Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007579.1 Corchorus capsularis cultivar CVL-1 contig07600, 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: 16466
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Found at i:5682 original size:42 final size:42
Alignment explanation
Indices: 5630--5709 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
5620 CGACATCCCA
5630 ACATAGATGAAGGGAAAAAATGATGA-GAGGTAAACTCTGTTG
1 ACATAGATGAAGGGAAAAAATGAT-ATGAGGTAAACTCTGTTG
* *
5672 ACATGGATGAAGGGAAAAATTGATATGAGGTAAACTCT
1 ACATAGATGAAGGGAAAAAATGATATGAGGTAAACTCT
5710 CTATGTGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (42 bp):
ACATAGATGAAGGGAAAAAATGATATGAGGTAAACTCTGTTG
Found at i:7546 original size:8 final size:8
Alignment explanation
Indices: 7533--7557 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
7523 ACTGTGCTTT
7533 TGGAAATA
1 TGGAAATA
7541 TGGAAATA
1 TGGAAATA
7549 TGGAAATA
1 TGGAAATA
7557 T
1 T
7558 ACTAAACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (8 bp):
TGGAAATA
Found at i:7665 original size:16 final size:16
Alignment explanation
Indices: 7631--7668 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
7621 TTGTAAAATA
*
7631 AAATAATATAAGTATC
1 AAATAATATAAGTAAC
7647 AAATAATATAA-TCAAC
1 AAATAATATAAGT-AAC
7663 AAATAA
1 AAATAA
7669 ATTCAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAATATAAGTAAC
Found at i:9279 original size:45 final size:45
Alignment explanation
Indices: 9229--9314 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
9219 ACTTCTCAAG
* *
9229 CTCATCATTAA-TCTGGGGTAGGGATTTTTTAGTAATTCCACCCAC
1 CTCATCATTAATTC-GGGGTAGGAATCTTTTAGTAATTCCACCCAC
9274 CTCATCATTAATTCGGGGTAGGAATCTTTTAGTAATTCCAC
1 CTCATCATTAATTCGGGGTAGGAATCTTTTAGTAATTCCAC
9315 TAGTCTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
45 36 0.95
46 2 0.05
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (45 bp):
CTCATCATTAATTCGGGGTAGGAATCTTTTAGTAATTCCACCCAC
Found at i:10512 original size:25 final size:25
Alignment explanation
Indices: 10472--10519 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
10462 TTTTTAACTC
10472 ATTATTTTTTATTTAAAATATATTT
1 ATTATTTTTTATTTAAAATATATTT
*
10497 ATTATTTATTTA-TTAATATATAT
1 ATTATTT-TTTATTTAAAATATAT
10520 CTAAGACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTATTTTTTATTTAAAATATATTT
Found at i:11349 original size:13 final size:13
Alignment explanation
Indices: 11333--11359 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11323 TTTGATAACC
11333 TAACTATGAAACT
1 TAACTATGAAACT
11346 TAACTATGAAACT
1 TAACTATGAAACT
11359 T
1 T
11360 TATTAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TAACTATGAAACT
Found at i:14372 original size:22 final size:21
Alignment explanation
Indices: 14318--14373 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
14308 ACGTATTTAA
*
14318 ATAATTCA-TATGAAATTATG
1 ATAATTCACTATTAAATTATG
*
14338 ATAATCTCTCTATTAAATTATG
1 ATAAT-TCACTATTAAATTATG
14360 ATAATTACACTATT
1 ATAATT-CACTATT
14374 TTTTATGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 5 0.17
21 3 0.10
22 22 0.73
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (21 bp):
ATAATTCACTATTAAATTATG
Found at i:14413 original size:22 final size:22
Alignment explanation
Indices: 14388--14901 Score: 140
Period size: 22 Copynumber: 23.6 Consensus size: 22
14378 ATGATCCCAT
14388 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** *
14410 TATGAAA-TTTGAATAACAATAC
1 TATGAAATTTTG-ATAACCTTCC
* * * * **
14432 TATGGAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
14454 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
14476 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
14498 TAAGGAATTTTGA-AGAGC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
14520 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * **
14542 AATGAAAATTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
14565 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
14586 ATATG--ATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
14607 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
14628 ACATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
14651 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
14673 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
**
14695 TATGAAATTTTGATACATATTCC
1 TATGAAATTTTGATA-ACCTTCC
* * *
14718 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * **
14741 TATAAAATTTTGATAACTTTTT
1 TATGAAATTTTGATAACCTTCC
*
14763 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
14780 TA-CAAATTTTGATATCCTTCC
1 TATGAAATTTTGATAACCTTCC
* *
14801 TAT-AATTTTTTGATAACC-TCAT
1 TATGAA-ATTTTGATAACCTTC-C
** **
14823 TATGAAATTTTTTTAATTTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
14845 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
14867 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
14889 TATGAAATTTTGA
1 TATGAAATTTTGA
14902 AAACTAAACT
Statistics
Matches: 359, Mismatches: 97, Indels: 72
0.68 0.18 0.14
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
20 16 0.04
21 22 0.06
22 237 0.66
23 69 0.19
24 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:14725 original size:23 final size:23
Alignment explanation
Indices: 14694--14756 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
14684 GATAACCTCG
* * *
14694 CTATGAAATTTTGATACATATTC
1 CTATAAAATTTTGATAAATATCC
*
14717 CTATAAAATTTTGATAAATCTCC
1 CTATAAAATTTTGATAAATATCC
14740 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
14757 CTTTTTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATATCC
Found at i:14963 original size:20 final size:20
Alignment explanation
Indices: 14914--14963 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
14904 ACTAAACTAA
* *
14914 GAAATTTAGATATCCTCTCT
1 GAAATTTTGATATCCTCCCT
* *
14934 G-AATTCTGATATCTTCCCT
1 GAAATTTTGATATCCTCCCT
14953 GAAATTTTGAT
1 GAAATTTTGAT
14964 TACTCCATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (20 bp):
GAAATTTTGATATCCTCCCT
Found at i:15093 original size:78 final size:78
Alignment explanation
Indices: 15011--15186 Score: 325
Period size: 78 Copynumber: 2.3 Consensus size: 78
15001 GTAACCATAC
* *
15011 TATGAAACTTTGATAACCTCCCTAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAAT
1 TATGAAATTTTGATAACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAAT
*
15076 TTGATAACCTTTT
66 TTGATAACCTCTT
15089 TATGAAATTTTGATAACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAAT
1 TATGAAATTTTGATAACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAAT
15154 TTGATAACCTCTT
66 TTGATAACCTCTT
15167 TATGAAATTTTGATAACCTC
1 TATGAAATTTTGATAACCTC
15187 TTTATAAAAT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 95 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (78 bp):
TATGAAATTTTGATAACCTCCCCAGAAATACCACTATGAAATTTTTGTAATCACATTTTGAAAAT
TTGATAACCTCTT
Found at i:15218 original size:22 final size:22
Alignment explanation
Indices: 15147--15538 Score: 106
Period size: 22 Copynumber: 17.6 Consensus size: 22
15137 AATCACATTT
* * *
15147 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
15169 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
15191 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* * * *
15213 TGAAATTCTAATAATCACAT-TA
1 TGAAATTTTGATAA-CCCCTCTA
* * * * *
15235 TGTAATTTTTATAACCTCGCTT
1 TGAAATTTTGATAACCCCTCTA
** *
15257 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCCCTCTA
****
15279 TGAAATTTTGATAATATTTCTA
1 TGAAATTTTGATAACCCCTCTA
*
15301 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--CCTCTA
* * * *
15325 TGAAATTTCGACAATCACTCTA
1 TGAAATTTTGATAACCCCTCTA
* * *
15347 TGAGA-TTCGATAA-CCTTCTA
1 TGAAATTTTGATAACCCCTCTA
* * *
15367 TCAAATTTTGGT-ACTCCT-TA
1 TGAAATTTTGATAACCCCTCTA
* *
15387 TGAAATTGAGACTTTTATAA-CCTTCATA
1 TGAAA-T-----TTTGATAACCCCTC-TA
* *
15415 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
15437 TAAAATTTTGATAACCTCC-CCA
1 TGAAATTTTGATAACC-CCTCTA
* *
15459 TGAAATATT-AGTAACCTCCT-AA
1 TGAAATTTTGA-TAACC-CCTCTA
*** *
15481 TGAAATTTT-ATTAATTACACTA
1 TGAAATTTTGA-TAACCCCTCTA
* *
15503 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCCCTCTA
*
15525 TGACATTTTGATAA
1 TGAAATTTTGATAA
15539 TCTCTTTGAT
Statistics
Matches: 271, Mismatches: 75, Indels: 48
0.69 0.19 0.12
Matches are distributed among these distances:
20 15 0.06
21 31 0.11
22 184 0.68
23 9 0.03
24 7 0.03
25 10 0.04
26 6 0.02
27 2 0.01
28 7 0.03
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:15285 original size:88 final size:88
Alignment explanation
Indices: 15122--15288 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 88
15112 AGAAATACCA
* ** * * **
15122 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC
1 CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
**
15187 TTTATAAAATTTTGTTGACCCCT
66 ACTATAAAATTTTGTTGACCCCT
* * *
15210 CTATGAAATTCTAATAATCACATTATGTAATTTTTATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAA
*
15274 CACTATGAAATTTTG
65 CACTATAAAATTTTG
15289 ATAATATTTC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
88 63 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (88 bp):
CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAAC
ACTATAAAATTTTGTTGACCCCT
Found at i:15638 original size:24 final size:22
Alignment explanation
Indices: 15581--15639 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
15571 AATTAATCAC
*
15581 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTAATAACCAA
* * *
15603 CCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAACC--AA
15627 CCTATGAAATTTT
1 CCTATGAAATTTT
15640 GGTAACCACA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 17 0.59
24 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (22 bp):
CCTATGAAATTTTAATAACCAA
Done.