Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001029.1 Corchorus capsularis cultivar CVL-1 contig01029, 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: 8206
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1265 original size:93 final size:93
Alignment explanation
Indices: 1106--1286 Score: 263
Period size: 93 Copynumber: 1.9 Consensus size: 93
1096 ATTCAAAGAT
1106 ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAAGACCAAATAAGGGTGAACACCATGTAAA
1 ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAAGACCAAATAAGGGTGAACACCATGTAAA
1171 ATTACATACAAAATATTAAGAAATCGGC
66 ATTACATACAAAATATTAAGAAATCGGC
* * ** * ** **
1199 ATTTTGACGAGTTAATTAATTGAGGGTGGGCATCTAGGACCATGTAAGGGTGGGCACCATGTAAA
1 ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAAGACCAAATAAGGGTGAACACCATGTAAA
* *
1264 ATTACATAGAAAATGTTAAGAAA
66 ATTACATACAAAATATTAAGAAA
1287 GTTGAAGGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (93 bp):
ATTTTGACAAGTTAATCAATTGAGGGTGAACATCTAAGACCAAATAAGGGTGAACACCATGTAAA
ATTACATACAAAATATTAAGAAATCGGC
Found at i:1734 original size:12 final size:12
Alignment explanation
Indices: 1717--1746 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1707 TAGAGTTTTG
*
1717 GAGGATATTGAA
1 GAGGATATTAAA
1729 GAGGATATTAAA
1 GAGGATATTAAA
1741 GAGGAT
1 GAGGAT
1747 TGGTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.23
Consensus pattern (12 bp):
GAGGATATTAAA
Found at i:3649 original size:2 final size:2
Alignment explanation
Indices: 3642--3684 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3632 ATATCTGCAG
* * *
3642 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3684 A
1 A
3685 GCAAGATGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:5465 original size:32 final size:32
Alignment explanation
Indices: 5419--5480 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
5409 CACTTCCAGT
*
5419 ACACGTGGCATGACACGTGTCACTTTTTTGGC
1 ACACATGGCATGACACGTGTCACTTTTTTGGC
*
5451 ACACATGGCATGACATGTGTCACTTTTTTG
1 ACACATGGCATGACACGTGTCACTTTTTTG
5481 TACACGTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (32 bp):
ACACATGGCATGACACGTGTCACTTTTTTGGC
Found at i:5503 original size:31 final size:31
Alignment explanation
Indices: 5383--5524 Score: 142
Period size: 31 Copynumber: 4.6 Consensus size: 31
5373 GCACGTGTCC
* * *
5383 TTTTGTGCACGTGGCATGCCACGTGTCAC-T
1 TTTTGTACACGTGGCATGACATGTGTCACTT
*** *
5413 TCCAGTACACGTGGCATGACACGTGTCACTT
1 TTTTGTACACGTGGCATGACATGTGTCACTT
* *
5444 TTTTGGCACACATGGCATGACATGTGTCACTT
1 TTTT-GTACACGTGGCATGACATGTGTCACTT
* * *
5476 TTTTGTACACGTGGCGTGTCATATGTCACTT
1 TTTTGTACACGTGGCATGACATGTGTCACTT
* *
5507 TTTGGTATACGTGGCATG
1 TTTTGTACACGTGGCATG
5525 TCACGTCAGA
Statistics
Matches: 91, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
30 24 0.26
31 39 0.43
32 28 0.31
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (31 bp):
TTTTGTACACGTGGCATGACATGTGTCACTT
Found at i:7712 original size:30 final size:30
Alignment explanation
Indices: 7625--8194 Score: 843
Period size: 30 Copynumber: 18.7 Consensus size: 30
7615 ATAAATCTCC
* * *
7625 ATTGACACCAGAAGTTGTCAGTGGTCTTACA
1 ATTGACACCAGAAGTTGTCA-TGATTTTGCA
* *
7656 ATTGACACCAGAAGTTGTCAATGATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATTTTGCA
* * * *
7687 AATGACACTAGAAGTTGTCATGATCTTACA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
* *
7717 ATTAACACCAGAAGTTGTCATGATTAATTTCTA
1 ATTGACACCAGAAGTTGTCATGATT--TTGC-A
* *
7750 AATGACACCAGAAGTTGTCATGATCTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
* *
7780 ATTGACACTAGAAGTTGTCATGATTAATTTCCA
1 ATTGACACCAGAAGTTGTCATGA-T--TTTGCA
*
7813 AATGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
*
7843 ATTGACACCAGAAGTTGTCATGATTTTTCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
* *
7873 ATGGACACCAGAAGTTATCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
*
7903 ATTGACACCAGAAGTTGTCATGATTTTTCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
*
7933 ATGGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
7963 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
*
7993 ATTGACACCAGAAGTTTTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
8023 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
8053 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
8083 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
8113 ATTGACACCAGAAGTTGTCATGATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATTTTGCA
* *
8143 GTTGACACCAGAAGTTGTCATGATTTATTCA
1 ATTGACACCAGAAGTTGTCATGATTT-TGCA
8174 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
8195 ATACACCATG
Statistics
Matches: 496, Mismatches: 35, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
30 371 0.75
31 72 0.15
32 5 0.01
33 48 0.10
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATTTTGCA
Done.