Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005072.1 Corchorus capsularis cultivar CVL-1 contig05090, 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: 25090
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1085 original size:16 final size:16
Alignment explanation
Indices: 1052--1105 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1042 GTTCCTACTC
* **
1052 TACTCACCCAATAAAA
1 TACTCACCCAGTGCAA
1068 TACTCACCCAGTGCAA
1 TACTCACCCAGTGCAA
* **
1084 TACCCACTTAGTGCAA
1 TACTCACCCAGTGCAA
1100 TACTCA
1 TACTCA
1106 ATTAGTGAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.22
Consensus pattern (16 bp):
TACTCACCCAGTGCAA
Found at i:1110 original size:16 final size:16
Alignment explanation
Indices: 1077--1121 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1067 ATACTCACCC
* *
1077 AGTGCAATACCCACTT
1 AGTGCAATACTCAATT
1093 AGTGCAATACTCAATT
1 AGTGCAATACTCAATT
1109 AGTG-AGATACTCA
1 AGTGCA-ATACTCA
1122 CTTACAAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (16 bp):
AGTGCAATACTCAATT
Found at i:5770 original size:60 final size:60
Alignment explanation
Indices: 5676--5792 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
5666 CCTATTTGAT
** * * ** *
5676 CAAATTAAAAGCATGTTGCCTAAATTGAGTATTTTTGTATATATTAGGGCCTTATTTAAC
1 CAAATTAAAAGCATGAGGCCTAAAATAAGTATTTTTAAATACATTAGGGCCTTATTTAAC
*
5736 CAAATTAAAAGCATGAGGCCTAAAATAACG-ATTTTTAAATACGTTAGGGCCTTATTT
1 CAAATTAAAAGCATGAGGCCTAAAATAA-GTATTTTTAAATACATTAGGGCCTTATTT
5793 GAACAATTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 47 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (60 bp):
CAAATTAAAAGCATGAGGCCTAAAATAAGTATTTTTAAATACATTAGGGCCTTATTTAAC
Found at i:8808 original size:25 final size:25
Alignment explanation
Indices: 8780--8827 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
8770 TCACCCAAAA
8780 AAAAAGTTTTTAGTGTAATAATTGG
1 AAAAAGTTTTTAGTGTAATAATTGG
*
8805 AAAATGTTTTTAGTGTAATAATT
1 AAAAAGTTTTTAGTGTAATAATT
8828 TGAAGCCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.44
Consensus pattern (25 bp):
AAAAAGTTTTTAGTGTAATAATTGG
Found at i:9074 original size:2 final size:2
Alignment explanation
Indices: 9067--9096 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9057 CTTTTATTAC
*
9067 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9097 GTTGGTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22888 original size:2 final size:2
Alignment explanation
Indices: 22881--22910 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22871 GATGCTCCCA
22881 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
22911 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22915 original size:2 final size:2
Alignment explanation
Indices: 22910--22946 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22900 TATATATATA
22910 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
22947 TTATAATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:24486 original size:15 final size:13
Alignment explanation
Indices: 24458--24496 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
24448 ATGAAACTTC
24458 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
24471 AAAAAAAAGATTAAG
1 AAAAAAAAGA--AAG
*
24486 AACAAAAAGAA
1 AAAAAAAAGAA
24497 GTGGTGGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 11 0.48
15 12 0.52
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Done.