Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013827.1 Corchorus olitorius cultivar O-4 contig13860, 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: 28386
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1014 original size:416 final size:424
Alignment explanation
Indices: 221--1128 Score: 1117
Period size: 416 Copynumber: 2.1 Consensus size: 424
211 GTCATTTACA
* * * * * *
221 AATCGATTTAACACTTTAG--GTA-TTTTTTTTCTGTTGGTCCGATTAAGGTGACTCAGGTGTCT
1 AATCGATTTAACACTTAAGTTTTATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAGGTGCCT
*
283 ATTAAAAGATAATTTCATGATTTACAACTTGCATGAAGGACTCAAAAGCCAATTTTAATGTTTCA
66 ATTAAAAGATAATTTCATGATCTACAACTTGCATGAAGGACTCAAAAGCCAATTTTAATGTTTCA
** * *
348 ATTCAAAAAAATGATTCTGAAATTTGGTGATTTTGATTGCCGATCTATTAAATATATCATATAAT
131 ATTCAAAAAAA-GATTC----ATTT-GCCA-TTCGATTGCCGATCTATT--ATATACCATATAAT
* * *
413 TTCGATCCACATGTCCAATTAATGTTATTGAAGTGTCACTTAAAAGGCTATTGCATGATCTACGA
187 TTCGATCCACATGTCCAATTAAAGTTATTGAAGTATCACTTAAAAAGCTATTGCATGATCTACGA
* * * *
478 CTTTCATGAAGGACCCGAAGGCTAAATTTGATCTACGAGTATCATTAAGGGTTCAAAATGGAATT
252 CTTTCATGAAGGACCCAAAGCCTAAATTTGATCTACGAG-A-CATGAAGGGTTCAAAAGGGAATT
*
543 TTTATGTTTCAAGATCTCCATCAACAAACATTTTCTTATTTAGATTATTTATCAAATAACCCTCA
315 TTTATGTTTCAAGATCTACATCAACAAACATTTTCTTATTTAGATTATTTATCAAATAACCCTCA
*
608 TATTTTTCTAC-TTATACTACTTAGTCCTTTACTAATTCTATCTT
380 TATTTTTCTACTTTATACTACTTAGTCCTTTACAAATTCTATCTT
652 AATCGATTTAACACTTAAGTTTTATTTTTTATTTCTATTTGTCCGATTAAGGTGATTCAGGT-CC
1 AATCGATTTAACACTTAAGTTTTATTTTTT-TTTCTATTTGTCCGATTAAGGTGATTCAGGTGCC
* * * * *
716 TATTAAAAGGTAATTTCATGATCTCCAACTTTCATGAAGGACTCAAAAGTCAATTTTTATGTTTC
65 TATTAAAAGATAATTTCATGATCTACAACTTGCATGAAGGACTCAAAAGCCAATTTTAATGTTTC
* * *
781 AATTC-AAAAAA-ATTC-TTT-CCA-TCGATTGTCGCTCTATT-TGATACCATATAATTTTGGAT
130 AATTCAAAAAAAGATTCATTTGCCATTCGATTGCCGATCTATTAT-ATACCATATAA-TTTCGAT
* * * * * *
840 CCACATGTCCGATTAAAGTTATTTAAGTATCAGTTAAAAAGTTATTGCGTTATCTACGACTTTCA
193 CCACATGTCCAATTAAAGTTATTGAAGTATCACTTAAAAAGCTATTGCATGATCTACGACTTTCA
*
905 TGAAGGACCCCAAAGCCT-AATTTGATCTAC-A-A-ATGAAGGGTTCAAAAGGGAGTTTTTATGT
258 TGAAGGA-CCCAAAGCCTAAATTTGATCTACGAGACATGAAGGGTTCAAAAGGGAATTTTTATGT
* * * *
966 TTTAAGATCTATATCAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATATTTTT
322 TTCAAGATCTACATCAACAAACATTTTCTTATTTAGATTATTTATCAAATAACCCTCATATTTTT
* *
1031 CTACTTTATACTATTTAGTCCTTTACAAATTCTATTTT
387 CTACTTTATACTACTTAGTCCTTTACAAATTCTATCTT
* * * * * * * *
1069 ACTCAATTTAACGCCTCAGTTTTTTTTTCTTTGTTCTATTTGTCCAATTAAGGTTATTCA
1 AATCGATTTAACACTTAAGTTTTATTTT-TTT-TTCTATTTGTCCGATTAAGGTGATTCA
1129 TGAAGAACTC
Statistics
Matches: 418, Mismatches: 49, Indels: 33
0.84 0.10 0.07
Matches are distributed among these distances:
416 90 0.22
417 53 0.13
418 28 0.07
419 1 0.00
420 11 0.03
421 81 0.19
422 22 0.05
424 1 0.00
426 3 0.01
431 22 0.05
433 8 0.02
434 70 0.17
435 28 0.07
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (424 bp):
AATCGATTTAACACTTAAGTTTTATTTTTTTTTCTATTTGTCCGATTAAGGTGATTCAGGTGCCT
ATTAAAAGATAATTTCATGATCTACAACTTGCATGAAGGACTCAAAAGCCAATTTTAATGTTTCA
ATTCAAAAAAAGATTCATTTGCCATTCGATTGCCGATCTATTATATACCATATAATTTCGATCCA
CATGTCCAATTAAAGTTATTGAAGTATCACTTAAAAAGCTATTGCATGATCTACGACTTTCATGA
AGGACCCAAAGCCTAAATTTGATCTACGAGACATGAAGGGTTCAAAAGGGAATTTTTATGTTTCA
AGATCTACATCAACAAACATTTTCTTATTTAGATTATTTATCAAATAACCCTCATATTTTTCTAC
TTTATACTACTTAGTCCTTTACAAATTCTATCTT
Found at i:2680 original size:16 final size:16
Alignment explanation
Indices: 2659--2695 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2649 GGCAGATGGG
*
2659 GGGTTGGGTTAGATTT
1 GGGTTGGGTCAGATTT
*
2675 GGGTTGGGTCAGTTTT
1 GGGTTGGGTCAGATTT
2691 GGGTT
1 GGGTT
2696 AAGAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.03, G:0.46, T:0.43
Consensus pattern (16 bp):
GGGTTGGGTCAGATTT
Found at i:4457 original size:16 final size:16
Alignment explanation
Indices: 4436--4490 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
4426 GGTTGATCGA
4436 GTTCGGGTCATTTTGG
1 GTTCGGGTCATTTTGG
*
4452 GTTCGGGTC-GTTTGG
1 GTTCGGGTCATTTTGG
* * *
4467 ATTCGGGTAATTTCGG
1 GTTCGGGTCATTTTGG
*
4483 GTTTGGGT
1 GTTCGGGT
4491 ACCCAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.07, C:0.11, G:0.40, T:0.42
Consensus pattern (16 bp):
GTTCGGGTCATTTTGG
Found at i:4471 original size:15 final size:16
Alignment explanation
Indices: 4437--4474 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4427 GTTGATCGAG
* *
4437 TTCGGGTCATTTTGGG
1 TTCGGGTCAGTTTGGA
4453 TTCGGGTC-GTTTGGA
1 TTCGGGTCAGTTTGGA
4468 TTCGGGT
1 TTCGGGT
4475 AATTTCGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.05, C:0.13, G:0.39, T:0.42
Consensus pattern (16 bp):
TTCGGGTCAGTTTGGA
Found at i:11975 original size:20 final size:20
Alignment explanation
Indices: 11950--11987 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
11940 AGTTAATTGT
11950 ACCCATTCGCACACAAAACA
1 ACCCATTCGCACACAAAACA
11970 ACCCATTCGCACACAAAA
1 ACCCATTCGCACACAAAA
11988 TATCCTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.39, G:0.05, T:0.11
Consensus pattern (20 bp):
ACCCATTCGCACACAAAACA
Found at i:14345 original size:22 final size:22
Alignment explanation
Indices: 14320--14372 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
14310 AAGGGCTGAA
14320 AATTATTAATTATTA-AATAAAT
1 AATTATTAATTATTAGAAT-AAT
* *
14342 AATTATTATTTTTTAGAATAAT
1 AATTATTAATTATTAGAATAAT
*
14364 TATTATTAA
1 AATTATTAA
14373 AATTTCCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTATTAATTATTAGAATAAT
Found at i:17190 original size:16 final size:16
Alignment explanation
Indices: 17169--17204 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17159 TGGGTTTGGA
* *
17169 TGGATAGTCGGATTCT
1 TGGATAATCCGATTCT
17185 TGGATAATCCGATTCT
1 TGGATAATCCGATTCT
17201 TGGA
1 TGGA
17205 CAGGTCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (16 bp):
TGGATAATCCGATTCT
Found at i:25249 original size:13 final size:12
Alignment explanation
Indices: 25218--25251 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
25208 CGTTGAGGAA
25218 ACTGTTTTA-TT
1 ACTGTTTTATTT
25229 ACTGTTTTATTT
1 ACTGTTTTATTT
25241 ACGTGTTTTAT
1 AC-TGTTTTAT
25252 AAATGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 4 0.19
13 8 0.38
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.62
Consensus pattern (12 bp):
ACTGTTTTATTT
Done.