Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017408.1 Corchorus olitorius cultivar O-4 contig17441, 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: 9107
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:205 original size:10 final size:10
Alignment explanation
Indices: 180--212 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
170 GTTCTAAAAC
180 TTTTCTTTTA
1 TTTTCTTTTA
190 -TTTCTTTTA
1 TTTTCTTTTA
199 TTTTCTTTTTA
1 TTTTC-TTTTA
210 TTT
1 TTT
213 ATTTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 4 0.19
11 8 0.38
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:223 original size:20 final size:20
Alignment explanation
Indices: 180--221 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
170 GTTCTAAAAC
*
180 TTTTC-TTTTATTTCTTTTA
1 TTTTCTTTTTATTTATTTTA
199 TTTTCTTTTTATTTA-TTTA
1 TTTTCTTTTTATTTATTTTA
218 TTTT
1 TTTT
222 TCCTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTCTTTTTATTTATTTTA
Found at i:228 original size:20 final size:20
Alignment explanation
Indices: 180--228 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
170 GTTCTAAAAC
*
180 TTTT-CTTTTATTTCTTTTA
1 TTTTCCTTTTATTTATTTTA
*
199 TTTTCTTTTTATTTA-TTTA
1 TTTTCCTTTTATTTATTTTA
218 TTTTTCCTTTT
1 -TTTTCCTTTT
229 CTTTTTCCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCCTTTTATTTATTTTA
Found at i:387 original size:6 final size:6
Alignment explanation
Indices: 296--384 Score: 133
Period size: 6 Copynumber: 14.8 Consensus size: 6
286 TTTTTTCTTT
296 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * * *
344 TTATTA TTATTT TTATTT TTATTT TTATTT TTATTT TTATT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATT
385 TTTTTTGGCT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTATTA
Found at i:453 original size:35 final size:35
Alignment explanation
Indices: 414--506 Score: 141
Period size: 35 Copynumber: 2.7 Consensus size: 35
404 TGGGGCCCAA
*
414 GCCTGGCCTAGGCGCTGGGCCGCGTTGGCCAGCAC
1 GCCTGGCCTAGGCGCTGGGCCGCGCTGGCCAGCAC
* * *
449 GCCTGGCCTGGGCGCTGGGCCGCGCTGGCCCGCGC
1 GCCTGGCCTAGGCGCTGGGCCGCGCTGGCCAGCAC
*
484 GCCTGGCCTAGGCGTTGGGCCGC
1 GCCTGGCCTAGGCGCTGGGCCGC
507 ACCAGGCCGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.04, C:0.39, G:0.43, T:0.14
Consensus pattern (35 bp):
GCCTGGCCTAGGCGCTGGGCCGCGCTGGCCAGCAC
Found at i:2495 original size:29 final size:29
Alignment explanation
Indices: 2462--2517 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2452 ACAAACTAAA
* *
2462 GAATTATGTAACACGTTTATTGGTAGATG
1 GAATTATGTAACACATATATTGGTAGATG
*
2491 GAATTATGTAGCACATATATTGGTAGA
1 GAATTATGTAACACATATATTGGTAGA
2518 CAGAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (29 bp):
GAATTATGTAACACATATATTGGTAGATG
Found at i:2523 original size:29 final size:29
Alignment explanation
Indices: 2461--2524 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2451 AACAAACTAA
* * *
2461 AGAATTATGTAACACGTTTATTGGTAGAT
1 AGAATTATGTAACACATATATTGGTAGAC
* *
2490 GGAATTATGTAGCACATATATTGGTAGAC
1 AGAATTATGTAACACATATATTGGTAGAC
2519 AGAATT
1 AGAATT
2525 TTAATGATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (29 bp):
AGAATTATGTAACACATATATTGGTAGAC
Found at i:4095 original size:30 final size:30
Alignment explanation
Indices: 4061--4384 Score: 459
Period size: 30 Copynumber: 10.7 Consensus size: 30
4051 ACTCTTTAAA
4061 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
4091 TGACACCAGAAGTTGTCATGGTCTTGCAAA
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
4121 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
4151 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
4181 TGACACCAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
4211 TGACACCAGAAGCTGTCATGGTTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
4241 TGACACCAGAAGCTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * *
4271 TGACACCAAAAGCTGTCATGATGTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
4301 TGACACCATAAGTTGTCATGATCATGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* * * *
4331 TGACACCATAAGTTGTCATAATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TCT-TGCAAT
4363 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
4385 AAATTTCCAA
Statistics
Matches: 274, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
30 248 0.91
31 2 0.01
32 24 0.09
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:4413 original size:33 final size:33
Alignment explanation
Indices: 4371--4476 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 33
4361 ATTGACACCA
*
4371 GAAGTTGTCATGATAAATTTCCAATAGACACTT
1 GAAGATGTCATGATAAATTTCCAATAGACACTT
* ** * * **
4404 GAAAATGTCAT-A-ATTTTATTCAATTGACACCA
1 GAAGATGTCATGATAAATT-TCCAATAGACACTT
*
4436 GAAGTTGTCATGATAAATTTCCAATAGACACTT
1 GAAGATGTCATGATAAATTTCCAATAGACACTT
4469 GAAGATGT
1 GAAGATGT
4477 TGTAGACACC
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
31 3 0.06
32 20 0.38
33 27 0.51
34 3 0.06
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (33 bp):
GAAGATGTCATGATAAATTTCCAATAGACACTT
Found at i:4428 original size:65 final size:65
Alignment explanation
Indices: 4344--4476 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
4334 CACCATAAGT
4344 TGTCATAATTTTATTCAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAAA
1 TGTCATAATTTTATTCAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAAA
*
4409 TGTCATAATTTTATTCAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAGA
1 TGTCATAATTTTATTCAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAAA
4474 TGT
1 TGT
4477 TGTAGACACC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (65 bp):
TGTCATAATTTTATTCAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACACTTGAAAA
Found at i:4616 original size:27 final size:28
Alignment explanation
Indices: 4544--4622 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
4534 GCATTATGGT
* * *
4544 CATCC-GGGGGTATTTTAGCCATTTGCA
1 CATCCAGGGGGCATTTTGGTCATTTGCA
4571 CATCCAGGGGGCATTTTGGTCATTTGCA
1 CATCCAGGGGGCATTTTGGTCATTTGCA
*
4599 CATTCA-GGGGCATTTTGGTCATTT
1 CATCCAGGGGGCATTTTGGTCATTT
4623 TAAGTTCACA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
27 23 0.49
28 24 0.51
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (28 bp):
CATCCAGGGGGCATTTTGGTCATTTGCA
Done.