Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010425.1 Corchorus capsularis cultivar CVL-1 contig10446, 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: 9566
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--50 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 AT AT AT AT
1 AT AT AT AT
51 TAAAGATTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1627 original size:112 final size:112
Alignment explanation
Indices: 1430--1653 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
1420 AAAACATTAG
1430 ATTCCCGATGAAGTTATAATTTAAAGCTTTTAAAGTTATTGAAGTAATATTTACTATTGTTTTTT
1 ATTCCCGATGAAGTTATAATTTAAAGCTTTTAAAGTTATTGAAGTAATATTTACTATTGTTTTTT
1495 TTTCAATGTTTGGAGGTGGAAAAGGATGAAAATAGTGTGAGAAGTTT
66 TTTCAATGTTTGGAGGTGGAAAAGGATGAAAATAGTGTGAGAAGTTT
1542 ATTCCCGATGAAGTTATAATTTAAAGCTTTTAAAGTTATTGAAGTAATATTTACTATTGTTTTTT
1 ATTCCCGATGAAGTTATAATTTAAAGCTTTTAAAGTTATTGAAGTAATATTTACTATTGTTTTTT
1607 TTTCAATGTTTGGAGGTGGAAAAGGATGAAAATAGTGTGAGAAGTTT
66 TTTCAATGTTTGGAGGTGGAAAAGGATGAAAATAGTGTGAGAAGTTT
1654 GTATGCAAGG
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (112 bp):
ATTCCCGATGAAGTTATAATTTAAAGCTTTTAAAGTTATTGAAGTAATATTTACTATTGTTTTTT
TTTCAATGTTTGGAGGTGGAAAAGGATGAAAATAGTGTGAGAAGTTT
Found at i:1922 original size:13 final size:13
Alignment explanation
Indices: 1904--1951 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
1894 ATCTAACTGT
1904 TTTGGTTTATTA-
1 TTTGGTTTATTAC
1916 TTCTGGTTTATTAC
1 TT-TGGTTTATTAC
*
1930 TTTGGTTTATGAC
1 TTTGGTTTATTAC
*
1943 TTTGATTTA
1 TTTGGTTTA
1952 GGATTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:3391 original size:17 final size:18
Alignment explanation
Indices: 3361--3394 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3351 TCTTTTCTTA
3361 TAAACTTTCCTTCTAGCC
1 TAAACTTTCCTTCTAGCC
*
3379 TAAA-TTTCTTTCTAGC
1 TAAACTTTCCTTCTAGC
3395 TTGATCTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (18 bp):
TAAACTTTCCTTCTAGCC
Found at i:3874 original size:75 final size:75
Alignment explanation
Indices: 3688--3904 Score: 397
Period size: 75 Copynumber: 2.9 Consensus size: 75
3678 TTTTATTTAA
3688 TTAAATCTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAGAAAAC---
1 TTAAAT-TAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAGAAAACTTA
3750 T-TATATTAGT
65 TATATATTAGT
3760 TTAAATTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAGAAAACTTAT
1 TTAAATTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAGAAAACTTAT
3825 ATATATTAGT
66 ATATATTAGT
3835 TTAAATTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAGAAAACTTAT
1 TTAAATTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAGAAAACTTAT
3900 ATATA
66 ATATA
3905 CCATTTTACT
Statistics
Matches: 141, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
71 55 0.39
72 6 0.04
74 1 0.01
75 79 0.56
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (75 bp):
TTAAATTAATATCCTTATAACTATTTAATTTTTACCATTTTACTATTTTAATTAAGAAAACTTAT
ATATATTAGT
Found at i:4937 original size:19 final size:19
Alignment explanation
Indices: 4891--4938 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
4881 TTTAGATCCT
* *
4891 TAAATTAAATATAATATTA
1 TAAACTAAATATAATATGA
4910 TAAACTAAATATAATTATGA
1 TAAACTAAATATAA-TATGA
*
4930 -AAAGTAAAT
1 TAAACTAAAT
4939 TATTAATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
TAAACTAAATATAATATGA
Found at i:5164 original size:2 final size:2
Alignment explanation
Indices: 5157--5182 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5147 GTAAGATAAG
5157 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5183 GTATGCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6460 original size:42 final size:43
Alignment explanation
Indices: 6409--6502 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
6399 AGTGCATTAC
* *
6409 CTAA-ATTCTA-CTCCATTTCTAGGTAATTCATCAAAAGAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAAGAAAA
* * *
6450 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCATAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAAGAAAA
6495 CTAATATT
1 CTAATATT
6503 AATTGTTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAAGAAAA
Done.