Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007690.1 Corchorus capsularis cultivar CVL-1 contig07711, 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: 8906
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:169 original size:45 final size:45
Alignment explanation
Indices: 84--171 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
74 GTTATTCGGA
* * *
84 ATGCAGAACGTGAAGGAAAACAATTTTTTTTTTGTTTTTTTAGAC
1 ATGCAGAACGTAAAGGAAAACAATTTTTTTGTTGTCTTTTTAGAC
*
129 ATGCAGAATGTAAAGGAAAACAATTTTTTGTGTTG-CTTTTTAG
1 ATGCAGAACGTAAAGGAAAACAATTTTTT-TGTTGTCTTTTTAG
172 GCATTTACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 34 0.89
46 4 0.11
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (45 bp):
ATGCAGAACGTAAAGGAAAACAATTTTTTTGTTGTCTTTTTAGAC
Found at i:458 original size:59 final size:59
Alignment explanation
Indices: 386--505 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
376 AAGGACTTAA
386 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCAAGCAATAT
1 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCAAGCAATAT
* * *
445 GCTCTATGATTAAAATGCAACACTACTAAATTACTTAATGAAAAGAAATCATGCAATAT
1 GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCAAGCAATAT
504 GC
1 GC
506 GAAAATGCTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (59 bp):
GCTCTATGATTAAAATGCAACACTACTAAATTACTAAATGAAAAGAAACCAAGCAATAT
Found at i:633 original size:28 final size:28
Alignment explanation
Indices: 601--673 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
591 GTAGATTAAG
*
601 AATGACCAAAATACCCCATAAATACAAA
1 AATGACCAAAATGCCCCATAAATACAAA
* * ***
629 AATGACCAAAATGCCCCCTATATGTGAA
1 AATGACCAAAATGCCCCATAAATACAAA
657 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
674 TGGATGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.47, C:0.27, G:0.10, T:0.16
Consensus pattern (28 bp):
AATGACCAAAATGCCCCATAAATACAAA
Found at i:1254 original size:16 final size:16
Alignment explanation
Indices: 1209--1255 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1199 TTTTGCTAAA
1209 AAATAATATAA-TA-T
1 AAATAATATAATTACT
1223 AAAT-ATATAATCTACT
1 AAATAATATAAT-TACT
*
1239 AAATAAAATAATTACT
1 AAATAATATAATTACT
1255 A
1 A
1256 TATAGAAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 6 0.21
14 4 0.14
15 2 0.07
16 10 0.36
17 6 0.21
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATAATATAATTACT
Found at i:1491 original size:11 final size:11
Alignment explanation
Indices: 1475--1500 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1465 GTACAGAAAT
1475 TATATAATATA
1 TATATAATATA
1486 TATATAATATA
1 TATATAATATA
1497 TATA
1 TATA
1501 GTATGTGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATAATATA
Found at i:2112 original size:217 final size:219
Alignment explanation
Indices: 1721--2160 Score: 794
Period size: 217 Copynumber: 2.0 Consensus size: 219
1711 CAAGTTATTC
* *
1721 AAGTTTGAGTCGTTTTGATCTCTGGTTAGTTGGGTCTTAGGTCGGGCGTGTTCCACTTGTTTACT
1 AAGTTTGAGTCGTTTAGATCTCTGGTTAGTTGGGTCTTAGGTCGGGCGCGTTCCACTTGTTTACT
1786 TTTCATGATTAAATTGGGTTAAATGGGGGTTTTTGATTCTTTTTTTTGGCATCAAAATGGGGTTT
66 TTTCATGATTAAATTGGGTTAAA-GGGGGTTTTTGATTCTTTTTTTTGGCATCAAAATGGGGTTT
*
1851 TTGAATTTAGACAACTATTTTACAGCTCTAATTGTGGTTTATCTTTTTAATTGTTACATCAAGTA
130 TTGAATTTAGACAACTATTTTACAGCTCTAATTGTGATTTATCTTTTTAATTGTTACATCAAGTA
1916 AGAAAATCTTGTGGGGCTAATTTTA
195 AGAAAATCTTGTGGGGCTAATTTTA
* *
1941 AAGTTTGAGTCGTTTAGATCTCTGGTTAGTTGGGTCTTAGGTCGGGGGCGTTCCGCTTGTTTACT
1 AAGTTTGAGTCGTTTAGATCTCTGGTTAGTTGGGTCTTAGGTCGGGCGCGTTCCACTTGTTTACT
2006 TTTCATGATTAAATTGGGTT-AA-GGGGTTTTTGATTCTTTTTTTTGGCATCAAAATGGGGTTTT
66 TTTCATGATTAAATTGGGTTAAAGGGGGTTTTTGATTCTTTTTTTTGGCATCAAAATGGGGTTTT
* *
2069 TGAATTTAGGCAACTTTTTTACAGCTCTAATTGTGATTTATCTTTTTAATTGTTACATCAAGTAA
131 TGAATTTAGACAACTATTTTACAGCTCTAATTGTGATTTATCTTTTTAATTGTTACATCAAGTAA
2134 GAAAATCTTGTGGGGCTAATTTTA
196 GAAAATCTTGTGGGGCTAATTTTA
2158 AAG
1 AAG
2161 GTTAAAAGCA
Statistics
Matches: 213, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
217 130 0.61
219 2 0.01
220 81 0.38
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.44
Consensus pattern (219 bp):
AAGTTTGAGTCGTTTAGATCTCTGGTTAGTTGGGTCTTAGGTCGGGCGCGTTCCACTTGTTTACT
TTTCATGATTAAATTGGGTTAAAGGGGGTTTTTGATTCTTTTTTTTGGCATCAAAATGGGGTTTT
TGAATTTAGACAACTATTTTACAGCTCTAATTGTGATTTATCTTTTTAATTGTTACATCAAGTAA
GAAAATCTTGTGGGGCTAATTTTA
Found at i:5743 original size:32 final size:32
Alignment explanation
Indices: 5702--5767 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
5692 GCCACTACTG
5702 GACCAACTGATTTATGTGTATACAAAAATTTT
1 GACCAACTGATTTATGTGTATACAAAAATTTT
*
5734 GACCAACTGATTTATGTGTATTCAAAAATTTT
1 GACCAACTGATTTATGTGTATACAAAAATTTT
5766 GA
1 GA
5768 AGCAATTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (32 bp):
GACCAACTGATTTATGTGTATACAAAAATTTT
Found at i:7431 original size:2 final size:2
Alignment explanation
Indices: 7424--7457 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7414 GCATTTTCTA
7424 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
7458 GTTCAAAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7934 original size:12 final size:12
Alignment explanation
Indices: 7917--7941 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7907 GTCCACCCTC
7917 AAACTTTCTCCT
1 AAACTTTCTCCT
7929 AAACTTTCTCCT
1 AAACTTTCTCCT
7941 A
1 A
7942 GGCAAACAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (12 bp):
AAACTTTCTCCT
Done.