Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010696.1 Corchorus capsularis cultivar CVL-1 contig10717, 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: 77908
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:9941 original size:2 final size:2
Alignment explanation
Indices: 9934--9967 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9924 CAGTGAGCAA
9934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9968 GTTAATCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13198 original size:31 final size:31
Alignment explanation
Indices: 13155--13258 Score: 136
Period size: 31 Copynumber: 3.4 Consensus size: 31
13145 TTCGACGTGA
*
13155 CATGTCACGTGTACCAAAAAGTGACATGTGG
1 CATGCCACGTGTACCAAAAAGTGACATGTGG
** *
13186 CACACCACGTGTACCAAAAAGTGACACGTGG
1 CATGCCACGTGTACCAAAAAGTGACATGTGG
* ** *
13217 CATGCCACATGTTTCAAAATGTGACATGTGG
1 CATGCCACGTGTACCAAAAAGTGACATGTGG
13248 CATGCCACGTG
1 CATGCCACGTG
13259 CACAAAAGGA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (31 bp):
CATGCCACGTGTACCAAAAAGTGACATGTGG
Found at i:19629 original size:52 final size:55
Alignment explanation
Indices: 19532--19643 Score: 167
Period size: 59 Copynumber: 2.0 Consensus size: 55
19522 ATTACTTTTA
19532 TTATTTTGAATTTCAAGTTTTCATTAGCAAGCTTTTGTTGTCTTGTATTGAAAATGGTG
1 TTATTTTGAATTTCAAGTTTTCATT---AAGC-TTTGTTGTCTTGTATTGAAAATGGTG
19591 TTATTTTGAATTTCAAGTTTTCATT-AGC-TT-TTGTCTTGTATTGAAAATGGTG
1 TTATTTTGAATTTCAAGTTTTCATTAAGCTTTGTTGTCTTGTATTGAAAATGGTG
19643 T
1 T
19644 CTTTTTCTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
52 23 0.43
53 2 0.04
55 3 0.06
59 25 0.47
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (55 bp):
TTATTTTGAATTTCAAGTTTTCATTAAGCTTTGTTGTCTTGTATTGAAAATGGTG
Found at i:25025 original size:26 final size:26
Alignment explanation
Indices: 24989--25039 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
24979 ATGTGCCCTT
24989 GGATGGCTTTTGACTACATAAATATC
1 GGATGGCTTTTGACTACATAAATATC
25015 GGATGGCTTTTGACTACATAAATAT
1 GGATGGCTTTTGACTACATAAATAT
25040 ATATAGGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (26 bp):
GGATGGCTTTTGACTACATAAATATC
Found at i:48826 original size:23 final size:23
Alignment explanation
Indices: 48778--48826 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
48768 ATTTATTAGA
* *
48778 CATAGTTTGTATTTGCAATTTTT
1 CATAGTTTGTATATGCAATTTCT
*
48801 CATAGTTTGTGTATGCGAA-TTCT
1 CATAGTTTGTATATGC-AATTTCT
48824 CAT
1 CAT
48827 TGTAACTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (23 bp):
CATAGTTTGTATATGCAATTTCT
Found at i:53024 original size:2 final size:2
Alignment explanation
Indices: 53017--53047 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
53007 GCCAATGATC
*
53017 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53048 ATTTATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58751 original size:27 final size:27
Alignment explanation
Indices: 58720--58772 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
58710 ACTCCCTCTG
*
58720 TTCCTTTTTAATTGTCTATTTCCCTTA
1 TTCCTTTTTAATTGTCCATTTCCCTTA
58747 TTCCTTTTTAATTGTCCATTTCCCTT
1 TTCCTTTTTAATTGTCCATTTCCCTT
58773 GTTTTCCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.13, C:0.25, G:0.04, T:0.58
Consensus pattern (27 bp):
TTCCTTTTTAATTGTCCATTTCCCTTA
Found at i:59370 original size:1 final size:1
Alignment explanation
Indices: 59364--59397 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
59354 GCTGAAATTC
59364 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
59398 GAGAAGATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:61800 original size:3 final size:3
Alignment explanation
Indices: 61786--61817 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
61776 CTCTCACCTG
61786 TTC TTCC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC T
61818 GCTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Done.