Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024275.1 Corchorus olitorius cultivar O-4 contig24308, 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, 847
Length: 1413
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.40
Found at i:376 original size:201 final size:202
Alignment explanation
Indices: 12--419 Score: 741
Period size: 201 Copynumber: 2.0 Consensus size: 202
2 TTTCCTTAAT
12 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
*
77 ATTTAATAAACCAACCACTAATGTTAAACTATTTTTTTTGGTATAGTTCTATATATATAATAGTA
66 ATTTAATAAACCAACCACTAATGTTAAACTATTTTTTTTGGTATAGTTCTATATATATAATAATA
142 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
207 ACCATTG
196 ACCATTG
214 ATAAA-AAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
278 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTT-T-TATATATAATAA
65 AATTTAATAAACCAACCACTAATGTTAAACTA-TTTTTTTTGGTATAGTTCTATATATATAATAA
*
341 TAATGTGTTGTATCTTATTCACTATAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
129 TAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACAT
406 TCACCATTG
194 TCACCATTG
415 ATAAA
1 ATAAA
420 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
201 99 0.50
202 84 0.42
203 17 0.09
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAACCAACCACTAATGTTAAACTATTTTTTTTGGTATAGTTCTATATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Found at i:976 original size:36 final size:36
Alignment explanation
Indices: 936--1005 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
926 GAGATTTTGG
* *
936 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
972 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
1006 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.