Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015488.1 Corchorus capsularis cultivar CVL-1 contig15509, 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: 41660
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4811 original size:106 final size:106
Alignment explanation
Indices: 4636--4896 Score: 409
Period size: 106 Copynumber: 2.5 Consensus size: 106
4626 TTTTTCTAAT
** *
4636 CCTTAAAATAAAATTTTAATTTTAATTT-GGGTTAAACTTAGT-GAATTAGTTATATATTTTATT
1 CCTTAAAATAAAA-TAAAATTTTAATTTGGGGCTAAACTTAGTGGAATTAGTTATATATTTTATT
*
4699 TCTAAAACCCTATAACAATAAATTATTAATTATGGAATTTAC
65 TCTAAAACCCTATAACAATAAATTATTAATTATGAAATTTAC
* *
4741 CCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGGAATTAGTTTTGTATTTTATTT
1 CCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGGAATTAGTTATATATTTTATTT
* *
4806 CTAAAATCCTATAACAATAAATTATTAATTTTGAAATTTAC
66 CTAAAACCCTATAACAATAAATTATTAATTATGAAATTTAC
*
4847 CCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 CCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGGAATTA
4897 AGGCAAAACT
Statistics
Matches: 144, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
104 12 0.08
105 26 0.18
106 67 0.47
107 39 0.27
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (106 bp):
CCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGGAATTAGTTATATATTTTATTT
CTAAAACCCTATAACAATAAATTATTAATTATGAAATTTAC
Found at i:10312 original size:3 final size:3
Alignment explanation
Indices: 10304--10375 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
10294 GATCATATGC
* * **
10304 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATTC ACC A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA
10349 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
10376 CTATTAAAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 1 0.02
3 59 0.95
4 2 0.03
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:17444 original size:22 final size:19
Alignment explanation
Indices: 17397--17444 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
17387 TAGAACCGAA
17397 TATATTTTAATTACTTTTT
1 TATATTTTAATTACTTTTT
17416 T-TA-TTTAATTTACATATTTT
1 TATATTTTAA-TTAC-T-TTTT
17436 TATATTTTA
1 TATATTTTA
17445 GAATTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 2 0.08
22 4 0.17
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTAATTACTTTTT
Found at i:17655 original size:22 final size:21
Alignment explanation
Indices: 17630--17677 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17620 CCATACCGAC
*
17630 AACCGACCCGCTAACCCGAATA
1 AACCGACACGCTAA-CCGAATA
**
17652 AACCGACACTTTAACCGAATA
1 AACCGACACGCTAACCGAATA
17673 AACCG
1 AACCG
17678 CGAAACCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.40, C:0.35, G:0.12, T:0.12
Consensus pattern (21 bp):
AACCGACACGCTAACCGAATA
Found at i:18461 original size:66 final size:66
Alignment explanation
Indices: 18300--18496 Score: 315
Period size: 66 Copynumber: 3.0 Consensus size: 66
18290 ACTAGACTTT
* ** *
18300 TTGGTCATTTCTCAATTGATTTTAATAGAGTAGTGGAATTACTAAAAGATTCCTACCGTG-TTTG
1 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATTCCTACCAAGACTTG
18364 C
66 C
*
18365 TTGGTCATTTCTCAATTGACTTTAATAGAGTATTGGAATTACTAAAAGATTCCTACCAAGACTTG
1 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATTCCTACCAAGACTTG
18430 C
66 C
* * *
18431 TTGGTCATCTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTATCAAGACTTG
1 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATTCCTACCAAGACTTG
18496 C
66 C
18497 ATTTGGAGCT
Statistics
Matches: 122, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 56 0.46
66 66 0.54
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (66 bp):
TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATTCCTACCAAGACTTG
C
Found at i:18748 original size:166 final size:167
Alignment explanation
Indices: 18431--18779 Score: 506
Period size: 166 Copynumber: 2.1 Consensus size: 167
18421 CAAGACTTGC
* * * * *
18431 TTGGTCATCTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTATCAAGACTTG
1 TTGGTCATTTCTCAATCGACTTGAATAGAGTAGTGGAATTACTAAAAGATCCCCATCAAGAATTG
* * * ***
18496 CATTTGGAGCTAGAGAACTTATTTTTTTCGTCTTTTTCTACTTGGCAGATCACTTAAATGTCCTA
66 CATATGGAGCTAGAGAACTAATCTTTTTCGTCTTCACCTACTTGGCAGATCACTTAAATGTCCTA
* * *
18561 ACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTT
131 ACTTTTAATTCTTGAGGGGATTAAATAACTAAACTTT
18598 TTGGTCATTTCTCAATCGACTTGAATAGAGTAGTGGAATTACTAAAAGATCCCCATCAAGAATTG
1 TTGGTCATTTCTCAATCGACTTGAATAGAGTAGTGGAATTACTAAAAGATCCCCATCAAGAATTG
*
18663 -ATGAT-GAGCTAGAGAACTAATCTTTTTCGTCTTCACCTACTTGGCAGAT-ACTTAACTGTCCT
66 CAT-ATGGAGCTAGAGAACTAATCTTTTTCGTCTTCACCTACTTGGCAGATCACTTAAATGTCCT
* *
18725 AATTTTTTAATTCTTGAGGGGATTAATTAACTAAACTTT
130 AA-CTTTTAATTCTTGAGGGGATTAAATAACTAAACTTT
18764 TTGGTCATTTCTCAAT
1 TTGGTCATTTCTCAAT
18780 TGACAAATGA
Statistics
Matches: 163, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
165 14 0.09
166 88 0.54
167 61 0.37
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (167 bp):
TTGGTCATTTCTCAATCGACTTGAATAGAGTAGTGGAATTACTAAAAGATCCCCATCAAGAATTG
CATATGGAGCTAGAGAACTAATCTTTTTCGTCTTCACCTACTTGGCAGATCACTTAAATGTCCTA
ACTTTTAATTCTTGAGGGGATTAAATAACTAAACTTT
Found at i:21605 original size:20 final size:19
Alignment explanation
Indices: 21580--21619 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21570 CCACTTAGCA
21580 TTTTGGTCCAAACGTGGCAT
1 TTTTGGTCC-AACGTGGCAT
*
21600 TTTTGGTCCGACGTGGCAT
1 TTTTGGTCCAACGTGGCAT
21619 T
1 T
21620 GTCACACGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.38
Consensus pattern (19 bp):
TTTTGGTCCAACGTGGCAT
Found at i:26564 original size:17 final size:17
Alignment explanation
Indices: 26542--26575 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
26532 ATACATAGAG
26542 TTATCTAGTATAACAAA
1 TTATCTAGTATAACAAA
* *
26559 TTATCTGGTGTAACAAA
1 TTATCTAGTATAACAAA
26576 CTTTACAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
TTATCTAGTATAACAAA
Done.