Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012952.1 Corchorus olitorius cultivar O-4 contig12985, 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: 19025
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Found at i:1327 original size:27 final size:28
Alignment explanation
Indices: 1296--1364 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 28
1286 CATGTACTTG
* * *
1296 AAATGACTAAAATGCCCCTGGTCGTGC-
1 AAATGACCAAAATGCCCCTGGACATGCA
*
1323 AAATGACCAAAATGCCCTTGGACATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
1351 AAATGACCAAAATG
1 AAATGACCAAAATG
1365 AGAAGTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:1804 original size:50 final size:50
Alignment explanation
Indices: 1584--1811 Score: 366
Period size: 50 Copynumber: 4.5 Consensus size: 50
1574 CGATCAACTT
* * * * *
1584 CTTTGAATTGTCTTCCAATTCAAATATAAAAAGGATCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTC-ACTCTTAAAAGGACCGTCTTCCGCTTATC
*
1635 CTTTGAACTGTCTTCCAATCCACTCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTTCCGCTTATC
*
1685 CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTCCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTTCCGCTTATC
*
1735 CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTTCCACTTATC
1 CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTTCCGCTTATC
*
1785 CTTTGAACTGTCTTCCAATTCGCTCTT
1 CTTTGAACTGTCTTCCAATTCACTCTT
1812 CTGGATATCT
Statistics
Matches: 166, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 147 0.89
51 19 0.11
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.36
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:2493 original size:2 final size:2
Alignment explanation
Indices: 2486--2513 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2476 GGAATTTAAC
2486 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
2514 GAGTACCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11986 original size:8 final size:8
Alignment explanation
Indices: 11973--11998 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11963 TTAATATGAG
11973 TGAATGGA
1 TGAATGGA
11981 TGAATGGA
1 TGAATGGA
11989 TGAATGGA
1 TGAATGGA
11997 TG
1 TG
11999 CCCTAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (8 bp):
TGAATGGA
Found at i:15371 original size:5 final size:5
Alignment explanation
Indices: 15357--15399 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
15347 AGTAAAACAT
* *
15357 CAAAA C-AAA CAAAA CAAAC CAAAA CAAAC CAAAA CAAAA CAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
15400 GCAACCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:15381 original size:10 final size:10
Alignment explanation
Indices: 15357--15399 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
15347 AGTAAAACAT
15357 CAAAACAAA-
1 CAAAACAAAC
15366 CAAAACAAAC
1 CAAAACAAAC
15376 CAAAACAAAC
1 CAAAACAAAC
*
15386 CAAAACAAAA
1 CAAAACAAAC
15396 CAAA
1 CAAA
15400 GCAACCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 9 0.28
10 23 0.72
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAACAAAC
Done.