Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000699.1 Kokia drynarioides strain JFW-HI SEQ_111700, 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: 22423
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6965 original size:17 final size:17
Alignment explanation
Indices: 6924--6965 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
6914 TTGTTTGGTC
6924 ATATTTTTATCTCAAAA
1 ATATTTTTATCTCAAAA
* *
6941 GTATTTTTTTCTCAAAA
1 ATATTTTTATCTCAAAA
6958 ATGATTTT
1 AT-ATTTT
6966 GAGAAGCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (17 bp):
ATATTTTTATCTCAAAA
Found at i:8640 original size:52 final size:52
Alignment explanation
Indices: 8555--8665 Score: 186
Period size: 52 Copynumber: 2.1 Consensus size: 52
8545 ATGCATATGT
*
8555 AATTATAGATAATTATGATATAATTAATCTTGTTAAATAAAGGATTGTATAA
1 AATTATAGATAATTATGATATAATTAATCTTGTTAAATAAAAGATTGTATAA
* * *
8607 AATTGTAGATAATTATGATATGATTAATTTTGTTAAATAAAAGATTGTATAA
1 AATTATAGATAATTATGATATAATTAATCTTGTTAAATAAAAGATTGTATAA
8659 AATTATA
1 AATTATA
8666 ATTTCACGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.41
Consensus pattern (52 bp):
AATTATAGATAATTATGATATAATTAATCTTGTTAAATAAAAGATTGTATAA
Found at i:9065 original size:25 final size:23
Alignment explanation
Indices: 9016--9065 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
9006 GTATGTATCA
* * *
9016 ATTAAAATATGTTATATTTATTT
1 ATTAAAAAATATTATATATATTT
9039 ATTAAAAAATATTATATAATATGTT
1 ATTAAAAAATATTATAT-ATAT-TT
9064 AT
1 AT
9066 ATTTTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 3 0.14
25 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTAAAAAATATTATATATATTT
Found at i:10088 original size:28 final size:28
Alignment explanation
Indices: 10021--10089 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
10011 AGTGAACCTT
* *
10021 TTATAAGCAAGCCCTTGTATGCAAACCC
1 TTATAAGCGAGCCCCTGTATGCAAACCC
* *
10049 TTATAGGTGAGCCCCTGTATGCAAACCC
1 TTATAAGCGAGCCCCTGTATGCAAACCC
10077 TTATAAGCGAGCC
1 TTATAAGCGAGCC
10090 TCTATATGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (28 bp):
TTATAAGCGAGCCCCTGTATGCAAACCC
Found at i:11903 original size:20 final size:20
Alignment explanation
Indices: 11866--11906 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11856 TTTGTTTGTT
*
11866 AAATGCATCTTTGCTTAATA
1 AAATGCATCTTTACTTAATA
* *
11886 AAATGTATCTTTATTTAATA
1 AAATGCATCTTTACTTAATA
11906 A
1 A
11907 TCTACATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
AAATGCATCTTTACTTAATA
Found at i:14834 original size:40 final size:40
Alignment explanation
Indices: 14776--15095 Score: 336
Period size: 40 Copynumber: 8.0 Consensus size: 40
14766 TGTAAATTCC
14776 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
1 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
*
14816 CCAGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
1 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
* * * * *
14856 CCGGTGTGTTTATCGAGCTTAGTGCTTTGTATGCTTCGTG
1 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
* * *
14896 TCGAT-TTTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
1 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
* * * * *
14935 CCGGTGTATTTATCGGGCTTGGTGCATAGCAAGCTTCATG
1 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
* * * *
14975 CTGGTGTATTTATCGAGCTTAGTGCCTAGCAAGCTTCGTG
1 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
*** * * * * *
15015 ATAGTGTATTTATCGAGCTTTGTGCCTAGTAGGCTTCATG
1 CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
* * * * * *
15055 CCGATGTGTACTATCAGGCTTTGAGCCTAGCAGGTTTCGTG
1 CCGGTGTGT-TTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
15096 TTGATGCTAT
Statistics
Matches: 233, Mismatches: 45, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
39 31 0.13
40 178 0.76
41 24 0.10
ACGTcount: A:0.15, C:0.20, G:0.30, T:0.36
Consensus pattern (40 bp):
CCGGTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTG
Found at i:14995 original size:119 final size:120
Alignment explanation
Indices: 14779--15057 Score: 364
Period size: 119 Copynumber: 2.3 Consensus size: 120
14769 AAATTCCCCG
* * * *
14779 GTGTGTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCAGTGTGTTTATCGGGCTTAGTGCCTA
1 GTGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTAGTGCATA
* * * * * * * *
14844 GCAGGCTTCGTGCCGGTGTGTTTATCGAGCTTAGTGCTTTGTATGCTTCGTG-TC
66 GCAAGCTTCATGCCGGTGTATTTATCGAGCTTAGTGCCTAGCAAGCTTCGTGATA
* *
14898 GAT-TTTTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTGGTGCAT
1 G-TGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTAGTGCAT
*
14962 AGCAAGCTTCATGCTGGTGTATTTATCGAGCTTAGTGCCTAGCAAGCTTCGTGATA
65 AGCAAGCTTCATGCCGGTGTATTTATCGAGCTTAGTGCCTAGCAAGCTTCGTGATA
* * * *
15018 GTGTATTTATCGAGCTTTGTGCCTAGTAGGCTTCATGCCG
1 GTGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCG
15058 ATGTGTACTA
Statistics
Matches: 138, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
119 103 0.75
120 35 0.25
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (120 bp):
GTGTATTTATCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTATCGGGCTTAGTGCATA
GCAAGCTTCATGCCGGTGTATTTATCGAGCTTAGTGCCTAGCAAGCTTCGTGATA
Done.