Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015278.1 Corchorus capsularis cultivar CVL-1 contig15299, 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: 13993
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Found at i:929 original size:134 final size:134
Alignment explanation
Indices: 767--1035 Score: 529
Period size: 134 Copynumber: 2.0 Consensus size: 134
757 TCTTTTTCAG
767 TACCAAATCTCCTTCTTTGAACTCTCTCGGGCGTATTTTCTTGTTAAATGCCCGCTCCATCCTCT
1 TACCAAATCTCCTTCTTTGAACTCTCTCGGGCGTATTTTCTTGTTAAATGCCCGCTCCATCCTCT
832 TTTGGTACATTTGGCCATGACATAAAGTCGTTACCCTTTTCTCGTCAACCAAGTTAAGCTGATCA
66 TTTGGTACATTTGGCCATGACATAAAGTCGTTACCCTTTTCTCGTCAACCAAGTTAAGCTGATCA
897 TACC
131 TACC
*
901 TACCAAATCTCCTTGTTTGAACTCTCTCGGGCGTATTTTCTTGTTAAATGCCCGCTCCATCCTCT
1 TACCAAATCTCCTTCTTTGAACTCTCTCGGGCGTATTTTCTTGTTAAATGCCCGCTCCATCCTCT
966 TTTGGTACATTTGGCCATGACATAAAGTCGTTACCCTTTTCTCGTCAACCAAGTTAAGCTGATCA
66 TTTGGTACATTTGGCCATGACATAAAGTCGTTACCCTTTTCTCGTCAACCAAGTTAAGCTGATCA
1031 TACC
131 TACC
1035 T
1 T
1036 CTCTTGAACC
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (134 bp):
TACCAAATCTCCTTCTTTGAACTCTCTCGGGCGTATTTTCTTGTTAAATGCCCGCTCCATCCTCT
TTTGGTACATTTGGCCATGACATAAAGTCGTTACCCTTTTCTCGTCAACCAAGTTAAGCTGATCA
TACC
Found at i:12141 original size:13 final size:13
Alignment explanation
Indices: 12096--12142 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
12086 ATCATTTTTA
*
12096 CTCTTTTCTTACT
1 CTCTTTTCTTATT
*
12109 CT-TTTTACTAATT
1 CTCTTTT-CTTATT
12122 ACTCTTTTCTTATT
1 -CTCTTTTCTTATT
12136 CTCTTTT
1 CTCTTTT
12143 ATTGATTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 13 0.46
14 7 0.25
15 4 0.14
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (13 bp):
CTCTTTTCTTATT
Found at i:12249 original size:21 final size:21
Alignment explanation
Indices: 12202--12249 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
12192 TTACTCTTTG
12202 AATTACTGATCACCCTTTACT
1 AATTACTGATCACCCTTTACT
** *
12223 CTTTACTGATTACTCC-TTACT
1 AATTACTGATCAC-CCTTTACT
12244 AATTAC
1 AATTAC
12250 CATTTTGCTC
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.27, C:0.27, G:0.04, T:0.42
Consensus pattern (21 bp):
AATTACTGATCACCCTTTACT
Found at i:12269 original size:21 final size:21
Alignment explanation
Indices: 12245--12299 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
12235 CTCCTTACTA
* **
12245 ATTACCATTTTGCTCTTTCTG
1 ATTACCATTTTACTCTGACTG
*
12266 ATTACTATTTTACTCTGACTG
1 ATTACCATTTTACTCTGACTG
12287 ATTACC-TTTTACT
1 ATTACCATTTTACT
12300 GATTACTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTACCATTTTACTCTGACTG
Found at i:12302 original size:14 final size:14
Alignment explanation
Indices: 12283--12327 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
12273 TTTTACTCTG
12283 ACTGATTACCTTTT
1 ACTGATTACCTTTT
*
12297 ACTGATTA-CTATT
1 ACTGATTACCTTTT
*
12310 ACCTGATTACATTTT
1 A-CTGATTACCTTTT
12325 ACT
1 ACT
12328 ACTCGTTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.19
14 17 0.65
15 4 0.15
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (14 bp):
ACTGATTACCTTTT
Found at i:12428 original size:26 final size:27
Alignment explanation
Indices: 12382--12449 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
12372 CTCTTTACTG
**
12382 ATTACTATTTT-ACCCTCTTGAACTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
*
12408 ATTACTATTTTCATTCT-TTGAATTTA
1 ATTACTATTTTCATTCTCTTGAACTTA
* *
12434 ATCACCATTTGTCATT
1 ATTACTATTT-TCATT
12450 TTACTCTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.50
Consensus pattern (27 bp):
ATTACTATTTTCATTCTCTTGAACTTA
Found at i:12458 original size:32 final size:32
Alignment explanation
Indices: 12422--12491 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
12412 CTATTTTCAT
12422 TCTTTGAATTTAATCACCATTTGT-CATTTTAC
1 TCTTTGAATTTAATCACCATTT-TACATTTTAC
* **
12454 TCTTTGGATTTAATTGCCATTTTACCATTTTAC
1 TCTTTGAATTTAATCACCATTTTA-CATTTTAC
12487 TCTTT
1 TCTTT
12492 ACCGATTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 1 0.03
32 19 0.58
33 13 0.39
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (32 bp):
TCTTTGAATTTAATCACCATTTTACATTTTAC
Found at i:12541 original size:40 final size:41
Alignment explanation
Indices: 12490--12603 Score: 167
Period size: 42 Copynumber: 2.8 Consensus size: 41
12480 ATTTTACTCT
*
12490 TTACCGATTTACTGATTACTTCTTTTACTTTTA-CTCTTAA
1 TTACCAATTTACTGATTACTTCTTTTACTTTTACCTCTTAA
* * *
12530 TTACCATTTTACTGATTACTTCTTTTGCTTTTACTCTCTTGA
1 TTACCAATTTACTGATTACTTCTTTTACTTTTAC-CTCTTAA
*
12572 TTACCAACTTACTGATTACTTCTTTTACTTTT
1 TTACCAATTTACTGATTACTTCTTTTACTTTT
12604 GCCCTTTTAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 30 0.46
42 35 0.54
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (41 bp):
TTACCAATTTACTGATTACTTCTTTTACTTTTACCTCTTAA
Done.