Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010385.1 Corchorus capsularis cultivar CVL-1 contig10406, 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: 46196
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5197 original size:11 final size:11
Alignment explanation
Indices: 5181--5214 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5171 TCATTCAAGT
5181 GTAAAATAATA
1 GTAAAATAATA
*
5192 GTAAAATCATA
1 GTAAAATAATA
*
5203 GTAAAATGATA
1 GTAAAATAATA
5214 G
1 G
5215 AAATCATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (11 bp):
GTAAAATAATA
Found at i:5220 original size:20 final size:21
Alignment explanation
Indices: 5181--5223 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5171 TCATTCAAGT
5181 GTAAAATAATAGTAAAATCATA
1 GTAAAATAATAG-AAAATCATA
*
5203 GTAAAATGATAG-AAATCATA
1 GTAAAATAATAGAAAATCATA
5223 G
1 G
5224 GAGGAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (21 bp):
GTAAAATAATAGAAAATCATA
Found at i:12160 original size:33 final size:33
Alignment explanation
Indices: 12118--12183 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
12108 ACTCTGACTC
12118 ACGGGGACTAACCAACTTCTTCTCAGGTTCGGG
1 ACGGGGACTAACCAACTTCTTCTCAGGTTCGGG
12151 ACGGGGACTAACCAACTTCTTCTCAGGTTCGGG
1 ACGGGGACTAACCAACTTCTTCTCAGGTTCGGG
12184 CTTAGCTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (33 bp):
ACGGGGACTAACCAACTTCTTCTCAGGTTCGGG
Found at i:15479 original size:6 final size:6
Alignment explanation
Indices: 15468--15553 Score: 57
Period size: 6 Copynumber: 13.8 Consensus size: 6
15458 CTGAAGTGTA
** * * * *
15468 TCTTCC TCTTCC TCTTTT TCTTCC TCATCC TCGTCTC GCTTCT TCTTCC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTC-C TCTTCC TCTTCC
* *
15517 TCTTTC TCTTCT TCAATTCC -CTCTCC TCTTCC TCTTC
1 TCTTCC TCTTCC TC--TTCC TCT-TCC TCTTCC TCTTC
15554 ATCGTCCTCC
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
5 1 0.02
6 49 0.82
7 7 0.12
8 3 0.05
ACGTcount: A:0.03, C:0.43, G:0.02, T:0.51
Consensus pattern (6 bp):
TCTTCC
Found at i:25727 original size:30 final size:30
Alignment explanation
Indices: 25693--25751 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
25683 GAGAAATTGT
*
25693 GCCCTTACCTTAGTAGAAGCTAAAAACTTA
1 GCCCTTACCTTACTAGAAGCTAAAAACTTA
25723 GCCCTTACCTTACTAGAAGCTAAAAACTT
1 GCCCTTACCTTACTAGAAGCTAAAAACTT
25752 GTTTCGAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (30 bp):
GCCCTTACCTTACTAGAAGCTAAAAACTTA
Found at i:31036 original size:209 final size:209
Alignment explanation
Indices: 30676--31095 Score: 804
Period size: 209 Copynumber: 2.0 Consensus size: 209
30666 TATGAACTTT
30676 CTTTGTTATTAGTTTAATGTGTCCCATATTCATAAAACTGTTCAGTTAAAATGATTAGTAGTCCT
1 CTTTGTTATTAGTTTAATGTGTCCCATATTCATAAAACTGTTCAGTTAAAATGATTAGTAGTCCT
30741 TTGCTGCTACATATATTAATAAAGTTTATAACGATTTCTCGAGCATCTCAAGGGTGCTTACTTTG
66 TTGCTGCTACATATATTAATAAAGTTTATAACGATTTCTCGAGCATCTCAAGGGTGCTTACTTTG
30806 TCTCTGTATAATGTGACACTGCACATTTTCATTTTTCTCATGATCGGCATCTTCCATTGAAGATG
131 TCTCTGTATAATGTGACACTGCACATTTTCATTTTTCTCATGATCGGCATCTTCCATTGAAGATG
30871 TGCTCATTCTGGCG
196 TGCTCATTCTGGCG
*
30885 CTTTGTTATTAGTTTAATGTGTCCCATATTCATAAAACTGTTTAGTTAAAATGATTAGTAGTCCT
1 CTTTGTTATTAGTTTAATGTGTCCCATATTCATAAAACTGTTCAGTTAAAATGATTAGTAGTCCT
* *
30950 TTGCTGCTACATGTATTAATAAAGTTTATAACGATTTCTCGAGCATCTCAAGGGTGCTTATTTTG
66 TTGCTGCTACATATATTAATAAAGTTTATAACGATTTCTCGAGCATCTCAAGGGTGCTTACTTTG
*
31015 TCTCTGTATAATGTGACACTGCACATTTTCATTTTTCTCATGATCGGCATCTTCTATTGAAGATG
131 TCTCTGTATAATGTGACACTGCACATTTTCATTTTTCTCATGATCGGCATCTTCCATTGAAGATG
31080 TGCTCATTCTGGCG
196 TGCTCATTCTGGCG
31094 CT
1 CT
31096 CTTGCTTGTG
Statistics
Matches: 207, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
209 207 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (209 bp):
CTTTGTTATTAGTTTAATGTGTCCCATATTCATAAAACTGTTCAGTTAAAATGATTAGTAGTCCT
TTGCTGCTACATATATTAATAAAGTTTATAACGATTTCTCGAGCATCTCAAGGGTGCTTACTTTG
TCTCTGTATAATGTGACACTGCACATTTTCATTTTTCTCATGATCGGCATCTTCCATTGAAGATG
TGCTCATTCTGGCG
Found at i:32403 original size:16 final size:16
Alignment explanation
Indices: 32382--32414 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
32372 GCTTTTACAG
32382 GAATAAAGTTAATGAT
1 GAATAAAGTTAATGAT
32398 GAATAAAGTTAATGAT
1 GAATAAAGTTAATGAT
32414 G
1 G
32415 TAAAATCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (16 bp):
GAATAAAGTTAATGAT
Found at i:37354 original size:5 final size:5
Alignment explanation
Indices: 37344--37372 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
37334 AGGGGGGAAT
37344 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
37373 TCCAATGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Done.