Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006022.1 Corchorus capsularis cultivar CVL-1 contig06040, 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: 12102
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Found at i:1505 original size:3 final size:3
Alignment explanation
Indices: 1499--1525 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1489 GGCTTATTAT
1499 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1526 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8309 original size:19 final size:19
Alignment explanation
Indices: 8285--8322 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
8275 AAAGAATTAA
8285 GGATCTATTTGATTTGCAT
1 GGATCTATTTGATTTGCAT
8304 GGATCTATTTGATTTGCAT
1 GGATCTATTTGATTTGCAT
8323 AGAGGAGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (19 bp):
GGATCTATTTGATTTGCAT
Found at i:9984 original size:28 final size:29
Alignment explanation
Indices: 9947--10020 Score: 132
Period size: 28 Copynumber: 2.6 Consensus size: 29
9937 ACTATAGTAT
9947 AAAAATACTCATTCACTTCTACC-AAAAA
1 AAAAATACTCATTCACTTCTACCAAAAAA
9975 AAAAATACTCATTCACTTCTACCAAAAAA
1 AAAAATACTCATTCACTTCTACCAAAAAA
10004 AAAAATTACTCATTCAC
1 AAAAA-TACTCATTCAC
10021 ATTACATTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 23 0.52
29 10 0.23
30 11 0.25
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAAATACTCATTCACTTCTACCAAAAAA
Found at i:10921 original size:7 final size:7
Alignment explanation
Indices: 10908--10947 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
10898 CTATTGACTT
10908 TTTCTTC
1 TTTCTTC
*
10915 CTTCTTC
1 TTTCTTC
10922 TTTCTTC
1 TTTCTTC
10929 TTTCTTTC
1 TTTC-TTC
10937 TTTCTTTC
1 TTTC-TTC
10945 TTT
1 TTT
10948 TTTTTTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCTTC
Found at i:10926 original size:4 final size:4
Alignment explanation
Indices: 10919--10947 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
10909 TTCTTCCTTC
10919 TTCT TTC- TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
10948 TTTTTTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:11367 original size:6 final size:6
Alignment explanation
Indices: 11356--11385 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11346 TATGTACAAA
11356 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
11386 TCAATATCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:11713 original size:2 final size:2
Alignment explanation
Indices: 11702--11736 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
11692 ATTCATATTC
11702 AT AT -T 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
11737 CAAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.