12 0.02
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTCTTTATG
Found at i:4877 original size:44 final size:44
Alignment explanation
Indices: 4827--5674 Score: 302
Period size: 44 Copynumber: 19.1 Consensus size: 44
4817 TACCACTCTA
* * *
4827 AAATTTTGATAATCACACTATAAAATTTTGATAACCTCTTTATG
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCATTATG
* * * * * *
4871 AAATTTTAAT-ACCTCTCTATTAAAGTTTGTTAACGTCTCA--ATG
1 AAATTTTGATAACCACACTATGAAATTTTGATAAC--CTCATTATG
** * * *
4914 AAATTTTGATAACCACGGTATGAAATTTCGATAACCTCGTTATA
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCATTATG
* * * * *
4958 AAATTTTGATAACCTCATTTTAAAATTTTGATAACCTCATTGTG
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCATTATG
* *
5002 AAATTTTAATAACCTTCA-TATGAAATTTTGATAA-CTGCATTATG
1 AAATTTTGATAACC-ACACTATGAAATTTTGATAACCT-CATTATG
*
5046 AAAATTTGATAA-CATTC-CTATGAAATTTTGATAA-CTACATTATG
1 AAATTTTGATAACCA--CACTATGAAATTTTGATAACCT-CATTATG
* * *
5090 AAAATTTGATAA-TATTC-CTATGAAATTTTGGTAACCTTC-TTATG
1 AAATTTTGATAACCA--CACTATGAAATTTTGATAACC-TCATTATG
** * ** * *
5134 AAATTTTGATAATTTGACCTCTATGAAAAATTAATAACCAC-TCTATG
1 AAATTTTGATAA--CCA-CACTATGAAATTTTGATAACCTCAT-TATG
* * * * * * * * *
5181 AGATATTGATAATCTC-CGTATGAATTTTTTTATAACCACACTATA
1 AAATTTTGATAACCACAC-TATGAA-ATTTTGATAACCTCATTATG
* * * * ** *
5226 AAATTTTGATAACTTAC-CTATTAAATTTTGATAACTTTACAATT
1 AAATTTTGATAAC-CACACTATGAAATTTTGATAACCTCATTATG
* * * * * *
5270 AAATTTTGACAACTTACTTA-TGAAATTGAGATTTTTATAACCTTACTATG
1 AAATTTTGATAAC-CAC--ACT---A-TGAAATTTTGATAACCTCATTATG
* * ** * * * *
5320 AAACTTTGGTAGTCACACTATAAAATTTTGATAACCACACTATA
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCATTATG
* *
5364 AAATTTTGATAACCTCCCTATGAAATTTTGACT--CC-CA--ATG
1 AAATTTTGATAACCACACTATGAAATTTTGA-TAACCTCATTATG
* *
5404 TAATTTT-AGTAATCTC-CA-TATGAAATTTCGATAACCAT-ACTT-TG
1 AAATTTTGA-TAA-C-CACACTATGAAATTTTGATAACC-TCA-TTATG
*** * *
5448 AAATTTTG-TAACCTGGCTATGAAATTTTTATAACCTTC-TTTTG
1 AAATTTTGATAACCACACTATGAAATTTTGATAACC-TCATTATG
*** * ** *
5491 AAATTTTGATAACC-TTTTGATGAAATTTTAATAATTTGATCCTATGG
1 AAATTTTGATAACCACACT-ATGAAATTTTGATAACCTCAT--TAT-G
* * ** * * *
5538 AATTTTTGATAACTATTCTATGAAATCTTGATAATCTTC-CTATG
1 AAATTTTGATAACCACACTATGAAATTTTGATAA-CCTCATTATG
* * *
5582 AAATTTTGGTAACCAAACAATGAAATTTTGATAACCTCCATGTA--
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCT-CAT-TATG
* * *
5626 AAATTTT-AGTAACCACATTATGAAAATTTGATAACCTCCTTATG
1 AAATTTTGA-TAACCACACTATGAAATTTTGATAACCTCATTATG
5670 AAATT
1 AAATT
5675 ATAATTCCTT
Statistics
Matches: 610, Mismatches: 135, Indels: 118
0.71 0.16 0.14
Matches are distributed among these distances:
39 2 0.00
40 23 0.04
41 5 0.01
42 12 0.02
43 72 0.12
44 351 0.58
45 42 0.07
46 11 0.02
47 57 0.09
48 6 0.01
49 3 0.00
50 26 0.04
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (44 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAACCTCATTATG
Found at i:5471 original size:43 final size:44
Alignment explanation
Indices: 5422--5505 Score: 118
Period size: 43 Copynumber: 1.9 Consensus size: 44
5412 GTAATCTCCA
5422 TATGAAATTTCGATAACCATAC-TTTGAAATTTTG-TAACCTGGC
1 TATGAAATTTCGATAACC-TACTTTTGAAATTTTGATAACCTGGC
** *
5465 TATGAAATTTTTATAACCTTCTTTTGAAATTTTGATAACCT
1 TATGAAATTTCGATAACCTACTTTTGAAATTTTGATAACCT
5506 TTTGATGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 2 0.06
43 28 0.78
44 6 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (44 bp):
TATGAAATTTCGATAACCTACTTTTGAAATTTTGATAACCTGGC
Found at i:5561 original size:47 final size:45
Alignment explanation
Indices: 5466--5588 Score: 108
Period size: 47 Copynumber: 2.7 Consensus size: 45
5456 TAACCTGGCT
* * * * *
5466 ATGAAATTTTTATAACCTTCTTTTGAAA-TTTTGATAACCTTTTG
1 ATGAAATCTTAATAATCTTCCTATGAAATTTTTGATAACCTTTTG
* * *
5510 ATGAAATTTTAATAATTTGATCCTATGGAATTTTTGATAA-CTATTCT-
1 ATGAAATCTTAATAATCT--TCCTATGAAATTTTTGATAACCT-TT-TG
*
5557 ATGAAATCTTGATAATCTTCCTATGAAATTTT
1 ATGAAATCTTAATAATCTTCCTATGAAATTTT
5589 GGTAACCAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
44 15 0.23
45 13 0.20
46 9 0.14
47 26 0.41
48 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.47
Consensus pattern (45 bp):
ATGAAATCTTAATAATCTTCCTATGAAATTTTTGATAACCTTTTG
Found at i:5933 original size:16 final size:16
Alignment explanation
Indices: 5903--5932 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5893 AGTTAGCTTA
5903 GTATTTTAATTTTTTG
1 GTATTTTAATTTTTTG
5919 GTATTTT-ATTTTTT
1 GTATTTTAATTTTTT
5933 TTAACAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (16 bp):
GTATTTTAATTTTTTG
Found at i:8415 original size:26 final size:25
Alignment explanation
Indices: 8367--8433 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
8357 TAATAATTTT
8367 AGTTTTAATTTATAATTTATATATA
1 AGTTTTAATTTATAATTTATATATA
*
8392 AGTTGTTAATTT-TAATGTTTTATAATA
1 AGTT-TTAATTTATAAT-TTATAT-ATA
8419 A-TTTATATATTTATA
1 AGTTT-TA-ATTTATA
8434 TTCAACATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 9 0.26
26 16 0.46
27 8 0.23
28 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (25 bp):
AGTTTTAATTTATAATTTATATATA
Found at i:9089 original size:36 final size:38
Alignment explanation
Indices: 9014--9092 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 38
9004 CTGGATGCGT
9014 ACTTTTTAAGTGAGAATTAAAGTCAAATAGTAGTAAGTA
1 ACTTTTTAAGTGAGAATTAAAGTC-AATAGTAGTAAGTA
9053 ACTTTTTAAGTGAGAATTAAAGTC-A-AGTAGTAAGTA
1 ACTTTTTAAGTGAGAATTAAAGTCAATAGTAGTAAGTA
9089 ACTT
1 ACTT
9093 ATTGACTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 15 0.38
37 1 0.03
39 24 0.60
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (38 bp):
ACTTTTTAAGTGAGAATTAAAGTCAATAGTAGTAAGTA
Found at i:12883 original size:17 final size:19
Alignment explanation
Indices: 12842--12890 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
12832 TATTAACTTT
*
12842 TAAATATAGTAAAAAAATC
1 TAAATATAGTAAAAAAATA
*
12861 TGAATATA-TAAAAAAA-A
1 TAAATATAGTAAAAAAATA
12878 TAAATA-AGTAAAA
1 TAAATATAGTAAAA
12891 TCTTTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 8 0.31
19 7 0.27
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (19 bp):
TAAATATAGTAAAAAAATA
Found at i:12912 original size:13 final size:13
Alignment explanation
Indices: 12896--12920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12886 TAAAATCTTT
12896 CAAAAAAATTAAA
1 CAAAAAAATTAAA
12909 CAAAAAAATTAA
1 CAAAAAAATTAA
12921 TATGCAACCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
CAAAAAAATTAAA
Found at i:15606 original size:3 final size:3
Alignment explanation
Indices: 15598--15628 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
15588 AACAAGTTTG
15598 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
15629 GTTGAGGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:21197 original size:40 final size:40
Alignment explanation
Indices: 21139--21216 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
21129 GTCTCTCCTA
* * *
21139 ATAATTAAGGAAACAAATTATATTCAGGTTTAGCCCCTTG
1 ATAATTAAGGAAACAAATTAAATCCAGGTTGAGCCCCTTG
* *
21179 ATAATTAAGGTAATAAATTAAATCCAGGTTGAGCCCCT
1 ATAATTAAGGAAACAAATTAAATCCAGGTTGAGCCCCT
21217 AGTTATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (40 bp):
ATAATTAAGGAAACAAATTAAATCCAGGTTGAGCCCCTTG
Done.