Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017484.1 Corchorus olitorius cultivar O-4 contig17517, 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: 30887
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1720 original size:9 final size:9
Alignment explanation
Indices: 1706--1735 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1696 CTCCATAATT
1706 TTTTATTTA
1 TTTTATTTA
1715 TTTTATTTA
1 TTTTATTTA
1724 -TTTATTTA
1 TTTTATTTA
1732 TTTT
1 TTTT
1736 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1729 original size:17 final size:16
Alignment explanation
Indices: 1703--1742 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
1693 TTGCTCCATA
1703 ATTTTTTATTTATTTT
1 ATTTTTTATTTATTTT
1719 ATTTATTTATTTATTTT
1 ATTT-TTTATTTATTTT
*
1736 CTTTTTT
1 ATTTTTT
1743 TTTTGGCCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
ATTTTTTATTTATTTT
Found at i:10296 original size:3 final size:3
Alignment explanation
Indices: 10288--10330 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
10278 CATGTTTCAG
*
10288 GAT GAT GAT GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
10331 TCAATGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:11117 original size:34 final size:34
Alignment explanation
Indices: 11074--11143 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
11064 AAGGCTCAGA
*
11074 AAGTGTTTACAATGATACTTACAAATTATTCACC
1 AAGTGTTTACAATGATACTTACAAATTATCCACC
*
11108 AAGTGTTTACAGTGATACTTACAAATTATCCACC
1 AAGTGTTTACAATGATACTTACAAATTATCCACC
11142 AA
1 AA
11144 CGAGGGCCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (34 bp):
AAGTGTTTACAATGATACTTACAAATTATCCACC
Found at i:19389 original size:21 final size:22
Alignment explanation
Indices: 19365--19421 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
19355 ATCAACATAC
* *
19365 AAAACCCACATACATTCAAAAA
1 AAAATCCACAAACATTCAAAAA
*
19387 AAAATCCACAAACATTC-AAGA
1 AAAATCCACAAACATTCAAAAA
19408 AAAATCCACAAACA
1 AAAATCCACAAACA
19422 AATCCACATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.60, C:0.26, G:0.02, T:0.12
Consensus pattern (22 bp):
AAAATCCACAAACATTCAAAAA
Found at i:24468 original size:3 final size:3
Alignment explanation
Indices: 24462--24493 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24452 TCGTAGAACG
24462 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24494 TATATATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:26887 original size:11 final size:11
Alignment explanation
Indices: 26871--26897 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
26861 GTGTGTATTG
26871 GTGTGTTTACA
1 GTGTGTTTACA
26882 GTGTGTTTACA
1 GTGTGTTTACA
26893 GTGTG
1 GTGTG
26898 CTTCATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.44
Consensus pattern (11 bp):
GTGTGTTTACA
Found at i:30044 original size:76 final size:76
Alignment explanation
Indices: 29907--30058 Score: 168
Period size: 76 Copynumber: 2.0 Consensus size: 76
29897 ACAAGGACCC
* * *
29907 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
29972 GGG-TAGTGTCA
66 GGGCT-GTGTCA
* * * **
29983 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
30045 GATGGGCTGTGTCA
63 GATGGGCTGTGTCA
30059 AAGCTCATCA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
75 4 0.06
76 53 0.83
77 7 0.11
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCTGTGTCA
Done.