Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011048.1 Corchorus capsularis cultivar CVL-1 contig11069, 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: 87837
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:2591 original size:14 final size:14
Alignment explanation
Indices: 2572--2604 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2562 ATGAGTACTA
2572 GAGAGGGAGAAGGG
1 GAGAGGGAGAAGGG
2586 GAGAGGGAGAAGGG
1 GAGAGGGAGAAGGG
2600 GAGAG
1 GAGAG
2605 AGAAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAAGGG
Found at i:6804 original size:78 final size:78
Alignment explanation
Indices: 6722--6890 Score: 243
Period size: 78 Copynumber: 2.2 Consensus size: 78
6712 TTGTTTAGGT
* *
6722 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATA-TTTATAAC
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATA-ACCTTATAAC
6785 TATTATATTTTACCA
64 TATTATATTTTACCA
* * *
6800 TTTTACTATTTTACTCAATTAAAAACTCTATTTTTATATAATTAAATCTATTAACCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA
**
6865 TTATATTTTAATA
66 TTATATTTTACCA
6878 TTTTACTATTTTA
1 TTTTACTATTTTA
6891 ATTAAAAAAC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
77 1 0.01
78 79 0.96
79 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA
TTATATTTTACCA
Found at i:7006 original size:23 final size:23
Alignment explanation
Indices: 6980--7023 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6970 AAACTTTTGC
*
6980 AATTGAAAACACTATTTTTATTT
1 AATTGAAAACAATATTTTTATTT
**
7003 AATTGAATTCAATATTTTTAT
1 AATTGAAAACAATATTTTTAT
7024 AATTATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
AATTGAAAACAATATTTTTATTT
Found at i:13510 original size:2 final size:2
Alignment explanation
Indices: 13505--13541 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13495 TAAGGTGTGT
13505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13542 TGTACGTGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14325 original size:13 final size:13
Alignment explanation
Indices: 14307--14333 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14297 CGTGTCAGAC
14307 CACTTAAACCAAT
1 CACTTAAACCAAT
14320 CACTTAAACCAAT
1 CACTTAAACCAAT
14333 C
1 C
14334 GATTATATTG
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:0.33, G:0.00, T:0.22
Consensus pattern (13 bp):
CACTTAAACCAAT
Found at i:32643 original size:9 final size:9
Alignment explanation
Indices: 32627--32663 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
32617 GGTAACAGAA
32627 TTGATATTG
1 TTGATATTG
*
32636 TCGATATTG
1 TTGATATTG
32645 ATTGATATTG
1 -TTGATATTG
32655 TTGATATTG
1 TTGATATTG
32664 CTGAGGATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (9 bp):
TTGATATTG
Found at i:32650 original size:19 final size:19
Alignment explanation
Indices: 32626--32663 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
32616 CGGTAACAGA
32626 ATTGATATTGTCGATATTG
1 ATTGATATTGTCGATATTG
*
32645 ATTGATATTGTTGATATTG
1 ATTGATATTGTCGATATTG
32664 CTGAGGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (19 bp):
ATTGATATTGTCGATATTG
Found at i:36227 original size:3 final size:3
Alignment explanation
Indices: 36219--36251 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
36209 TTGTATAACA
*
36219 CCG CCG CCG CCG CCG CCG CCG CCG CCT CCG CCG
1 CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG
36252 TGATTTCCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.67, G:0.30, T:0.03
Consensus pattern (3 bp):
CCG
Found at i:37738 original size:27 final size:30
Alignment explanation
Indices: 37685--37743 Score: 70
Period size: 32 Copynumber: 2.0 Consensus size: 30
37675 GTATACCTAT
*
37685 TATATAAAATAAAATACTACATATATATATTA
1 TATATAAAATAAAATACT--ATATATACATTA
37717 TATATAAAATAAAATA-T-T-TATACATTA
1 TATATAAAATAAAATACTATATATACATTA
37744 AAAAATACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 8 0.31
28 1 0.04
31 1 0.04
32 16 0.62
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (30 bp):
TATATAAAATAAAATACTATATATACATTA
Found at i:47638 original size:13 final size:13
Alignment explanation
Indices: 47610--47656 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
47600 CCATTTAAAA
**
47610 AAAAAAAAAACCC
1 AAAAAAAAAAGAC
47623 AAAAAAAAAAGAC
1 AAAAAAAAAAGAC
*
47636 AAAAACAAAAGGA-
1 AAAAA-AAAAAGAC
47649 AAAAAAAA
1 AAAAAAAA
47657 TCGTTACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 3 0.10
13 21 0.70
14 6 0.20
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAC
Found at i:52669 original size:30 final size:29
Alignment explanation
Indices: 52607--52676 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
52597 ACCGAACCGT
****
52607 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
52636 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
52666 CAAATAAGCCC
1 CAAATAAGCCC
52677 TATTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:66233 original size:39 final size:39
Alignment explanation
Indices: 66176--66253 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
66166 CCTGCAAAAC
*
66176 GAAGGTGAAGATAGAAGAAAATGGTTGTAAAAACTAAAT
1 GAAGGTGAAGATAAAAGAAAATGGTTGTAAAAACTAAAT
*
66215 GAAGGTGAAGATAAAAGAAAATGGTTGTAAATACTAAAT
1 GAAGGTGAAGATAAAAGAAAATGGTTGTAAAAACTAAAT
66254 AGAGGTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.51, C:0.03, G:0.24, T:0.22
Consensus pattern (39 bp):
GAAGGTGAAGATAAAAGAAAATGGTTGTAAAAACTAAAT
Found at i:73497 original size:36 final size:36
Alignment explanation
Indices: 73450--73519 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
73440 AGTAATACCA
73450 ACATATAAGGATGTGCTCATTCATGTAAGATCTGAT
1 ACATATAAGGATGTGCTCATTCATGTAAGATCTGAT
73486 ACATATAAGGATGTGCTCATTCATGTAAGATCTG
1 ACATATAAGGATGTGCTCATTCATGTAAGATCTG
73520 CTTCAGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (36 bp):
ACATATAAGGATGTGCTCATTCATGTAAGATCTGAT
Found at i:76549 original size:13 final size:13
Alignment explanation
Indices: 76517--76541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76507 ATTTATGAGG
76517 GACAAATTAGAGA
1 GACAAATTAGAGA
76530 GACAAATTAGAG
1 GACAAATTAGAG
76542 GATCAAATAG
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:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (13 bp):
GACAAATTAGAGA
Found at i:77632 original size:2 final size:2
Alignment explanation
Indices: 77625--77651 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
77615 ACTATAGTAC
77625 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
77652 TCAAATGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79733 original size:102 final size:102
Alignment explanation
Indices: 79557--79750 Score: 237
Period size: 102 Copynumber: 1.9 Consensus size: 102
79547 GTTAAAGATC
* ** * *
79557 AGCCTCAATTTGATAAACCCTTTCACCATCACTTGTTAGATTCCATTACTCTGCCCATTCTCCAT
1 AGCCTCAATTTGATAAACCATTTCACCATCACTTACTAAATTCCATTACTCTGCCCATTCTCCAA
* *
79622 CTTTTCACTTTCGAGAAAAACCAGGAGGAATCTGATG
66 CTATTCACTTTCGAGAAAAACAAGGAGGAATCTGATG
* * * * * *
79659 AGCCTGAATTTGATGAACCATTTCACTATCACTTACTAAATTCCATTATTGTGCCCATT-TGTCA
1 AGCCTCAATTTGATAAACCATTTCACCATCACTTACTAAATTCCATTACTCTGCCCATTCT-CCA
* *
79723 ACTATTCACTTTGGGGAAAAACAAGGAG
65 ACTATTCACTTTCGAGAAAAACAAGGAG
79751 AAATTTTGGC
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 1 0.01
102 75 0.99
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (102 bp):
AGCCTCAATTTGATAAACCATTTCACCATCACTTACTAAATTCCATTACTCTGCCCATTCTCCAA
CTATTCACTTTCGAGAAAAACAAGGAGGAATCTGATG
Found at i:80358 original size:29 final size:29
Alignment explanation
Indices: 80300--80368 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
80290 ACCGAACCGT
* ***
80300 CAAATAAGCCACTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTATAAAGGC
80329 CAAATAAGCCCCTGAACTATTGA-AAAGGC
1 CAAATAAGCCCCTGAACTATT-ATAAAGGC
80358 CAAATAAGCCC
1 CAAATAAGCCC
80369 TATTGCCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 34 0.97
30 1 0.03
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTATAAAGGC
Found at i:86297 original size:52 final size:52
Alignment explanation
Indices: 86219--86322 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
86209 TTAATGAGTA
86219 ATGACCATGTATTAGGGTAAAATCGAGCTCGACTTTGCTGAAGATTTAGGGT
1 ATGACCATGTATTAGGGTAAAATCGAGCTCGACTTTGCTGAAGATTTAGGGT
*
86271 ATGACCATGTATTAGGGTAGAATCGAGCTCGACTTTGCTGAAGATTTAGGGT
1 ATGACCATGTATTAGGGTAAAATCGAGCTCGACTTTGCTGAAGATTTAGGGT
86323 TAGCTTTCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (52 bp):
ATGACCATGTATTAGGGTAAAATCGAGCTCGACTTTGCTGAAGATTTAGGGT
Done.