Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023083.1 Corchorus olitorius cultivar O-4 contig23116, 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: 2469
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Found at i:766 original size:196 final size:199
Alignment explanation
Indices: 396--798 Score: 706
Period size: 196 Copynumber: 2.0 Consensus size: 199
386 TTCCTTAATA
* * *
396 ATAAATAAATCGGATCTTAATATCTTTTATATTTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCAGATCTTAATA-CTTTTAAAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
461 ATTTAATAAATCAACCACTAATATTCAACTAATTTTTTTGGTATAGTTCTATATATATAATAGTA
65 ATTTAATAAATCAACCACTAATATTCAACTAA--TTTTTGGTATAGTTCTATATATATAATAGTA
526 ATGTATTGTATCTTATTCAGTACAACTTTGTTAGTAATCTTAGACTTAAAAAA-TAATAACATTC
128 ATGTATTGTATCTTATTCAGTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
*
590 ACCATTG
193 AACATTG
597 ATAAATAAATCAGATCTTTAATA-TTTTAAAATTTTGAAATTTTGTTTGACATTGATCTAA-TTA
1 ATAAATAAATCAGATC-TTAATACTTTTAAAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
660 ATTTAATAAATCAACCACTAATATTCAACTAA-TTTTGGTATAGTTCTATATATATAATAGTAAT
65 ATTTAATAAATCAACCACTAATATTCAACTAATTTTTGGTATAGTTCTATATATATAATAGTAAT
724 GTATTGTATCTTATTCAGTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAA
130 GTATTGTATCTTATTCAGTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAA
789 CATTG
195 CATTG
794 ATAAA
1 ATAAA
799 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
196 83 0.42
197 22 0.11
199 35 0.18
200 35 0.18
201 15 0.08
202 6 0.03
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (199 bp):
ATAAATAAATCAGATCTTAATACTTTTAAAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
TTTAATAAATCAACCACTAATATTCAACTAATTTTTGGTATAGTTCTATATATATAATAGTAATG
TATTGTATCTTATTCAGTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAAC
ATTG
Found at i:1371 original size:36 final size:36
Alignment explanation
Indices: 1317--1386 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1307 GAGATTTTGG
* * *
1317 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAATA
*
1353 AGAAATATAATAACCAAAATCACAAAAGATGTAA
1 AGAAATATAATAACCAAAATCACAAAAAATGTAA
1387 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (36 bp):
AGAAATATAATAACCAAAATCACAAAAAATGTAATA
Done.