Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008156.1 Corchorus capsularis cultivar CVL-1 contig08177, 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: 39188
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:877 original size:29 final size:30
Alignment explanation
Indices: 812--880 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
802 TTTGTTGTTT
*
812 AACTAAGGTCAAAGTATTTGGCCAAAAAAAA
1 AACTAAGGTCAAAGTATATGG-CAAAAAAAA
843 AACTAAGGTCAAAGTAATAT-G-AAAAAAAA
1 AACTAAGGTCAAAGT-ATATGGCAAAAAAAA
872 AACTAAGGT
1 AACTAAGGT
881 GAAATTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 17 0.47
31 16 0.44
32 3 0.08
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (30 bp):
AACTAAGGTCAAAGTATATGGCAAAAAAAA
Found at i:10673 original size:23 final size:23
Alignment explanation
Indices: 10643--10691 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
10633 ATCCTAAACC
*
10643 TATGTGTTCTTGGATCTTTCAGG
1 TATGTGTTCTTGGATCTTTCAAG
*
10666 TATGTGTTCTTGGGTCTTTCAAG
1 TATGTGTTCTTGGATCTTTCAAG
10689 TAT
1 TAT
10692 ATATGCCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.49
Consensus pattern (23 bp):
TATGTGTTCTTGGATCTTTCAAG
Found at i:11346 original size:1 final size:1
Alignment explanation
Indices: 11340--11379 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
11330 TTGAAATTTC
11340 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11380 CAAGAAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18172 original size:71 final size:71
Alignment explanation
Indices: 18085--18237 Score: 279
Period size: 71 Copynumber: 2.2 Consensus size: 71
18075 AGAACATATT
*
18085 TCCCTTTTCTTTCAAATTTTAAATTTTTTATATGCATAGAACAATTTTTATTACCAACTTGATAA
1 TCCCTTTTCTTTCAAATTTTAAATTTTTTATATGCATAGAACAATTATTATTACCAACTTGATAA
18150 ATAACA
66 ATAACA
* *
18156 TCTCTTTTCTTTCAAATTTTAATTTTTTTATATGCATAGAACAATTATTATTACCAACTTGATAA
1 TCCCTTTTCTTTCAAATTTTAAATTTTTTATATGCATAGAACAATTATTATTACCAACTTGATAA
18221 ATAACA
66 ATAACA
18227 TCCCTTTTCTT
1 TCCCTTTTCTT
18238 ATACGCGTAC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (71 bp):
TCCCTTTTCTTTCAAATTTTAAATTTTTTATATGCATAGAACAATTATTATTACCAACTTGATAA
ATAACA
Found at i:18392 original size:3 final size:3
Alignment explanation
Indices: 18384--18418 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
18374 GCATCCGGTT
18384 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
18419 TGTAGAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:18819 original size:218 final size:218
Alignment explanation
Indices: 18436--18857 Score: 808
Period size: 218 Copynumber: 1.9 Consensus size: 218
18426 ATTCAATGCC
18436 GGTTAAGGCTAGAAGCTGAATATGGAAAATGGGAGGAAAAACCTATCTTCATTAATTGATTACAG
1 GGTTAAGGCTAGAAGCTGAATATGGAAAATGGGAGGAAAAACCTATCTTCATTAATTGATTACAG
*
18501 GGTATTTATACAATACATGAGTTTGAGTATAAGGCAAATACATAGAGTTATTTAGTGTAACAAAC
66 GGTATTTATACAATACATGAGTTTAAGTATAAGGCAAATACATAGAGTTATTTAGTGTAACAAAC
*
18566 TATCTGGTGTAACAACTTTACAAATCAAATATTGAATTTAAGATGAAGGATAAGTTGGTCACTTA
131 TATCTGGTGTAACAACTTTACAAATCAAATATTGAATTTAAAATGAAGGATAAGTTGGTCACTTA
18631 TCCCTTACACGTACCCTCAAGAT
196 TCCCTTACACGTACCCTCAAGAT
18654 GGTTAAGGCTAGAAGCTGAATATGGAAAATGGGAGGAAAAACCTATCTTCATTAATTGATTACAG
1 GGTTAAGGCTAGAAGCTGAATATGGAAAATGGGAGGAAAAACCTATCTTCATTAATTGATTACAG
*
18719 GGTATTTATACAATACATGAGTTTAAGTATAAGTCAAATACATAGAGTTATTTAGTGTAACAAAC
66 GGTATTTATACAATACATGAGTTTAAGTATAAGGCAAATACATAGAGTTATTTAGTGTAACAAAC
*
18784 TATCTGGTGTAACAACTTTACAAATCAACTATTGAATTTAAAATGAAGGATAAGTTGGTCACTTA
131 TATCTGGTGTAACAACTTTACAAATCAAATATTGAATTTAAAATGAAGGATAAGTTGGTCACTTA
18849 TCCCTTACA
196 TCCCTTACA
18858 ATCATCATCA
Statistics
Matches: 200, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
218 200 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (218 bp):
GGTTAAGGCTAGAAGCTGAATATGGAAAATGGGAGGAAAAACCTATCTTCATTAATTGATTACAG
GGTATTTATACAATACATGAGTTTAAGTATAAGGCAAATACATAGAGTTATTTAGTGTAACAAAC
TATCTGGTGTAACAACTTTACAAATCAAATATTGAATTTAAAATGAAGGATAAGTTGGTCACTTA
TCCCTTACACGTACCCTCAAGAT
Found at i:23963 original size:85 final size:86
Alignment explanation
Indices: 23819--24043 Score: 389
Period size: 87 Copynumber: 2.6 Consensus size: 86
23809 TTGGTACATT
23819 ATTGAATGTTTTCATTACCAAGCATATATAATTGATGAATGATTGTGTATAATTGTGATCATAAT
1 ATTGAATG-TTTCATTACCAAGCATATATAATTGATGAATGATTGTGTATAATTGTGATCATAAT
23884 TAAAATC-AAATTGCATTCACC
65 TAAAATCAAAATTGCATTCACC
**
23905 ATTGAATGTTTCATTACCAAGCACGTATAATTGATGAATGATTGTGTATAATTGTGATCATAATT
1 ATTGAATGTTTCATTACCAAGCATATATAATTGATGAATGATTGTGTATAATTGTGATCATAATT
23970 AAAATCAAAAATTGCATTCACC
66 AAAATC-AAAATTGCATTCACC
* *
23992 ATTGAATGTTTCATTACCAACCATATATAATTGACGAATGATTGTGTATAAT
1 ATTGAATGTTTCATTACCAAGCATATATAATTGATGAATGATTGTGTATAAT
24044 GATATTATTA
Statistics
Matches: 131, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
85 61 0.47
86 8 0.06
87 62 0.47
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (86 bp):
ATTGAATGTTTCATTACCAAGCATATATAATTGATGAATGATTGTGTATAATTGTGATCATAATT
AAAATCAAAATTGCATTCACC
Found at i:24777 original size:18 final size:18
Alignment explanation
Indices: 24756--24802 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
24746 GTTAATCATC
*
24756 ATCATCATTATTTTTATT
1 ATCATCATTATTATTATT
*
24774 ATCATCATCATTATTATT
1 ATCATCATTATTATTATT
24792 AT-AT-ATTATTA
1 ATCATCATTATTA
24803 CTATATGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 6 0.23
17 2 0.08
18 18 0.69
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (18 bp):
ATCATCATTATTATTATT
Found at i:24779 original size:21 final size:21
Alignment explanation
Indices: 24753--24793 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
24743 CCGGTTAATC
*
24753 ATCATCATCATTATTTTTATT
1 ATCATCATCATTATTATTATT
24774 ATCATCATCATTATTATTAT
1 ATCATCATCATTATTATTAT
24794 ATATTATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.54
Consensus pattern (21 bp):
ATCATCATCATTATTATTATT
Found at i:24852 original size:2 final size:2
Alignment explanation
Indices: 24845--24872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24835 CTACTTTAAA
24845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24873 TCTCAAAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33271 original size:31 final size:31
Alignment explanation
Indices: 33233--33313 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
33223 GTATTGCCAG
*
33233 CTATATGCATATCTTTTTTCCAGCCCGGATA
1 CTATATGCATATCTTTTTTCCAGCCCAGATA
*
33264 CTATATGCATATCTTTTATCCAGCCCAGATA
1 CTATATGCATATCTTTTTTCCAGCCCAGATA
*
33295 CCATATGCATATCTTTTTT
1 CTATATGCATATCTTTTTT
33314 TGAAAGATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.41
Consensus pattern (31 bp):
CTATATGCATATCTTTTTTCCAGCCCAGATA
Found at i:34521 original size:31 final size:31
Alignment explanation
Indices: 34481--34549 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
34471 ACATGGCATG
*
34481 CCACATGGATAAAAAAGTAACACGTGGCACA
1 CCACGTGGATAAAAAAGTAACACGTGGCACA
* *
34512 CCACGTGGATCAAAAAGTGACACGTGGCACA
1 CCACGTGGATAAAAAAGTAACACGTGGCACA
*
34543 TCACGTG
1 CCACGTG
34550 TGCCAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.14
Consensus pattern (31 bp):
CCACGTGGATAAAAAAGTAACACGTGGCACA
Found at i:34557 original size:31 final size:31
Alignment explanation
Indices: 34492--34564 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
34482 CACATGGATA
* *
34492 AAAAAGTAACACGTGGCACACCACGTGGATC
1 AAAAAGTGACACGTGGCACACCACGTGGACC
*
34523 AAAAAGTGACACGTGGCACATCACGTGTG-CC
1 AAAAAGTGACACGTGGCACACCACGTG-GACC
34554 AAAAAGTGACA
1 AAAAAGTGACA
34565 TGTCATGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGTGACACGTGGCACACCACGTGGACC
Found at i:34583 original size:53 final size:53
Alignment explanation
Indices: 34520--34620 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
34510 CACCACGTGG
* * * *
34520 ATCAAAAAGTGACACGTGGCACATCACGTGTGCCAAAAAGTGACATGTCATGT
1 ATCAAAAAGTGACACGTGGCACACCACATGTACCAAAAAGCGACATGTCATGT
* *
34573 ATCAAAAAGTGATACGTGGCACGCCACATGTACCAAAAAGCGACATGT
1 ATCAAAAAGTGACACGTGGCACACCACATGTACCAAAAAGCGACATGT
34621 GGCATGCCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (53 bp):
ATCAAAAAGTGACACGTGGCACACCACATGTACCAAAAAGCGACATGTCATGT
Found at i:34623 original size:31 final size:31
Alignment explanation
Indices: 34568--34629 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
34558 AGTGACATGT
* * *
34568 CATGTATCAAAAAGTGATACGTGGCACGCCA
1 CATGTACCAAAAAGCGACACGTGGCACGCCA
* *
34599 CATGTACCAAAAAGCGACATGTGGCATGCCA
1 CATGTACCAAAAAGCGACACGTGGCACGCCA
34630 TGCACACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (31 bp):
CATGTACCAAAAAGCGACACGTGGCACGCCA
Found at i:37939 original size:13 final size:13
Alignment explanation
Indices: 37921--37945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37911 TTCGAATTCC
37921 AAATAATATTTAT
1 AAATAATATTTAT
37934 AAATAATATTTA
1 AAATAATATTTA
37946 GATTGAATTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:38544 original size:17 final size:17
Alignment explanation
Indices: 38507--38547 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
38497 ATTACCACCC
**
38507 AGATCACCAGTGATCTT
1 AGATCACCAGTGATCCA
*
38524 AGATCACCATTGATCCA
1 AGATCACCAGTGATCCA
38541 AGATCAC
1 AGATCAC
38548 TGGTAATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (17 bp):
AGATCACCAGTGATCCA
Found at i:38963 original size:3 final size:3
Alignment explanation
Indices: 38955--39010 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
38945 GATTTGTATG
* *
38955 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA -TA TATA CGTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA
*
39001 TCA TTA TTA T
1 TTA TTA TTA T
39011 ATATATCTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.87
4 4 0.09
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:39006 original size:25 final size:25
Alignment explanation
Indices: 38968--39015 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
38958 TTATTATTAT
*
38968 TATTATTATTATTAGTATATATACG
1 TATTATTATCATTAGTATATATACG
*
38993 TATTATTATCATTATTATATATA
1 TATTATTATCATTAGTATATATA
39016 TCTACTATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
TATTATTATCATTAGTATATATACG
Done.