Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021791.1 Corchorus olitorius cultivar O-4 contig21824, 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: 13822
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:2309 original size:57 final size:57
Alignment explanation
Indices: 2221--2334 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
2211 TCTAGGCCGC
2221 GTGAAATCCAATTGTTTGGTTGGTGAGAAAATTTCACCAAAGAAGAAAAAGAAAGCA
1 GTGAAATCCAATTGTTTGGTTGGTGAGAAAATTTCACCAAAGAAGAAAAAGAAAGCA
2278 GTGAAATCCAATTGTTTGGTTGGTGAGAAAATTTCACCAAAGAAGAAAAAGAAAGCA
1 GTGAAATCCAATTGTTTGGTTGGTGAGAAAATTTCACCAAAGAAGAAAAAGAAAGCA
2335 TATGTAGCGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23
Consensus pattern (57 bp):
GTGAAATCCAATTGTTTGGTTGGTGAGAAAATTTCACCAAAGAAGAAAAAGAAAGCA
Found at i:2672 original size:19 final size:19
Alignment explanation
Indices: 2627--2663 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2617 AATAATAATA
*
2627 AATAGATTAAAATTAAATG
1 AATAAATTAAAATTAAATG
2646 AATAAATTAAAATTAAAT
1 AATAAATTAAAATTAAAT
2664 TGTATAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAAATTAAAATTAAATG
Found at i:3021 original size:17 final size:17
Alignment explanation
Indices: 2994--3048 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2984 CTTTAGAATA
2994 TTTACTTTCCTTTTTACT
1 TTTA-TTTCCTTTTTACT
3012 TTTATTTCCTTTTGTA-T
1 TTTATTTCCTTTT-TACT
*
3029 TTTTTTTCCTGTTTT-CT
1 TTTATTTCCT-TTTTACT
3046 TTT
1 TTT
3049 TGTTTTATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.73
Consensus pattern (17 bp):
TTTATTTCCTTTTTACT
Found at i:5499 original size:2 final size:2
Alignment explanation
Indices: 5492--5560 Score: 58
Period size: 2 Copynumber: 34.5 Consensus size: 2
5482 TTATAGTAAT
5492 TA TA TA TA TA TA TA TA TA CTA -A TA CTA -A TA CTA -A TA CTA -A
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA -TA TA
5532 TA CTA -A 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 TA T
5561 TATTTGAAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
1 5 0.09
2 42 0.74
3 10 0.18
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5560 original size:12 final size:12
Alignment explanation
Indices: 5483--5557 Score: 70
Period size: 12 Copynumber: 6.3 Consensus size: 12
5473 TTTATCTAAT
*
5483 TATAGTAAT-TA
1 TATACTAATATA
5494 TATA-TATATATA
1 TATACTA-ATATA
5506 TATACTAATACTA
1 TATACTAATA-TA
5519 -ATACTAATACTA
1 TATACTAATA-TA
5531 -ATACTAATATA
1 TATACTAATATA
5542 TATA-TATATATA
1 TATACTA-ATATA
5554 TATA
1 TATA
5558 TATTATTTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.03
11 10 0.17
12 42 0.72
13 4 0.07
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (12 bp):
TATACTAATATA
Found at i:6441 original size:128 final size:130
Alignment explanation
Indices: 6298--6543 Score: 363
Period size: 129 Copynumber: 1.9 Consensus size: 130
6288 AAACTTTTAC
* * *
6298 TATAATTTTACTCAACTAAAAACTCTA-TTTTTATTTACTTAAATC-TAATATCTTTATAACTAC
1 TATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCGT-ATATCCTTATAACTAA
* *
6361 TTAATTTTTACCATTTTACTATTTTAATT-AAAAACTTATATATATTAGAATTTTTTAAATATTT
65 TTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTTAAATATTT
6425 T
130 T
* * *
6426 TATAGTTTTATTCAACTAAAAACTCTATTTTTTATTTAATTAAATCGTATATCCTTATACCTAAT
1 TATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCGTATATCCTTATAACTAAT
* * *
6491 TTATTTTTATCATTTTATTAATTTAATTAAAAAACTTAGATATATTAGAATTT
66 TAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTT
6544 GGATAAATGT
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
128 25 0.24
129 55 0.53
130 24 0.23
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.50
Consensus pattern (130 bp):
TATAATTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCGTATATCCTTATAACTAAT
TAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTTAAATATTTT
Found at i:10972 original size:26 final size:26
Alignment explanation
Indices: 10943--11010 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
10933 TTAGTAGAAT
10943 AAAACTGTAAAATTTATTTCTAACAA
1 AAAACTGTAAAATTTATTTCTAACAA
10969 AAAACTGTAAAATTTATTTCTAACAA
1 AAAACTGTAAAATTTATTTCTAACAA
10995 AAAACTGTAAAATTTA
1 AAAACTGTAAAATTTA
11011 AATAATGTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAACTGTAAAATTTATTTCTAACAA
Found at i:11170 original size:22 final size:22
Alignment explanation
Indices: 11145--11191 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11135 TTTTTAGTTG
*
11145 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
11167 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
11189 AGT
1 AGT
11192 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:11170 original size:93 final size:93
Alignment explanation
Indices: 11068--11252 Score: 300
Period size: 93 Copynumber: 2.0 Consensus size: 93
11058 ACTTTTTAAT
* *
11068 TAAATTAGTAATATCATAAAAATAAAATAGGTATAAGGATA-TGAGATTTAATTAAATAAAAATA
1 TAAAATAGTAAAATCATAAAAATAAAATAGGTATAAGGATATTG-GATTTAATTAAATAAAAATA
*
11132 GAGTTTTTAGTTGAGTAAAACTATAAAAG
65 GAGTTTTTAGTTGACTAAAACTATAAAAG
** *
11161 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTGGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCATAAAAATAAAATAGGTATAAGGATATTGGATTTAATTAAATAAAAATAG
11226 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAACTATAAAA
11253 ATTAAAACAA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
93 83 0.98
94 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (93 bp):
TAAAATAGTAAAATCATAAAAATAAAATAGGTATAAGGATATTGGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:11454 original size:2 final size:2
Alignment explanation
Indices: 11447--11477 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11437 ATGAACTGGT
11447 TA TA 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 TA TA T
11478 CAATTTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.