Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023487.1 Corchorus olitorius cultivar O-4 contig23520, 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: 17948
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:5586 original size:2 final size:2
Alignment explanation
Indices: 5575--5649 Score: 59
Period size: 2 Copynumber: 39.0 Consensus size: 2
5565 ATCGACCGTT
* *
5575 TA TA TA -A TA TA TA TA TA TA TA TA -A TA TA TCA GA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * *
5616 TA TA -A T- TC TT TA TA TA TA TA AA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5650 ATAATTTATA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
1 4 0.07
2 53 0.91
3 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5658 original size:30 final size:31
Alignment explanation
Indices: 5598--5659 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
5588 TATATATATA
* **
5598 ATATATCAGATATATTTATATAATTCTTTAT
1 ATATATCAAATATATTTATATAATAATTTAT
5629 ATATAT-AAATATATATT-TATAATAATTTAT
1 ATATATCAAATATAT-TTATATAATAATTTAT
5659 A
1 A
5660 AAATTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (31 bp):
ATATATCAAATATATTTATATAATAATTTAT
Found at i:5659 original size:16 final size:15
Alignment explanation
Indices: 5608--5659 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
5598 ATATATCAGA
5608 TATATTTATATAATT
1 TATATTTATATAATT
* * *
5623 CTTTATATATATAAATA
1 -TATATTTATAT-AATT
5640 TATATTTATAATAATT
1 TATATTTAT-ATAATT
5656 TATA
1 TATA
5660 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTTATATAATT
Found at i:9494 original size:14 final size:14
Alignment explanation
Indices: 9477--9503 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9467 GCTTTGGACT
9477 TTGGTAGTTGGTAC
1 TTGGTAGTTGGTAC
9491 TTGGTAGTTGGTA
1 TTGGTAGTTGGTA
9504 AAAATCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.37, T:0.44
Consensus pattern (14 bp):
TTGGTAGTTGGTAC
Found at i:11318 original size:2 final size:2
Alignment explanation
Indices: 11313--11357 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
11303 TATATATATA
11313 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
11355 TG T
1 TG T
11358 ATTTATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:12345 original size:61 final size:62
Alignment explanation
Indices: 12280--12399 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 62
12270 TGCACGTGAC
* * *
12280 CCAATATGTTTAAATTAAATTAAAATTAAAATCTTAAGTATATTACTAATTTTA-CGTGCAA
1 CCAATATGTTTAAATTAAATGAAAATTAAAATCTTAAGCATACTACTAATTTTATCGTGCAA
*
12341 CCAATATGTTTAAATTAAATGAAAATTAAAATTTTAAGCATACTACTAATTTTATCGTG
1 CCAATATGTTTAAATTAAATGAAAATTAAAATCTTAAGCATACTACTAATTTTATCGTG
12400 AAGAATCTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
61 50 0.93
62 4 0.07
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (62 bp):
CCAATATGTTTAAATTAAATGAAAATTAAAATCTTAAGCATACTACTAATTTTATCGTGCAA
Found at i:14457 original size:124 final size:123
Alignment explanation
Indices: 14214--14460 Score: 293
Period size: 124 Copynumber: 2.0 Consensus size: 123
14204 CCTTTTAAAT
*
14214 TAAAATAGTAAAAATAAAATAATTATAAAAATATTTAATTTAATTAAATGAAAATAGAGTTTTTA
1 TAAAATAGTAAAAATAAAATAATTATAAAAATATTTAATTTAATTAAATAAAAATAGAGTTTTTA
* *** ** *
14279 GTAGAATAAAATTTTATATTAAATTTTTTTAATATATCCAAGTTTTTAATGAAAAATAG
66 GTAGAATAAAATTATATATT-AATTTAAGTAATATATCCAAGAATATAATGAAAAATAG
* * *
14338 TAAAATGGTAAAAATAAAGTAATTATAAAGATA-TTAGATTTAATTAAATAAAAATAGAGTTTTT
1 TAAAATAGTAAAAATAAAATAATTATAAAAATATTTA-ATTTAATTAAATAAAAATAGAGTTTTT
* ** *
14402 AGTAGAATAAAATTATA-ATT-GTTTAAGTAATAGTATTTAAGAAATATATTCGAAAAATA
65 AGTAGAATAAAATTATATATTAATTTAAGTAATA-TATCCAAG-AATATAAT-GAAAAATA
14461 AGGATATAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
121 8 0.08
122 6 0.06
123 10 0.10
124 80 0.77
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (123 bp):
TAAAATAGTAAAAATAAAATAATTATAAAAATATTTAATTTAATTAAATAAAAATAGAGTTTTTA
GTAGAATAAAATTATATATTAATTTAAGTAATATATCCAAGAATATAATGAAAAATAG
Found at i:15257 original size:13 final size:13
Alignment explanation
Indices: 15241--15265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15231 CATAAACAAC
15241 CCTAATAATTTCT
1 CCTAATAATTTCT
15254 CCTAATAATTTC
1 CCTAATAATTTC
15266 AAATTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (13 bp):
CCTAATAATTTCT
Done.