Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015018.1 Corchorus capsularis cultivar CVL-1 contig15039, 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: 27077
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:4074 original size:32 final size:32
Alignment explanation
Indices: 4008--4105 Score: 124
Period size: 32 Copynumber: 3.1 Consensus size: 32
3998 GTCCGAACTT
* * * * *
4008 GAACCCGAATTAATCTAACCCAAAATTGACCC
1 GAACCCGAATCAACCTGACCCAAATTTAACCC
*
4040 GAACCCGAATCAACCTGACCCAAATTTAATCC
1 GAACCCGAATCAACCTGACCCAAATTTAACCC
* *
4072 GAACCTGATTCAACCTGACCCAAATTTAACCC
1 GAACCCGAATCAACCTGACCCAAATTTAACCC
4104 GA
1 GA
4106 CCTGACACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.19
Consensus pattern (32 bp):
GAACCCGAATCAACCTGACCCAAATTTAACCC
Found at i:4107 original size:16 final size:16
Alignment explanation
Indices: 4051--4107 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
4041 AACCCGAATC
*
4051 AACCTGACCCAAATTT
1 AACCCGACCCAAATTT
* * ** *
4067 AATCCGAACCTGATTC
1 AACCCGACCCAAATTT
*
4083 AACCTGACCCAAATTT
1 AACCCGACCCAAATTT
4099 AACCCGACC
1 AACCCGACC
4108 TGACACAAGT
Statistics
Matches: 28, Mismatches: 13, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.21
Consensus pattern (16 bp):
AACCCGACCCAAATTT
Found at i:7130 original size:74 final size:74
Alignment explanation
Indices: 7009--7160 Score: 286
Period size: 74 Copynumber: 2.1 Consensus size: 74
6999 GTTGAAAGGT
* *
7009 AAAGCTCTTATAACCGTTATATGTAAGATCTGTTTTGTTGGTGTATATATTCCTTTTTGCGGCTT
1 AAAGCTCTTATAACCGTTATATGCAAGATCTATTTTGTTGGTGTATATATTCCTTTTTGCGGCTT
7074 CAATCAATA
66 CAATCAATA
7083 AAAGCTCTTATAACCGTTATATGCAAGATCTATTTTGTTGGTGTATATATTCCTTTTTGCGGCTT
1 AAAGCTCTTATAACCGTTATATGCAAGATCTATTTTGTTGGTGTATATATTCCTTTTTGCGGCTT
7148 CAATCAATA
66 CAATCAATA
7157 AAAG
1 AAAG
7161 TTAACCTTTG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (74 bp):
AAAGCTCTTATAACCGTTATATGCAAGATCTATTTTGTTGGTGTATATATTCCTTTTTGCGGCTT
CAATCAATA
Found at i:12203 original size:9 final size:9
Alignment explanation
Indices: 12189--12226 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
12179 CTAAAGCAAC
12189 TTTTTCTCT
1 TTTTTCTCT
12198 TTTTTCT-T
1 TTTTTCTCT
*
12206 TTTTTTTCTT
1 TTTTTCTC-T
12216 TTTTTCTCT
1 TTTTTCTCT
12225 TT
1 TT
12227 CTTTAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 10 0.40
10 8 0.32
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:12210 original size:10 final size:10
Alignment explanation
Indices: 12197--12226 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12187 ACTTTTTCTC
12197 TTTTTTCTTT
1 TTTTTTCTTT
12207 TTTTTTCTTT
1 TTTTTTCTTT
*
12217 TTTTCTCTTT
1 TTTTTTCTTT
12227 CTTTAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:13295 original size:29 final size:29
Alignment explanation
Indices: 13259--13318 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
13249 AATTAGGCAT
* *
13259 TACCTAAGTTTGGAAAGTTGGGTATTACC
1 TACCTAAGTTAGGAAAGTTAGGTATTACC
*
13288 TACCTAAGTTAGGAAAGTTAGGTTTTACC
1 TACCTAAGTTAGGAAAGTTAGGTATTACC
13317 TA
1 TA
13319 AGTTAGGCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (29 bp):
TACCTAAGTTAGGAAAGTTAGGTATTACC
Found at i:13322 original size:25 final size:26
Alignment explanation
Indices: 13258--13325 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 26
13248 TAATTAGGCA
* *
13258 TTACCTAAGTTTGGAAAGTTGGGTAT
1 TTACCTAAGTTAGGAAAGTTAGGTAT
13284 TACCTACCTAAGTTAGGAAAGTTAGGT-T
1 T---TACCTAAGTTAGGAAAGTTAGGTAT
13312 TTACCTAAGTTAGG
1 TTACCTAAGTTAGG
13326 CAAATTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 13 0.35
26 1 0.03
28 2 0.05
29 21 0.57
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (26 bp):
TTACCTAAGTTAGGAAAGTTAGGTAT
Found at i:15756 original size:2 final size:2
Alignment explanation
Indices: 15749--15778 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15739 TAACTTGAAA
15749 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
15779 TCTTTGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22426 original size:8 final size:8
Alignment explanation
Indices: 22415--22445 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
22405 ATTTAAGCAT
22415 TTTATAGA
1 TTTATAGA
22423 TTTATAGA
1 TTTATAGA
22431 TTTATAGA
1 TTTATAGA
22439 TGTTATA
1 T-TTATA
22446 TAAACAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (8 bp):
TTTATAGA
Done.