Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008703.1 Corchorus capsularis cultivar CVL-1 contig08724, 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: 40888
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Found at i:7475 original size:75 final size:75
Alignment explanation
Indices: 7352--7727 Score: 563
Period size: 75 Copynumber: 5.0 Consensus size: 75
7342 CCATGTCAAA
7352 TCCAAGCGTGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGTGCC
1 TCCAAGCGTGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGTGCC
*
7417 CCCGTATAAT
66 CCCGTATAAC
* * * * *
7427 TCCAAGCGTGGTTGAACATCCCAGCAGACGTCACCCGCAGATGGCTGAGCACCTAGACTGGGGCT
1 TCCAAGCGTGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGTGCC
*
7492 CCCATATAAC
66 CCCGTATAAC
* *
7502 TCCAAGCATGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTTGTGCC
1 TCCAAGCGTGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGTGCC
*
7567 CCCGTGTAAC
66 CCCGTATAAC
* * * * * *
7577 TCCAAACGAGGTCGAACGTCCAAGCAGGCGTCACCAGCAGACGGCTGGGCACCTAGACTGGTGCC
1 TCCAAGCGTGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGTGCC
7642 CCCGTATAAC
66 CCCGTATAAC
* * * * *
7652 TCCAAGTGTGGTCGAACGTCCCAGCAGACGTCACCCTCAGATGGCTGGGCACCTAGATTGGTGCC
1 TCCAAGCGTGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGTGCC
7717 CCCGTATAAC
66 CCCGTATAAC
7727 T
1 T
7728 TCGAATTCGG
Statistics
Matches: 267, Mismatches: 34, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 267 1.00
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (75 bp):
TCCAAGCGTGGTCGAACGTCCCAGCAGACGTCACCCGCAGACGGCTGAGCACCTAGACTGGTGCC
CCCGTATAAC
Found at i:11499 original size:21 final size:21
Alignment explanation
Indices: 11472--11519 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
11462 TGTCAGCCCG
*
11472 CCAAAATTCGAAATTTGAATT
1 CCAAAATTCGAAATTCGAATT
* *
11493 TCAAAATTTGAAATTCGAATT
1 CCAAAATTCGAAATTCGAATT
11514 CCAAAA
1 CCAAAA
11520 AAAAAACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (21 bp):
CCAAAATTCGAAATTCGAATT
Found at i:13107 original size:2 final size:2
Alignment explanation
Indices: 13102--13131 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13092 GAGAAAAAAA
13102 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13132 AGAGTATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16015 original size:11 final size:11
Alignment explanation
Indices: 16001--16034 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
15991 GCTAGTTCAA
16001 GGCAATTTCCT
1 GGCAATTTCCT
* *
16012 GGCAACTTCTT
1 GGCAATTTCCT
16023 GGCAATTTCCT
1 GGCAATTTCCT
16034 G
1 G
16035 AAGATTGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (11 bp):
GGCAATTTCCT
Found at i:33197 original size:37 final size:38
Alignment explanation
Indices: 33143--33217 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
33133 GATTTTCATA
33143 AAAGAAAGTTGATTTAACTTGTTACCATTCATCAAATT
1 AAAGAAAGTTGATTTAACTTGTTACCATTCATCAAATT
33181 AAAGAAAG-TGATTTAACTTGTTACCATTCATCAAATT
1 AAAGAAAGTTGATTTAACTTGTTACCATTCATCAAATT
33218 GAGCACCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (38 bp):
AAAGAAAGTTGATTTAACTTGTTACCATTCATCAAATT
Found at i:35253 original size:18 final size:16
Alignment explanation
Indices: 35212--35255 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
35202 TTTTCCCTTT
*
35212 TTTATTTTTATATTTA
1 TTTATTTTAATATTTA
35228 TTTCATTTCTAATATTTAA
1 TTT-ATTT-TAATATTT-A
35247 TTTATTTTA
1 TTTATTTTA
35256 GGTATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.12
17 6 0.25
18 11 0.46
19 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTTAATATTTA
Found at i:36855 original size:73 final size:73
Alignment explanation
Indices: 36768--36903 Score: 245
Period size: 73 Copynumber: 1.9 Consensus size: 73
36758 TATGTACGAG
* *
36768 ATTTCCGTTGGTAAGTTCGTTTGTACTATATACCAACAGAATTAGAAACGAAAATATCAATACTG
1 ATTTCCGTTGGTAAGTCCGTTTGTACTATATACCAACAGAATCAGAAACGAAAATATCAATACTG
36833 AATCAGGA
66 AATCAGGA
*
36841 ATTTCCGTTGGTAAGTCCGTTTGTACTATATACCAACAGAATCAGAAACGGAAATATCAATAC
1 ATTTCCGTTGGTAAGTCCGTTTGTACTATATACCAACAGAATCAGAAACGAAAATATCAATAC
36904 AAAAACAAGA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (73 bp):
ATTTCCGTTGGTAAGTCCGTTTGTACTATATACCAACAGAATCAGAAACGAAAATATCAATACTG
AATCAGGA
Found at i:37047 original size:6 final size:6
Alignment explanation
Indices: 37022--37060 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
37012 TTTATAATTC
*
37022 ATTTA- ATTAAT ATATTAT ATTTAT ATTTAT ATTTAT ATT
1 ATTTAT ATTTAT AT-TTAT ATTTAT ATTTAT ATTTAT ATT
37061 AAAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 4 0.13
6 21 0.70
7 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
ATTTAT
Found at i:40752 original size:6 final size:6
Alignment explanation
Indices: 40734--40765 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
40724 AAGAAGGTAA
40734 TTTCTT ATTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT T
40766 CGTAAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Done.