Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012435.1 Kokia drynarioides strain JFW-HI SEQ_127439, 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: 28627
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:3282 original size:17 final size:17
Alignment explanation
Indices: 3260--3299 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3250 AGGTGAAAAA
* *
3260 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTGGAGAATT
3277 CTTGTTCGTGGAGAATT
1 CTTGTTCGTGGAGAATT
3294 CTTGTT
1 CTTGTT
3300 AAGGTGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.47
Consensus pattern (17 bp):
CTTGTTCGTGGAGAATT
Found at i:14676 original size:15 final size:15
Alignment explanation
Indices: 14656--14687 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
14646 TAAATCTCTT
*
14656 ATAATAAATGAATAA
1 ATAATAAAGGAATAA
14671 ATAATAAAGGAATAA
1 ATAATAAAGGAATAA
14686 AT
1 AT
14688 GGATTCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (15 bp):
ATAATAAAGGAATAA
Found at i:14796 original size:29 final size:30
Alignment explanation
Indices: 14738--14799 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
14728 ATTTCAAAAT
* *
14738 TATATATGAATTTTGATTTAAAGTGTAATTA
1 TATATATGAATTTTAATTT-AAGTGCAATTA
*
14769 TATATATGAATTTTAATTT-GGTGCAATTA
1 TATATATGAATTTTAATTTAAGTGCAATTA
14798 TA
1 TA
14800 CACGTGAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.36
31 18 0.64
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (30 bp):
TATATATGAATTTTAATTTAAGTGCAATTA
Found at i:15857 original size:17 final size:17
Alignment explanation
Indices: 15832--15873 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
15822 AATCAAAGTG
*
15832 ATTTCATTTAGTTATAT
1 ATTTTATTTAGTTATAT
* *
15849 ATTTTATTTATTTTTAT
1 ATTTTATTTAGTTATAT
15866 -TTTTATTT
1 ATTTTATTT
15874 CTATTTACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTTATTTAGTTATAT
Found at i:15866 original size:6 final size:6
Alignment explanation
Indices: 15855--15908 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
15845 ATATATTTTA
* *
15855 TTTATT TTTATT TTTATT TCTA-- TTTACT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
15901 TTTATT TT
1 TTTATT TT
15909 ATTATATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
4 3 0.07
6 40 0.93
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:15918 original size:12 final size:11
Alignment explanation
Indices: 15846--15918 Score: 69
Period size: 12 Copynumber: 6.5 Consensus size: 11
15836 CATTTAGTTA
15846 TATATTTTATT
1 TATATTTTATT
15857 TAT-TTTTATT
1 TATATTTTATT
*
15867 TTTATTTCTATT
1 TATATTT-TATT
*
15879 TA-CTTTTATT
1 TATATTTTATT
*
15889 TTTATTTTTATT
1 TATA-TTTTATT
*
15901 TTTATTTTATT
1 TATATTTTATT
15912 ATATATT
1 -TATATT
15919 GTACTTTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
10 14 0.27
11 16 0.31
12 21 0.41
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (11 bp):
TATATTTTATT
Found at i:25685 original size:18 final size:18
Alignment explanation
Indices: 25664--25708 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
25654 ACAACTTGAG
*
25664 TTGAGCTCGTTGCTTTAA
1 TTGAGCTCGTAGCTTTAA
25682 TTGAGCTCGTAGCTTTAA
1 TTGAGCTCGTAGCTTTAA
25700 TTGAGCTCG
1 TTGAGCTCG
25709 CATATGGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (18 bp):
TTGAGCTCGTAGCTTTAA
Done.