Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007578.1 Corchorus capsularis cultivar CVL-1 contig07599, 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: 7373
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:918 original size:22 final size:21
Alignment explanation
Indices: 892--947 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
882 TTCGTGTTTA
*
892 AAGATTATTTGAAGATAATTTG
1 AAGATTATTTGAAGACAA-TTG
914 AAG---ATTTGAAGACAATTG
1 AAGATTATTTGAAGACAATTG
*
932 AAGAATTATTTCAAGA
1 AAG-ATTATTTGAAGA
948 AGCAAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 11 0.39
22 11 0.39
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.34
Consensus pattern (21 bp):
AAGATTATTTGAAGACAATTG
Found at i:922 original size:19 final size:18
Alignment explanation
Indices: 898--935 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
888 TTTAAAGATT
*
898 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
917 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
935 A
1 A
936 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:2329 original size:15 final size:15
Alignment explanation
Indices: 2309--2338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2299 TAGTATTTAG
*
2309 TTTAATTGTTTTCTT
1 TTTAATTGCTTTCTT
2324 TTTAATTGCTTTCTT
1 TTTAATTGCTTTCTT
2339 AAAATCCCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTAATTGCTTTCTT
Found at i:2626 original size:19 final size:19
Alignment explanation
Indices: 2584--2626 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2574 GTTTTTTCTA
2584 AAAAAAAAAAAATTTCGTC
1 AAAAAAAAAAAATTTCGTC
*
2603 GAAAAAAAAAAATTGT-GTC
1 AAAAAAAAAAAATT-TCGTC
2622 AAAAA
1 AAAAA
2627 TAAATTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.65, C:0.07, G:0.09, T:0.19
Consensus pattern (19 bp):
AAAAAAAAAAAATTTCGTC
Found at i:5219 original size:21 final size:19
Alignment explanation
Indices: 5194--5232 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
5184 TATGACTCAT
5194 ATGCTATGAATGCTATGATTG
1 ATGCTATGAAT-CT-TGATTG
*
5215 ATGCTTTGAATCTTGATT
1 ATGCTATGAATCTTGATT
5233 TGCTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
ATGCTATGAATCTTGATTG
Found at i:6663 original size:22 final size:21
Alignment explanation
Indices: 6637--6692 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
6627 TTCATGTTTA
*
6637 AAGATTATTTGAAGATAATTTG
1 AAGATTATTTGAAGACAA-TTG
6659 AAG---ATTTGAAGACAATTG
1 AAGATTATTTGAAGACAATTG
*
6677 AAGAATTATTTCAAGA
1 AAG-ATTATTTGAAGA
6693 AGCAAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 11 0.39
22 11 0.39
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.34
Consensus pattern (21 bp):
AAGATTATTTGAAGACAATTG
Found at i:6667 original size:19 final size:18
Alignment explanation
Indices: 6643--6680 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
6633 TTTAAAGATT
*
6643 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
6662 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
6680 A
1 A
6681 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Done.