Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009262.1 Corchorus capsularis cultivar CVL-1 contig09283, 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: 49079
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Found at i:3142 original size:20 final size:20
Alignment explanation
Indices: 3117--3154 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3107 ATTAGTTATA
3117 AGTGAAAATTGAAAATTCTC
1 AGTGAAAATTGAAAATTCTC
3137 AGTGAAAATTGAAAATTC
1 AGTGAAAATTGAAAATTC
3155 CCTGTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (20 bp):
AGTGAAAATTGAAAATTCTC
Found at i:8713 original size:3 final size:3
Alignment explanation
Indices: 8705--8731 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8695 CAACCCAAAG
8705 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
8732 CCCTGCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:21077 original size:29 final size:29
Alignment explanation
Indices: 21034--21089 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
21024 TATATTTAGA
*
21034 AAATTTTATCTATTAGATCTGGAAATGAG
1 AAATTTTATCCATTAGATCTGGAAATGAG
*
21063 AAATTTTGTCCATTAGATCTGGAAATG
1 AAATTTTATCCATTAGATCTGGAAATG
21090 GGAATGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (29 bp):
AAATTTTATCCATTAGATCTGGAAATGAG
Found at i:25377 original size:87 final size:87
Alignment explanation
Indices: 25273--25435 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 87
25263 TCAAAAAAAT
* * * *
25273 GTGATCTTCCTTATGGAGATAT-GGATGGTTATGGTGCAAAATCTTTGGAAACT-ATTATGGTAG
1 GTGATCTTCCTAATGGAGATATAGTA-AGTTATGATGCAAAATCTTTGGAAACTGATT-TGGTAG
*
25336 AGGATATTTTGAATTGAAATATTA
64 AGGATATGTTGAATTGAAATATTA
* * *
25360 GTGATCTTCCTAATGGAGTTATAGTAAGTTATGATGCAAAATCTTTGGAAACTGATTTGGTGGTG
1 GTGATCTTCCTAATGGAGATATAGTAAGTTATGATGCAAAATCTTTGGAAACTGATTTGGTAGAG
25425 GATATGTTGAA
66 GATATGTTGAA
25436 CAAATCGGAG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 61 0.92
88 5 0.08
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.37
Consensus pattern (87 bp):
GTGATCTTCCTAATGGAGATATAGTAAGTTATGATGCAAAATCTTTGGAAACTGATTTGGTAGAG
GATATGTTGAATTGAAATATTA
Found at i:27448 original size:2 final size:2
Alignment explanation
Indices: 27441--27469 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27431 TACTATCAGA
27441 AT AT 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 AT AT A
27470 AATCATGTTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35051 original size:2 final size:2
Alignment explanation
Indices: 35046--35084 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
35036 TGTCTTTGTT
* *
35046 TC TC TC TC T- TC TC TC TG TC TC TC TG TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
35085 CAGCACACAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.44, G:0.05, T:0.51
Consensus pattern (2 bp):
TC
Found at i:35063 original size:25 final size:27
Alignment explanation
Indices: 35030--35081 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
35020 AATTTCTTCC
*
35030 TCTCTCTGTCT-T-TGTTTCTCTCTCT
1 TCTCTCTGTCTCTCTGTCTCTCTCTCT
35055 TCTCTCTGTCTCTCTGTCTCTCTCTCT
1 TCTCTCTGTCTCTCTGTCTCTCTCTCT
35082 CTCCAGCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 11 0.46
26 1 0.04
27 12 0.50
ACGTcount: A:0.00, C:0.37, G:0.08, T:0.56
Consensus pattern (27 bp):
TCTCTCTGTCTCTCTGTCTCTCTCTCT
Found at i:39170 original size:39 final size:38
Alignment explanation
Indices: 39116--39191 Score: 143
Period size: 39 Copynumber: 2.0 Consensus size: 38
39106 GCTCTATTTC
39116 TTAGGATTCACAAGGTTAAGTTCTACTTTTTAAAAAAAA
1 TTAGGATTCACAAGGTTAAGTTCTAC-TTTTAAAAAAAA
39155 TTAGGATTCACAAGGTTAAGTTCTACTTTTAAAAAAA
1 TTAGGATTCACAAGGTTAAGTTCTACTTTTAAAAAAA
39192 TTAAAATCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 11 0.30
39 26 0.70
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (38 bp):
TTAGGATTCACAAGGTTAAGTTCTACTTTTAAAAAAAA
Found at i:39205 original size:36 final size:39
Alignment explanation
Indices: 39123--39208 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
39113 TTCTTAGGAT
* *
39123 TCACAAGGTTAAGTTCTACTTTTTAAAAAAAATTAGGAT
1 TCACAAGGTTAAGTTCTACTTTTTAAAAAAAATTAGAAA
39162 TCACAAGGTTAAGTTCTAC-TTTT-AAAAAAATTA-AAA
1 TCACAAGGTTAAGTTCTACTTTTTAAAAAAAATTAGAAA
*
39198 TCTCAAGGTTA
1 TCACAAGGTTA
39209 GTCTAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 11 0.25
37 10 0.23
38 4 0.09
39 19 0.43
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (39 bp):
TCACAAGGTTAAGTTCTACTTTTTAAAAAAAATTAGAAA
Found at i:40325 original size:159 final size:159
Alignment explanation
Indices: 40036--40351 Score: 497
Period size: 159 Copynumber: 2.0 Consensus size: 159
40026 CCGAGAACGC
* * *
40036 CTCTCTTTCTGGGTCTTTTGAGGAACAAAAGAAAGTTGATGTGAAAATCAAAGAGGGTCCCTTTG
1 CTCTCTTTCTGGGTCTTTTCAGGAACAAAAGAAAGATGATGTGAAAAGCAAAGAGGGTCCCTTTG
* * * * *
40101 GAGTTCAAGATTTTGATAATCTTGTCAACAATGCCATCGAAGTTGATACGGATTCTGTAATTGAA
66 GAGTTCAAGATGTTGATAACCTTGTCAACAATGCAATCGAAGTTGATACGGAGTCTGTAACTGAA
*
40166 GCTGATAAGAAGGAACATCCAGGGACTTG
131 GCTGATAAGAAGGAACACCCAGGGACTTG
* * *
40195 CTCTCTTTCTGGGTCTTTTCAGGAAGAAAAGAAAGATGGTGTGAAAAGCAAAGAGGGTTCCTTTG
1 CTCTCTTTCTGGGTCTTTTCAGGAACAAAAGAAAGATGATGTGAAAAGCAAAGAGGGTCCCTTTG
* * *
40260 GAGTTCAAGATGTTGATAACCTTGTCAACAATGCAATTGAAGTTGATATGGAGTCTGTCACTGAA
66 GAGTTCAAGATGTTGATAACCTTGTCAACAATGCAATCGAAGTTGATACGGAGTCTGTAACTGAA
40325 GCTGATAAGAAGGAACACCCAGGGACT
131 GCTGATAAGAAGGAACACCCAGGGACT
40352 AGCTTGGAAT
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
159 142 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (159 bp):
CTCTCTTTCTGGGTCTTTTCAGGAACAAAAGAAAGATGATGTGAAAAGCAAAGAGGGTCCCTTTG
GAGTTCAAGATGTTGATAACCTTGTCAACAATGCAATCGAAGTTGATACGGAGTCTGTAACTGAA
GCTGATAAGAAGGAACACCCAGGGACTTG
Found at i:46103 original size:2 final size:2
Alignment explanation
Indices: 46096--46131 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46086 GTACTACTTA
46096 AT AT AT AT 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 AT AT AT AT
46132 CAGATTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.