Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009882.1 Corchorus capsularis cultivar CVL-1 contig09903, 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: 15947
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:132 original size:2 final size:2
Alignment explanation
Indices: 127--156 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
117 TATTACTGAC
127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
157 ATAACTATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3420 original size:18 final size:17
Alignment explanation
Indices: 3397--3433 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3387 CAGACAAGTT
*
3397 AAACAATATTTTAAACAA
1 AAACAAAATTTTAAA-AA
3415 AAACAAAATTTTAAAAA
1 AAACAAAATTTTAAAAA
3432 AA
1 AA
3434 GCCACCTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
AAACAAAATTTTAAAAA
Found at i:7612 original size:1 final size:1
Alignment explanation
Indices: 7606--7639 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
7596 CGACAGACTC
7606 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7640 CCTATTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:7739 original size:18 final size:18
Alignment explanation
Indices: 7716--7757 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
7706 ACTGCCCTCC
7716 TTTTTATAATTTTTGACA
1 TTTTTATAATTTTTGACA
7734 TTTTTATAATTTTTGACA
1 TTTTTATAATTTTTGACA
7752 TTTTTA
1 TTTTTA
7758 CTCTTTGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTTTATAATTTTTGACA
Found at i:8005 original size:15 final size:15
Alignment explanation
Indices: 7943--8006 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
7933 TAATTAAGAG
* * *
7943 TAATTAATCATAAAT
1 TAATTAATTAAAAAC
*
7958 TAACTAATT-AAAAC
1 TAATTAATTAAAAAC
* *
7972 TAAGTAATTAAATAC
1 TAATTAATTAAAAAC
*
7987 TAATTAATTAAAAAA
1 TAATTAATTAAAAAC
8002 TAATT
1 TAATT
8007 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 11 0.28
15 28 0.72
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (15 bp):
TAATTAATTAAAAAC
Found at i:8859 original size:27 final size:27
Alignment explanation
Indices: 8828--8883 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
8818 AACCTTTTAA
*
8828 ATTAAATGGTAAAAATAAAATAATTAT
1 ATTAAATGATAAAAATAAAATAATTAT
8855 ATTAAATGATAAAAATAAAATAATTAT
1 ATTAAATGATAAAAATAAAATAATTAT
8882 AT
1 AT
8884 AATATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (27 bp):
ATTAAATGATAAAAATAAAATAATTAT
Found at i:10824 original size:13 final size:13
Alignment explanation
Indices: 10806--10834 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10796 AAAATATATC
10806 ATAAGATAAAATT
1 ATAAGATAAAATT
10819 ATAAGATAAAATT
1 ATAAGATAAAATT
10832 ATA
1 ATA
10835 GAATGTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
ATAAGATAAAATT
Found at i:11514 original size:33 final size:33
Alignment explanation
Indices: 11440--11541 Score: 152
Period size: 33 Copynumber: 3.0 Consensus size: 33
11430 TACTACCTTG
11440 TATATTAGTGACACCTGAAGTTGTCACATGATCAAGA
1 TATATTAGTGACACCTGAAGTTGTCAC---ATCAA-A
*
11477 -ATATTAGTGGCACCTGAAGTTGTCACATCAAA
1 TATATTAGTGACACCTGAAGTTGTCACATCAAA
11509 TATATTAGTGACACCTGAAGTTGTCACATCAAA
1 TATATTAGTGACACCTGAAGTTGTCACATCAAA
11542 GAAATAGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
32 1 0.02
33 36 0.58
36 25 0.40
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (33 bp):
TATATTAGTGACACCTGAAGTTGTCACATCAAA
Found at i:11763 original size:16 final size:16
Alignment explanation
Indices: 11742--11772 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11732 ATGATTTCTT
*
11742 TGTTTGATGTATTTCA
1 TGTTTGATGAATTTCA
11758 TGTTTGATGAATTTC
1 TGTTTGATGAATTTC
11773 TTAATCTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (16 bp):
TGTTTGATGAATTTCA
Found at i:13376 original size:20 final size:19
Alignment explanation
Indices: 13330--13376 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13320 GGCCCAAAGC
* *
13330 AATTTAAGGCCCAATGGGA
1 AATTTAAAGCCCAAGGGGA
*
13349 AATCTAAAGCCCAAGGGGAA
1 AATTTAAAGCCCAAGGGG-A
13369 AATTTAAA
1 AATTTAAA
13377 CCCTACTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (19 bp):
AATTTAAAGCCCAAGGGGA
Found at i:15592 original size:6 final size:6
Alignment explanation
Indices: 15573--15650 Score: 56
Period size: 6 Copynumber: 12.3 Consensus size: 6
15563 AAGTCAACGT
15573 CCCGAA CCCG-- CCCGAA CCCGAA CCCGAAATTA CCCGAA CCCGAAAATA
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCG--A--A CCCGAA CCCG---A-A
15621 CCCGAA CCCG-- CCCGAA CCCGAA CCCGAA CC
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CC
15651 GAGCCCGAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
4 8 0.13
6 38 0.63
7 1 0.02
8 2 0.03
9 1 0.02
10 10 0.17
ACGTcount: A:0.32, C:0.49, G:0.15, T:0.04
Consensus pattern (6 bp):
CCCGAA
Found at i:15594 original size:16 final size:16
Alignment explanation
Indices: 15573--15646 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
15563 AAGTCAACGT
**
15573 CCCGAACCCGCCCGAA
1 CCCGAACCCGCAAGAA
* **
15589 CCCGAACCCGAAATTA
1 CCCGAACCCGCAAGAA
*
15605 CCCGAACCCG-AAAATA
1 CCCGAACCCGCAAGA-A
**
15621 CCCGAACCCGCCCGAA
1 CCCGAACCCGCAAGAA
15637 CCCGAACCCG
1 CCCGAACCCG
15647 AACCGAGCCC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
15 2 0.04
16 43 0.93
17 1 0.02
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (16 bp):
CCCGAACCCGCAAGAA
Done.