Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016698.1 Corchorus olitorius cultivar O-4 contig16731, 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: 16587
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Found at i:264 original size:15 final size:16
Alignment explanation
Indices: 244--273 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
234 TGTAAGTTTA
244 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
259 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
274 GAATTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:11833 original size:12 final size:12
Alignment explanation
Indices: 11816--11841 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11806 ATGTAAATTC
11816 ACACCTTGAAAT
1 ACACCTTGAAAT
11828 ACACCTTGAAAT
1 ACACCTTGAAAT
11840 AC
1 AC
11842 TATTCAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (12 bp):
ACACCTTGAAAT
Found at i:12573 original size:13 final size:13
Alignment explanation
Indices: 12557--12581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12547 CTAAGTCAAC
12557 CTGCCACGTCATT
1 CTGCCACGTCATT
12570 CTGCCACGTCAT
1 CTGCCACGTCAT
12582 CACTGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (13 bp):
CTGCCACGTCATT
Found at i:12589 original size:44 final size:44
Alignment explanation
Indices: 12526--12704 Score: 175
Period size: 44 Copynumber: 4.0 Consensus size: 44
12516 CAATCCGCTG
* * *
12526 CTGCCACATCATCACTGTTGACTAAGTCAACCTGCCACGTCATT
1 CTGCCACGTCATCACTGTTGACTAAGTCAACCTGCCACATCATC
*
12570 CTGCCACGTCATCACTGTTGACTAAGTCAACCCGCCACATCATC
1 CTGCCACGTCATCACTGTTGACTAAGTCAACCTGCCACATCATC
* * * ** *
12614 CTACCACGTCATCCATTGACCGTTTACCGAGTCAACCTGCCACATCATG
1 CTGCCACGTCAT-C----ACTGTTGACTAAGTCAACCTGCCACATCATC
* * *
12663 CTGCCACGTCAT-AC-GTTGAC-CAGTCAACCTACCACGTCATC
1 CTGCCACGTCATCACTGTTGACTAAGTCAACCTGCCACATCATC
12704 C
1 C
12705 GTTGACCAGT
Statistics
Matches: 113, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
41 18 0.16
42 5 0.04
43 2 0.02
44 51 0.45
45 1 0.01
49 36 0.32
ACGTcount: A:0.25, C:0.37, G:0.14, T:0.24
Consensus pattern (44 bp):
CTGCCACGTCATCACTGTTGACTAAGTCAACCTGCCACATCATC
Found at i:12698 original size:28 final size:28
Alignment explanation
Indices: 12666--12738 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
12656 CATCATGCTG
*
12666 CCACGTCATACGTTGACCAGTCAACCTA
1 CCACGTCATCCGTTGACCAGTCAACCTA
12694 CCACGTCATCCGTTGACCAGTCAACCTA
1 CCACGTCATCCGTTGACCAGTCAACCTA
12722 CCACGTCATCCGTTGAC
1 CCACGTCATCCGTTGAC
12739 TGGGTCAACC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.22
Consensus pattern (28 bp):
CCACGTCATCCGTTGACCAGTCAACCTA
Found at i:12958 original size:18 final size:18
Alignment explanation
Indices: 12935--13058 Score: 133
Period size: 18 Copynumber: 7.3 Consensus size: 18
12925 CTATTTTCTG
12935 CCTGTTTGACCTCTTGGT
1 CCTGTTTGACCTCTTGGT
12953 CCTGTTTGACCTCTTGGT
1 CCTGTTTGACCTCTTGGT
12971 CCTGTTTGACC-CTTTGGT
1 CCTGTTTGACCTC-TTGGT
12989 CCTGTTT----TC-T-G-
1 CCTGTTTGACCTCTTGGT
* *
13000 CTTGTTCGACCTCTTGGT
1 CCTGTTTGACCTCTTGGT
13018 CCTGTTTGACCT-TTCGGT
1 CCTGTTTGACCTCTT-GGT
13036 CCTGTTTGACCT-TTCGGT
1 CCTGTTTGACCTCTT-GGT
13054 CCTGT
1 CCTGT
13059 ATTTTAGCCC
Statistics
Matches: 92, Mismatches: 4, Indels: 20
0.79 0.03 0.17
Matches are distributed among these distances:
11 5 0.05
12 1 0.01
13 1 0.01
15 3 0.03
16 1 0.01
17 4 0.04
18 77 0.84
ACGTcount: A:0.05, C:0.28, G:0.22, T:0.45
Consensus pattern (18 bp):
CCTGTTTGACCTCTTGGT
Found at i:13057 original size:65 final size:65
Alignment explanation
Indices: 12910--13058 Score: 232
Period size: 65 Copynumber: 2.3 Consensus size: 65
12900 AGTTTGCTCC
* *
12910 GTTTGACCTTTC-GTCCTATTTTCTGCCTGTTTGACCTCTTGGTCCTGTTTGACCTCTTGGTCCT
1 GTTTGACCTTTCGGTCCTGTTTTCTGCCTGTTCGACCTCTTGGTCCTGTTTGACCTCTTGGTCCT
*
12974 GTTTGACCCTTT-GGTCCTGTTTTCTGCTTGTTCGACCTCTTGGTCCTGTTTGACCT-TTCGGTC
1 GTTTGA-CCTTTCGGTCCTGTTTTCTGCCTGTTCGACCTCTTGGTCCTGTTTGACCTCTT-GGTC
13037 CT
64 CT
13039 GTTTGACCTTTCGGTCCTGT
1 GTTTGACCTTTCGGTCCTGT
13059 ATTTTAGCCC
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
64 13 0.17
65 65 0.83
ACGTcount: A:0.05, C:0.28, G:0.21, T:0.46
Consensus pattern (65 bp):
GTTTGACCTTTCGGTCCTGTTTTCTGCCTGTTCGACCTCTTGGTCCTGTTTGACCTCTTGGTCCT
Found at i:13324 original size:12 final size:12
Alignment explanation
Indices: 13307--13332 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13297 ATGTAAATTC
13307 ACACCTTGAAAT
1 ACACCTTGAAAT
13319 ACACCTTGAAAT
1 ACACCTTGAAAT
13331 AC
1 AC
13333 TATTCAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (12 bp):
ACACCTTGAAAT
Done.