Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015008.1 Corchorus olitorius cultivar O-4 contig15041, 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: 2253
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Found at i:316 original size:14 final size:14
Alignment explanation
Indices: 297--330 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
287 TTTTATAATT
297 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
311 ATTTTATTTTTACT
1 ATTTTATTTTTACC
325 ATTTTA
1 ATTTTA
331 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:378 original size:15 final size:15
Alignment explanation
Indices: 358--388 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
348 GATTAACCTG
358 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
373 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
388 T
1 T
389 AATGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:851 original size:14 final size:14
Alignment explanation
Indices: 832--865 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
822 TTTTATAATT
832 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
846 ATTTTATTTTTACT
1 ATTTTATTTTTACC
860 ATTTTA
1 ATTTTA
866 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:913 original size:15 final size:15
Alignment explanation
Indices: 893--923 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
883 GATTAACCTG
893 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
908 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
923 T
1 T
924 AATGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:1912 original size:123 final size:123
Alignment explanation
Indices: 1712--1966 Score: 330
Period size: 123 Copynumber: 2.0 Consensus size: 123
1702 CATTGTTTAA
* * **
1712 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTATTATTTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATCCTTATAAT
* ** *
1777 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 CTTTATAATTTTACTATTTTAATTAAAAAACCTATATATATTAGAATTTTTTAAATAT
* * *
1835 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATCCTTATA-A
*
1900 TACTTTATTTTTACCATTTTACTATTTTATTTAAAAAACCTATATATATTAGAATTTTTTAAATA
65 T-CTTTA----TA--ATTTTACTATTTTAATTAAAAAACCTATATATATTAGAATTTTTTAAATA
1965 T
123 T
1966 A
1 A
1967 TTTCTTAAAT
Statistics
Matches: 112, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
123 57 0.51
124 1 0.01
125 4 0.04
131 50 0.45
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.49
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATCCTTATAAT
CTTTATAATTTTACTATTTTAATTAAAAAACCTATATATATTAGAATTTTTTAAATAT
Found at i:1956 original size:131 final size:123
Alignment explanation
Indices: 1712--1966 Score: 375
Period size: 131 Copynumber: 2.0 Consensus size: 123
1702 CATTGTTTAA
* *
1712 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTATTATTTTTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATTTTTATAAT
*
1777 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACCTATATATATTAGAATTTTTTAAATAT
* *
1835 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATAT--TT-T---
* *
1900 TACTTTATTTTTACCATTTTACTATTTTATTTAAAAAACCTATATATATTAGAATTTTTTAAATA
60 TA--TAATTTTTACCATTTTACTATTTTAATTAAAAAACCTATATATATTAGAATTTTTTAAATA
1965 T
123 T
1966 A
1 A
1967 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 52 0.44
125 2 0.02
126 1 0.01
129 2 0.02
131 60 0.51
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.49
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATGTTATTTAATTAAATCTAATATTTTTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAACCTATATATATTAGAATTTTTTAAATAT
Found at i:1988 original size:14 final size:13
Alignment explanation
Indices: 1952--1990 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1942 TATATATTAG
1952 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
1965 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
1979 AATTTTTTAAAT
1 AATTTTTTAAAT
1991 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Done.