Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011133.1 Corchorus capsularis cultivar CVL-1 contig11154, 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: 121375
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:814 original size:2 final size:2
Alignment explanation
Indices: 807--839 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
797 GACGTTGAAT
807 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 T
840 TTTATGGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6113 original size:6 final size:6
Alignment explanation
Indices: 6102--6140 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
6092 ATTAGTAAAC
6102 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG
6141 CCCTTTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:34240 original size:69 final size:70
Alignment explanation
Indices: 34162--34313 Score: 218
Period size: 69 Copynumber: 2.2 Consensus size: 70
34152 GTTTTTTAAT
* * * * *
34162 TAAAATAGTAAAATATAATAGTTATAAGGATATTAGATTAAATTATATAAAAA-AGAGTTTTTAG
1 TAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTAAATTAAACAAAAATAGAGTTTTTAG
34226 TTGAG
66 TTGAG
* *
34231 TAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAACAAAAATAGAGTTTTTAG
1 TAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTAAATTAAACAAAAATAGAGTTTTTAG
34296 TTGAG
66 TTGAG
34301 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
34314 ACCTAAACAA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
69 46 0.62
70 26 0.35
71 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.35
Consensus pattern (70 bp):
TAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTAAATTAAACAAAAATAGAGTTTTTAG
TTGAG
Found at i:51521 original size:14 final size:14
Alignment explanation
Indices: 51502--51530 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
51492 ATCGTATTTG
51502 GAGATAAAAAAACT
1 GAGATAAAAAAACT
51516 GAGATAAAAAAACT
1 GAGATAAAAAAACT
51530 G
1 G
51531 CTTCTCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.07, G:0.17, T:0.14
Consensus pattern (14 bp):
GAGATAAAAAAACT
Found at i:60691 original size:30 final size:30
Alignment explanation
Indices: 60655--60725 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
60645 TTGGCAACAA
****
60655 GGCTTATTTGACTTTTTTTAAGAGTTCAGG
1 GGCTTATTTGACTTAAAATAAGAGTTCAGG
* *
60685 GGCTTATTTG-GTTAAAATAATAGTTCAGG
1 GGCTTATTTGACTTAAAATAAGAGTTCAGG
60714 GGCTTATTTGAC
1 GGCTTATTTGAC
60726 GGTTCGGTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (30 bp):
GGCTTATTTGACTTAAAATAAGAGTTCAGG
Found at i:69854 original size:16 final size:16
Alignment explanation
Indices: 69833--69866 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
69823 TAACATCCTA
69833 TACATTTCATTCTTGC
1 TACATTTCATTCTTGC
69849 TACATTTCATTCTTGC
1 TACATTTCATTCTTGC
69865 TA
1 TA
69867 GTCACATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.06, T:0.50
Consensus pattern (16 bp):
TACATTTCATTCTTGC
Found at i:71351 original size:167 final size:167
Alignment explanation
Indices: 71075--71413 Score: 669
Period size: 167 Copynumber: 2.0 Consensus size: 167
71065 GATGATAATC
71075 ATTTTGTGATGTTTAATATGCTACATGATTTCATGTACATTATTGTTATGGATTGTATGAGAATC
1 ATTTTGTGATGTTTAATATGCTACATGATTTCATGTACATTATTGTTATGGATTGTATGAGAATC
71140 TCTTTTCAAGACTTATTTGATTTAATATTATGCTTGCCTTTAAAAAAGGAAAATGGTAAAGCACA
66 TCTTTTCAAGACTTATTTGATTTAATATTATGCTTGCCTTTAAAAAAGGAAAATGGTAAAGCACA
*
71205 TTTATCATCATTGACATTAAGAATCATATTGAAGAAA
131 TTTATCATCATTGACATTAAGAATCACATTGAAGAAA
71242 ATTTTGTGATGTTTAATATGCTACATGATTTCATGTACATTATTGTTATGGATTGTATGAGAATC
1 ATTTTGTGATGTTTAATATGCTACATGATTTCATGTACATTATTGTTATGGATTGTATGAGAATC
71307 TCTTTTCAAGACTTATTTGATTTAATATTATGCTTGCCTTTAAAAAAGGAAAATGGTAAAGCACA
66 TCTTTTCAAGACTTATTTGATTTAATATTATGCTTGCCTTTAAAAAAGGAAAATGGTAAAGCACA
71372 TTTATCATCATTGACATTAAGAATCACATTGAAGAAA
131 TTTATCATCATTGACATTAAGAATCACATTGAAGAAA
71409 ATTTT
1 ATTTT
71414 AGAAAAAAGG
Statistics
Matches: 171, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 171 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (167 bp):
ATTTTGTGATGTTTAATATGCTACATGATTTCATGTACATTATTGTTATGGATTGTATGAGAATC
TCTTTTCAAGACTTATTTGATTTAATATTATGCTTGCCTTTAAAAAAGGAAAATGGTAAAGCACA
TTTATCATCATTGACATTAAGAATCACATTGAAGAAA
Found at i:93397 original size:42 final size:42
Alignment explanation
Indices: 93350--93434 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
93340 GAAGCCCTGT
93350 ATTTATATTCGATCCAATAGAGCCTAAACTGGAAATTTAATA
1 ATTTATATTCGATCCAATAGAGCCTAAACTGGAAATTTAATA
93392 ATTTATATTCGATCCAATAGAGCCTAAACTGGAAATTTAATA
1 ATTTATATTCGATCCAATAGAGCCTAAACTGGAAATTTAATA
93434 A
1 A
93435 CAAGACGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (42 bp):
ATTTATATTCGATCCAATAGAGCCTAAACTGGAAATTTAATA
Found at i:107587 original size:3 final size:3
Alignment explanation
Indices: 107565--107692 Score: 157
Period size: 3 Copynumber: 42.7 Consensus size: 3
107555 GGAGGAGGAT
* * * * * *
107565 GAA GAA AAA GAT GTA GAA GAA GAA GGA GAA GAA GAA GAA AAA GAT GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
107613 CAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA CAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
107661 CAA GAA GGA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
107693 TGTTCCAGAA
Statistics
Matches: 103, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.63, C:0.02, G:0.31, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:118874 original size:2 final size:2
Alignment explanation
Indices: 118867--118895 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
118857 TTTGTCTTAT
118867 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 T
118896 GCCATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:120019 original size:16 final size:18
Alignment explanation
Indices: 119977--120015 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
119967 TTCTCTCATC
119977 CTCCATATTTTATTGTCT
1 CTCCATATTTTATTGTCT
119995 CTCCATATTTTATTGTCT
1 CTCCATATTTTATTGTCT
120013 CTC
1 CTC
120016 TATTCTCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.26, G:0.05, T:0.54
Consensus pattern (18 bp):
CTCCATATTTTATTGTCT
Found at i:120156 original size:53 final size:53
Alignment explanation
Indices: 120073--120179 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
120063 TTGTTATCAT
* *
120073 TTCACAACAAAATTTGATTTCTTAATTGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
120126 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
120179 T
1 T
120180 AAAACAGCCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTATAAAA
Done.