Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006010.1 Corchorus capsularis cultivar CVL-1 contig06028, 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: 6666
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Found at i:1977 original size:21 final size:21
Alignment explanation
Indices: 1951--2075 Score: 105
Period size: 21 Copynumber: 5.8 Consensus size: 21
1941 TTTTACTGAA
1951 TTACTGATTACCATTATTA-TT
1 TTACTGATTACCATT-TTACTT
*
1972 TTACTGATTA--TTCTTTACTT
1 TTACTGATTACCAT-TTTACTT
* *
1992 TGTACTGATTACTATTTTACTC
1 T-TACTGATTACCATTTTACTT
**
2014 TTGTTGATTACC-TTCTTACTTT
1 TTACTGATTACCATT-TTAC-TT
2036 TTACTGATTACCATTTTACTCTT
1 TTACTGATTACCATTTTA--CTT
*
2059 TTACTGATTACTATTTT
1 TTACTGATTACCATTTT
2076 CTGCTCCTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.05
20 6 0.07
21 31 0.37
22 21 0.25
23 21 0.25
24 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.55
Consensus pattern (21 bp):
TTACTGATTACCATTTTACTT
Found at i:2069 original size:15 final size:15
Alignment explanation
Indices: 2051--2106 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
2041 GATTACCATT
2051 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
2066 TTACTATTTT-CTG-
1 TTACTCTTTTACTGA
* * *
2079 CTCCTTTTTTACTGA
1 TTACTCTTTTACTGA
2094 TTACTCTTTTACT
1 TTACTCTTTTACT
2107 TCTTACTGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.57
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:2133 original size:21 final size:21
Alignment explanation
Indices: 2087--2173 Score: 88
Period size: 21 Copynumber: 4.1 Consensus size: 21
2077 TGCTCCTTTT
* *
2087 TTACTGATTACTCTTTTACTTC
1 TTACTGATTACTATTTGAC-TC
2109 TTACTGATTACTATTTGACTC
1 TTACTGATTACTATTTGACTC
*
2130 TTACTAATTACTACTTTG-CTC
1 TTACTGATTACTA-TTTGACTC
* * *
2151 TCACTGGTTACTGTTT-ACTC
1 TTACTGATTACTATTTGACTC
2171 TTA
1 TTA
2174 ATGGTTACCT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
20 8 0.15
21 26 0.47
22 21 0.38
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.49
Consensus pattern (21 bp):
TTACTGATTACTATTTGACTC
Found at i:2170 original size:71 final size:73
Alignment explanation
Indices: 2018--2172 Score: 176
Period size: 73 Copynumber: 2.2 Consensus size: 73
2008 TTACTCTTGT
* * * *
2018 TGATTAC-CTTCTTACTTTTTACTGATTACCATTTTACTCTTTTACTGATTACTATTTTCTGCTC
1 TGATTACTCTTCTTACTTCTTACTGATTACCATTTGACTC-TTTACTAATTACTATTTGCTGCTC
**
2082 CTTTTTTAC
65 CTTGGTTAC
*
2091 TGATTACTCTT-TTACTTCTTACTGATTACTATTTGACTC-TTACTAATTACTACTTTGCT-CTC
1 TGATTACTCTTCTTACTTCTTACTGATTACCATTTGACTCTTTACTAATTACTA-TTTGCTGCTC
2153 AC-TGGTTAC
65 -CTTGGTTAC
*
2162 TGTTTACTCTT
1 TGATTACTCTT
2173 AATGGTTACC
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
71 30 0.42
72 6 0.08
73 32 0.45
74 3 0.04
ACGTcount: A:0.19, C:0.22, G:0.07, T:0.52
Consensus pattern (73 bp):
TGATTACTCTTCTTACTTCTTACTGATTACCATTTGACTCTTTACTAATTACTATTTGCTGCTCC
TTGGTTAC
Found at i:2338 original size:35 final size:34
Alignment explanation
Indices: 2281--2437 Score: 136
Period size: 35 Copynumber: 4.4 Consensus size: 34
2271 TTACTTTTTG
*
2281 CTGATTATCCTTTTACTCTTTACCATTCTTTCTTTA
1 CTGATTATTC-TTTACTCTTTACCATTC-TTCTTTA
* *
2317 CTGATTATTCTTTACTTTTTACCATTCTTCTTTTG
1 CTGATTATTCTTTACTCTTTACCATTCTTC-TTTA
* * *
2352 CTGATTACTTTTTTTACTCTTTACTAATTAC-TCCTTA
1 CTGATTA--TTCTTTACTCTTTAC-CATT-CTTCTTTA
* * * *
2389 GTGATTATTATTTACTCTTTATCATTTCTCCTTTA
1 CTGATTATTCTTTACTCTTTACCA-TTCTTCTTTA
*
2424 CTGATTACTCTTTA
1 CTGATTATTCTTTA
2438 GAATTTAATT
Statistics
Matches: 97, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
34 5 0.05
35 56 0.58
36 9 0.09
37 21 0.22
38 5 0.05
39 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.04, T:0.56
Consensus pattern (34 bp):
CTGATTATTCTTTACTCTTTACCATTCTTCTTTA
Found at i:2394 original size:72 final size:71
Alignment explanation
Indices: 2276--2433 Score: 169
Period size: 72 Copynumber: 2.2 Consensus size: 71
2266 TCTTTTTACT
* * * *
2276 TTTTGCTGATTA-TCCTTTTACTCTTTACCATTCTTTCTTTACTGATTATTCTTTACTTTTTACC
1 TTTTGCTGATTACTCCTTTTACTCTTTACAATTC-TTCCTTACTGATTATTATTTACTCTTTACC
2340 A-TTCTTC
65 ATTTC-TC
** * *
2347 TTTTGCTGATTACTTTTTTTACTCTTTACTAATTAC-TCCTTAGTGATTATTATTTACTCTTTAT
1 TTTTGCTGATTACTCCTTTTACTCTTTAC-AATT-CTTCCTTACTGATTATTATTTACTCTTTAC
2411 CATTTCTC
64 CATTTCTC
* *
2419 CTTTACTGATTACTC
1 TTTTGCTGATTACTC
2434 TTTAGAATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 12 0.17
72 53 0.74
73 6 0.08
74 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.56
Consensus pattern (71 bp):
TTTTGCTGATTACTCCTTTTACTCTTTACAATTCTTCCTTACTGATTATTATTTACTCTTTACCA
TTTCTC
Found at i:2750 original size:47 final size:47
Alignment explanation
Indices: 2644--2805 Score: 252
Period size: 47 Copynumber: 3.4 Consensus size: 47
2634 TTTTACTTGA
* * * **
2644 TTACTGATTTACTGATTACTATTACCTTGACTTTTGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGAC-TCCGATTAATCTCTTT
*
2692 TCACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
*
2739 TTACTGTTTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
1 TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
2786 TTACTGATTTACTGATTACC
1 TTACTGATTTACTGATTACC
2806 TTTTTACTAT
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 78 0.74
48 27 0.26
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.47
Consensus pattern (47 bp):
TTACTGATTTACTGATTACCATCACTTTGACTCCGATTAATCTCTTT
Found at i:3583 original size:50 final size:49
Alignment explanation
Indices: 3475--3969 Score: 402
Period size: 51 Copynumber: 9.8 Consensus size: 49
3465 AACTAATCAA
** * * * * *
3475 TTTATTTACTAATGGCCTAAAAAGTTTAAACTTCTAATTCAAAGGTAACA-T
1 TTTATTTACTAATTACTTAAAAA-TTCAATCTT-TTATTCAAAGTTAA-ATT
* * **
3526 TTTATTTACTAATTACTTAAAAGTTCAATCTTTCATTCAAATGTTAAAGC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAA-GTTAAATT
* * ** * * *
3576 TTTATTTACTAATCACTCTAAAGATTCAATCTTTTACCCAAACATGACA-T
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAA-GTTAAATT
* * *
3626 TTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAA-GTTAAATT
* * * *
3676 TTTATTTACTAATTACTCTAAAGATTCAATCTTTTACTCAAAGATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAG-TTAAATT
* * *
3727 TTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAAGCTTAAAAT
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAG-TTAAATT
* * ** **
3777 TTTATTTGCTAATCACTTTAAAAATTCAATCTTTTACCCAAA-TATGGCATT
1 TTTATTTACTAATTAC-TTAAAAATTCAATCTTTTATTCAAAGT-T-AAATT
* * * *
3828 TTTATTTTCCAATTACATAAAAATTCAATCTTTTATTCAAAGCTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAG-TTAAATT
* * ** * *
3878 TTTATTTGCTAATCACTTTAAAAATTCAATCTTTTACCCAAAGATGACATT
1 TTTATTTACTAATTAC-TTAAAAATTCAATCTTTTATTCAAAG-TTAAATT
* * *
3929 TTTATTTTCCAATTACTCAAAAATTCAATCTTTTATTCAAA
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAA
3970 TGATAAACTT
Statistics
Matches: 352, Mismatches: 80, Indels: 25
0.77 0.18 0.05
Matches are distributed among these distances:
49 34 0.10
50 157 0.45
51 160 0.45
52 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (49 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGTTAAATT
Found at i:3781 original size:101 final size:101
Alignment explanation
Indices: 3525--3969 Score: 646
Period size: 101 Copynumber: 4.4 Consensus size: 101
3515 AAAGGTAACA
* * * * *
3525 TTTTATTTACTAATTACTTAAAAGTTCAATCTTTCATTCAAATG-TTAAAGCTTTATTTACTAAT
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAA-GCTTAAATCTTTATTTACTAAT
* *
3589 CACTCTAAAGATTCAATCTTTTACCCAAACATGACA-
65 CACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
* * * *
3625 TTTTACTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATT
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAAGCTTAAATCTTTATTTACTAATC
* *
3690 ACTCTAAAGATTCAATCTTTTACTCAAAGATGACAT
66 ACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
*
3726 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAAGCTTAAAAT-TTTATTTGCTAAT
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAAGCTT-AAATCTTTATTTACTAAT
* * *
3790 CACTTTAAAAATTCAATCTTTTACCCAAATATGGCAT
65 CACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
* *
3827 TTTTATTTTCCAATTACATAAAAATTCAATCTTTTATTCAAAGCTTAAATCTTTATTTGCTAATC
1 TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAAGCTTAAATCTTTATTTACTAATC
*
3892 ACTTTAAAAATTCAATCTTTTACCCAAAGATGACAT
66 ACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
*
3928 TTTTATTTTCCAATTAC-TCAAAAATTCAATCTTTTATTCAAA
1 TTTTATTTACCAATTACAT-AAAAATTCAATCTTTTATTCAAA
3970 TGATAAACTT
Statistics
Matches: 319, Mismatches: 21, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
99 1 0.00
100 95 0.30
101 219 0.69
102 4 0.01
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.43
Consensus pattern (101 bp):
TTTTATTTACCAATTACATAAAAATTCAATCTTTTATTCAAAGCTTAAATCTTTATTTACTAATC
ACTCTAAAAATTCAATCTTTTACCCAAAGATGACAT
Found at i:6025 original size:16 final size:16
Alignment explanation
Indices: 6004--6037 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5994 CCTTGGGGAA
6004 CATTTCTTGTGCTTTG
1 CATTTCTTGTGCTTTG
* *
6020 CATTTCTTTTTCTTTG
1 CATTTCTTGTGCTTTG
6036 CA
1 CA
6038 AGGTCCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.21, G:0.12, T:0.59
Consensus pattern (16 bp):
CATTTCTTGTGCTTTG
Done.