Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014029.1 Corchorus olitorius cultivar O-4 contig14062, 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: 7553
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:936 original size:51 final size:50
Alignment explanation
Indices: 835--936 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
825 GTTCTTCGTA
* **
835 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
885 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
936 T
1 T
937 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:1533 original size:41 final size:42
Alignment explanation
Indices: 1476--1556 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 42
1466 CAATTAATTT
**
1476 TAGCTTTATTTTGATGAATT-TTTAGAGATGGAGTAGAATAA
1 TAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAGAATAA
1517 TAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAGAAT
1 TAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAGAAT
1557 TTAGGTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 20 0.54
42 17 0.46
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.40
Consensus pattern (42 bp):
TAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAGAATAA
Found at i:4576 original size:12 final size:12
Alignment explanation
Indices: 4552--4584 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
4542 TATAAGACTT
4552 TAACATAATATAA
1 TAACAT-ATATAA
4565 TAACATATATAA
1 TAACATATATAA
4577 TAACATAT
1 TAACATAT
4585 CTATATCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (12 bp):
TAACATATATAA
Found at i:4967 original size:30 final size:27
Alignment explanation
Indices: 4882--4964 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
4872 GTTAATTTAG
4882 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
4909 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
*
4939 ACTTATTATTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
4965 TTAGTGGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:5442 original size:9 final size:9
Alignment explanation
Indices: 5414--5495 Score: 60
Period size: 9 Copynumber: 8.6 Consensus size: 9
5404 TAATTTAGAC
*
5414 ATTATTATT
1 ATTATAATT
*
5423 ATAATAATT
1 ATTATAATT
5432 ATTA-AACTT
1 ATTATAA-TT
5441 ATTATTAATGGT
1 ATTA-TAAT--T
5453 ATTATAATT
1 ATTATAATT
*
5462 ATTAAACTTATT
1 ATT--A-TAATT
5474 ATTATAATT
1 ATTATAATT
5483 ATTAT-ATT
1 ATTATAATT
5491 ATTAT
1 ATTAT
5496 TAGTGGTATG
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
8 10 0.17
9 29 0.48
10 2 0.03
11 7 0.12
12 12 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (9 bp):
ATTATAATT
Found at i:5444 original size:12 final size:11
Alignment explanation
Indices: 5414--5487 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 11
5404 TAATTTAGAC
5414 ATTATTATTATA
1 ATTATTATTA-A
*
5426 ATAATTATTAA
1 ATTATTATTAA
5437 ACTTATTATT-A
1 A-TTATTATTAA
5448 ATGGTATTA-T-A
1 AT--TATTATTAA
5459 ATTATTA--AA
1 ATTATTATTAA
*
5468 CTTATTATTATA
1 ATTATTATTA-A
5480 ATTATTAT
1 ATTATTAT
5488 ATTATTATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
9 12 0.24
10 1 0.02
11 9 0.18
12 29 0.57
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
ATTATTATTAA
Found at i:5486 original size:30 final size:30
Alignment explanation
Indices: 5414--5494 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
5404 TAATTTAGAC
* *
5414 ATTATTATTATAATAATTATTAAACTTATT
1 ATTATAATTATTATAATTATTAAACTTATT
5444 A-T-TAATGGTATTATAATTATTAAACTTATT
1 ATTATAAT--TATTATAATTATTAAACTTATT
5474 ATTATAATTATTAT-ATTATTA
1 ATTATAATTATTATAATTATTA
5495 TTAGTGGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
28 3 0.07
29 8 0.18
30 29 0.64
31 1 0.02
32 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (30 bp):
ATTATAATTATTATAATTATTAAACTTATT
Found at i:5838 original size:531 final size:527
Alignment explanation
Indices: 4613--5729 Score: 1504
Period size: 531 Copynumber: 2.1 Consensus size: 527
4603 TAAGTCTAAA
* *** * ** ** * *
4613 CTTCAAAAACCTTGACCTGAAATATCTAAAATAGTCTTTTTAATTTTAAAATTTTAGTTATATTT
1 CTTCAAAAACCTAGAAAAGAAATAACTAAAATAG-CTTTTTAAGGTTAAAA-TAAAGTGACATTT
* * * * * ** *
4678 TTAAGGGTTAATATGTAATCTATCCAATCAGATTTTATTTCCATATTAAAAAAGTTTAAAATAAT
64 TTAAGCGTTAATATGTAATC-ATCCAATAAGATTTCAATTCCAAATTAAAAAAGTCAAAAAAAAT
** *** * *
4743 AACAATTATTTTTATATTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATA
128 AACAAGGAAAATAAGATTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATA
4808 TAATTACGTTTTCCTTTCCATATCACAAAAGTCCAATCTAATATAATACTAACAATTTTTTCACG
193 TAATTACGTTTTCCTTTCCATATCACAAAAGTCCAATCTAATATAATACTAACAATTTTTTCACG
*
4873 TTAATTTAGACTTATTATTATTATAATAATTATTAAACTTATTATTAGTGGTATTATAATTATTA
258 TTAATTTAGAC-TATTATTATTATAATAATTATTAAACTTATTATTAATGGTATTATAATTATTA
4938 AACTTATTATTATAATAATAATTATTATTAGTGGTATGTATTTTTTTCCTTCATCTTTTCTTAGA
322 AACTTATTATTATAATAATAATTATTATTAGTGGTATGTATTTTTTTCCTTCATCTTTTCTTAGA
5003 TAATTTAGACTATTTCAAAGTTGAGTATATAATATTTTTTTCTAAAAAAACAAATAAAAACAAAA
387 TAATTTAGACTATTTCAAAGTTGAGTATATAATATTTTTTTCTAAAAAAACAAATAAAAACAAAA
5068 TCATATACTTCGACTTAATATGTAGCAAAAAAATACTTATCTTTTTGACCAAAAAAAAACTTCAA
452 TCATATACTTCGACTTAATATGTAGCAAAAAAATACTTATCTTTTTGACCAAAAAAAAACTTCAA
5133 CTTAATTGCCT
517 CTTAATTGCCT
* *** * ** ** * *
5144 CTTCAAAAACCTTGACCTGAAATATCTAAAATAGCCTTTTTAATTTTAAAATTTTAGTTATATTT
1 CTTCAAAAACCTAGAAAAGAAATAACTAAAATAG-CTTTTTAAGGTTAAAA-TAAAGTGACATTT
* * * * * * * *
5209 TTAAGGGTTAATATGTAATCTATCCAATCAGATTTTATTTCCATATTTAAAAAGTCTAAAATAAT
64 TTAAGCGTTAATATGTAATC-ATCCAATAAGATTTCAATTCCAAATTAAAAAAGTCAAAAAAAAT
** *** * *
5274 AACAATTATTTTTATATTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATA
128 AACAAGGAAAATAAGATTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATA
5339 TAATTACGTTTTCCTTTCCATATCACAAAAGTCCAATCT-ATATAATACTAACAATTTTTTCACG
193 TAATTACGTTTTCCTTTCCATATCACAAAAGTCCAATCTAATATAATACTAACAATTTTTTCACG
5403 TTAATTTAGAC-ATTATTATTATAATAATTATTAAACTTATTATTAATGGTATTATAATTATTAA
258 TTAATTTAGACTATTATTATTATAATAATTATTAAACTTATTATTAATGGTATTATAATTATTAA
* *
5467 ACTTATTATTATAATTATTATATTATTATTAGTGGTATGTATTTTTTTTCTTCATCTTTTCTTAG
323 ACTTATTATTATAA-TAATA-ATTATTATTAGTGGTATGTATTTTTTTCCTTCATCTTTTCTTAG
*
5532 ATAATTTAGACTATTTCAAAGTTGAGTA-ATAAT-TTTTTTTCTAAAAAAACAAATAAAAAATAA
386 ATAATTTAGACTATTTCAAAGTTGAGTATATAATATTTTTTTCTAAAAAAACAAAT-AAAAACAA
5595 AATCATATACTTCGACTTAATATGTAGCAAAAAAATACTTATC-TTTTGACC-AAAAAAAACTTC
450 AATCATATACTTCGACTTAATATGTAGCAAAAAAATACTTATCTTTTTGACCAAAAAAAAACTTC
5658 AACTTAATTGCCT
515 AACTTAATTGCCT
* * *
5671 CTTCAAGAA-C-AGAAAAAGAAA-AAC-ACATATAG-TTTTTCAGGTTAAAA-AAAG-GACATTT
1 CTTCAAAAACCTAG-AAAAGAAATAACTA-AAATAGCTTTTTAAGGTTAAAATAAAGTGACATTT
5729 T
64 T
5730 CCTCTTTAAA
Statistics
Matches: 560, Mismatches: 21, Indels: 21
0.93 0.03 0.03
Matches are distributed among these distances:
520 6 0.01
521 2 0.00
523 12 0.02
524 1 0.00
525 8 0.01
526 6 0.01
527 33 0.06
528 95 0.17
529 59 0.11
530 107 0.19
531 231 0.41
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (527 bp):
CTTCAAAAACCTAGAAAAGAAATAACTAAAATAGCTTTTTAAGGTTAAAATAAAGTGACATTTTT
AAGCGTTAATATGTAATCATCCAATAAGATTTCAATTCCAAATTAAAAAAGTCAAAAAAAATAAC
AAGGAAAATAAGATTAAACAACTTATTATTATAATTATTAAAATTATTATTAGTTATATATATAA
TTACGTTTTCCTTTCCATATCACAAAAGTCCAATCTAATATAATACTAACAATTTTTTCACGTTA
ATTTAGACTATTATTATTATAATAATTATTAAACTTATTATTAATGGTATTATAATTATTAAACT
TATTATTATAATAATAATTATTATTAGTGGTATGTATTTTTTTCCTTCATCTTTTCTTAGATAAT
TTAGACTATTTCAAAGTTGAGTATATAATATTTTTTTCTAAAAAAACAAATAAAAACAAAATCAT
ATACTTCGACTTAATATGTAGCAAAAAAATACTTATCTTTTTGACCAAAAAAAAACTTCAACTTA
ATTGCCT
Done.