Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004881.1 Corchorus capsularis cultivar CVL-1 contig04899, 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: 38595
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:836 original size:16 final size:15
Alignment explanation
Indices: 815--844 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
805 AATAGATTGT
815 TTTTTTTTCTTTTTTC
1 TTTTTTTT-TTTTTTC
831 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
845 TGCATGACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (15 bp):
TTTTTTTTTTTTTTC
Found at i:9316 original size:24 final size:24
Alignment explanation
Indices: 9289--9359 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
9279 GAAGAGCAAC
9289 TGAGGTGGTGAGAGGGAAAAAAAA
1 TGAGGTGGTGAGAGGGAAAAAAAA
* * * ** *
9313 TGAGGAGTTGA-AAGGAAGAGCAAC
1 TGAGGTGGTGAGAGGGAA-AAAAAA
9337 TGAGGTGGTGAGAGGGAAAAAAA
1 TGAGGTGGTGAGAGGGAAAAAAA
9360 CGAGAGAAAC
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
23 5 0.15
24 24 0.71
25 5 0.15
ACGTcount: A:0.44, C:0.03, G:0.41, T:0.13
Consensus pattern (24 bp):
TGAGGTGGTGAGAGGGAAAAAAAA
Found at i:9321 original size:48 final size:48
Alignment explanation
Indices: 9265--9359 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
9255 TGATCAACAC
9265 TGAGGAGTTGAAAGGAAGAGCAACTGAGGTGGTGAGAGGGAAAAAAAA
1 TGAGGAGTTGAAAGGAAGAGCAACTGAGGTGGTGAGAGGGAAAAAAAA
9313 TGAGGAGTTGAAAGGAAGAGCAACTGAGGTGGTGAGAGGGAAAAAAA
1 TGAGGAGTTGAAAGGAAGAGCAACTGAGGTGGTGAGAGGGAAAAAAA
9360 CGAGAGAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.43, C:0.04, G:0.40, T:0.13
Consensus pattern (48 bp):
TGAGGAGTTGAAAGGAAGAGCAACTGAGGTGGTGAGAGGGAAAAAAAA
Found at i:19535 original size:57 final size:57
Alignment explanation
Indices: 19455--19576 Score: 235
Period size: 57 Copynumber: 2.1 Consensus size: 57
19445 GATTGCTGAA
19455 GCATCTGACGAGCGGGTAACTGAGAGTCATCAGACTCCTATTCTGGAACAAGATTCT
1 GCATCTGACGAGCGGGTAACTGAGAGTCATCAGACTCCTATTCTGGAACAAGATTCT
*
19512 GCATCTGATGAGCGGGTAACTGAGAGTCATCAGACTCCTATTCTGGAACAAGATTCT
1 GCATCTGACGAGCGGGTAACTGAGAGTCATCAGACTCCTATTCTGGAACAAGATTCT
19569 GCATCTGA
1 GCATCTGA
19577 AGTCGGTTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (57 bp):
GCATCTGACGAGCGGGTAACTGAGAGTCATCAGACTCCTATTCTGGAACAAGATTCT
Found at i:32361 original size:57 final size:57
Alignment explanation
Indices: 32273--32389 Score: 207
Period size: 57 Copynumber: 2.1 Consensus size: 57
32263 TTGTCCAATA
* *
32273 ATTTCCAATATATTATTGGATGATTGTCACCTATTAAAATTAGATTGAATGGTTGAG
1 ATTTCCAATATATTATTGAATGATTGCCACCTATTAAAATTAGATTGAATGGTTGAG
*
32330 ATTTCCAATATATTATTGAATGATTGCCACCTATTAAAATTAGGTTGAATGGTTGAG
1 ATTTCCAATATATTATTGAATGATTGCCACCTATTAAAATTAGATTGAATGGTTGAG
32387 ATT
1 ATT
32390 AAAATGTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.40
Consensus pattern (57 bp):
ATTTCCAATATATTATTGAATGATTGCCACCTATTAAAATTAGATTGAATGGTTGAG
Found at i:33242 original size:46 final size:46
Alignment explanation
Indices: 33177--33269 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
33167 CAACCATTCA
33177 AAATCATTTTAACCGGTGCCCATCATCCAAAAGTGCATTGGATATC
1 AAATCATTTTAACCGGTGCCCATCATCCAAAAGTGCATTGGATATC
33223 AAATCATTTTAACCGGTGCCCATCATCCAAAAGTGCATTGGATATC
1 AAATCATTTTAACCGGTGCCCATCATCCAAAAGTGCATTGGATATC
33269 A
1 A
33270 TTGGATGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (46 bp):
AAATCATTTTAACCGGTGCCCATCATCCAAAAGTGCATTGGATATC
Found at i:34504 original size:15 final size:15
Alignment explanation
Indices: 34484--34517 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
34474 TAGATTTGCA
34484 GATTATAATAGGATT
1 GATTATAATAGGATT
34499 GATTATAATAGGATT
1 GATTATAATAGGATT
34514 GATT
1 GATT
34518 GCTATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
GATTATAATAGGATT
Found at i:35963 original size:16 final size:16
Alignment explanation
Indices: 35939--35969 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35929 ACTTTACCAT
*
35939 TGTATATATCATCAAA
1 TGTACATATCATCAAA
35955 TGTACATATCATCAA
1 TGTACATATCATCAA
35970 GGTGTATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (16 bp):
TGTACATATCATCAAA
Done.