Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004365.1 Kokia drynarioides strain JFW-HI SEQ_117721, 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: 30083
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:684 original size:61 final size:61
Alignment explanation
Indices: 437--844 Score: 391
Period size: 61 Copynumber: 6.9 Consensus size: 61
427 GGGGAAGTTA
** * * * *
437 GTGTCGGCCATTACATGGTCAACACCAAAAAA-TTT--AATTTTTTAC-CAAATAAAAAGGGG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTC-GA-GAAAAGGGG
** * *
496 GTGTTAGCCA-TTGCATGGCCAATACCAAAAAATTTTGAAATTTTTTT-TCGAGAAAAGCGG
1 GTGTCGGCCATTTG-ATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGG
* *** * * * **
556 GTGTCAGCCATGCAATGGCAAACACCCAAAAA---TG-CATTTTTTT-TTTAGAAATA-GGG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAA-AGGGG
*
612 GTGTCGACCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGG
*
673 GTGTCGGCCATTTGATGACCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGG
** *** * * *
734 GTGTCGATCATGCAATGGCCAACACCCAAAAA---TGCAATTTTTTT-TCGAAAAAAGGGG
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGG
*
791 GTGTCGGCCATTTGAT-GCCAACACCAAAAAATTTTGAAATTTTTTTCTCAAGAA
1 GTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAA
845 GCCAACACCC
Statistics
Matches: 281, Mismatches: 51, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
56 55 0.20
57 26 0.09
58 12 0.04
59 37 0.13
60 48 0.17
61 94 0.33
62 9 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (61 bp):
GTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGG
Found at i:752 original size:178 final size:177
Alignment explanation
Indices: 456--844 Score: 533
Period size: 178 Copynumber: 2.2 Consensus size: 177
446 ATTACATGGT
* * * *
456 CAACACCAAAAAA-TTT--AATTTTTTAC-CAAATAAAAAGGGGGTGTTAGCCATTGCATGGCCA
1 CAACACCAAAAAATTTTGAAATTTTTTTCTC-AA-GAAAAGGGGGTGTCAGCCATTGCATGACCA
*
517 ATACCAAAAAATTTTGAAATTTTTTTTCGAGAAAAGCGGGTGTCAGCCATGCAATGGCAAACACC
64 ACACCAAAAAATTTTGAAATTTTTTTTCGAGAAAAGCGGGTGTCAGCCATGCAATGGCAAACACC
* *
582 CAAAAATGCATTTTTTTTTTAG-AAATA-GGGGTGTCGACCATTTGATGGC
129 CAAAAATGCA-ATTTTTTTTAGAAAAAAGGGGGTGTCGACCATTTGAT-GC
* *
631 CAACACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTG-ATGACCAA
1 CAACACCAAAAAATTTTGAAATTTTTTTCTCAAGAAAAGGGGGTGTCAGCCA-TTGCATGACCAA
* * *
695 CACCAAAAAATTTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTC-GATCATGCAATGGCCAACAC
65 CACCAAAAAATTTTGAAATTTTTTT-TCGAGAAAAGCGGGTGTCAG-CCATGCAATGGCAAACAC
* *
759 CCAAAAATGCAATTTTTTTTCGAAAAAAGGGGGTGTCGGCCATTTGATGC
128 CCAAAAATGCAATTTTTTTTAGAAAAAAGGGGGTGTCGACCATTTGATGC
809 CAACACCAAAAAATTTTGAAATTTTTTTCTCAAGAA
1 CAACACCAAAAAATTTTGAAATTTTTTTCTCAAGAA
845 GCCAACACCC
Statistics
Matches: 190, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
175 13 0.07
176 3 0.02
177 57 0.30
178 98 0.52
179 19 0.10
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (177 bp):
CAACACCAAAAAATTTTGAAATTTTTTTCTCAAGAAAAGGGGGTGTCAGCCATTGCATGACCAAC
ACCAAAAAATTTTGAAATTTTTTTTCGAGAAAAGCGGGTGTCAGCCATGCAATGGCAAACACCCA
AAAATGCAATTTTTTTTAGAAAAAAGGGGGTGTCGACCATTTGATGC
Found at i:896 original size:91 final size:94
Alignment explanation
Indices: 751--928 Score: 308
Period size: 92 Copynumber: 1.9 Consensus size: 94
741 TCATGCAATG
* *
751 GCCAACACCCAAAAATGCAATTTTTTTTCGAAAAAAGGGGGTGTCGGCCATTTGAT-GCCAACAC
1 GCCAACACCCAAAAATACAATTTTTTTTCG-AAAAAGGGGGTGTCGACCATTTGATGGCCAACAC
815 CAAAAAATTTTGAAATTTTTTTCTCAAGAA
65 CAAAAAATTTTGAAATTTTTTTCTCAAGAA
845 GCCAACACCCAAAAATACAATTTTTTTT-G-AAAAGGGGGTGTCGACCATTTGATGGCCAACACC
1 GCCAACACCCAAAAATACAATTTTTTTTCGAAAAAGGGGGTGTCGACCATTTGATGGCCAACACC
908 AAAAAATTTTGAAATTTTTTT
66 AAAAAATTTTGAAATTTTTTT
929 TTCTAAAAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
91 23 0.28
92 30 0.37
93 1 0.01
94 27 0.33
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (94 bp):
GCCAACACCCAAAAATACAATTTTTTTTCGAAAAAGGGGGTGTCGACCATTTGATGGCCAACACC
AAAAAATTTTGAAATTTTTTTCTCAAGAA
Found at i:19766 original size:20 final size:20
Alignment explanation
Indices: 19738--19775 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19728 GATATGATCC
*
19738 TTGTGATCTTAGAGATTTGA
1 TTGTAATCTTAGAGATTTGA
19758 TTGTAATCTTAGAGATTT
1 TTGTAATCTTAGAGATTT
19776 TTTTTGTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (20 bp):
TTGTAATCTTAGAGATTTGA
Found at i:21049 original size:19 final size:18
Alignment explanation
Indices: 21017--21052 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21007 ATTTTAAGAA
*
21017 TAAAAATAAGAAAAAAAT
1 TAAAAATAAAAAAAAAAT
21035 TAAAATATAAAAAAAAAA
1 TAAAA-ATAAAAAAAAAA
21053 CCTCCATACA
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:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAAAAAAAT
Found at i:29734 original size:24 final size:26
Alignment explanation
Indices: 29688--29736 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
29678 CGTCATCTAG
29688 AAAAAATCTTATAAAATCTTTAAAAA
1 AAAAAATCTTATAAAATCTTTAAAAA
29714 AAAAAAT-TTA-AAAAT-TATTAAAA
1 AAAAAATCTTATAAAATCT-TTAAAA
29737 TCTTAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 1 0.05
24 11 0.50
25 3 0.14
26 7 0.32
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAAATCTTATAAAATCTTTAAAAA
Done.