Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016020.1 Corchorus capsularis cultivar CVL-1 contig16041, 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: 32952
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1659 original size:2 final size:2
Alignment explanation
Indices: 1652--1686 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1642 AAAATGATGT
1652 TA TA TA TA 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 TA TA TA TA T
1687 TGGCCAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4536 original size:7 final size:7
Alignment explanation
Indices: 4521--4554 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
4511 GATGGGTGGT
4521 GAAATGG
1 GAAATGG
*
4528 GAGATGG
1 GAAATGG
4535 GAAATGG
1 GAAATGG
4542 GAAATGG
1 GAAATGG
4549 GAAATG
1 GAAATG
4555 TTTTTTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (7 bp):
GAAATGG
Found at i:6533 original size:64 final size:64
Alignment explanation
Indices: 6396--6520 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
6386 GGGAGCTAAC
* * *
6396 AGGTTAAAGTCATCCTAACAAATGTGTTTTCGAGTAATTAAATTTGTATTTTCACTATTGTCAT
1 AGGTTAAAGTCATCCTAACAAATGTGTTTTCGAGTAAATAAATTTGTATTCTCACCATTGTCAT
*
6460 AGGTTAAAGTCATCCTAACAAATGTGTTTTTGAGTAAATAAATTTGTATTCTCACCATTGT
1 AGGTTAAAGTCATCCTAACAAATGTGTTTTCGAGTAAATAAATTTGTATTCTCACCATTGT
6521 TTTCGAGTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (64 bp):
AGGTTAAAGTCATCCTAACAAATGTGTTTTCGAGTAAATAAATTTGTATTCTCACCATTGTCAT
Found at i:12497 original size:38 final size:38
Alignment explanation
Indices: 12455--12528 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
12445 ACTTTAAGGT
* *
12455 AATTTTTTTTTGGGTATCTAAACCTGAGGTAATTTTAG
1 AATTTTTTTTCGGGTATCTAAACCTAAGGTAATTTTAG
12493 AATTTTTTTTCGGGTATCTAAACCTAAGGTAATTTT
1 AATTTTTTTTCGGGTATCTAAACCTAAGGTAATTTT
12529 CGGCCCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.47
Consensus pattern (38 bp):
AATTTTTTTTCGGGTATCTAAACCTAAGGTAATTTTAG
Found at i:13633 original size:17 final size:19
Alignment explanation
Indices: 13611--13645 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13601 TTTATAATTA
13611 ATAATT-AT-ATTATATTT
1 ATAATTAATGATTATATTT
13628 ATAATTAATGATTATATT
1 ATAATTAATGATTATATT
13646 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATAATTAATGATTATATTT
Found at i:13633 original size:24 final size:24
Alignment explanation
Indices: 13591--13651 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
13581 ATCTAATTAC
13591 TATATTATATTTTATAATTAATAAT
1 TATATTATA-TTTATAATTAATAAT
*
13616 TATATTATATTTATAATTAATGAT
1 TATATTATATTTATAATTAATAAT
13640 TATATTATATTT
1 TATATTATATTT
13652 TTATCCAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 26 0.74
25 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATATTATATTTATAATTAATAAT
Found at i:21108 original size:28 final size:28
Alignment explanation
Indices: 21075--21131 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
21065 TAACTATCTA
* *
21075 TTTTGGGACAAATTGACCCCTTAATTTT
1 TTTTGGGACAAATTGACCCATTAACTTT
*
21103 TTTTGGGACAAATTGGCCCATTAACTTT
1 TTTTGGGACAAATTGACCCATTAACTTT
21131 T
1 T
21132 AAAAACGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (28 bp):
TTTTGGGACAAATTGACCCATTAACTTT
Found at i:21858 original size:29 final size:29
Alignment explanation
Indices: 21822--21879 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
21812 TCTCGTTTTT
*
21822 AAAAGTTAAGGGGACAATTTGTCCAAAAA
1 AAAAGTTAAGAGGACAATTTGTCCAAAAA
* *
21851 AAAAGTTAAGAGGCCAATTTGTCCCAAAA
1 AAAAGTTAAGAGGACAATTTGTCCAAAAA
21880 TGGATAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.21
Consensus pattern (29 bp):
AAAAGTTAAGAGGACAATTTGTCCAAAAA
Found at i:21901 original size:31 final size:28
Alignment explanation
Indices: 21822--21902 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 28
21812 TCTCGTTTTT
21822 AAAAGTTAAGGGGACAATTTGTCCAAAAA
1 AAAAGTTAA-GGGACAATTTGTCCAAAAA
* *
21851 AAAAGTTAAGAGGCCAATTTGTCCCAAAATG
1 AAAAGTTAAG-GGACAATTTGT-CCAAAA-A
* *
21882 GATAGTTAAGGGACTAATTTG
1 AAAAGTTAAGGGAC-AATTTG
21903 GATATTAAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.44
30 9 0.21
31 14 0.33
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (28 bp):
AAAAGTTAAGGGACAATTTGTCCAAAAA
Found at i:28503 original size:24 final size:22
Alignment explanation
Indices: 28450--28508 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
28440 ACTGTTCATC
28450 TTCTTTTTTTTT-CTTTTTCTT
1 TTCTTTTTTTTTCCTTTTTCTT
* *
28471 TAACGTTTTTTTTCCCTTTTTCTT
1 T-TC-TTTTTTTTTCCTTTTTCTT
28495 GTTCTTTTTTTTTC
1 -TTCTTTTTTTTTC
28509 TTTAACGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 1 0.03
22 1 0.03
23 17 0.57
24 10 0.33
25 1 0.03
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (22 bp):
TTCTTTTTTTTTCCTTTTTCTT
Done.