Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013140.1 Corchorus olitorius cultivar O-4 contig13173, 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: 30313
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:639 original size:24 final size:23
Alignment explanation
Indices: 598--649 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
588 AAACACAACT
* * *
598 AAACAAAACAGACCTCAATAAAAC
1 AAACAAAAAAAACATCAA-AAAAC
*
622 AAACAAAAAAAACATCAAAGAAC
1 AAACAAAAAAAACATCAAAAAAC
645 AAACA
1 AAACA
650 GGAAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.06
Consensus pattern (23 bp):
AAACAAAAAAAACATCAAAAAAC
Found at i:2172 original size:20 final size:19
Alignment explanation
Indices: 2149--2191 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2139 AAACAATTAC
2149 AAAAACAAAAACAG-GAAAA
1 AAAAACAAAAA-AGCGAAAA
**
2168 AAAAACGCAAAAGCGAAAA
1 AAAAACAAAAAAGCGAAAA
2187 AAAAA
1 AAAAA
2192 ACTTGTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.77, C:0.12, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAGCGAAAA
Found at i:10266 original size:24 final size:24
Alignment explanation
Indices: 10239--10286 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
10229 TTTATCTTTC
*
10239 TACTTTTTTGCTTCAATTTAGTCA
1 TACTTTTTTGATTCAATTTAGTCA
* *
10263 TACTTTTTTTATTCTATTTAGTCA
1 TACTTTTTTGATTCAATTTAGTCA
10287 ATTAAGATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.58
Consensus pattern (24 bp):
TACTTTTTTGATTCAATTTAGTCA
Found at i:14653 original size:13 final size:13
Alignment explanation
Indices: 14610--14660 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
14600 AAAAAGGGTG
14610 AAGGAATTGCTTA
1 AAGGAATTGCTTA
** *
14623 AAGATGAAGAGTTTA
1 AAG--GAATTGCTTA
14638 AAGGAATTGCTTA
1 AAGGAATTGCTTA
14651 AAGGAATTGC
1 AAGGAATTGC
14661 GTTTTATCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
13 20 0.67
15 10 0.33
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.27
Consensus pattern (13 bp):
AAGGAATTGCTTA
Found at i:16666 original size:15 final size:13
Alignment explanation
Indices: 16628--16659 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
16618 TTTAGAGATC
16628 TATATAACAAATA
1 TATATAACAAATA
16641 TATATAACAAATA
1 TATATAACAAATA
16654 TATATA
1 TATATA
16660 CCTCAAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (13 bp):
TATATAACAAATA
Found at i:17054 original size:28 final size:29
Alignment explanation
Indices: 16994--17063 Score: 133
Period size: 28 Copynumber: 2.4 Consensus size: 29
16984 ACGTATAAAG
16994 AGTCATTCATGTATGTGTCAAAAAAAAAA
1 AGTCATTCATGTATGTGTCAAAAAAAAAA
17023 AGTCATTCATGTATGTGTC-AAAAAAAAA
1 AGTCATTCATGTATGTGTCAAAAAAAAAA
17051 AGTCATTCATGTA
1 AGTCATTCATGTA
17064 GATACACGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 22 0.54
29 19 0.46
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (29 bp):
AGTCATTCATGTATGTGTCAAAAAAAAAA
Found at i:24305 original size:29 final size:30
Alignment explanation
Indices: 24249--24307 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
24239 GAGTTTTTGA
*
24249 CCAAACCATTGTAGTTTTTAAAAATAATTC
1 CCAAACCATTGTAGCTTTTAAAAATAATTC
*
24279 CCAAACCATTGT-GCTTTTAAAATTAATTC
1 CCAAACCATTGTAGCTTTTAAAAATAATTC
24308 TCATTCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (30 bp):
CCAAACCATTGTAGCTTTTAAAAATAATTC
Found at i:25441 original size:30 final size:29
Alignment explanation
Indices: 25383--25441 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
25373 AAGGGAATGA
** *
25383 GAATTAATTTTAAAAGTACAATGGTTTGG
1 GAATTAATTTTAAAACCACAATGCTTTGG
*
25412 GAATTATTTTTAAAAACCACAATGCTTTGG
1 GAATTAATTTT-AAAACCACAATGCTTTGG
25442 TCAAAAACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (29 bp):
GAATTAATTTTAAAACCACAATGCTTTGG
Found at i:29705 original size:25 final size:25
Alignment explanation
Indices: 29673--29725 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
29663 TTAATTTCTT
29673 ATATATTAATATTTCTCACATTTGG
1 ATATATTAATATTTCTCACATTTGG
*
29698 ATATATTAATATTTCTTACATTTGG
1 ATATATTAATATTTCTCACATTTGG
29723 ATA
1 ATA
29726 ATTTGTAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (25 bp):
ATATATTAATATTTCTCACATTTGG
Found at i:30034 original size:79 final size:78
Alignment explanation
Indices: 29940--30096 Score: 251
Period size: 79 Copynumber: 2.0 Consensus size: 78
29930 AGATTTTCGA
* *
29940 TTGCTTGCCCGCTACTCCCTTCCGTTCCCACCCACTCCCCTGATTTTCCTCGATTTCCCTGTGGT
1 TTGCTTGCCCACTACTCCCTTCCATTCCCACCCACTCCCCTGATTTTCCTCGATTTCCCTGTGG-
30005 TGGCCACCTGCTCC
65 TGGCCACCTGCTCC
* *
30019 TTGCTTGCCCACTACTCGCTTCCATTCCCACCCACTCCCCTGGTTTTCCTCGATTTCCCTGTGGT
1 TTGCTTGCCCACTACTCCCTTCCATTCCCACCCACTCCCCTGATTTTCCTCGATTTCCCTGTGGT
* *
30084 GGGCATCTGCTCC
66 GGCCACCTGCTCC
30097 CTTTCTTCTT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 12 0.17
79 60 0.83
ACGTcount: A:0.08, C:0.43, G:0.16, T:0.33
Consensus pattern (78 bp):
TTGCTTGCCCACTACTCCCTTCCATTCCCACCCACTCCCCTGATTTTCCTCGATTTCCCTGTGGT
GGCCACCTGCTCC
Done.