Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009958.1 Corchorus capsularis cultivar CVL-1 contig09979, 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: 13296
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:76 original size:39 final size:39
Alignment explanation
Indices: 22--111 Score: 171
Period size: 39 Copynumber: 2.3 Consensus size: 39
12 CATGGGTCGC
*
22 TCCCGGATCGCGGCCCACCATTGGGCGGGTCGCACGCGA
1 TCCCGGGTCGCGGCCCACCATTGGGCGGGTCGCACGCGA
61 TCCCGGGTCGCGGCCCACCATTGGGCGGGTCGCACGCGA
1 TCCCGGGTCGCGGCCCACCATTGGGCGGGTCGCACGCGA
100 TCCCGGGTCGCG
1 TCCCGGGTCGCG
112 ACCCCTCACT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.10, C:0.39, G:0.38, T:0.13
Consensus pattern (39 bp):
TCCCGGGTCGCGGCCCACCATTGGGCGGGTCGCACGCGA
Found at i:147 original size:13 final size:13
Alignment explanation
Indices: 129--156 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
119 ACTGTTCATC
129 TTTCTCTTTTTTT
1 TTTCTCTTTTTTT
142 TTTCTCTTTTTTT
1 TTTCTCTTTTTTT
155 TT
1 TT
157 CCTTGTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTCTCTTTTTTT
Found at i:176 original size:32 final size:27
Alignment explanation
Indices: 140--213 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 27
130 TTCTCTTTTT
140 TTTTTCTCTTTTTTTTTCCTTGTTCTTTAAC
1 TTTTT-TCTTTTTTTTTCCTTGTTC-TT--C
*
171 GTTTTTT-TTTCTTTTT-CTTGTTCTTC
1 -TTTTTTCTTTTTTTTTCCTTGTTCTTC
197 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTTTTTTTTC
214 TTTAACGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 6 0.16
26 9 0.24
28 2 0.05
29 7 0.18
30 8 0.21
31 1 0.03
32 5 0.13
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTTTTCTTTTTTTTTCCTTGTTCTTC
Found at i:187 original size:6 final size:6
Alignment explanation
Indices: 127--216 Score: 51
Period size: 6 Copynumber: 14.8 Consensus size: 6
117 TCACTGTTCA
* * * * *
127 TCTTTC TCTTTT T-TTTT TCTCTTT T-TTTT TCCTTGT TCTTTA ACGTTT
1 TCTTTT TCTTTT TCTTTT TCT-TTT TCTTTT T-CTTTT TCTTTT TCTTTT
* * *
175 T-TTTT TCTTTT TCTTGT TCTTCTT TTTTCTT TTTTTT TCTTT
1 TCTTTT TCTTTT TCTTTT TCTT-TT TCTT-TT TCTTTT TCTTT
217 AACGTTTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
5 13 0.20
6 33 0.51
7 19 0.29
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (6 bp):
TCTTTT
Found at i:203 original size:22 final size:20
Alignment explanation
Indices: 175--215 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
165 TTTAACGTTT
175 TTTTTTCTTTTTCTTGTTCTTC
1 TTTTTTCTTTTT-TT-TTCTTC
197 TTTTTTCTTTTTTTTTCTT
1 TTTTTTCTTTTTTTTTCTT
216 TAACGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTTCTTC
Found at i:216 original size:10 final size:10
Alignment explanation
Indices: 137--216 Score: 70
Period size: 10 Copynumber: 7.3 Consensus size: 10
127 TCTTTCTCTT
137 TTTTTTTTCTC
1 TTTTTTTT-TC
148 TTTTTTTTTCC
1 TTTTTTTTT-C
**
159 TTGTTCTTTAAC
1 TT-TT-TTTTTC
171 GTTTTTTTTTC
1 -TTTTTTTTTC
182 TTTTTCTTGTTC
1 TTTTT-TT-TTC
*
194 TTCTTTTTTC
1 TTTTTTTTTC
204 TTTTTTTTTC
1 TTTTTTTTTC
214 TTT
1 TTT
217 AACGTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
10 21 0.37
11 19 0.33
12 12 0.21
13 5 0.09
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:4641 original size:144 final size:144
Alignment explanation
Indices: 4377--4660 Score: 471
Period size: 144 Copynumber: 2.0 Consensus size: 144
4367 CAGGGCACAA
4377 ACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTTTAAACAACA
1 ACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTTTAAACAACA
* * *
4442 GTGAAACGGTTCAAAAGTATACCATGCCGAATAAGTACTTTTTTACTATTAGTTTTGGCTTCATC
66 GTGAAAAGGTTCAAAAGTATACCACGCCGAATAAGTACTTCTTTACTATTAGTTTTGGCTTCATC
4507 CAGTAGATCAGGGC
131 CAGTAGATCAGGGC
4521 ACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTTTAAACAACA
1 ACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTTTAAACAACA
* *** * *
4586 GTGAAAAGGTTCAAAATTATACCACGCTTCATAAGTTCTTCTTTACT-TTGGGTTTTGGCTTCAT
66 GTGAAAAGGTTCAAAAGTATACCACGCCGAATAAGTACTTCTTTACTATT-AGTTTTGGCTTCAT
4650 CCAGTAGATCA
130 CCAGTAGATCA
4661 ACTAATCGAA
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
143 2 0.02
144 128 0.98
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (144 bp):
ACAAAGCAGCAATTTTCAGATATAAAAAGTTTGAAAGGTGAAAAGGATATAATTTTTAAACAACA
GTGAAAAGGTTCAAAAGTATACCACGCCGAATAAGTACTTCTTTACTATTAGTTTTGGCTTCATC
CAGTAGATCAGGGC
Found at i:5571 original size:22 final size:22
Alignment explanation
Indices: 5543--5590 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
5533 TCAGATGATG
5543 TAAAGAAAATTTTGTGTATTAT
1 TAAAGAAAATTTTGTGTATTAT
5565 TAAAGAAAATTTTGTGTATTAT
1 TAAAGAAAATTTTGTGTATTAT
5587 TAAA
1 TAAA
5591 TTTTACCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (22 bp):
TAAAGAAAATTTTGTGTATTAT
Found at i:7442 original size:93 final size:92
Alignment explanation
Indices: 7266--7443 Score: 311
Period size: 93 Copynumber: 1.9 Consensus size: 92
7256 TCATGACAAA
* *
7266 ACTAATTATCATCTGTTGTTTTGATTCAATTCAAAGTAAAGAAATTCAAAAGACCTCATTAACGG
1 ACTAATTATCATCTGTTGTTTTGATTCAATTCAAAGTAAAGAAATTCAAAAGAACTCATTAAAGG
* *
7331 AGCAAGGACTACTCATGGAAAAACCTC
66 AACAAGGACGACTCATGGAAAAACCTC
7358 ACTAATTATCATCTGTTGTTTTGATTCAATTCAAAGTAAAAGAAATTCAAAAGAACTCATTAAAG
1 ACTAATTATCATCTGTTGTTTTGATTCAATTCAAAGT-AAAGAAATTCAAAAGAACTCATTAAAG
7423 GAACAAGGACGACTCATGGAA
65 GAACAAGGACGACTCATGGAA
7444 CTTCTTTACC
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 37 0.46
93 44 0.54
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (92 bp):
ACTAATTATCATCTGTTGTTTTGATTCAATTCAAAGTAAAGAAATTCAAAAGAACTCATTAAAGG
AACAAGGACGACTCATGGAAAAACCTC
Found at i:11416 original size:2 final size:2
Alignment explanation
Indices: 11409--11435 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11399 ATCTTTCTTT
11409 TA 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 T
11436 CTATCTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.