Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011193.1 Corchorus capsularis cultivar CVL-1 contig11214, 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: 21946
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Found at i:228 original size:2 final size:2
Alignment explanation
Indices: 221--256 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
211 TTGTATGATG
*
221 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
257 CTTTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1606 original size:48 final size:48
Alignment explanation
Indices: 1533--1628 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
1523 CGGAGGGACT
*
1533 AACGTGTCCTCAAATTGCAAGTTTAAGGGGCAAAAAGTCCCAAATTAA
1 AACGTGTCCTCAAATTGCAAGTTTAAGGAGCAAAAAGTCCCAAATTAA
* *
1581 AACGTGTCCTTAAATTTGCAA-TTTAAGGAGCAAAAAGTCTCAAATTAA
1 AACGTGTCCTCAAA-TTGCAAGTTTAAGGAGCAAAAAGTCCCAAATTAA
1629 TATTTAGGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 38 0.86
49 6 0.14
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (48 bp):
AACGTGTCCTCAAATTGCAAGTTTAAGGAGCAAAAAGTCCCAAATTAA
Found at i:2567 original size:18 final size:18
Alignment explanation
Indices: 2544--2578 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2534 CTAAAAGGAT
2544 GGGAAAGTTACCTTTCCC
1 GGGAAAGTTACCTTTCCC
2562 GGGAAAGTTACCTTTCC
1 GGGAAAGTTACCTTTCC
2579 TAGGAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (18 bp):
GGGAAAGTTACCTTTCCC
Found at i:2584 original size:18 final size:18
Alignment explanation
Indices: 2545--2587 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2535 TAAAAGGATG
*
2545 GGAAAGTTACCTTTCCCG
1 GGAAAGTTACCTTTCCCA
*
2563 GGAAAGTTACCTTTCCTA
1 GGAAAGTTACCTTTCCCA
2581 GGAAAGT
1 GGAAAGT
2588 ATTACTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (18 bp):
GGAAAGTTACCTTTCCCA
Found at i:10557 original size:2 final size:2
Alignment explanation
Indices: 10552--10576 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10542 ATAAGATACG
10552 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10577 CTAAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13350 original size:70 final size:71
Alignment explanation
Indices: 13247--13389 Score: 234
Period size: 70 Copynumber: 2.0 Consensus size: 71
13237 ACTAAAATCC
* *
13247 TAATAGACTCACTAAATAAAAAACTCTCAATTAAATTAAACTTAATTAAATAAATAAAGAGCTCA
1 TAATAGACCCACTAAATAAAAAACTCTCAATTAAATTAAACTTAATTAAATAAATAAAAAGCTCA
13312 TAAAAA
66 TAAAAA
* * *
13318 TAATTGACCCACTAAAT-AAAAACTCTCGATTAAATTAAACTTAATTAAATAAATAAAAATCTCA
1 TAATAGACCCACTAAATAAAAAACTCTCAATTAAATTAAACTTAATTAAATAAATAAAAAGCTCA
13382 TAAAAA
66 TAAAAA
13388 TA
1 TA
13390 TTATTGGCCT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 52 0.78
71 15 0.22
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.28
Consensus pattern (71 bp):
TAATAGACCCACTAAATAAAAAACTCTCAATTAAATTAAACTTAATTAAATAAATAAAAAGCTCA
TAAAAA
Found at i:19395 original size:61 final size:64
Alignment explanation
Indices: 19305--19430 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 64
19295 ATGACAATTA
*
19305 TAAAGGCATGCTCATGATTACATAGAC-A-AAT-AATTTCAAGTATTAACATGGCAAAGACAAT
1 TAAAGGCATGCTCATGATTACATAGACAATAATGAATTTCAAATATTAACATGGCAAAGACAAT
* *
19366 TAAAGGCATGCTCATG-TTAACATATACAAATAATGAATTTCAAATTTTAACATGGCAAAGACAA
1 TAAAGGCATGCTCATGATT-ACATAGAC-AATAATGAATTTCAAATATTAACATGGCAAAGACAA
19430 T
64 T
19431 CCAATAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
60 2 0.04
61 23 0.40
63 1 0.02
64 3 0.05
65 28 0.49
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.28
Consensus pattern (64 bp):
TAAAGGCATGCTCATGATTACATAGACAATAATGAATTTCAAATATTAACATGGCAAAGACAAT
Found at i:21027 original size:18 final size:18
Alignment explanation
Indices: 21004--21038 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20994 AGAAAAATCA
21004 AATAATAATATATATAAT
1 AATAATAATATATATAAT
21022 AATAATAATATATATAA
1 AATAATAATATATATAA
21039 GACTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAATAATATATATAAT
Found at i:21398 original size:45 final size:45
Alignment explanation
Indices: 21340--21425 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
21330 AAGATCTCAA
* * *
21340 TATGAAATTTTGATAACTTCGCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCTC-CATATGAAATATTGATAACCAACAC
* *
21385 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
21426 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 2 0.06
45 33 0.94
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:21419 original size:22 final size:22
Alignment explanation
Indices: 21296--21794 Score: 169
Period size: 22 Copynumber: 23.0 Consensus size: 22
21286 TAAACTTTCT
* *
21296 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCA
* * * *
21318 TAAGGAATTTTGA-AGATCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
21340 TATGAAATTTTGATAACTTCGCA
1 TATGAAATTTTGATAACCTC-CA
**
21363 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
21384 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
21407 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* * * *
21429 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
*
21451 TATG-AATTGTTAATAA--TCACA
1 TATGAAATT-TTGATAACCTC-CA
* *
21472 CTTTAAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
*
21494 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
* *
21517 TATGAAATTTTGATAAATCTTTC-
1 TATGAAATTTTGAT-AA-CCTCCA
* * *
21540 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * *
21563 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTCCA
*
21585 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* ** *
21602 TA-CAAATTTTGATAAGTTCCT
1 TATGAAATTTTGATAACCTCCA
**
21623 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * ** *
21644 TTATTAAATTTTGTTAATTTCCC
1 -TATGAAATTTTGATAACCTCCA
* * * *
21667 TATAAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
*
21689 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
21711 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* * *
21732 CTATGAAAATTTGATGACCTTCA
1 -TATGAAATTTTGATAACCTCCA
*
21755 TATGAAATTTTGATATCCT-CA
1 TATGAAATTTTGATAACCTCCA
* *
21776 -CTG-AATTTTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
21795 CTGAATTTTG
Statistics
Matches: 355, Mismatches: 93, Indels: 60
0.70 0.18 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 14 0.04
20 6 0.02
21 19 0.05
22 235 0.66
23 62 0.17
24 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:21572 original size:46 final size:45
Alignment explanation
Indices: 21475--21578 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 45
21465 AATCACACTT
* * *
21475 TAAAATTTTGAT-AATCACACTATGAAATTGTGATAACCTCGCTA
1 TAAAATTTTGATAAATCACACTATAAAATTGTAATAACCTCCCTA
* *** *
21519 TGAAATTTTGATAAATCTTTCTATAAAATTTTAATAAACCTCCCTA
1 TAAAATTTTGATAAATCACACTATAAAATTGTAAT-AACCTCCCTA
21565 TAAAATTTTGATAA
1 TAAAATTTTGATAA
21579 CTTTCTTATG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 11 0.22
45 16 0.33
46 22 0.45
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (45 bp):
TAAAATTTTGATAAATCACACTATAAAATTGTAATAACCTCCCTA
Found at i:21784 original size:19 final size:19
Alignment explanation
Indices: 21760--21826 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
21750 CTTCATATGA
*
21760 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
21779 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
* *
21798 AATTTTGGTATCCTCCCTAA
1 AATTTTGATATCCTCCCT-G
21818 AATTTTGAT
1 AATTTTGAT
21827 TACTCCATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 35 0.81
20 8 0.19
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.43
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Done.