Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009327.1 Corchorus capsularis cultivar CVL-1 contig09348, 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: 17566
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4795 original size:19 final size:18
Alignment explanation
Indices: 4771--4806 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4761 TGAAGATTTC
4771 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
4790 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
4807 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:6486 original size:20 final size:21
Alignment explanation
Indices: 6461--6513 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
6451 ACTAGCGCTG
*
6461 GGCG-CCCATGTGGTTTGCTT
1 GGCGACCCATGTGGTTTGCCT
*
6481 GGCGCCCCATGTGGTTTGCCT
1 GGCGACCCATGTGGTTTGCCT
*
6502 CGCGACCCATGT
1 GGCGACCCATGT
6514 ACTCCAGTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.08, C:0.32, G:0.32, T:0.28
Consensus pattern (21 bp):
GGCGACCCATGTGGTTTGCCT
Found at i:9179 original size:19 final size:19
Alignment explanation
Indices: 9155--9191 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
9145 ATAATAGTTA
9155 AAAAAAAAGAT-TTTTCATT
1 AAAAAAAAG-TGTTTTCATT
9174 AAAAAAAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
9192 GAATGAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
AAAAAAAAGTGTTTTCATT
Found at i:14198 original size:24 final size:24
Alignment explanation
Indices: 14171--14248 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
14161 ACCATTTAAT
14171 ATAAAGTCCATTGTATCTCAAATC
1 ATAAAGTCCATTGTATCTCAAATC
* ** * * **
14195 ATAATAGGCCGCGTGTTTAATTTAAT-
1 ATAA-AGTCC-ATTGTAT-CTCAAATC
14221 ATAAAGTCCATTGTATCTCAAATC
1 ATAAAGTCCATTGTATCTCAAATC
14245 ATAA
1 ATAA
14249 TAGGCCGCGT
Statistics
Matches: 36, Mismatches: 14, Indels: 8
0.62 0.24 0.14
Matches are distributed among these distances:
23 4 0.11
24 12 0.33
25 8 0.22
26 8 0.22
27 4 0.11
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (24 bp):
ATAAAGTCCATTGTATCTCAAATC
Found at i:14235 original size:50 final size:50
Alignment explanation
Indices: 14164--14264 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
14154 TGAATATACC
14164 ATTTAATATAAAGTCCATTGTATCTCAAATCATAATAGGCCGCGTGTTTA
1 ATTTAATATAAAGTCCATTGTATCTCAAATCATAATAGGCCGCGTGTTTA
*
14214 ATTTAATATAAAGTCCATTGTATCTCAAATCATAATAGGCCGCGTTTTTA
1 ATTTAATATAAAGTCCATTGTATCTCAAATCATAATAGGCCGCGTGTTTA
14264 A
1 A
14265 CGAAAGTCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (50 bp):
ATTTAATATAAAGTCCATTGTATCTCAAATCATAATAGGCCGCGTGTTTA
Found at i:15725 original size:12 final size:12
Alignment explanation
Indices: 15706--15760 Score: 83
Period size: 12 Copynumber: 4.5 Consensus size: 12
15696 CATCGATACC
15706 TCGATATATCCG
1 TCGATATATCCG
*
15718 TTGATATATCCG
1 TCGATATATCCG
15730 TCGATATATCCG
1 TCGATATATCCG
*
15742 TTCGATAAATCCG
1 -TCGATATATCCG
15755 TCGATA
1 TCGATA
15761 CCTGTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
12 28 0.72
13 11 0.28
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:15754 original size:25 final size:24
Alignment explanation
Indices: 15706--15760 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
15696 CATCGATACC
*
15706 TCGATATATCCGTTGATATATCCG
1 TCGATATATCCGTTGATAAATCCG
15730 TCGATATATCCGTTCGATAAATCCG
1 TCGATATATCCGTT-GATAAATCCG
15755 TCGATA
1 TCGATA
15761 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (24 bp):
TCGATATATCCGTTGATAAATCCG
Done.