Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009536.1 Corchorus capsularis cultivar CVL-1 contig09557, 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: 50477
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:9621 original size:6 final size:6
Alignment explanation
Indices: 9610--9639 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
9600 CTGAGTACAC
*
9610 AACAAG AACAAG AACAAG AACAAC AACAAG
1 AACAAG AACAAG AACAAG AACAAG AACAAG
9640 GCTCCTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.67, C:0.20, G:0.13, T:0.00
Consensus pattern (6 bp):
AACAAG
Found at i:10397 original size:2 final size:2
Alignment explanation
Indices: 10392--10420 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10382 GTATTCCACT
10392 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10421 CCCCTACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12115 original size:2 final size:2
Alignment explanation
Indices: 12108--12134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12098 AATTGAGACA
12108 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12135 CACGTCGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15460 original size:25 final size:25
Alignment explanation
Indices: 15432--15482 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
15422 ACTAAAATTA
15432 TTTTATGCTATTTTATATATGTTCT
1 TTTTATGCTATTTTATATATGTTCT
15457 TTTTATGCTATTTTATATATGTTCT
1 TTTTATGCTATTTTATATATGTTCT
15482 T
1 T
15483 GATCGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.65
Consensus pattern (25 bp):
TTTTATGCTATTTTATATATGTTCT
Found at i:17248 original size:31 final size:32
Alignment explanation
Indices: 17208--17269 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
17198 TTTTTAACCT
17208 AATAACCAAAACCGCACCG-AAACCATTTAAC
1 AATAACCAAAACCGCACCGAAAACCATTTAAC
* *
17239 AATATCCAAATCCGCACCGCAAAACCATTTA
1 AATAACCAAAACCGCACCG-AAAACCATTTA
17270 TTAAGCGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 17 0.63
33 10 0.37
ACGTcount: A:0.45, C:0.32, G:0.06, T:0.16
Consensus pattern (32 bp):
AATAACCAAAACCGCACCGAAAACCATTTAAC
Found at i:21211 original size:5 final size:5
Alignment explanation
Indices: 21203--21230 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
21193 TTCCCACCAA
21203 TTGGT TTGGT TTGGT TTGGT TTGGT TTG
1 TTGGT TTGGT TTGGT TTGGT TTGGT TTG
21231 ATATCTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (5 bp):
TTGGT
Found at i:23556 original size:25 final size:25
Alignment explanation
Indices: 23525--23604 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
23515 CCTCTGCTAA
23525 AGAAAATGACATTGATGGAGGGAAG
1 AGAAAATGACATTGATGGAGGGAAG
* * *
23550 AGAAAAT-ACCGATTCA-AGA-GTAA-
1 AGAAAATGA-C-ATTGATGGAGGGAAG
23573 AGAAAATGACATTGATGGAGGGAAG
1 AGAAAATGACATTGATGGAGGGAAG
23598 AGAAAAT
1 AGAAAAT
23605 ACCGATTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
22 4 0.09
23 10 0.23
24 8 0.19
25 17 0.40
26 4 0.09
ACGTcount: A:0.49, C:0.06, G:0.29, T:0.16
Consensus pattern (25 bp):
AGAAAATGACATTGATGGAGGGAAG
Found at i:23593 original size:48 final size:48
Alignment explanation
Indices: 23522--23617 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
23512 TGGCCTCTGC
23522 TAAAGAAAATGACATTGATGGAGGGAAGAGAAAATACCGATTCAAGAG
1 TAAAGAAAATGACATTGATGGAGGGAAGAGAAAATACCGATTCAAGAG
23570 TAAAGAAAATGACATTGATGGAGGGAAGAGAAAATACCGATTCAAGAG
1 TAAAGAAAATGACATTGATGGAGGGAAGAGAAAATACCGATTCAAGAG
23618 AGTTGGAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.08, G:0.27, T:0.17
Consensus pattern (48 bp):
TAAAGAAAATGACATTGATGGAGGGAAGAGAAAATACCGATTCAAGAG
Found at i:23598 original size:23 final size:23
Alignment explanation
Indices: 23524--23598 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
23514 GCCTCTGCTA
23524 AAGAAAATGACATTGATGGAGGG
1 AAGAAAATGACATTGATGGAGGG
* * **
23547 AAGAGAAAAT-ACCGATTCA-AGAGTA
1 -A-AGAAAATGA-C-ATTGATGGAGGG
23572 AAGAAAATGACATTGATGGAGGG
1 AAGAAAATGACATTGATGGAGGG
23595 AAGA
1 AAGA
23599 GAAAATACCG
Statistics
Matches: 38, Mismatches: 8, Indels: 11
0.67 0.14 0.19
Matches are distributed among these distances:
22 4 0.11
23 15 0.39
24 4 0.11
25 11 0.29
26 4 0.11
ACGTcount: A:0.48, C:0.07, G:0.29, T:0.16
Consensus pattern (23 bp):
AAGAAAATGACATTGATGGAGGG
Found at i:34265 original size:13 final size:13
Alignment explanation
Indices: 34244--34273 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34234 TGGAAATATA
*
34244 TATAGTATGGGTT
1 TATAATATGGGTT
34257 TATAATATGGGTT
1 TATAATATGGGTT
34270 TATA
1 TATA
34274 TATAATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (13 bp):
TATAATATGGGTT
Found at i:40198 original size:3 final size:3
Alignment explanation
Indices: 40192--40222 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
40182 GAAGAAGACA
40192 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G
40223 AGTTTGGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:41785 original size:2 final size:2
Alignment explanation
Indices: 41778--41805 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41768 CAAACAAAGA
41778 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
41806 CTACCATGTT
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:46113 original size:2 final size:2
Alignment explanation
Indices: 46108--46135 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46098 ATATGTATGA
46108 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
46136 GTTTTTCAAG
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:49204 original size:2 final size:2
Alignment explanation
Indices: 49197--49222 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49187 TAATAAATTA
49197 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
49223 TTGTTCGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.