Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016187.1 Corchorus capsularis cultivar CVL-1 contig16208, 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: 15009
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:1437 original size:2 final size:2
Alignment explanation
Indices: 1430--1464 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1420 ATACCAGGTA
1430 AT AT AT AT AT 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 AT AT AT AT AT A
1465 ATACAATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2729 original size:57 final size:57
Alignment explanation
Indices: 2668--2786 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
2658 CAATAGTTTC
* * * * *
2668 TTTTTCT-ATTCTACTTTCATTTGTCTCATTGTTAATAGCAAATTCTTCAATAATCAT
1 TTTTTCTCATT-TACTTGCATATGGCTCATTGTTAATAACAAATTCTTCAACAATCAT
* * *
2725 TTTTTTTCCTTTACTTGCATATGGCTCATTGTTAATAACAAATTCTTCAACAATCTT
1 TTTTTCTCATTTACTTGCATATGGCTCATTGTTAATAACAAATTCTTCAACAATCAT
2782 TTTTT
1 TTTTT
2787 TTTATTTGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 51 0.96
58 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (57 bp):
TTTTTCTCATTTACTTGCATATGGCTCATTGTTAATAACAAATTCTTCAACAATCAT
Found at i:5376 original size:17 final size:18
Alignment explanation
Indices: 5347--5380 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5337 TTGAAGAAAA
5347 AGAAAAAGAAAAGGGAAG
1 AGAAAAAGAAAAGGGAAG
5365 AGAAAAAG-AAAGGGAA
1 AGAAAAAGAAAAGGGAA
5381 AAGGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAAAGGGAAG
Found at i:5387 original size:18 final size:18
Alignment explanation
Indices: 5344--5389 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5334 AATTTGAAGA
5344 AAAAGAAAAAGAAAAGGG
1 AAAAGAAAAAGAAAAGGG
*
5362 AAGAGAAAAAG-AAAGGG
1 AAAAGAAAAAGAAAAGGG
5379 AAAAGGAAAAA
1 AAAA-GAAAAA
5390 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGGG
Found at i:6162 original size:24 final size:24
Alignment explanation
Indices: 6135--6180 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
6125 CTTGGTTTTG
* *
6135 GATTGATTATCTTGATTTTACTAT
1 GATTGATGATCATGATTTTACTAT
* *
6159 GATTTATGATCATGGTTTTACT
1 GATTGATGATCATGATTTTACT
6181 GATTTTCCTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (24 bp):
GATTGATGATCATGATTTTACTAT
Found at i:6389 original size:14 final size:13
Alignment explanation
Indices: 6331--6390 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
6321 GATGGACTTA
*
6331 TTTTTATT-ACTG
1 TTTTTATTAAATG
*
6343 TTTTTAATAAATTG
1 TTTTTATTAAA-TG
*
6357 TTTTTTTATAAATG
1 TTTTTAT-TAAATG
6371 ATTTTTATTAAGATG
1 -TTTTTATTAA-ATG
6386 TTTTT
1 TTTTT
6391 GGTGAATTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 7 0.18
13 1 0.03
14 17 0.45
15 13 0.34
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (13 bp):
TTTTTATTAAATG
Found at i:11149 original size:20 final size:20
Alignment explanation
Indices: 11124--11181 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
11114 AATAAGTTTT
11124 TAAGGTTATTAAAAAATTTA
1 TAAGGTTATTAAAAAATTTA
* * *
11144 TAAGGTGACTAATAAATTTA
1 TAAGGTTATTAAAAAATTTA
* *
11164 AAATGTTATTGAAAAAAT
1 TAAGGTTATT-AAAAAAT
11182 AAAGTTAGTT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 23 0.79
21 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (20 bp):
TAAGGTTATTAAAAAATTTA
Found at i:11516 original size:16 final size:16
Alignment explanation
Indices: 11491--11521 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11481 TCTACAAATT
11491 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
11507 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
11522 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:12451 original size:2 final size:2
Alignment explanation
Indices: 12438--12478 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
12428 TGTCTAATCT
12438 TA TA TCA TA TA TA TA TA TA TA TGA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
12479 TTAAAACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12464 original size:17 final size:17
Alignment explanation
Indices: 12438--12476 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12428 TGTCTAATCT
12438 TATATCATATATATATA
1 TATATCATATATATATA
*
12455 TATATGATATATATATA
1 TATATCATATATATATA
12472 TATAT
1 TATAT
12477 ATTTAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
TATATCATATATATATA
Found at i:14240 original size:26 final size:27
Alignment explanation
Indices: 14184--14247 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
14174 ATATTGATGA
14184 AAGGTTACT-AAAATTTCTAAGAATGC
1 AAGGTTACTAAAAATTTCTAAGAATGC
* *
14210 AAGGTCACTAAAAATTTC-AAGAATGT
1 AAGGTTACTAAAAATTTCTAAGAATGC
*
14236 GAGGTTACTAAA
1 AAGGTTACTAAA
14248 TTTATGCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 25 0.76
27 8 0.24
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (27 bp):
AAGGTTACTAAAAATTTCTAAGAATGC
Found at i:14340 original size:43 final size:42
Alignment explanation
Indices: 14313--14398 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 42
14303 CATTAAATTA
14313 ACCAATAATAGTTTAAAAAAGTTTTAAAAATGTAAAGTAAAAT
1 ACCAATAATAGTTTAAAAAAGTTTTAAAAATG-AAAGTAAAAT
14356 ACCAATAATAGTTTAAAAAAGTTTTAAAAATGTAAAGTAAAAT
1 ACCAATAATAGTTTAAAAAAGTTTTAAAAATG-AAAGTAAAAT
14399 TTCCAAGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (42 bp):
ACCAATAATAGTTTAAAAAAGTTTTAAAAATGAAAGTAAAAT
Done.