Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011171.1 Corchorus capsularis cultivar CVL-1 contig11192, 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: 16319
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:980 original size:39 final size:39
Alignment explanation
Indices: 926--1073 Score: 287
Period size: 39 Copynumber: 3.8 Consensus size: 39
916 ATTGGGTGTA
926 CAAAATTGGTTACTAATTACTAATTCATATATCGTTGTT
1 CAAAATTGGTTACTAATTACTAATTCATATATCGTTGTT
*
965 CAAAATTGGTTACTAATTACTAATTCATATATCGTTGTA
1 CAAAATTGGTTACTAATTACTAATTCATATATCGTTGTT
1004 CAAAATTGGTTACTAATTACTAATTCATATATCGTTGTT
1 CAAAATTGGTTACTAATTACTAATTCATATATCGTTGTT
1043 CAAAATTGGTTACTAATTACTAATTCATATA
1 CAAAATTGGTTACTAATTACTAATTCATATA
1074 ACCTTCATTT
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 107 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (39 bp):
CAAAATTGGTTACTAATTACTAATTCATATATCGTTGTT
Found at i:5901 original size:18 final size:18
Alignment explanation
Indices: 5878--5913 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5868 GATGACAACA
5878 GATATATGAAGTTGCAAT
1 GATATATGAAGTTGCAAT
5896 GATATATGAAGTTGCAAT
1 GATATATGAAGTTGCAAT
5914 TATTAGGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (18 bp):
GATATATGAAGTTGCAAT
Found at i:7433 original size:2 final size:2
Alignment explanation
Indices: 7426--7475 Score: 66
Period size: 2 Copynumber: 24.5 Consensus size: 2
7416 TTATTTAATA
*
7426 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AC ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
7468 ACT AT AT A
1 A-T AT AT A
7476 CTCCCTCTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 1 0.02
2 39 0.91
3 3 0.07
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7436 original size:17 final size:19
Alignment explanation
Indices: 7414--7474 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 19
7404 TGGCTAAGAT
*
7414 TATTATTTA-ATA-ATATA
1 TATTATATATATATATATA
7431 TATTATATATATATATATA
1 TATTATATATATATATATA
*
7450 TATATATATACACTATATACTA
1 TAT-TATATATA-TATATA-TA
7472 TAT
1 TAT
7475 ACTCCCTCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.22
18 3 0.08
19 8 0.22
20 7 0.19
21 6 0.16
22 5 0.14
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATATATATATATATA
Found at i:7665 original size:17 final size:19
Alignment explanation
Indices: 7628--7667 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
7618 AATTCATTTT
7628 GACTAAGTGGGAGGAGAGA
1 GACTAAGTGGGAGGAGAGA
* *
7647 GACTTAGTGGGGGGAGAGA
1 GACTAAGTGGGAGGAGAGA
7666 GA
1 GA
7668 AGAGGGGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.50, T:0.12
Consensus pattern (19 bp):
GACTAAGTGGGAGGAGAGA
Found at i:12225 original size:15 final size:15
Alignment explanation
Indices: 12205--12234 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12195 AATTTTTTTC
12205 TAATAAGATATCCTT
1 TAATAAGATATCCTT
12220 TAATAAGATATCCTT
1 TAATAAGATATCCTT
12235 GAACAGCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
TAATAAGATATCCTT
Found at i:14238 original size:3 final size:3
Alignment explanation
Indices: 14230--14283 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
14220 TCCCTACCCA
14230 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14278 TAT TAT
1 TAT TAT
14284 ATATAAATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15014 original size:24 final size:25
Alignment explanation
Indices: 14987--15040 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
14977 AAGAAGTAAA
14987 AATAATTCAAAAAATAGTAA-TAAT
1 AATAATTCAAAAAATAGTAACTAAT
* **
15011 AAT-ATTTAAAATGTAGTAACTAAT
1 AATAATTCAAAAAATAGTAACTAAT
*
15035 TATAAT
1 AATAAT
15041 ATATATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 13 0.54
24 9 0.38
25 2 0.08
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (25 bp):
AATAATTCAAAAAATAGTAACTAAT
Done.