Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010626.1 Corchorus olitorius cultivar O-4 contig10658, 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: 9573
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:1841 original size:26 final size:26
Alignment explanation
Indices: 1808--1950 Score: 277
Period size: 26 Copynumber: 5.5 Consensus size: 26
1798 TTTTAGGGGC
1808 AAAATGGTAATTTTCCCACTAAGGGT
1 AAAATGGTAATTTTCCCACTAAGGGT
1834 AAAATGGTAATTTTCCCACTAAGGGT
1 AAAATGGTAATTTTCCCACTAAGGGT
1860 AAAATGGTAATTTTCCCACTAAGGGT
1 AAAATGGTAATTTTCCCACTAAGGGT
*
1886 AAAATGGTAATTTTTCCACTAAGGGT
1 AAAATGGTAATTTTCCCACTAAGGGT
1912 AAAATGGTAATTTTCCCACTAAGGGT
1 AAAATGGTAATTTTCCCACTAAGGGT
1938 AAAATGGTAATTT
1 AAAATGGTAATTT
1951 CACTTGTATT
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 115 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (26 bp):
AAAATGGTAATTTTCCCACTAAGGGT
Found at i:3361 original size:21 final size:24
Alignment explanation
Indices: 3332--3382 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
3322 TTTTGAACTC
3332 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
3355 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
3378 ATTAT
1 ATTAT
3383 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:3377 original size:25 final size:25
Alignment explanation
Indices: 3332--3380 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3322 TTTTGAACTC
*
3332 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
3357 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
3381 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:4150 original size:55 final size:55
Alignment explanation
Indices: 4066--4176 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
4056 ACGATTTTGA
*
4066 AAGTAGTCTTGTTGGCTAAGTAGTTTTAAATTAAGACATAATTACAAG-AACTTCT
1 AAGTAGTCTTGTTGGCTAAGTAATTTTAAATTAAGACATAATTA-AAGCAACTTCT
4121 AAGTAGTCTTGTTGGCTAAGTAATTTTAAATTAAGACATAATTAAAGCAACTTCT
1 AAGTAGTCTTGTTGGCTAAGTAATTTTAAATTAAGACATAATTAAAGCAACTTCT
4176 A
1 A
4177 GTTTAAAAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
54 3 0.06
55 51 0.94
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (55 bp):
AAGTAGTCTTGTTGGCTAAGTAATTTTAAATTAAGACATAATTAAAGCAACTTCT
Found at i:4476 original size:50 final size:49
Alignment explanation
Indices: 4418--4516 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 49
4408 TCTTTAGGGG
4418 AATATGATTTAAGTTAAATCCTTTAAAT-GGTAGGGATTAATATGGCTAAT
1 AATATGATTTAAGTTAAATCCTTT-AATGGGT-GGGATTAATATGGCTAAT
*
4468 AATATGATTTAAGTTAAATCCTTTGATGGGTGGGATTAATATGGCTAAT
1 AATATGATTTAAGTTAAATCCTTTAATGGGTGGGATTAATATGGCTAAT
4517 TGTTTCTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
49 20 0.43
50 27 0.57
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (49 bp):
AATATGATTTAAGTTAAATCCTTTAATGGGTGGGATTAATATGGCTAAT
Done.