Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022307.1 Corchorus olitorius cultivar O-4 contig22340, 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: 30278
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:180 original size:29 final size:30
Alignment explanation
Indices: 138--217 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
128 CTCATTTTTG
* * *
138 AAACGTAATGGATTAATTTT-TCCCGAAA-A
1 AAACATAAGGGATT-ATTTTGTCCCAAAACA
167 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA-CA
*
198 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
218 GGTATTTAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.11
29 19 0.43
31 20 0.45
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (30 bp):
AAACATAAGGGATTATTTTGTCCCAAAACA
Found at i:8223 original size:19 final size:19
Alignment explanation
Indices: 8183--8219 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8173 AATTTTTAAG
8183 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
8202 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
8220 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:15815 original size:27 final size:27
Alignment explanation
Indices: 15777--15829 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
15767 ACGTGGCATT
15777 CCCTCTGTTCCTTTTTATTTGTCATCA
1 CCCTCTGTTCCTTTTTATTTGTCATCA
*
15804 CCCTTTGTTCCTTTTTATTTGTCATC
1 CCCTCTGTTCCTTTTTATTTGTCATC
15830 TTACACTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.09, C:0.28, G:0.08, T:0.55
Consensus pattern (27 bp):
CCCTCTGTTCCTTTTTATTTGTCATCA
Found at i:15994 original size:15 final size:16
Alignment explanation
Indices: 15974--16003 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15964 AACTTTTCTT
15974 GGTTATT-AATTTGTA
1 GGTTATTGAATTTGTA
15989 GGTTATTGAATTTGT
1 GGTTATTGAATTTGT
16004 CTATAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (16 bp):
GGTTATTGAATTTGTA
Found at i:16408 original size:22 final size:23
Alignment explanation
Indices: 16363--16411 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
16353 TTCTTAAGTA
* **
16363 TTTTTAGTAATCTTATTAGTATT
1 TTTTTAATAATCTTATTAAAATT
16386 TTTTTAATAATCTTA-TAAAATT
1 TTTTTAATAATCTTATTAAAATT
16408 TTTT
1 TTTT
16412 AACACCTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTTTAATAATCTTATTAAAATT
Found at i:17008 original size:13 final size:13
Alignment explanation
Indices: 16992--17017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16982 TTGATCACTT
16992 GTGGTGATCTTAG
1 GTGGTGATCTTAG
17005 GTGGTGATCTTAG
1 GTGGTGATCTTAG
17018 ATCACCCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (13 bp):
GTGGTGATCTTAG
Found at i:23000 original size:22 final size:22
Alignment explanation
Indices: 22972--23030 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
22962 TTTCTAATAG
*
22972 AAAACTCAGGTTCAACCGCACC
1 AAAACTCAGGTTCAACCCCACC
22994 AAAACTCAGGTTCAACCCCACC
1 AAAACTCAGGTTCAACCCCACC
23016 AAAACTCAGGTTCAA
1 AAAACTCAGGTTCAA
23031 GCTCCAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.39, C:0.34, G:0.12, T:0.15
Consensus pattern (22 bp):
AAAACTCAGGTTCAACCCCACC
Found at i:26473 original size:148 final size:148
Alignment explanation
Indices: 26205--26504 Score: 564
Period size: 148 Copynumber: 2.0 Consensus size: 148
26195 GAGCAATAAG
26205 TGTACTTTTCCAAGAATAATTTCTTAAGGCTCGTCCAAGAGGTGATTGAACCAGTAGGTAGGAGG
1 TGTACTTTTCCAAGAATAATTTCTTAAGGCTCGTCCAAGAGGTGATTGAACCAGTAGGTAGGAGG
* *
26270 TACAACTAATCTTTTGCACGATCCACAAGAGTGAACAGAAAAGTTATTAGCTTGAATTGATCTTT
66 TACAACCAATCTTTTGCACGATCCACAAGAGTGAACAGAAAAGTTATTAGATTGAATTGATCTTT
26335 AGGAATACCTTGAATACT
131 AGGAATACCTTGAATACT
*
26353 TGTACTTTTCCAAGAATAATTTCTTAAGGCTCGTCCAAGAGGTGATTGAACCGGTAGGTAGGAGG
1 TGTACTTTTCCAAGAATAATTTCTTAAGGCTCGTCCAAGAGGTGATTGAACCAGTAGGTAGGAGG
*
26418 TACAACCAATCTTTTGCACGATCCACAAGAGTGAACAGAAAAGTTCTTAGATTGAATTGATCTTT
66 TACAACCAATCTTTTGCACGATCCACAAGAGTGAACAGAAAAGTTATTAGATTGAATTGATCTTT
26483 AGGAATACCTTGAATACT
131 AGGAATACCTTGAATACT
26501 TGTA
1 TGTA
26505 ATTGCACAGG
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
148 148 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (148 bp):
TGTACTTTTCCAAGAATAATTTCTTAAGGCTCGTCCAAGAGGTGATTGAACCAGTAGGTAGGAGG
TACAACCAATCTTTTGCACGATCCACAAGAGTGAACAGAAAAGTTATTAGATTGAATTGATCTTT
AGGAATACCTTGAATACT
Found at i:30005 original size:20 final size:20
Alignment explanation
Indices: 29980--30019 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29970 GAAGTGGAGT
*
29980 AGCAGATCCGGGATGAGGAA
1 AGCAGATACGGGATGAGGAA
*
30000 AGCAGATATGGGATGAGGAA
1 AGCAGATACGGGATGAGGAA
30020 GAGAAGCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.40, T:0.12
Consensus pattern (20 bp):
AGCAGATACGGGATGAGGAA
Done.