Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013355.1 Corchorus capsularis cultivar CVL-1 contig13376, 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: 32352
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12248 original size:1 final size:1
Alignment explanation
Indices: 12242--12274 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
12232 ACCAAGAGAC
12242 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12275 CCCTACTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19073 original size:2 final size:2
Alignment explanation
Indices: 19066--19096 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19056 TTTATGGCAT
19066 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19097 GTTTGATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20766 original size:2 final size:2
Alignment explanation
Indices: 20759--20791 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20749 ATTAAAGCGT
20759 TA TA 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 TA TA T
20792 CAGTATATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24529 original size:33 final size:33
Alignment explanation
Indices: 24480--24547 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
24470 GGCAATTTAG
*
24480 AAATATATTTTGAAAAAAAAAGGTATAATC-GA
1 AAATATATTTTGAAAAAAAAAGGTACAATCGGA
24512 AAATAT-TATTTGAAAAAAAAAGGTACAATCGGA
1 AAATATAT-TTTGAAAAAAAAAGGTACAATCGGA
24545 AAA
1 AAA
24548 CATAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.03
32 27 0.82
33 5 0.15
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.25
Consensus pattern (33 bp):
AAATATATTTTGAAAAAAAAAGGTACAATCGGA
Found at i:29783 original size:2 final size:2
Alignment explanation
Indices: 29776--29800 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29766 ATAATTAGTT
29776 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 T
29801 TAAGGGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30319 original size:29 final size:29
Alignment explanation
Indices: 30287--30345 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
30277 TTTTGTTCCC
* *
30287 TGAACTTTAATTTTGGACATTTTACCCCA
1 TGAACTTCAATTTGGGACATTTTACCCCA
* *
30316 TGAACTTCAATTTGGGACGTTTTGCCCCA
1 TGAACTTCAATTTGGGACATTTTACCCCA
30345 T
1 T
30346 CAGACTAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (29 bp):
TGAACTTCAATTTGGGACATTTTACCCCA
Found at i:30764 original size:7 final size:7
Alignment explanation
Indices: 30752--30781 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
30742 ATATAGTACT
30752 TATTATA
1 TATTATA
30759 TATTATA
1 TATTATA
30766 TATTATA
1 TATTATA
30773 TATTATA
1 TATTATA
30780 TA
1 TA
30782 AAGCATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTATA
Found at i:30765 original size:21 final size:21
Alignment explanation
Indices: 30741--30781 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30731 TATAAAAAAC
30741 TATATAGTACT-TATTATATAT
1 TATATAGTA-TATATTATATAT
*
30762 TATATATTATATATTATATA
1 TATATAGTATATATTATATA
30782 AAGCATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TATATAGTATATATTATATAT
Done.