Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007204.1 Corchorus capsularis cultivar CVL-1 contig07225, 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: 64963
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:6572 original size:2 final size:2
Alignment explanation
Indices: 6560--6590 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6550 GGATAAGTTT
*
6560 TA TA GA 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 T
6591 TTTACGCAAG
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):
TA
Found at i:9099 original size:21 final size:21
Alignment explanation
Indices: 9057--9100 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9047 AGGGCACATA
* *
9057 GGTGCCCAGGCCAACCGGCTG
1 GGTGCCCAGGCAAACCGCCTG
* *
9078 GGTGCGCAGGCAAAGCGCCTG
1 GGTGCCCAGGCAAACCGCCTG
9099 GG
1 GG
9101 CGCACAGCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.43, T:0.09
Consensus pattern (21 bp):
GGTGCCCAGGCAAACCGCCTG
Found at i:9252 original size:19 final size:20
Alignment explanation
Indices: 9214--9254 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
9204 GCTTGGTCCC
*
9214 TTTTTGCTCCCAAATTTCAA
1 TTTTTGCTCCCAAATCTCAA
*
9234 TTTTTGCTTCCAAA-CTCAA
1 TTTTTGCTCCCAAATCTCAA
9253 TT
1 TT
9255 CCAACTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTTTGCTCCCAAATCTCAA
Found at i:33935 original size:12 final size:11
Alignment explanation
Indices: 33917--33947 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
33907 ATTATACAGC
33917 CTTTTTTTTTT
1 CTTTTTTTTTT
33928 CTTTTTTTTTT
1 CTTTTTTTTTT
*
33939 GTTTTTTTT
1 CTTTTTTTT
33948 GTCTAGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:40888 original size:2 final size:2
Alignment explanation
Indices: 40881--40931 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
40871 ATTTCCATGC
40881 AT AT AT AT AT AT AT AT AT AT AT A- 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 AT AT AT AT
40922 AT AT AT AT AT
1 AT AT AT AT AT
40932 TTGGTCAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47600 original size:15 final size:15
Alignment explanation
Indices: 47580--47610 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47570 TTTCTTTTCT
47580 TTTCAAATAAGTCCC
1 TTTCAAATAAGTCCC
*
47595 TTTCAATTAAGTCCC
1 TTTCAAATAAGTCCC
47610 T
1 T
47611 GAAACTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
TTTCAAATAAGTCCC
Found at i:49147 original size:288 final size:283
Alignment explanation
Indices: 48631--49202 Score: 991
Period size: 288 Copynumber: 2.0 Consensus size: 283
48621 AGCTTCAATT
* *
48631 AATAAAGGAAATCTTCCCAAAGGATATGTATTATGTATCTAAAATTTTCATCATAGCAGCAGCCA
1 AATAAAGGAAATCTTCCCAAAGGATATGTATTATGTATCCAAAATTTTCATCACAGCAGCAGCCA
* *
48696 TCCTCTGTTTAGAGTATGTTATTGCTACTTAAATTGAAGTTAAAATTTTAAGTTTCTTTCCCCCA
66 TCCTCCGTTCAGAGTATGTTATTGCTACTTAAATTGAAGTTAAAATTTTAAGTTTCTTTCCCCCA
* *
48761 GAATTATACTAAAATGTTCCTTTGCCTACTTAACCTCTTCCTAATTCGTATAGAAGCTATATGAT
131 GAATTATACTAAAATGTTCCTTTGCCTACTTAACCTCCTCCTAATTCGCATAGAAGCTATATGAT
*
48826 GTTAAGAGACAATATCCATGAAATACTCTGGGAAATTAAAGATCAAAACTATAAAAAAAAAAGAA
196 GTTAAGAGACAACATCCATGAAATACTCTGGGAAATTAAAGATCAAAACTAT----AAAAAA-AA
48891 ACTAAATTTTACCACTTATTGTTGATTA
256 ACTAAATTTTACCACTTATTGTTGATTA
* *
48919 AATAAAGGAAATCTTCCCAATGGATATGTATTATGTATCCAGAATTTTCATCACAGCAGCAGCCA
1 AATAAAGGAAATCTTCCCAAAGGATATGTATTATGTATCCAAAATTTTCATCACAGCAGCAGCCA
48984 TCCTCCGTTCAGAGTATGTTATTGCTACTTAAATTGAAGTTAAAATTTTAAGTTTCTTTCCCCCA
66 TCCTCCGTTCAGAGTATGTTATTGCTACTTAAATTGAAGTTAAAATTTTAAGTTTCTTTCCCCCA
***
49049 GAATTATACTTTCATGTTCCTTTGCCTACTTAACCTCCTCCTAATTCGCATAGAAGCTATATGAT
131 GAATTATACTAAAATGTTCCTTTGCCTACTTAACCTCCTCCTAATTCGCATAGAAGCTATATGAT
49114 GTTAAGAGACAACATCCATGAAATACTCTGGGAAATTAAAGATCAAAACTATAAAAAAAAACTAA
196 GTTAAGAGACAACATCCATGAAATACTCTGGGAAATTAAAGATCAAAACTATAAAAAAAAACTAA
49179 ATTTTACCACTTATTGTTGATTA
261 ATTTTACCACTTATTGTTGATTA
49202 A
1 A
49203 CTAACGAGGG
Statistics
Matches: 272, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
283 31 0.11
284 6 0.02
288 235 0.86
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (283 bp):
AATAAAGGAAATCTTCCCAAAGGATATGTATTATGTATCCAAAATTTTCATCACAGCAGCAGCCA
TCCTCCGTTCAGAGTATGTTATTGCTACTTAAATTGAAGTTAAAATTTTAAGTTTCTTTCCCCCA
GAATTATACTAAAATGTTCCTTTGCCTACTTAACCTCCTCCTAATTCGCATAGAAGCTATATGAT
GTTAAGAGACAACATCCATGAAATACTCTGGGAAATTAAAGATCAAAACTATAAAAAAAAACTAA
ATTTTACCACTTATTGTTGATTA
Found at i:49456 original size:31 final size:31
Alignment explanation
Indices: 49419--49483 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
49409 TTGGGTTATC
49419 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
49450 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
49481 AGT
1 AGT
49484 TAATTCAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:62906 original size:2 final size:2
Alignment explanation
Indices: 62899--62933 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
62889 TACTCCGTAC
62899 TA TA TA TA TA TA TA TA -A TA -A 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 TA T
62934 GTTGTGAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.