Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011333.1 Corchorus capsularis cultivar CVL-1 contig11354, 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: 34244
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8515 original size:17 final size:17
Alignment explanation
Indices: 8493--8550 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
8483 ATAGATCCAT
8493 GTGATCTTGTATCACTG
1 GTGATCTTGTATCACTG
*
8510 GTGATCTTGCATCACTG
1 GTGATCTTGTATCACTG
*
8527 GTGATCTT-TGATCACTA
1 GTGATCTTGT-ATCACTG
8544 GTGATCT
1 GTGATCT
8551 GGGGAGTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (17 bp):
GTGATCTTGTATCACTG
Found at i:8800 original size:59 final size:59
Alignment explanation
Indices: 8727--8841 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
8717 CTAAATCAAA
8727 GAGCATAACATCATCTCTTATTCTAAATCGAAAGAATGCATGTTTTTAATTAATTCCTG
1 GAGCATAACATCATCTCTTATTCTAAATCGAAAGAATGCATGTTTTTAATTAATTCCTG
*
8786 GAGCATAAGATCATCTCTTATTCTAAATCGAAAGAATGCATGTTTTTAATTAATTC
1 GAGCATAACATCATCTCTTATTCTAAATCGAAAGAATGCATGTTTTTAATTAATTC
8842 TTGTTGCTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (59 bp):
GAGCATAACATCATCTCTTATTCTAAATCGAAAGAATGCATGTTTTTAATTAATTCCTG
Found at i:9792 original size:9 final size:9
Alignment explanation
Indices: 9780--9814 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
9770 AAAATAAAAT
9780 AAATTAATA
1 AAATTAATA
9789 AAATTAATA
1 AAATTAATA
*
9798 AATAGTAATA
1 AA-ATTAATA
9808 AAATTAA
1 AAATTAA
9815 AATTAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
AAATTAATA
Found at i:14849 original size:2 final size:2
Alignment explanation
Indices: 14842--14866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14832 TACCTAGTAG
14842 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
14867 TTTTTTCAAA
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:15594 original size:2 final size:2
Alignment explanation
Indices: 15582--15612 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15572 AAATTGGAAG
*
15582 GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
15613 GATTGGGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:18257 original size:1 final size:1
Alignment explanation
Indices: 18251--18281 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
18241 CATTCTTAGC
*
18251 AAAAAAAAAAAAAAAAAAGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18282 CAGTTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:29266 original size:6 final size:6
Alignment explanation
Indices: 29257--29284 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29247 TTAATTTGGG
29257 AAGAAC AAGAAC AAGAAC AAGAAC AAGA
1 AAGAAC AAGAAC AAGAAC AAGAAC AAGA
29285 TTAGATGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.14, G:0.18, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:31146 original size:4 final size:4
Alignment explanation
Indices: 31137--31171 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
31127 GGCCAACGAT
31137 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
31172 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:34220 original size:2 final size:2
Alignment explanation
Indices: 34213--34242 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34203 AATTATTAAG
34213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34243 CA
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):
AT
Done.