Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011055.1 Corchorus capsularis cultivar CVL-1 contig11076, 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: 80607
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2550 original size:16 final size:16
Alignment explanation
Indices: 2531--2581 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2521 CCGAAACCGG
2531 AAATGACCCGAACCAA
1 AAATGACCCGAACCAA
* * *
2547 AAATTA-CCTAGACCCA
1 AAATGACCCGA-ACCAA
2563 AAATGACCCGAACCCAA
1 AAATGACCCGAA-CCAA
2580 AA
1 AA
2582 GATTAACTCG
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 3 0.12
16 15 0.58
17 8 0.31
ACGTcount: A:0.49, C:0.31, G:0.10, T:0.10
Consensus pattern (16 bp):
AAATGACCCGAACCAA
Found at i:13286 original size:30 final size:29
Alignment explanation
Indices: 13250--13333 Score: 116
Period size: 30 Copynumber: 2.9 Consensus size: 29
13240 TTATTTTGAT
*
13250 AAAAAAAAATAACAAATTGAAATTTTTACC
1 AAAAAAAAATAACAAAATGAAATTTTT-CC
* *
13280 AAAAAAAAATAACAAAATGAAAATCTTCC
1 AAAAAAAAATAACAAAATGAAATTTTTCC
*
13309 -AAAAAAATTAACAAAATGAAATTTT
1 AAAAAAAAATAACAAAATGAAATTTT
13334 AAAGAATGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 22 0.46
29 2 0.04
30 24 0.50
ACGTcount: A:0.63, C:0.10, G:0.04, T:0.24
Consensus pattern (29 bp):
AAAAAAAAATAACAAAATGAAATTTTTCC
Found at i:13479 original size:24 final size:24
Alignment explanation
Indices: 13452--13500 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13442 ACTTTTACAC
13452 ATTTCTATTTTTAATTATAAAATT
1 ATTTCTATTTTTAATTATAAAATT
13476 ATTTCTATTTTTAATTATAAAATT
1 ATTTCTATTTTTAATTATAAAATT
13500 A
1 A
13501 CTAATGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTCTATTTTTAATTATAAAATT
Found at i:23196 original size:39 final size:39
Alignment explanation
Indices: 23135--23215 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
23125 TAGGAGTTAG
*
23135 ATAGGATCAGGAAACAATAGTAATTATCAAAGCCAACAA
1 ATAGGATCAGGAAACAACAGTAATTATCAAAGCCAACAA
*
23174 ATAGGATCAGGAAATAACAGTAATTATCAAAGCCAACAA
1 ATAGGATCAGGAAACAACAGTAATTATCAAAGCCAACAA
23213 ATA
1 ATA
23216 TGTTATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (39 bp):
ATAGGATCAGGAAACAACAGTAATTATCAAAGCCAACAA
Found at i:35893 original size:2 final size:2
Alignment explanation
Indices: 35886--35916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35876 CTCTAGTTCC
35886 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
35917 GCTTCCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:49795 original size:1 final size:1
Alignment explanation
Indices: 49789--49814 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
49779 GTTGAAACCT
49789 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
49815 TCCCTGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:61989 original size:3 final size:3
Alignment explanation
Indices: 61983--62035 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
61973 TTGATGATGA
* * *
61983 TGG TGG TGG TGG TGG TGG TGG TGAG TTGG CGG CGG CGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TG-G -TGG TGG TGG TGG TGG TGG TGG
62030 TGG TGG
1 TGG TGG
62036 CGGAGATGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 42 0.91
4 2 0.04
5 2 0.04
ACGTcount: A:0.02, C:0.06, G:0.64, T:0.28
Consensus pattern (3 bp):
TGG
Found at i:74588 original size:4 final size:4
Alignment explanation
Indices: 74581--74619 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
74571 TTCTGCTTTC
* * *
74581 TCTT TCTT TCTT TCTT TTTT TCTC TCTC TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
74620 CTTTATTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TCTT
Found at i:74612 original size:16 final size:16
Alignment explanation
Indices: 74579--74621 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
74569 TTTTCTGCTT
74579 TCTCTTTCTTTCT-T-
1 TCTCTTTCTTTCTCTC
74593 TCT-TTT-TTTCTCTC
1 TCTCTTTCTTTCTCTC
74607 TCTCTTTCTTTCTCT
1 TCTCTTTCTTTCTCT
74622 TTATTGCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.20
13 4 0.16
14 6 0.24
15 3 0.12
16 7 0.28
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TCTCTTTCTTTCTCTC
Found at i:76161 original size:30 final size:30
Alignment explanation
Indices: 76127--76187 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
76117 TCATGAAATC
76127 AAGTGTACCATAAAAATAATTTAAGGATTA
1 AAGTGTACCATAAAAATAATTTAAGGATTA
76157 AAGTGTACCATAAAAATAATTTAAGGATTA
1 AAGTGTACCATAAAAATAATTTAAGGATTA
76187 A
1 A
76188 TTTACTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.30
Consensus pattern (30 bp):
AAGTGTACCATAAAAATAATTTAAGGATTA
Found at i:76588 original size:20 final size:19
Alignment explanation
Indices: 76542--76594 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
76532 AGCTAAGATG
*
76542 TAGTCATAATATATTGTTTA
1 TAGTCATAAT-TATTGTCTA
**
76562 TTTTCATAATTATTGTACTA
1 TAGTCATAATTATTGT-CTA
76582 TAGTCATTAATTA
1 TAGTCA-TAATTA
76595 GGAACGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (19 bp):
TAGTCATAATTATTGTCTA
Done.