Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010678.1 Corchorus olitorius cultivar O-4 contig10710, 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: 3308
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Found at i:2297 original size:21 final size:20
Alignment explanation
Indices: 2272--2316 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
2262 ACTTTCTAAG
2272 GTTACTAAAAAGCTTAACAAA
1 GTTACTAAAAAGCTT-ACAAA
* *
2293 GTTACTAAAATGCTTACTAA
1 GTTACTAAAAAGCTTACAAA
2313 GTTA
1 GTTA
2317 TATATTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (20 bp):
GTTACTAAAAAGCTTACAAA
Found at i:2302 original size:40 final size:40
Alignment explanation
Indices: 2219--2302 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
2209 ATGATAAAAA
* *
2219 AAAACTTATCCAAGTTACTAAAAAGTTTACACGAGTATAT
1 AAAACTTATCCAAGTTACTAAAAAGTTAACACAAGTATAT
*
2259 AAAACTT-TCTAAGGTTACTAAAAAGCTTAACA-AAGT-TACT
1 AAAACTTATCCAA-GTTACTAAAAAG-TTAACACAAGTATA-T
2299 AAAA
1 AAAA
2303 TGCTTACTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
39 6 0.16
40 27 0.71
41 5 0.13
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (40 bp):
AAAACTTATCCAAGTTACTAAAAAGTTAACACAAGTATAT
Found at i:2525 original size:22 final size:21
Alignment explanation
Indices: 2473--2575 Score: 68
Period size: 21 Copynumber: 4.9 Consensus size: 21
2463 AAAACTTAAT
* **
2473 GTTACAAAAAAAGCGTAATAA
1 GTTACTAAAAAAGTTTAATAA
*
2494 GATCAC-AAAAAAGTTTAATAA
1 G-TTACTAAAAAAGTTTAATAA
* *
2515 GTTTATTAAAAACA-CTTAATAAA
1 G-TTACTAAAAA-AGTTTAAT-AA
2538 GTTACT-AAAAAGTTTAATAA
1 GTTACTAAAAAAGTTTAATAA
* * *
2558 ATCACTAAAAGAGTTTAA
1 GTTACTAAAAAAGTTTAA
2576 GATTATTATA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
20 7 0.11
21 36 0.56
22 17 0.27
23 4 0.06
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (21 bp):
GTTACTAAAAAAGTTTAATAA
Found at i:2558 original size:21 final size:21
Alignment explanation
Indices: 2501--2668 Score: 75
Period size: 21 Copynumber: 8.0 Consensus size: 21
2491 TAAGATCACA
*
2501 AAAAAGTTTAAT-AAGTTTATT
1 AAAAAGTTTAATAAAG-TTACT
**
2522 AAAAACACTTAATAAAGTTACT
1 AAAAA-GTTTAATAAAGTTACT
*
2544 AAAAAGTTTAATAAA-TCACT
1 AAAAAGTTTAATAAAGTTACT
* *
2564 AAAAGAGTTTAAGATTA-TTA-T
1 AAAA-AGTTTAATA-AAGTTACT
* *
2585 AAAAAGCTT-A-CAAGATTACT
1 AAAAAGTTTAATAAAG-TTACT
* *
2605 -AAAATTTTAATAAAGCCTACT
1 AAAAAGTTTAATAAAG-TTACT
*
2626 AAAAA-TTGTAATAAGGGTTACT
1 AAAAAGTT-TAATAA-AGTTACT
* *
2648 AAAACA-TTTAGTAAGGTTACT
1 AAAA-AGTTTAATAAAGTTACT
2669 TAAACATTTA
Statistics
Matches: 114, Mismatches: 20, Indels: 26
0.71 0.12 0.16
Matches are distributed among these distances:
17 1 0.01
19 10 0.09
20 14 0.12
21 42 0.37
22 40 0.35
23 7 0.06
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGTTTAATAAAGTTACT
Found at i:2647 original size:22 final size:20
Alignment explanation
Indices: 2600--2678 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 20
2590 GCTTACAAGA
* *
2600 TTACTAAAATTTTAATAAAGC
1 TTACTAAAAATTTAAT-AAGG
*
2621 CTACTAAAAATTGTAATAAGGG
1 TTACTAAAAATT-TAATAA-GG
*
2643 TTACTAAAACATTTAGTAAGG
1 TTACTAAAA-ATTTAATAAGG
*
2664 TTACTTAAACATTTA
1 TTAC-TAAAAATTTA
2679 TTAACTTACT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 23 0.48
22 22 0.46
23 3 0.06
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
TTACTAAAAATTTAATAAGG
Found at i:2841 original size:20 final size:21
Alignment explanation
Indices: 2801--2842 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2791 TTAGTGAGGT
*
2801 TATTGAAAAGCTTACTTAAGGG
1 TATTAAAAAGCTTA-TTAAGGG
2823 TATTAAAAAGCTT-TTAAGGG
1 TATTAAAAAGCTTATTAAGGG
2843 CTGTCGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33
Consensus pattern (21 bp):
TATTAAAAAGCTTATTAAGGG
Found at i:2966 original size:24 final size:24
Alignment explanation
Indices: 2929--2979 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2919 TAAGATTTCT
2929 AAAAAACTCAATAAAGTTACTAAA
1 AAAAAACTCAATAAAGTTACTAAA
* *
2953 AAAAAACTTC-ATAAGGTTACTATA
1 AAAAAAC-TCAATAAAGTTACTAAA
2977 AAA
1 AAA
2980 TTCATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (24 bp):
AAAAAACTCAATAAAGTTACTAAA
Found at i:2985 original size:20 final size:21
Alignment explanation
Indices: 2955--2998 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
2945 TTACTAAAAA
2955 AAAACTTCATAAGGTT-ACTAT
1 AAAACTTCATAA-GTTAACTAT
2976 AAAA-TTCATAAGTTAACTAT
1 AAAACTTCATAAGTTAACTAT
2996 AAA
1 AAA
2999 TCTTACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAACTTCATAAGTTAACTAT
Done.