Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008834.1 Corchorus capsularis cultivar CVL-1 contig08855, 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: 44397
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:13512 original size:2 final size:2
Alignment explanation
Indices: 13500--13548 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
13490 GAATAAACAT
* *
13500 TA TA T- TA TA TA TA TA TA TA TA TA TA TG CA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13540 TA TA TA TA T
1 TA TA TA TA T
13549 TTCGGGGCCG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17248 original size:2 final size:2
Alignment explanation
Indices: 17241--17269 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17231 ATATTTTGCC
17241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17270 GATTTACCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22081 original size:3 final size:3
Alignment explanation
Indices: 22073--22103 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
22063 GAAGTTCTAG
22073 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22104 AAAGTAAATT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27344 original size:21 final size:21
Alignment explanation
Indices: 27319--27360 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27309 AAGTGAGGGC
27319 GGAGGAC-GAGCCAGAAGATGA
1 GGAGGACAGAGCC-GAAGATGA
*
27340 GGAGGACAGTGCCGAAGATGA
1 GGAGGACAGAGCCGAAGATGA
27361 TTAAGAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.36, C:0.14, G:0.43, T:0.07
Consensus pattern (21 bp):
GGAGGACAGAGCCGAAGATGA
Found at i:28411 original size:11 final size:11
Alignment explanation
Indices: 28395--28426 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28385 TATACTATAT
28395 CTAATTAATAA
1 CTAATTAATAA
*
28406 CTAATTAATAT
1 CTAATTAATAA
28417 CTAATTAATA
1 CTAATTAATA
28427 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:31808 original size:21 final size:21
Alignment explanation
Indices: 31783--31861 Score: 83
Period size: 21 Copynumber: 3.7 Consensus size: 21
31773 TATCTTAGAT
31783 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
31804 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* *
31825 ATAAATAAT-GATTTAAAATAA
1 AT-AATAATATATTTTAAATAA
31846 ATAAATAATATATTTT
1 AT-AATAATATATTTT
31862 TAATTACTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
20 8 0.16
21 21 0.43
22 13 0.27
23 7 0.14
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:31816 original size:25 final size:25
Alignment explanation
Indices: 31785--31833 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
31775 TCTTAGATAT
*
31785 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
31810 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
31834 GATTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:31822 original size:18 final size:19
Alignment explanation
Indices: 31801--31852 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
31791 TATTATTAAA
31801 TAAATAATAAATAT-ATTT
1 TAAATAATAAATATGATTT
31819 TAAATAATAAATAATGATTT
1 TAAATAATAAAT-ATGATTT
*
31839 AAAATAAATAAATA
1 TAAAT-AATAAATA
31853 ATATATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 12 0.40
19 2 0.07
20 9 0.30
21 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATAATAAATATGATTT
Found at i:38830 original size:24 final size:24
Alignment explanation
Indices: 38798--38876 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
38788 ATAATGGAGA
*
38798 ATCTTCTTCTTCGGCTATGCTATC
1 ATCTTCTTCTTCGGCTATGGTATC
*
38822 ATCTTCTTCGGCTACGGCTATGGTATC
1 ATCTTCTT---CTTCGGCTATGGTATC
**
38849 ATGATCTTCTTCGGCTATGGTATC
1 ATCTTCTTCTTCGGCTATGGTATC
38873 ATCT
1 ATCT
38877 CCACCATTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
24 25 0.56
27 20 0.44
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (24 bp):
ATCTTCTTCTTCGGCTATGGTATC
Found at i:38839 original size:27 final size:28
Alignment explanation
Indices: 38809--38865 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
38799 TCTTCTTCTT
38809 CGGCTATGCTATC-ATCTTCTTCGGCTA
1 CGGCTATGCTATCAATCTTCTTCGGCTA
*
38836 CGGCTATGGTATCATGATCTTCTTCGGCTA
1 CGGCTATGCTATCA--ATCTTCTTCGGCTA
38866 TGGTATCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.46
30 14 0.54
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (28 bp):
CGGCTATGCTATCAATCTTCTTCGGCTA
Done.