Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014312.1 Corchorus olitorius cultivar O-4 contig14345, 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: 31858
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:13295 original size:69 final size:70
Alignment explanation
Indices: 13183--13336 Score: 220
Period size: 69 Copynumber: 2.2 Consensus size: 70
13173 GCAACAACTT
* *
13183 CTGGACAAGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTT-TACGCTCCTCAAAAGCCC
1 CTGGACAGGACTTGGGTAACTCCTGCCCAGGCCTTGTCCTGTATTTCTACGCTCCTCAAAAGCCC
*
13247 ACGTC
66 AAGTC
* * * * * *
13252 TTGGACAGGAGTTGGGTAACTCCTGCCCATGCCTTGTCCTGTATTTCTGCGTTCCTCAACAGCCC
1 CTGGACAGGACTTGGGTAACTCCTGCCCAGGCCTTGTCCTGTATTTCTACGCTCCTCAAAAGCCC
13317 AAGTC
66 AAGTC
13322 CTGGACAGGACTTGG
1 CTGGACAGGACTTGG
13337 CCAAGATGTG
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
69 41 0.56
70 32 0.44
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (70 bp):
CTGGACAGGACTTGGGTAACTCCTGCCCAGGCCTTGTCCTGTATTTCTACGCTCCTCAAAAGCCC
AAGTC
Found at i:16923 original size:19 final size:18
Alignment explanation
Indices: 16890--16925 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16880 TGGAAATAAT
16890 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
16908 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
16926 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:17512 original size:3 final size:3
Alignment explanation
Indices: 17497--17527 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
17487 CATCCATCAG
*
17497 ATC ATC TTC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
17528 GCTGCAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:25673 original size:37 final size:36
Alignment explanation
Indices: 25594--25733 Score: 212
Period size: 37 Copynumber: 3.9 Consensus size: 36
25584 AAAAATGCTT
25594 TTGATGGGAACTTTCCCAATTTGAAAAC-T-AAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAACTTGAAAAC
* *
25628 CTGATGGGAATTTTCCCAATTTGAAAACTTGAAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAACTTG-AAAAC
*
25665 TTGATGGGAACTTTCCCAGTTTGAAAACTTTGAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAAC-TTGAAAAC
*
25702 TTGATGGGAATTTTCCCAATTTGAAAACTTGA
1 TTGATGGGAACTTTCCCAATTTGAAAACTTGA
25734 TGGGAACTTT
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.27
35 1 0.01
36 4 0.04
37 61 0.64
38 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (36 bp):
TTGATGGGAACTTTCCCAATTTGAAAACTTGAAAAC
Found at i:25725 original size:28 final size:28
Alignment explanation
Indices: 25693--25756 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
25683 GTTTGAAAAC
*
25693 TTTGAAAACTTGATGGGAATTTTCCCAA
1 TTTGAAAACTTGATGGGAACTTTCCCAA
25721 TTTGAAAACTTGATGGGAACTTTCCCAA
1 TTTGAAAACTTGATGGGAACTTTCCCAA
25749 TTTGAAAA
1 TTTGAAAA
25757 GAGCTAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (28 bp):
TTTGAAAACTTGATGGGAACTTTCCCAA
Found at i:25725 original size:74 final size:71
Alignment explanation
Indices: 25594--25733 Score: 235
Period size: 74 Copynumber: 1.9 Consensus size: 71
25584 AAAAATGCTT
25594 TTGATGGGAACTTTCCCAATTTGAAAACTAAAACCTGATGGGAATTTTCCCAATTTGAAAACTTG
1 TTGATGGGAACTTTCCCAATTTGAAAACTAAAACCTGATGGGAATTTTCCCAATTTGAAAACTTG
25659 AAAAAC
66 AAAAAC
* *
25665 TTGATGGGAACTTTCCCAGTTTGAAAACTTTGAAAACTTGATGGGAATTTTCCCAATTTGAAAAC
1 TTGATGGGAACTTTCCCAATTTGAAAAC--T-AAAACCTGATGGGAATTTTCCCAATTTGAAAAC
25730 TTGA
63 TTGA
25734 TGGGAACTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
71 27 0.42
73 1 0.02
74 36 0.56
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (71 bp):
TTGATGGGAACTTTCCCAATTTGAAAACTAAAACCTGATGGGAATTTTCCCAATTTGAAAACTTG
AAAAAC
Found at i:25780 original size:52 final size:52
Alignment explanation
Indices: 25721--25860 Score: 235
Period size: 52 Copynumber: 2.7 Consensus size: 52
25711 ATTTTCCCAA
* * *
25721 TTTGAAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATTGAATAC
1 TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACAC
*
25773 TTTGAAAACTTGATGGAAACTTTCCCACTTTGAAAAGACCTAAATTGAACAC
1 TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACAC
*
25825 TTTGAAAACTTGTTGGGAACTTTCCCACTTTGAAAA
1 TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
25861 CTTTGAAAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (52 bp):
TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACAC
Found at i:29635 original size:21 final size:21
Alignment explanation
Indices: 29601--29649 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
29591 TAAAAATCAC
* *
29601 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
29621 AATTAGAAAACAAAGCAAAGTA
1 AATTA-AAAACAAAGCAAAGTA
29643 AATTAAA
1 AATTAAA
29650 TCTAAGTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 11 0.44
22 9 0.36
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.18
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Done.