Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020013.1 Corchorus olitorius cultivar O-4 contig20046, 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: 24768
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2330 original size:17 final size:18
Alignment explanation
Indices: 2310--2349 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2300 TTCTTTGCAT
2310 ATTTAATTATCA-TTTTA
1 ATTTAATTATCATTTTTA
* *
2327 ATTTTATTATTATTTTTA
1 ATTTAATTATCATTTTTA
2345 ATTTA
1 ATTTA
2350 TATACTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATTATCATTTTTA
Found at i:5835 original size:19 final size:18
Alignment explanation
Indices: 5811--5846 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5801 TGAAGACTTA
*
5811 TTGAAGACTATTTGAAGAT
1 TTGAAGACCA-TTGAAGAT
5830 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
5847 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Found at i:15584 original size:19 final size:18
Alignment explanation
Indices: 15560--15596 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15550 AAGTTCGTGC
15560 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
15579 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
15597 ATTATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Found at i:24410 original size:20 final size:19
Alignment explanation
Indices: 24387--24461 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 19
24377 AAAAATATTA
24387 AAATAAAAAAAGTAATAGAT
1 AAATAAAAAAA-TAATAGAT
*
24407 AAATAAATAAATAAATAGAT
1 AAATAAAAAAAT-AATAGAT
24427 AAATAAGTAAAAATAATAGAT
1 AAATAA--AAAAATAATAGAT
*
24448 AAATAAAAAGATAA
1 AAATAAAAAAATAA
24462 ATAGGTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.16
20 23 0.47
21 13 0.27
22 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAAAAAAATAATAGAT
Found at i:24414 original size:4 final size:4
Alignment explanation
Indices: 24387--24464 Score: 61
Period size: 4 Copynumber: 19.2 Consensus size: 4
24377 AAAAATATTA
* * * *
24387 AAAT AAAA AAAGT -AAT AGAT AAAT AAAT AAAT AAAT AGAT AAAT AAGT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
24435 AAAA ATAAT AGAT AAAT AAA- AAGAT AAAT A
1 AAAT A-AAT AAAT AAAT AAAT AA-AT AAAT A
24465 GGTATATAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
3 3 0.05
4 49 0.86
5 5 0.09
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:24415 original size:12 final size:12
Alignment explanation
Indices: 24405--24528 Score: 84
Period size: 12 Copynumber: 11.0 Consensus size: 12
24395 AAAGTAATAG
*
24405 ATAAATAAATAA
1 ATAAATAGATAA
24417 ATAAATAGATAA
1 ATAAATAGATAA
*
24429 ATAAGTA-A-AA
1 ATAAATAGATAA
24439 AT-AATAGATAA
1 ATAAATAGATAA
*
24450 ATAAAAAGATAA
1 ATAAATAGATAA
** * *
24462 ATAGGTATATAG
1 ATAAATAGATAA
*
24474 ATAATTAGATAA
1 ATAAATAGATAA
** *
24486 ATAGGTAGGTAA
1 ATAAATAGATAA
*
24498 A-AAA-A-ATAG
1 ATAAATAGATAA
24507 AT-AATAG-TAA
1 ATAAATAGATAA
24517 ATAAATAGATAA
1 ATAAATAGATAA
24529 TAGCTAAATT
Statistics
Matches: 83, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
9 8 0.10
10 11 0.13
11 11 0.13
12 53 0.64
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (12 bp):
ATAAATAGATAA
Found at i:24547 original size:19 final size:18
Alignment explanation
Indices: 24400--24594 Score: 75
Period size: 16 Copynumber: 11.5 Consensus size: 18
24390 TAAAAAAAGT
*
24400 AATAGATAAATAAATAAATA
1 AATAGAT-AAT-AGTAAATA
*
24420 AATAGATAA-A-TAAGTA
1 AATAGATAATAGTAAATA
24436 AA-A-ATAATAGATAAATA
1 AATAGATAATAG-TAAATA
* **
24453 AAAAGATAA-A-TAGGTA
1 AATAGATAATAGTAAATA
* *
24469 TATAGATAAT--TAGATA
1 AATAGATAATAGTAAATA
* * *
24485 AATAGGT-A-GGTAAAAAA
1 AATAGATAATAGT-AAATA
24502 AATAGATAATAGTAAATA
1 AATAGATAATAGTAAATA
*
24520 AATAGATAATAGCTAAATT
1 AATAGATAATAG-TAAATA
*
24539 AAT-G--AATA--AAA-G
1 AATAGATAATAGTAAATA
*
24551 GATA-A-AATAGTAAATA
1 AATAGATAATAGTAAATA
*
24567 AATAGATAATAGTTAAATT
1 AATAGATAATAG-TAAATA
*
24586 AATAAATAA
1 AATAGATAA
24595 AAAAATCGTT
Statistics
Matches: 134, Mismatches: 21, Indels: 41
0.68 0.11 0.21
Matches are distributed among these distances:
12 2 0.01
13 7 0.05
14 4 0.03
15 6 0.04
16 36 0.27
17 18 0.13
18 25 0.19
19 29 0.22
20 7 0.05
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.26
Consensus pattern (18 bp):
AATAGATAATAGTAAATA
Found at i:24547 original size:27 final size:26
Alignment explanation
Indices: 24514--24595 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 26
24504 TAGATAATAG
24514 TAAATAAATAGATAATAGCTAAATTAA
1 TAAATAAATAGATAATAG-TAAATTAA
* * *
24541 TGAATAAA-AG--GATA--AAA-TAG
1 TAAATAAATAGATAATAGTAAATTAA
24561 TAAATAAATAGATAATAGTTAAATTAA
1 TAAATAAATAGATAATAG-TAAATTAA
24588 TAAATAAA
1 TAAATAAA
24596 AAAATCGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
20 9 0.21
21 5 0.12
23 3 0.07
24 3 0.07
26 5 0.12
27 17 0.40
ACGTcount: A:0.61, C:0.01, G:0.10, T:0.28
Consensus pattern (26 bp):
TAAATAAATAGATAATAGTAAATTAA
Done.