Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010028.1 Kokia drynarioides strain JFW-HI SEQ_124794, 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: 2028
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Found at i:681 original size:29 final size:29
Alignment explanation
Indices: 631--950 Score: 337
Period size: 30 Copynumber: 10.9 Consensus size: 29
621 GAGGTCTCTA
631 AACTGTCCAAAAATTCCATTTTT-CCCCAG
1 AACT-TCCAAAAATTCCATTTTTACCCCAG
*
660 AACTTCCAAAAATTCCATTTTTGACCTC-G
1 AACTTCCAAAAATTCCATTTTT-ACCCCAG
* *
689 AAACTTCCAAAAATTCCATTTTTGCCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCCAG
* * *
719 AACTTCCAAAAATTCCATTATTAACCTCAA
1 AACTTCCAAAAATTCCATT-TTTACCCCAG
* *
749 AACTTCCAAAAAATTCCATTTATGAACCC-G
1 AACTTCC-AAAAATTCCATTT-TTACCCCAG
779 AACTTCCAAAAATTCCATTTTTACCCCTA-
1 AACTTCCAAAAATTCCATTTTTACCCC-AG
* * * *
808 AACTTTCAAAAATTTCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCAG
*
838 AACTTCCAAAAACTCCATTTTTACCCTC-G
1 AACTTCCAAAAATTCCATTTTTACCC-CAG
* *
867 AACTTCCAAAAATTCCATTTTTAACCCTG
1 AACTTCCAAAAATTCCATTTTTACCCCAG
* *
896 AAACTTCTAAAAATTCCATTTTTATCCCA-
1 -AACTTCCAAAAATTCCATTTTTACCCCAG
* *
925 AACTTCCAAAAATTTCATTTTAACCC
1 AACTTCCAAAAATTCCATTTTTACCC
951 TCGAAACTCT
Statistics
Matches: 246, Mismatches: 31, Indels: 29
0.80 0.10 0.09
Matches are distributed among these distances:
28 46 0.19
29 90 0.37
30 94 0.38
31 16 0.07
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCAG
Found at i:730 original size:59 final size:58
Alignment explanation
Indices: 630--950 Score: 364
Period size: 59 Copynumber: 5.5 Consensus size: 58
620 GGAGGTCTCT
630 AAACTGTCCAAAAATTCCATTTTT-CCCCAGAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCAGAACTTCCAAAAATTCCATTTTT-ACCTCG
* * * *
689 AAACTTCCAAAAATTCCATTTTTGCCCCCGAACTTCCAAAAATTCCATTATTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCAGAACTTCCAAAAATTCCATT-TTTACCTCG
* * * *
748 AAACTTCCAAAAAATTCCATTTATGAACCC-GAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCC-AAAAATTCCATTT-TTACCCCAGAACTTCCAAAAATTCCATTTTTACCTCG
* * * * *
807 AAACTTTCAAAAATTTCATTTTTAACCCTAAAACTTCCAAAAACTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCAGAACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
867 -AACTTCCAAAAATTCCATTTTTAACCCTGAAACTTCTAAAAATTCCATTTTTATCC-C-
1 AAACTTCCAAAAATTCCATTTTTACCCCAG-AACTTCCAAAAATTCCATTTTTA-CCTCG
* *
924 AAACTTCCAAAAATTTCATTTTAACCC
1 AAACTTCCAAAAATTCCATTTTTACCC
951 TCGAAACTCT
Statistics
Matches: 223, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.00
58 60 0.27
59 120 0.54
60 38 0.17
61 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAGAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:1032 original size:30 final size:28
Alignment explanation
Indices: 631--1041 Score: 344
Period size: 29 Copynumber: 14.0 Consensus size: 28
621 GAGGTCTCTA
631 AACTGTCCAAAAATTCCATTTTT-CCCCAG
1 AACT-TCCAAAAATTCCATTTTTACCCC-G
*
660 AACTTCCAAAAATTCCATTTTTGACCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
*
689 AAACTTCCAAAAATTCCATTTTTGCCCCCG
1 -AACTTCCAAAAATTCCATTTTT-ACCCCG
* **
719 AACTTCCAAAAATTCCATTATTAACCTCAA
1 AACTTCCAAAAATTCCATT-TTTACC-CCG
* *
749 AACTTCCAAAAAATTCCATTTATGAACCCG
1 AACTTCC-AAAAATTCCATTT-TTACCCCG
*
779 AACTTCCAAAAATTCCATTTTTACCCCTA
1 AACTTCCAAAAATTCCATTTTTACCCC-G
* * **
808 AACTTTCAAAAATTTCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCC-CG
*
838 AACTTCCAAAAACTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
*
867 AACTTCCAAAAATTCCATTTTTAACCCTG
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
* * *
896 AAACTTCTAAAAATTCCATTTTTATCCCA
1 -AACTTCCAAAAATTCCATTTTTACCCCG
* *
925 AACTTCCAAAAATTTCATTTTAACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
** * *
954 AAAC-TCTTAAAATTACC-CTTTTACCCCC
1 -AACTTCCAAAAATT-CCATTTTTACCCCG
* * * *
982 AAATATCTAAGAATTTCATTTTTAACCCCG
1 AACT-TCCAAAAATTCCATTTTT-ACCCCG
*
1012 AACTTCCCAAAATTACCATTTTGT-CCCCG
1 AACTTCCAAAAATT-CCATTTT-TACCCCG
1041 A
1 A
1042 GAATCCAAAA
Statistics
Matches: 311, Mismatches: 50, Indels: 42
0.77 0.12 0.10
Matches are distributed among these distances:
27 2 0.01
28 47 0.15
29 130 0.42
30 116 0.37
31 16 0.05
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Done.