Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022615.1 Corchorus olitorius cultivar O-4 contig22648, 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: 10604
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:3383 original size:24 final size:24
Alignment explanation
Indices: 3356--3406 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3346 AAAAAGAAAA
*
3356 AAATGAAATTTGGTAACTAAGGTT
1 AAATGAAATTTGGTAACTAAAGTT
** *
3380 AAATGGTATTTGGTAATTAAAGTT
1 AAATGAAATTTGGTAACTAAAGTT
3404 AAA
1 AAA
3407 AGAGTAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (24 bp):
AAATGAAATTTGGTAACTAAAGTT
Found at i:3425 original size:33 final size:31
Alignment explanation
Indices: 3379--3518 Score: 116
Period size: 33 Copynumber: 4.6 Consensus size: 31
3369 TAACTAAGGT
3379 TAAATGGTATTTGGTAATTAAAGTTAAAAGA
1 TAAATGGTATTTGGTAATTAAAGTTAAAAGA
3410 GTAAACTGGTATTTGGT-ATTAAAGGTTAAAAGAA
1 -TAAA-TGGTATTTGGTAATTAAA-GTTAAAAG-A
* ** *
3444 AAAATGAAATTTGGTAACTAAAG-T------
1 TAAATGGTATTTGGTAATTAAAGTTAAAAGA
* *
3468 TAAATGGTATTTGGTAATTAAAGTAAAAATA
1 TAAATGGTATTTGGTAATTAAAGTTAAAAGA
3499 GTAAATTGGTATTTGGTAAT
1 -TAAA-TGGTATTTGGTAAT
3519 CAAGGTAAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 25
0.72 0.08 0.21
Matches are distributed among these distances:
24 19 0.22
31 1 0.01
32 24 0.28
33 41 0.48
34 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.20, T:0.35
Consensus pattern (31 bp):
TAAATGGTATTTGGTAATTAAAGTTAAAAGA
Found at i:3456 original size:32 final size:32
Alignment explanation
Indices: 3387--3471 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
3377 GTTAAATGGT
* * **
3387 ATTTGGTAATTAAAGTTAAAAGAGTAAACTGGT
1 ATTTGGT-ATTAAAGTTAAAAGAGAAAAATGAA
3420 ATTTGGTATTAAAGGTTAAAAGA-AAAAATGAA
1 ATTTGGTATTAAA-GTTAAAAGAGAAAAATGAA
*
3452 ATTTGGTAACTAAAGTTAAA
1 ATTTGGT-ATTAAAGTTAAA
3472 TGGTATTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 24 0.53
33 21 0.47
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.32
Consensus pattern (32 bp):
ATTTGGTATTAAAGTTAAAAGAGAAAAATGAA
Found at i:3472 original size:24 final size:24
Alignment explanation
Indices: 3445--3491 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3435 TTAAAAGAAA
3445 AAATGAAATTTGGTAACTAAAGTT
1 AAATGAAATTTGGTAACTAAAGTT
** *
3469 AAATGGTATTTGGTAATTAAAGT
1 AAATGAAATTTGGTAACTAAAGT
3492 AAAAATAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (24 bp):
AAATGAAATTTGGTAACTAAAGTT
Found at i:3485 original size:89 final size:90
Alignment explanation
Indices: 3315--3543 Score: 388
Period size: 89 Copynumber: 2.6 Consensus size: 90
3305 AGTAAAGAGT
*
3315 AAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGAAATTTGGTAACTAAGGTT
1 AAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGAAATTTGGTAACTAAAGTT
*
3380 AAATGGTATTTGGTAATTAAAGTTA
66 AAATGGTATTTGGTAATTAAAGTAA
* * * *
3405 AAAGAGTAAACTGGTATTTGGTATTAAAGGTTAAAAG-AAAAAATGAAATTTGGTAACTAAAGTT
1 AAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGAAATTTGGTAACTAAAGTT
3469 AAATGGTATTTGGTAATTAAAGTAA
66 AAATGGTATTTGGTAATTAAAGTAA
*
3494 AAATAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGAAAT
1 AAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGAAAT
3544 GTTGCAATTA
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
89 82 0.65
90 45 0.35
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (90 bp):
AAAGAGTAAATTGGTATTTGGTAATCAAGGTAAAAAGAAAAAAATGAAATTTGGTAACTAAAGTT
AAATGGTATTTGGTAATTAAAGTAA
Found at i:3527 original size:33 final size:32
Alignment explanation
Indices: 3468--3529 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
3458 TAACTAAAGT
*
3468 TAAATGGTATTTGGTAATTAAAGTAAAAATAG
1 TAAATGGTATTTGGTAATCAAAGTAAAAATAG
*
3500 TAAATTGGTATTTGGTAATCAAGGTAAAAA
1 TAAA-TGGTATTTGGTAATCAAAGTAAAAA
3530 GAAAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.34
Consensus pattern (32 bp):
TAAATGGTATTTGGTAATCAAAGTAAAAATAG
Found at i:3611 original size:16 final size:17
Alignment explanation
Indices: 3558--3611 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
3548 CAATTAAAAC
*
3558 AAAAAGAGTAATATGGT
1 AAAAAGAGTAAAATGGT
*
3575 AAAAAGAGATTAAA--GT
1 AAAAAGAG-TAAAATGGT
3591 AAAAAGAGTAAAATGGT
1 AAAAAGAGTAAAATGGT
3608 AAAA
1 AAAA
3612 CGAAATTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 14 0.45
18 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (17 bp):
AAAAAGAGTAAAATGGT
Found at i:3673 original size:33 final size:33
Alignment explanation
Indices: 3632--3720 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
3622 TAACTAAAGT
* *
3632 TAAA-TGGTATTCGGTAATTAAAATAAAAAGAG
1 TAAATTGGTATTTGGTAATTAAAATAAAAACAG
* * *
3664 TAAATTGGTATTTGGTAAATATAGTAAAAACAG
1 TAAATTGGTATTTGGTAATTAAAATAAAAACAG
*
3697 TAAAATTGGTATTTGCTAATTAAA
1 T-AAATTGGTATTTGGTAATTAAA
3721 GTAGAAATTG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 4 0.09
33 24 0.51
34 19 0.40
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (33 bp):
TAAATTGGTATTTGGTAATTAAAATAAAAACAG
Found at i:4312 original size:16 final size:16
Alignment explanation
Indices: 4291--4331 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
4281 CGACCGAACT
4291 CGAACCC-AAAATTACC
1 CGAACCCGAAAA-TACC
4307 CGAACCCGAAAATACC
1 CGAACCCGAAAATACC
4323 CGAACCCGA
1 CGAACCCGA
4332 GGCAGCCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.41, C:0.39, G:0.12, T:0.07
Consensus pattern (16 bp):
CGAACCCGAAAATACC
Found at i:4344 original size:6 final size:6
Alignment explanation
Indices: 4335--4393 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
4325 AACCCGAGGC
* * * *
4335 AGCCCG AGCCCG AACCTG A-CCCG AGACCG AGCCCG ATCCCG A-CCCG
1 AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG AGCCCG
*
4381 AGCCCG AACCCG A
1 AGCCCG AGCCCG A
4394 AATAATTTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 9 0.20
6 35 0.80
ACGTcount: A:0.24, C:0.47, G:0.25, T:0.03
Consensus pattern (6 bp):
AGCCCG
Found at i:4368 original size:23 final size:23
Alignment explanation
Indices: 4321--4394 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
4311 CCCGAAAATA
** *
4321 CCCGAACCCGAGGC-AGCCCGAG
1 CCCGAACCCGACCCGAGACCGAG
*
4343 CCCGAACCTGACCCGAGACCGAG
1 CCCGAACCCGACCCGAGACCGAG
* * *
4366 CCCGATCCCGACCCGAGCCCGAA
1 CCCGAACCCGACCCGAGACCGAG
4389 CCCGAA
1 CCCGAA
4395 ATAATTTGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 11 0.26
23 31 0.74
ACGTcount: A:0.24, C:0.47, G:0.26, T:0.03
Consensus pattern (23 bp):
CCCGAACCCGACCCGAGACCGAG
Found at i:4381 original size:17 final size:17
Alignment explanation
Indices: 4361--4393 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4351 TGACCCGAGA
*
4361 CCGAGCCCGATCCCGAC
1 CCGAGCCCGAACCCGAC
4378 CCGAGCCCGAACCCGA
1 CCGAGCCCGAACCCGA
4394 AATAATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.24, T:0.03
Consensus pattern (17 bp):
CCGAGCCCGAACCCGAC
Found at i:4501 original size:26 final size:26
Alignment explanation
Indices: 4463--4513 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
4453 ATATTTCCTT
4463 TTAATATTAAATAAAACTATTATATAAA
1 TTAATATTAAATAAAA-T-TTATATAAA
4491 TTAATA-T-AATAAAATTTATATAA
1 TTAATATTAAATAAAATTTATATAA
4514 TAATGATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.35
25 1 0.04
26 7 0.30
27 1 0.04
28 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAATATTAAATAAAATTTATATAAA
Found at i:4602 original size:2 final size:2
Alignment explanation
Indices: 4569--4593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4559 AAACTACTAA
4569 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4594 ACTTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4901 original size:31 final size:31
Alignment explanation
Indices: 4830--4901 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
4820 GTCTATCAGC
*
4830 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
4861 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
4891 GTTTTAATTTG
1 -TTTTAATTTG
4902 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:5190 original size:13 final size:12
Alignment explanation
Indices: 5154--5200 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
5144 TCAATCTTTA
*
5154 TATATATTGATAA
1 TATATATT-ATAT
*
5167 TA-ATGTTATAT
1 TATATATTATAT
5178 TATATTATTATAT
1 TATA-TATTATAT
5191 TATATATTAT
1 TATATATTAT
5201 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5381 original size:16 final size:16
Alignment explanation
Indices: 5359--5462 Score: 106
Period size: 16 Copynumber: 6.6 Consensus size: 16
5349 ACCCGAGACT
5359 GAACCCGAAAATACCC
1 GAACCCGAAAATACCC
* *
5375 AAACCCG-ACATAACCC
1 GAACCCGAAAAT-ACCC
*
5391 GAGCCCGAAAATACCC
1 GAACCCGAAAATACCC
**
5407 GAACCCG-ACTTAACCC
1 GAACCCGAAAAT-ACCC
*
5423 GAGCCCGAAAATACCC
1 GAACCCGAAAATACCC
*
5439 GAACCCG-AAGTACCC
1 GAACCCGAAAATACCC
5454 GAACCCGAA
1 GAACCCGAA
5463 CCCGCCCAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
15 19 0.27
16 46 0.66
17 5 0.07
ACGTcount: A:0.38, C:0.39, G:0.15, T:0.07
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:5400 original size:32 final size:32
Alignment explanation
Indices: 5362--5462 Score: 152
Period size: 32 Copynumber: 3.2 Consensus size: 32
5352 CGAGACTGAA
*
5362 CCCGAAAATACCCAAACCCGACATAACCCGAG
1 CCCGAAAATACCCGAACCCGACATAACCCGAG
*
5394 CCCGAAAATACCCGAACCCGACTTAACCCGAG
1 CCCGAAAATACCCGAACCCGACATAACCCGAG
*
5426 CCCGAAAATACCCGAACCCGA-AGT-ACCCGAA
1 CCCGAAAATACCCGAACCCGACA-TAACCCGAG
5457 CCCGAA
1 CCCGAA
5463 CCCGCCCAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 12 0.19
32 52 0.81
ACGTcount: A:0.38, C:0.41, G:0.15, T:0.07
Consensus pattern (32 bp):
CCCGAAAATACCCGAACCCGACATAACCCGAG
Done.