Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009213.1 Corchorus olitorius cultivar O-4 contig09241, 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, 710
Length: 1184
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Found at i:459 original size:21 final size:19
Alignment explanation
Indices: 423--464 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
413 TATATAATGC
*
423 ATATTTTATTTATATATTA
1 ATATTCTATTTATATATTA
442 ATATTCTATATTATTATATTA
1 ATATTCTAT-TTA-TATATTA
463 AT
1 AT
465 TTATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTCTATTTATATATTA
Found at i:477 original size:18 final size:18
Alignment explanation
Indices: 456--493 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
446 TCTATATTAT
456 TATATTAATTTATATAAA
1 TATATTAATTTATATAAA
* *
474 TATATTCATTTATATGAA
1 TATATTAATTTATATAAA
492 TA
1 TA
494 ATACTCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATATTAATTTATATAAA
Found at i:546 original size:29 final size:29
Alignment explanation
Indices: 506--569 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
496 ACTCTATTAT
*
506 TATTAATACTATTACAATTATTACATATA
1 TATTAATACTATTACAATTAGTACATATA
535 T-TTAATTACTATTACAATTAGTACATATA
1 TATTAA-TACTATTACAATTAGTACATATA
564 TATTAA
1 TATTAA
570 ATTTATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.12
29 24 0.75
30 4 0.12
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (29 bp):
TATTAATACTATTACAATTAGTACATATA
Found at i:576 original size:29 final size:28
Alignment explanation
Indices: 515--577 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
505 TTATTAATAC
*
515 TATTACAATTATTACATATATTTAATTA
1 TATTACAATTAGTACATATATTTAATTA
543 CTATTACAATTAGTACATATATATTAAATT-
1 -TATTACAATTAGTACATATAT-TT-AATTA
573 TATTA
1 TATTA
578 TTCCATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 25 0.81
30 2 0.06
31 4 0.13
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.48
Consensus pattern (28 bp):
TATTACAATTAGTACATATATTTAATTA
Found at i:596 original size:21 final size:22
Alignment explanation
Indices: 570--617 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
560 TATATATTAA
570 ATTTATTATTCCATTTATAT-T
1 ATTTATTATTCCATTTATATAT
*
591 ATTTATTATTCCGTTTATATAT
1 ATTTATTATTCCATTTATATAT
613 ATTTA
1 ATTTA
618 AATAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTATTATTCCATTTATATAT
Found at i:1135 original size:21 final size:21
Alignment explanation
Indices: 1107--1169 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
1097 TAGAACTACT
1107 ACTCTTAGAACCAGAAATAAA
1 ACTCTTAGAACCAGAAATAAA
*
1128 ACTTTTAGAACCAGAAATAAA
1 ACTCTTAGAACCAGAAATAAA
1149 ACTCTTAGAACCAGAAATAAA
1 ACTCTTAGAACCAGAAATAAA
1170 TAGGCTTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (21 bp):
ACTCTTAGAACCAGAAATAAA
Done.