Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013109.1 Corchorus olitorius cultivar O-4 contig13142, 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: 13879
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--38 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 ACCT
5 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39 ACGATCTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3219 original size:3 final size:3
Alignment explanation
Indices: 3211--3256 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
3201 TGGTGATTTA
*
3211 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ACTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
3257 TATTTCTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:8790 original size:151 final size:150
Alignment explanation
Indices: 8517--8821 Score: 601
Period size: 151 Copynumber: 2.0 Consensus size: 150
8507 AGATAGAGGG
8517 AATAGACTGGGGTGGCTGGATGTGTGGTAATCTTGCTATTAAGATTTGGCAGTTTGGACTCATTT
1 AATAGACTGGGGTGGCTGGATGTGTGGTAATCTTGCTATTAAGATTTGGCAGTTTGGACTCATTT
8582 TCTCAAGTTGGAAAAAGAACTAATGAAAGATGTTGTGTTGAGTCATGAGTTATATTTAACTATTT
66 TCTCAAGTTGGAAAAAGAACTAATGAAAGATGTTGTGTTGAGTCATGAGTTATATTTAACTATTT
8647 AAGCCTCTTCTGCATGAAGA
131 AAGCCTCTTCTGCATGAAGA
8667 AATAGACTGGGGTGGCTGGATGTGTGGTAATCTTTGCTATTAAGATTTGGCAGTTTGGACTCATT
1 AATAGACTGGGGTGGCTGGATGTGTGGTAATC-TTGCTATTAAGATTTGGCAGTTTGGACTCATT
8732 TTCTCAAGTTGGAAAAAGAACTAATGAAAGATGTTGTGTTGAGTCATGAGTTATATTTAACTATT
65 TTCTCAAGTTGGAAAAAGAACTAATGAAAGATGTTGTGTTGAGTCATGAGTTATATTTAACTATT
8797 TAAGCCTCTTCTGCATGAAGA
130 TAAGCCTCTTCTGCATGAAGA
8818 AATA
1 AATA
8822 TATGTTCCGC
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
150 32 0.21
151 122 0.79
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.35
Consensus pattern (150 bp):
AATAGACTGGGGTGGCTGGATGTGTGGTAATCTTGCTATTAAGATTTGGCAGTTTGGACTCATTT
TCTCAAGTTGGAAAAAGAACTAATGAAAGATGTTGTGTTGAGTCATGAGTTATATTTAACTATTT
AAGCCTCTTCTGCATGAAGA
Found at i:12672 original size:33 final size:34
Alignment explanation
Indices: 12614--12678 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
12604 CTTAGCATGG
12614 ATCTTGCGGTTCTTAATTTTGCATGGATCTTGGC
1 ATCTTGCGGTTCTTAATTTTGCATGGATCTTGGC
*
12648 ATCTTGCGGTTCTT-TTTTTGCATGGATCTTG
1 ATCTTGCGGTTCTTAATTTTGCATGGATCTTG
12679 CACTTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (34 bp):
ATCTTGCGGTTCTTAATTTTGCATGGATCTTGGC
Found at i:12916 original size:2 final size:2
Alignment explanation
Indices: 12909--12954 Score: 65
Period size: 2 Copynumber: 22.0 Consensus size: 2
12899 TTTAGTAAAT
*
12909 TA TA TA TA TA TA CTA TA TA TA TA TA TA TA TA TC TA TA TA CTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
12953 TA
1 TA
12955 AGTCTAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 36 0.90
3 4 0.10
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13191 original size:103 final size:103
Alignment explanation
Indices: 13007--13214 Score: 380
Period size: 103 Copynumber: 2.0 Consensus size: 103
12997 CCTTTTTAAT
* *
13007 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTTCA
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGATTCA
*
13072 ATATGTAATTTTATTTATCAATTAAATTAAATATATTA
66 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
*
13110 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGATTTA
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGATTCA
13175 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
66 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
13213 TT
1 TT
13215 ATATTAAAAT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (103 bp):
TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAACTTTTAAGATTCA
ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
Found at i:13382 original size:25 final size:24
Alignment explanation
Indices: 13346--13392 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
13336 AATACTTACA
*
13346 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGCTATTTTT
13370 TTAATTCAAATTCTTAGCTATTT
1 TTAATT-AAATTCTTAGCTATTT
13393 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGCTATTTTT
Found at i:13865 original size:201 final size:202
Alignment explanation
Indices: 13466--13873 Score: 746
Period size: 201 Copynumber: 2.0 Consensus size: 202
13456 TTCCTTAATA
*
13466 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
*
13531 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAGTA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
13596 ATGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
13661 ACCATTG
196 ACCATTG
13668 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
* * * *
13733 AATTTAATAATTCAACCACTAATGTTTAACT-ATTTTTTTTTGTATAGTTTTATATATAATAATA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
*
13797 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
13862 ACCATTG
196 ACCATTG
13869 ATAAA
1 ATAAA
13874 GTTATT
Statistics
Matches: 199, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
201 106 0.53
202 93 0.47
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
ATGTGTTATATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Done.