Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010321.1 Corchorus capsularis cultivar CVL-1 contig10342, 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: 47583
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:43 original size:2 final size:2
Alignment explanation
Indices: 38--64 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28 ATGGGAGATC
38 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 T
65 CTTACCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1852 original size:50 final size:50
Alignment explanation
Indices: 1777--1877 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
1767 TGAACGGGGG
*
1777 ACGGGGGAGTTTGTTGGAGTTCACATGTGAGTGTCGCATCCCACATCACA
1 ACGGGGAAGTTTGTTGGAGTTCACATGTGAGTGTCGCATCCCACATCACA
1827 ACGGGGAAGTTTGTTGGAGTTCACATGTGAGTGTCGCATCCCACATCACA
1 ACGGGGAAGTTTGTTGGAGTTCACATGTGAGTGTCGCATCCCACATCACA
1877 A
1 A
1878 AGGGATGGAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (50 bp):
ACGGGGAAGTTTGTTGGAGTTCACATGTGAGTGTCGCATCCCACATCACA
Found at i:2105 original size:3 final size:3
Alignment explanation
Indices: 2097--2140 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2087 CATTATATAT
2097 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2141 TTTGGTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3347 original size:22 final size:25
Alignment explanation
Indices: 3322--3367 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
3312 ATGATATCTA
3322 ATTATA-ATT-TTA-TTATTATTAT
1 ATTATAGATTATTATTTATTATTAT
3344 ATTATATGATTATTATTTATTATT
1 ATTATA-GATTATTATTTATTATT
3368 TTTTGGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
24 3 0.15
25 3 0.15
26 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTATAGATTATTATTTATTATTAT
Found at i:6507 original size:30 final size:30
Alignment explanation
Indices: 6471--6528 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6461 AGGAAATTCC
* *
6471 AAATTATTTATCTTTTATGCACTTCAATAT
1 AAATTATTCATCTTTTATACACTTCAATAT
6501 AAATTATTCATCTTTTATACACTTCAAT
1 AAATTATTCATCTTTTATACACTTCAAT
6529 GGAAATCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (30 bp):
AAATTATTCATCTTTTATACACTTCAATAT
Found at i:7251 original size:2 final size:2
Alignment explanation
Indices: 7244--7270 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7234 CCCAAAGCTT
7244 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 T
7271 TACATATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11446 original size:45 final size:44
Alignment explanation
Indices: 11395--11483 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 44
11385 TAATAAAGTA
*
11395 GTGGAATTACTAAAAGATGCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTA-CCCGAATTAATGATAAGCTGG
* *
11440 GTGGAATTACTAAAAGATCCCTACCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCGAATTAATGATAAGCTGG
11484 AGAAGTAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (44 bp):
GTGGAATTACTAAAAGATCCCTACCCGAATTAATGATAAGCTGG
Found at i:12903 original size:11 final size:11
Alignment explanation
Indices: 12887--12911 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12877 AATTAGAATC
12887 TCAAGTTCTAA
1 TCAAGTTCTAA
12898 TCAAGTTCTAA
1 TCAAGTTCTAA
12909 TCA
1 TCA
12912 CGAAAGTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (11 bp):
TCAAGTTCTAA
Found at i:25734 original size:39 final size:39
Alignment explanation
Indices: 25679--25765 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
25669 TATTAGTTTT
*
25679 AAATTTTGGCAACTTTGAATGAATTATGAATGAGGTATAC
1 AAATTTT-GCAACTTTGAATGAATTATAAATGAGGTATAC
25719 AAATTTTGCAACTTTGAATGAATTATAAATGAGGTATAC
1 AAATTTTGCAACTTTGAATGAATTATAAATGAGGTATAC
25758 AAATTTTG
1 AAATTTTG
25766 GCTTGTCATT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 39 0.85
40 7 0.15
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (39 bp):
AAATTTTGCAACTTTGAATGAATTATAAATGAGGTATAC
Found at i:29830 original size:6 final size:6
Alignment explanation
Indices: 29821--29847 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29811 TTGAATGGTT
29821 GAATTA GAATTA GAATTA GAATTA GAA
1 GAATTA GAATTA GAATTA GAATTA GAA
29848 GAAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.30
Consensus pattern (6 bp):
GAATTA
Found at i:31601 original size:22 final size:22
Alignment explanation
Indices: 31571--31612 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31561 GTTTTGCTTC
31571 TCCTAATTATTATGCTGTTGTT
1 TCCTAATTATTATGCTGTTGTT
* * *
31593 TCCTTATTATTTTTCTGTTG
1 TCCTAATTATTATGCTGTTG
31613 AGAGTTGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (22 bp):
TCCTAATTATTATGCTGTTGTT
Done.