Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003286.1 Kokia drynarioides strain JFW-HI SEQ_115958, 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: 12587
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:1251 original size:12 final size:12
Alignment explanation
Indices: 1236--1264 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1226 TAATAATGCT
1236 AATAATAATAAC
1 AATAATAATAAC
1248 AATAATAATAAC
1 AATAATAATAAC
1260 AATAA
1 AATAA
1265 AAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:2370 original size:29 final size:29
Alignment explanation
Indices: 2328--2673 Score: 206
Period size: 29 Copynumber: 11.7 Consensus size: 29
2318 CCGTAGAGGT
*
2328 CCCTAAACTGTCCAAAAATTACA-TTTTAC
1 CCCTAAACTTTCC-AAAATTACATTTTTAC
*
2357 CCCTAAACTTTCCAAAATTCCATTTTTGA-
1 CCCTAAACTTTCCAAAATTACATTTTT-AC
* * *
2386 CCCT-ACCTTTTCTAAAAAAATTACTTTTTTA-
1 CCCTAAAC-TTTC---CAAAATTACATTTTTAC
* *
2417 CCCTCAAACTTTCCAAAATTCCATTTTTAG
1 CCCT-AAACTTTCCAAAATTACATTTTTAC
* * * * * *
2447 CCTTTAATTTTGCAAAATTCCATTTTTAA
1 CCCTAAACTTTCCAAAATTACATTTTTAC
* * *
2476 CCATAAATTTTCCAAAAATTCCATTTTTAC
1 CCCTAAACTTTCC-AAAATTACATTTTTAC
* * *
2506 CCCCAAACTTAT-TAAAATT-CTATTATTGAC
1 CCCTAAACTT-TCCAAAATTAC-ATT-TTTAC
* *
2536 CTC-AAATTTTCCAAAAATTACATTTTTAC
1 CCCTAAACTTTCC-AAAATTACATTTTTAC
** *
2565 CCCTAAACTTTATAAAATTTCATTTTTGAC
1 CCCTAAACTTTCCAAAATTACATTTTT-AC
* ** *
2595 CCC-AAATTTTTTGAAAATAACATTTTTAC
1 CCCTAAA-CTTTCCAAAATTACATTTTTAC
* * * *
2624 CCCTAAACTCTCCAGAATT-CTATTTCTAA
1 CCCTAAACTTTCCAAAATTAC-ATTTTTAC
2653 CCCTAAACTTTCCAAAATTAC
1 CCCTAAACTTTCCAAAATTAC
2674 CAATTTACCC
Statistics
Matches: 247, Mismatches: 48, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
28 13 0.05
29 138 0.56
30 71 0.29
31 7 0.03
32 16 0.06
33 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTACATTTTTAC
Found at i:2523 original size:59 final size:58
Alignment explanation
Indices: 2460--2632 Score: 204
Period size: 59 Copynumber: 2.9 Consensus size: 58
2450 TTAATTTTGC
* * *
2460 AAAATTCCATTTTTAACCATAAATTTTCCAAAAATTCCATTTTTACCCCCAAAC-TTATT
1 AAAATTCCATTTTTGACC-TAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTA-T
* *
2519 AAAATTCTATTATTGACCTCAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTAT
1 AAAATTCCATTTTTGACCT-AAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTAT
* * *** *
2578 AAAATTTCATTTTTGACCCCAAATTTTTTGAAAATAACATTTTTACCCCTAAACT
1 AAAATTCCATTTTTGA-CCTAAATTTTCCAAAAATTACATTTTTACCCCTAAACT
2633 CTCCAGAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 1 0.01
59 92 0.94
60 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTAT
Found at i:2714 original size:29 final size:29
Alignment explanation
Indices: 2677--2834 Score: 101
Period size: 29 Copynumber: 5.4 Consensus size: 29
2667 AAATTACCAA
*
2677 TTTACCCTCGAATGTCTAAAAATTCCATT
1 TTTAACCTCGAATGTCTAAAAATTCCATT
* * * *
2706 TTTGACCTCGAGCT-TTTCAAAATTACCA-T
1 TTTAACCTCGA-ATGTCTAAAAATT-CCATT
* * *
2735 TTTAACGTC-AGATGTATAAAAATTCTATT
1 TTTAACCTCGA-ATGTCTAAAAATTCCATT
* * * *
2764 TTTGACCCCTAACCT-TCCAAAAATTACCA-T
1 TTTAACCTCGAA--TGTCTAAAAATT-CCATT
*
2794 TTTACCCTCGAATGTCTAAAAATTCCATT
1 TTTAACCTCGAATGTCTAAAAATTCCATT
*
2823 TTTAACCCCGAA
1 TTTAACCTCGAA
2835 CCTTTCGAAA
Statistics
Matches: 95, Mismatches: 24, Indels: 20
0.68 0.17 0.14
Matches are distributed among these distances:
28 9 0.09
29 61 0.64
30 22 0.23
31 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (29 bp):
TTTAACCTCGAATGTCTAAAAATTCCATT
Found at i:2816 original size:59 final size:58
Alignment explanation
Indices: 2662--2855 Score: 246
Period size: 59 Copynumber: 3.3 Consensus size: 58
2652 ACCCTAAACT
* * * *
2662 TTCCAAAATTACCAATTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCTCGAGCT
1 TTCCAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCCCGAACC
* * * * * *
2720 TTTCAAAATTACCATTTTAACGTC-AGATGTATAAAAATTCTATTTTTGACCCCTAACC
1 TTCCAAAATTACCATTTTACCCTCGA-ATGTCTAAAAATTCCATTTTTGACCCCGAACC
*
2778 TTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCCCGAACC
1 TTCC-AAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCCCGAACC
*
2837 TTTCGAAAATTACCATTTT
1 -TTCCAAAATTACCATTTT
2856 TTCCCGAAGC
Statistics
Matches: 114, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
57 1 0.01
58 49 0.43
59 60 0.53
60 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (58 bp):
TTCCAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCCCGAACC
Found at i:8672 original size:33 final size:31
Alignment explanation
Indices: 8605--8665 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
8595 TTGATGTAAT
8605 TATATAAATGAAAATTTAATTATAATTCAAA
1 TATATAAATGAAAATTTAATTATAATTCAAA
* * *
8636 TATATATATGAAACTTTAATTTTAATTCAA
1 TATATAAATGAAAATTTAATTATAATTCAA
8666 TCATATACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (31 bp):
TATATAAATGAAAATTTAATTATAATTCAAA
Done.