Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015086.1 Corchorus olitorius cultivar O-4 contig15119, 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: 53997
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7529 original size:3 final size:3
Alignment explanation
Indices: 7515--7547 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
7505 AATCAGTCGG
*
7515 AGA AGC AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
7548 GGAGGAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:15786 original size:21 final size:24
Alignment explanation
Indices: 15727--15807 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 24
15717 TTTAGTAATT
15727 TAATATATATTATTTATTTATTT--
1 TAATATATATTA-TTATTTATTTAA
*
15750 TGAA-CTA-ATTATT-TATTATTTAA
1 T-AATATATATTATTAT-TTATTTAA
*
15773 -AATATAT-TTATTATTTCTTTAA
1 TAATATATATTATTATTTATTTAA
15795 TAATATATATTAT
1 TAATATATATTAT
15808 ATCTAAGATA
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
20 1 0.02
21 10 0.22
22 18 0.39
23 11 0.24
24 6 0.13
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (24 bp):
TAATATATATTATTATTTATTTAA
Found at i:29754 original size:28 final size:27
Alignment explanation
Indices: 29722--29774 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
29712 CAATCAAGCC
29722 AAAAGTTTGATTAGATAGATAAGTAGCA
1 AAAAGTTTGATTAGATAGAT-AGTAGCA
29750 AAAAGTTTGATTAGATAGATAGTAG
1 AAAAGTTTGATTAGATAGATAGTAG
29775 TAGTCAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (27 bp):
AAAAGTTTGATTAGATAGATAGTAGCA
Found at i:32316 original size:1 final size:1
Alignment explanation
Indices: 32312--32342 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
32302 TAAGTTTGTC
32312 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32343 AAATTATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:36725 original size:18 final size:19
Alignment explanation
Indices: 36702--36742 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
36692 AAGATTCATA
36702 TGTATAATAA-TACGCATG
1 TGTATAATAATTACGCATG
*
36720 TGTAT-ATAATTACGTATG
1 TGTATAATAATTACGCATG
36738 -GTATA
1 TGTATA
36743 GTAGGTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTATAATAATTACGCATG
Found at i:39228 original size:23 final size:23
Alignment explanation
Indices: 39166--39229 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 23
39156 GAAAGAAAGA
39166 GACCTAAATTTTGATGTTGAAGT
1 GACCTAAATTTTGATGTTGAAGT
**
39189 GATGTGAAAAGAGTTTTGATGTTGAAGT
1 GACCT---AA-A-TTTTGATGTTGAAGT
39217 GACCTAAATTTTG
1 GACCTAAATTTTG
39230 GACTGGGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
23 8 0.25
24 1 0.03
25 2 0.06
26 2 0.06
27 1 0.03
28 18 0.56
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (23 bp):
GACCTAAATTTTGATGTTGAAGT
Found at i:42119 original size:158 final size:158
Alignment explanation
Indices: 41831--42141 Score: 604
Period size: 158 Copynumber: 2.0 Consensus size: 158
41821 AAAATGAGGG
*
41831 GAAAATTCAATATCCATTTTGGAATTGATATATCATTTCCTTACAAGGTTAAAATATCTATATCT
1 GAAAATTCAATATCCATTTTGGAATGGATATATCATTTCCTTACAAGGTTAAAATATCTATATCT
41896 ATACAAAACAAAGCACAAGGTCTTTATAAGCTATGCTAGCATGACATATGAAACAAGAGGGAAAT
66 ATACAAAACAAAGCACAAGGTCTTTATAAGCTATGCTAGCATGACATATGAAACAAGAGGGAAAT
*
41961 TTTGCAACACTGAGAGTTGCCTGTTGGA
131 TTCGCAACACTGAGAGTTGCCTGTTGGA
41989 GAAAATTCAATATCCATTTTGGAATGGATATATCATTTCCTTACAAGGTTAAAATATCTATATCT
1 GAAAATTCAATATCCATTTTGGAATGGATATATCATTTCCTTACAAGGTTAAAATATCTATATCT
42054 ATACAAAACAAAGCACAAGGTCTTTATAAGCTATGCTAGCATGACATATGAAACAAGAGGGAAAT
66 ATACAAAACAAAGCACAAGGTCTTTATAAGCTATGCTAGCATGACATATGAAACAAGAGGGAAAT
42119 TTCGCAACACTGAGAGTTGCCTG
131 TTCGCAACACTGAGAGTTGCCTG
42142 CTGACTATAC
Statistics
Matches: 151, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 151 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (158 bp):
GAAAATTCAATATCCATTTTGGAATGGATATATCATTTCCTTACAAGGTTAAAATATCTATATCT
ATACAAAACAAAGCACAAGGTCTTTATAAGCTATGCTAGCATGACATATGAAACAAGAGGGAAAT
TTCGCAACACTGAGAGTTGCCTGTTGGA
Done.