Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009707.1 Corchorus capsularis cultivar CVL-1 contig09728, 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: 33110
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:204 original size:15 final size:15
Alignment explanation
Indices: 184--216 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
174 AATCTTTTCG
184 TCTGATTTCCTTCCT
1 TCTGATTTCCTTCCT
199 TCTGATTTCCTTCCT
1 TCTGATTTCCTTCCT
214 TCT
1 TCT
217 TGCTCCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.33, G:0.06, T:0.55
Consensus pattern (15 bp):
TCTGATTTCCTTCCT
Found at i:514 original size:34 final size:34
Alignment explanation
Indices: 471--543 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
461 ATAAAACGTG
471 AAAAGACATAACCTCTGGTAACTGTCTCCTAATT
1 AAAAGACATAACCTCTGGTAACTGTCTCCTAATT
505 AAAAGACATAACCTCTGGTAACTGTCTCCTAATT
1 AAAAGACATAACCTCTGGTAACTGTCTCCTAATT
539 AAAAG
1 AAAAG
544 GTATCTATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (34 bp):
AAAAGACATAACCTCTGGTAACTGTCTCCTAATT
Found at i:1748 original size:1 final size:1
Alignment explanation
Indices: 1742--1769 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1732 AAATAATCGC
1742 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1770 CAACATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2701 original size:64 final size:64
Alignment explanation
Indices: 2628--2758 Score: 208
Period size: 64 Copynumber: 2.0 Consensus size: 64
2618 CGCAATGTCA
* * *
2628 AATAATTCTTGGTTTGTGTAAAAAGCTCATTTTGACCACAAAAACCAAACTAACTTGAAAAGCT
1 AATAATTCTTGATTTGTGTAAAAAACTCATTTTGACCACAAAAACCAAACCAACTTGAAAAGCT
* * *
2692 AATAATTCTTGATTTGTGTAAAAAACTTATTTTGACCACAAAAGCCAAGCCAACTTGAAAAGCT
1 AATAATTCTTGATTTGTGTAAAAAACTCATTTTGACCACAAAAACCAAACCAACTTGAAAAGCT
2756 AAT
1 AAT
2759 TCGTAGTTGC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (64 bp):
AATAATTCTTGATTTGTGTAAAAAACTCATTTTGACCACAAAAACCAAACCAACTTGAAAAGCT
Found at i:15432 original size:6 final size:6
Alignment explanation
Indices: 15421--15445 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15411 GTGCAAGTAA
15421 TTTCAT TTTCAT TTTCAT TTTCAT T
1 TTTCAT TTTCAT TTTCAT TTTCAT T
15446 CAATGTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:17513 original size:31 final size:29
Alignment explanation
Indices: 17470--17541 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
17460 AAATTGGGTG
*
17470 AGGGACCTAATTGCTGACTTAA-CTCAACTTC
1 AGGGACC-AATTGCTCAC-TAAGCTC-ACTTC
*
17501 AGGGACTCAATTGCTCACTAAGTTCACTTC
1 AGGGAC-CAATTGCTCACTAAGCTCACTTC
17531 AGGGACCAATT
1 AGGGACCAATT
17542 TGCACATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 5 0.14
30 14 0.38
31 17 0.46
32 1 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (29 bp):
AGGGACCAATTGCTCACTAAGCTCACTTC
Found at i:19297 original size:6 final size:6
Alignment explanation
Indices: 19288--19312 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19278 TCGGTGTCGG
19288 ATATTC ATATTC ATATTC ATATTC A
1 ATATTC ATATTC ATATTC ATATTC A
19313 ATATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTC
Found at i:23368 original size:33 final size:33
Alignment explanation
Indices: 23312--23403 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
23302 TTTGGATTCT
* *
23312 ATTGTTCCCACTAATATTATGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
* * *
23345 ATTGCTGCCACTGATGTTGTGCCTCAGAATGAG
1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
23378 ATTGCTCCCACTAATATTGTGCCTCA
1 ATTGCTCCCACTAATATTGTGCCTCA
23404 ACGAACACAC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (33 bp):
ATTGCTCCCACTAATATTGTGCCTCAGAATGAG
Found at i:29839 original size:6 final size:6
Alignment explanation
Indices: 29828--29852 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29818 GTGCAAGTAA
29828 TTTCAT TTTCAT TTTCAT TTTCAT T
1 TTTCAT TTTCAT TTTCAT TTTCAT T
29853 CAATGTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCAT
Found at i:31800 original size:20 final size:22
Alignment explanation
Indices: 31761--31805 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
31751 AAGCATGGAG
31761 GACTCTCAGTTAGAGAGAGAGA
1 GACTCTCAGTTAGAGAGAGAGA
31783 GACTCTCA-TTAGGAGAGAGAGA
1 GACTCTCAGTTA-GAGAGAGAGA
31805 G
1 G
31806 TATACAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (22 bp):
GACTCTCAGTTAGAGAGAGAGA
Done.