Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011452.1 Corchorus olitorius cultivar O-4 contig11485, 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: 39793
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3660 original size:13 final size:13
Alignment explanation
Indices: 3642--3666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3632 TTCAATGTTC
3642 TAAATATTATTTA
1 TAAATATTATTTA
3655 TAAATATTATTT
1 TAAATATTATTT
3667 GGAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:6341 original size:132 final size:130
Alignment explanation
Indices: 6203--6470 Score: 428
Period size: 130 Copynumber: 2.0 Consensus size: 130
6193 CATTGTTTAA
* *
6203 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATCTAATATC-CTATAAC
* * *
6268 TATTTAATTTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 TATTTAA-TTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAAT
6333 AT
129 AT
* *
6335 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATCTAATATCCTATACCT
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATCTAATATCCTATAACT
* *
6400 ATTTTATTTTTACCATTTTACTAATTTAATTGAAAAACTTAGATATATTAGAATTTTTAAAATAT
66 ATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
*
6465 ATTTTT
1 ACTTTT
6471 TAAATGAAAT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
130 60 0.48
131 11 0.09
132 55 0.44
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (130 bp):
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATCTAATATCCTATAACT
ATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATAT
Found at i:24825 original size:14 final size:14
Alignment explanation
Indices: 24786--24827 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
24776 CTAATTTATC
24786 TATTAGTCAATTTT
1 TATTAGTCAATTTT
*
24800 T-TT-GCCAGATTTT
1 TATTAGTCA-ATTTT
24813 TATTAGTCAATTTT
1 TATTAGTCAATTTT
24827 T
1 T
24828 TTTAAGAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 9 0.39
15 3 0.13
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (14 bp):
TATTAGTCAATTTT
Found at i:30748 original size:20 final size:22
Alignment explanation
Indices: 30723--30762 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
30713 TCAGATTTAT
30723 TGAATTAAAT-AT-TTAAAATA
1 TGAATTAAATGATATTAAAATA
30743 TGAATTAAATGATATTAAAA
1 TGAATTAAATGATATTAAAA
30763 AATTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
TGAATTAAATGATATTAAAATA
Found at i:35192 original size:429 final size:433
Alignment explanation
Indices: 34344--35345 Score: 1245
Period size: 429 Copynumber: 2.3 Consensus size: 433
34334 AAAAAAATCG
* * * * * * ** **
34344 TATGATATTAAGTAGATCGTCAATCGAAATCACAAAATTTCGGAAGCATTTTTTAAAATTGAAAC
1 TATGATAGTAAATAGACCGGCAATCGAAACCACCAAATTTAAGAAGCATTTTTTTGAATTGAAAC
* * * *
34409 ATAAAAATT-AGCTTTTGACTCCTTAATG--AA----AG-T--TGAAATTACCGTTTAATAGACA
66 ATAAAAATTGA-CTCTTGAGTCCTTCATGAAAATTGCAGATCATGAAATTACCTTTTAATAGACA
*
34464 CCTGAATTACCTTAATTGGACAAATAAAACAAAAAAATAAAGATGAAGTGTTAAATCGAGTAAAA
130 CCTGAATCACCTTAATTGG---AATAAAACAAAAAAATAAAGATGAAGTGTTAAATCGAGTAAAA
* * * *
34529 TAGAATTTATAAAAGACTATGTAGTATAAATTAGAATAGTGTGAGGGTCATTTGATAAATAATCC
192 TAGAATTTATAAAAGACTAAGTAGTATAAAATAGAAAAGTATGAGGGTCATTTGATAAATAATCC
* * * * * **
34594 AAATAAAACAATGTTTGTTGATAGAGATCTTGAAATATAAAAAATTCCCTTTTGGACCTTTCATG
257 AAATAAAACAATGTTTGTTAATAGAAATCTTGAAACATAAAAAATTCCCTTTTGAACCATTCACA
* *
34659 AAACTCGTAGATCAGATTTAACTTTTGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTT
322 AAACTCGTAGATCAGAATTAACTTTTGGGTCCTTCATGAAAGTCGTAAATAATGCAATAACCTTT
*
34724 TAATCGACACTTGAATAACTTTAATCGGACATGTGGATCGAAAATTA
387 TAATCGACACTTAAATAACTTTAATCGGACATGTGGATCGAAAATTA
* * * * *
34771 TATGATATTAAATAGATCGGCAATCGAAACCACCAAATTTAATAAGCATTTTTTTGAGTTGAAAT
1 TATGATAGTAAATAGACCGGCAATCGAAACCACCAAATTTAAGAAGCATTTTTTTGAATTGAAAC
* * *
34836 ATAAAAATTTG-CTCTTGAGTTCTTCATGAAAGTTGCAGATCATGAAATTACCTTTTAATAGACC
66 ATAAAAA-TTGACTCTTGAGTCCTTCATGAAAATTGCAGATCATGAAATTACCTTTTAATAGACA
* * * * *
34900 CCTGAATCACCTTAATTGG-AT-AGATATAAAAA-AAAGTTGAAGTGTTAAATCGATTAAAATAG
130 CCTGAATCACCTTAATTGGAATAAAACAAAAAAATAAAGATGAAGTGTTAAATCGAGTAAAATAG
* *
34962 AA-TTAGTAAAGGATTAAGTAGTATAAAATAGAAAAAG-ATGAGGGTCATTTGATAAATAATCCA
195 AATTTA-TAAAAGACTAAGTAGTATAAAATAG-AAAAGTATGAGGGTCATTTGATAAATAATCCA
* * *
35025 AATAAGAA-AATGTTTGTTAAT-GAAAATCTTGAAACAT-AAAAATTTCGTTTTGAACCATTCGC
258 AATAA-AACAATGTTTGTTAATAG-AAATCTTGAAACATAAAAAATTCCCTTTTGAACCATTCAC
* *
35087 AAAACTCGTAGATCA-AATTAAGCTTTTGGGTCCTTCATGAAAGTCGTAGATAATGTAATAACCT
321 AAAACTCGTAGATCAGAATTAA-CTTTTGGGTCCTTCATGAAAGTCGTAAATAATGCAATAACCT
*
35151 TTTAA-CTGACACTTAAATAACTTTAATCGGACATGTGGATCGAAAATTT
385 TTTAATC-GACACTTAAATAACTTTAATCGGACATGTGGATCGAAAATTA
* **
35200 TATGATAGTAAATAGACCGTCAATCGAAACCACCAAATTTTGGAAGCATTTTTTTGAATTGAAAC
1 TATGATAGTAAATAGACCGGCAATCGAAACCACCAAATTTAAGAAGCATTTTTTTGAATTGAAAC
* *
35265 ATAAAAATTGACTTTTGAGTCCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACAC
66 ATAAAAATTGACTCTTGAGTCCTTCATGAAAATTGCAGATCATGAAATTACCTTTTAATAGACAC
* *
35330 CTAAATCACCTAAATT
131 CTGAATCACCTTAATT
35346 AGACAAATAA
Statistics
Matches: 496, Mismatches: 61, Indels: 34
0.84 0.10 0.06
Matches are distributed among these distances:
427 74 0.15
428 11 0.02
429 249 0.50
430 105 0.21
431 14 0.03
432 2 0.00
433 2 0.00
434 1 0.00
436 38 0.08
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (433 bp):
TATGATAGTAAATAGACCGGCAATCGAAACCACCAAATTTAAGAAGCATTTTTTTGAATTGAAAC
ATAAAAATTGACTCTTGAGTCCTTCATGAAAATTGCAGATCATGAAATTACCTTTTAATAGACAC
CTGAATCACCTTAATTGGAATAAAACAAAAAAATAAAGATGAAGTGTTAAATCGAGTAAAATAGA
ATTTATAAAAGACTAAGTAGTATAAAATAGAAAAGTATGAGGGTCATTTGATAAATAATCCAAAT
AAAACAATGTTTGTTAATAGAAATCTTGAAACATAAAAAATTCCCTTTTGAACCATTCACAAAAC
TCGTAGATCAGAATTAACTTTTGGGTCCTTCATGAAAGTCGTAAATAATGCAATAACCTTTTAAT
CGACACTTAAATAACTTTAATCGGACATGTGGATCGAAAATTA
Found at i:36048 original size:37 final size:37
Alignment explanation
Indices: 36007--36080 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
35997 TTTTCACTTC
36007 CTCCTATTATTGTTCTTTATTTATTTATTTATAATTT
1 CTCCTATTATTGTTCTTTATTTATTTATTTATAATTT
36044 CTCCTATTATTGTTCTTTATTTATTTATTTATAATTT
1 CTCCTATTATTGTTCTTTATTTATTTATTTATAATTT
36081 ATAATATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.11, G:0.03, T:0.65
Consensus pattern (37 bp):
CTCCTATTATTGTTCTTTATTTATTTATTTATAATTT
Done.