Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012925.1 Kokia drynarioides strain JFW-HI SEQ_127941, 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: 12667
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Found at i:595 original size:29 final size:29
Alignment explanation
Indices: 543--714 Score: 143
Period size: 29 Copynumber: 5.8 Consensus size: 29
533 GGAGGTCCTA
* * *
543 GAACTTCTAAAAAGTTTCACTTTTACCCCT
1 GAACTTCCAAAAA-TTCCATTTTTACCCCT
* *
573 GAACTTCAAAAAATTCCATTTTTGAAACCCCA
1 GAACTTCCAAAAATTCCATTTTT---ACCCCT
* * *
605 AAACTTCCAAAAATTCCATTTCTACCCTT
1 GAACTTCCAAAAATTCCATTTTTACCCCT
* *
634 AAACTTCCAAAAATTCTATTTTTGACCCC-
1 GAACTTCCAAAAATTCCATTTTT-ACCCCT
*
663 GAAACTTCCAAAAATTACA-TTTTA-CCCT
1 G-AACTTCCAAAAATTCCATTTTTACCCCT
* *
691 CGAACCTCCAAAATTTCCATTTTT
1 -GAACTTCCAAAAATTCCATTTTT
715 GACCTAAAAA
Statistics
Matches: 116, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
27 3 0.03
28 15 0.13
29 42 0.36
30 31 0.27
32 25 0.22
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
GAACTTCCAAAAATTCCATTTTTACCCCT
Found at i:670 original size:30 final size:30
Alignment explanation
Indices: 574--785 Score: 175
Period size: 29 Copynumber: 7.1 Consensus size: 30
564 TTTACCCCTG
*
574 AACTTCAAAAAATTCCATTTTTGAAACCCCAA
1 AACTTCCAAAAATTCCATTTTTG--ACCCCAA
* **
606 AACTTCCAAAAATTCCATTTCT-ACCCTTA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
* *
635 AACTTCCAAAAATTCTATTTTTGACCCCGA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
* *
665 AACTTCCAAAAATTACA-TTTT-ACCCTC-G
1 AACTTCCAAAAATTCCATTTTTGACCC-CAA
* * **
693 AACCTCCAAAATTTCCATTTTTGACCTAAA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
* *
723 AACTTTCAAAAATTACCA-TTTTGCCCCCAA
1 AACTTCCAAAAATT-CCATTTTTGACCCCAA
** * * *
753 ATGTT-TAAAAACTCCATTTTTGACCTCAA
1 AACTTCCAAAAATTCCATTTTTGACCCCAA
782 AACT
1 AACT
786 CTCAAAATTA
Statistics
Matches: 142, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
28 21 0.15
29 52 0.37
30 46 0.32
31 3 0.02
32 20 0.14
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTGACCCCAA
Found at i:821 original size:58 final size:59
Alignment explanation
Indices: 706--830 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 59
696 CTCCAAAATT
* ** *
706 TCCATTTTTGACCTAAAAACTTTCAAAAATTACCATTTTGCCCCCAAATGTTTAAAAAC
1 TCCATTTTTGACCTAAAAACTCTCAAAAATTACCATTTTAACCCCAAATGTCTAAAAAC
* * * *
765 TCCATTTTTGACCTCAAAACTCTC-AAAATTACCCTTTTAACCCTAAATGTCTAAAAAT
1 TCCATTTTTGACCTAAAAACTCTCAAAAATTACCATTTTAACCCCAAATGTCTAAAAAC
823 TCCATTTT
1 TCCATTTT
831 AACCCAAACT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
58 36 0.62
59 22 0.38
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (59 bp):
TCCATTTTTGACCTAAAAACTCTCAAAAATTACCATTTTAACCCCAAATGTCTAAAAAC
Found at i:831 original size:28 final size:29
Alignment explanation
Indices: 730--892 Score: 95
Period size: 29 Copynumber: 5.7 Consensus size: 29
720 AAAAACTTTC
** * *
730 AAAAATTACCATTTTGCCCCCAAATGTTT
1 AAAAATTACCATTTTAACCCTAAATGTCT
* * **
759 AAAAACT-CCATTTTTGA-CCTCAAAACTCT
1 AAAAATTACCA-TTTTAACCCT-AAATGTCT
* *
788 CAAAATTACCCTTTTAACCCTAAATGTCT
1 AAAAATTACCATTTTAACCCTAAATGTCT
* *
817 AAAAATT-CCATTTTAACCC-AAACTTTCC
1 AAAAATTACCATTTTAACCCTAAA-TGTCT
* ** **
845 CAAAATTACCATTTTGCCCCTAAAAATC-
1 AAAAATTACCATTTTAACCCTAAATGTCT
*
873 CAAAATTACCATTTT-ACCCT
1 AAAAATTACCATTTTAACCCT
893 TCGAGTATCC
Statistics
Matches: 105, Mismatches: 22, Indels: 16
0.73 0.15 0.11
Matches are distributed among these distances:
27 7 0.07
28 40 0.38
29 50 0.48
30 8 0.08
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATTACCATTTTAACCCTAAATGTCT
Found at i:11719 original size:6 final size:6
Alignment explanation
Indices: 11697--11800 Score: 68
Period size: 6 Copynumber: 17.0 Consensus size: 6
11687 GTTTAAATTG
* * * * *
11697 ATTTAA ATTTAT TTTTAA ATTTAA ATTTATCT TTTTAA ATTTAA ATTT-G
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA--A ATTTAA ATTTAA ATTTAA
* * * * *
11746 CTTTAA ATTTAA ATTTATCT TTTTAA ATTTAA ATTT-G CTTTAA ATTTAA
1 ATTTAA ATTTAA ATTTA--A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
11795 ATTTAA
1 ATTTAA
11801 TCAAATTTGA
Statistics
Matches: 72, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
5 6 0.08
6 58 0.81
8 8 0.11
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:11800 original size:43 final size:37
Alignment explanation
Indices: 11710--11799 Score: 180
Period size: 37 Copynumber: 2.4 Consensus size: 37
11700 TAAATTTATT
11710 TTTAAATTTAAATTTATCTTTTTAAATTTAAATTTGC
1 TTTAAATTTAAATTTATCTTTTTAAATTTAAATTTGC
11747 TTTAAATTTAAATTTATCTTTTTAAATTTAAATTTGC
1 TTTAAATTTAAATTTATCTTTTTAAATTTAAATTTGC
11784 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
11800 ATCAAATTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (37 bp):
TTTAAATTTAAATTTATCTTTTTAAATTTAAATTTGC
Done.