Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021915.1 Corchorus olitorius cultivar O-4 contig21948, 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: 6956
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Found at i:68 original size:25 final size:24
Alignment explanation
Indices: 34--80 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
24 ACGTTTGCAC
34 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
59 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
81 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:125 original size:39 final size:40
Alignment explanation
Indices: 71--151 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
61 ATACCTAAGA
*
71 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
110 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
150 AT
1 AT
152 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:386 original size:6 final size:6
Alignment explanation
Indices: 368--404 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
358 GTTTAGACTT
368 ATATAG TATATAG ATATAG TATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG -ATATAG ATATAG ATATA
405 TCGGCACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.59
7 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (6 bp):
ATATAG
Found at i:386 original size:13 final size:13
Alignment explanation
Indices: 368--404 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
358 GTTTAGACTT
368 ATATAGTATATAG
1 ATATAGTATATAG
381 ATATAGTATATAG
1 ATATAGTATATAG
394 ATATAG-ATATA
1 ATATAGTATATA
405 TCGGCACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (13 bp):
ATATAGTATATAG
Found at i:767 original size:24 final size:23
Alignment explanation
Indices: 735--780 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
725 ATGTTTGCAC
735 AAATACCTAAGAATTTGAATTAAA
1 AAATACCTAAGAATTT-AATTAAA
759 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
781 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (23 bp):
AAATACCTAAGAATTTAATTAAA
Found at i:825 original size:39 final size:40
Alignment explanation
Indices: 771--851 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
761 ATACCTAAGA
*
771 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
810 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
850 AT
1 AT
852 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2417 original size:20 final size:20
Alignment explanation
Indices: 2354--2422 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
2344 CAAAAAATTG
*
2354 TAGGGAGATTAACAAAATCTCA
1 TAGGAAGATT-ACAAAAT-TCA
*
2376 TA-GAGAGATTATCAAAAATCA
1 TAGGA-AGATTA-CAAAATTCA
*
2397 TAGGAAGGTTACAAAATTCA
1 TAGGAAGATTACAAAATTCA
2417 TAGGAA
1 TAGGAA
2423 AGTTTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.35
21 12 0.30
22 14 0.35
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (20 bp):
TAGGAAGATTACAAAATTCA
Found at i:2473 original size:22 final size:23
Alignment explanation
Indices: 2366--2529 Score: 82
Period size: 22 Copynumber: 7.6 Consensus size: 23
2356 GGGAGATTAA
* *
2366 CAAAATCTCATAG-AGAGATTAT
1 CAAAATTTCATAGTAGAGTTTAT
* * *
2388 CAAAA-ATCATAGGA-AGGTTA-
1 CAAAATTTCATAGTAGAGTTTAT
* *
2408 CAAAA-TTCATAGGAAAGTTTAT
1 CAAAATTTCATAGTAGAGTTTAT
*
2430 TAAAATTTCATAGTTAG-G-TTAT
1 CAAAATTTCATAG-TAGAGTTTAT
*
2452 CAAAGTTTCATA-TAGAGTTTAT
1 CAAAATTTCATAGTAGAGTTTAT
* *
2474 CACAATTTTATAGGTA-A--TTAT
1 CAAAATTTCATA-GTAGAGTTTAT
* * * *
2495 CAAAATTTTATA-TGGTGGTTAT
1 CAAAATTTCATAGTAGAGTTTAT
*
2517 CAAAATTTAATAG
1 CAAAATTTCATAG
2530 GGTAATTATC
Statistics
Matches: 113, Mismatches: 16, Indels: 25
0.73 0.10 0.16
Matches are distributed among these distances:
19 1 0.01
20 16 0.14
21 32 0.28
22 52 0.46
23 9 0.08
24 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (23 bp):
CAAAATTTCATAGTAGAGTTTAT
Found at i:2496 original size:21 final size:22
Alignment explanation
Indices: 2470--2550 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
2460 CATATAGAGT
*
2470 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTTATAGGGTAA
* **
2491 TTATCAAAATTTTATATGGTGG
1 TTATCAAAATTTTATAGGGTAA
*
2513 TTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTTATAGGGTAA
2535 TTATCAAAATTTTATA
1 TTATCAAAATTTTATA
2551 AAAATATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 15 0.29
22 36 0.71
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGTAA
Done.