Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013093.1 Kokia drynarioides strain JFW-HI SEQ_128111, 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: 1714
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.33
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:680 original size:30 final size:29
Alignment explanation
Indices: 584--1068 Score: 266
Period size: 30 Copynumber: 16.5 Consensus size: 29
574 AAACTATCAA
* *
584 AAAATTACATTTTGA-CCTCAAACTTCTCC
1 AAAATTACATTTTTACCCCCAAACTT-TCC
* * * *
613 AAAATTATATTTTTAACCCTAAACTTTCAAA
1 AAAATTACATTTTTACCCCCAAACTTTC--C
*
644 AAAATTACATTATTACCCCCAAACTTCTCC
1 AAAATTACATTTTTACCCCCAAACTT-TCC
* * * *
674 AAAATTATATTTTGACCCCCGAACTTTCTA
1 AAAATTACATTTTTACCCCCAAACTTTC-C
***
704 AAAATTACATTTTTACCCTTGAACTTTCC
1 AAAATTACATTTTTACCCCCAAACTTTCC
* *
733 AAAATTCCA-TTTGA-CCCCAAACTTTCC
1 AAAATTACATTTTTACCCCCAAACTTTCC
* * *
760 AAAATTACTTTTTTACCCTCGAAC-TTCC
1 AAAATTACATTTTTACCCCCAAACTTTCC
* * * *
788 TAAAATTCCATTTTTGA-CCTC-GATTTTCCC
1 -AAAATTACATTTTT-ACCCCCAAACTTT-CC
*
818 AAAAATTACATTTTTACCCCTAAACTTTCC
1 -AAAATTACATTTTTACCCCCAAACTTTCC
* * * *
848 AAATTTCCATTTTTGA-CCTC-GA-TTTCACC
1 AAAATTACATTTTT-ACCCCCAAACTTT--CC
* *
877 AAAAAATTTCCA-TTTTACCCCCAAAC-ATCC
1 --AAAA-TTACATTTTTACCCCCAAACTTTCC
*
907 AAAAATT-CTATTTTTGACCCCAAAAC-TTCC
1 -AAAATTAC-ATTTTT-ACCCCCAAACTTTCC
*
937 AAAAATTACA-TTTTACCCCTAAAC-TTCC
1 -AAAATTACATTTTTACCCCCAAACTTTCC
* * *
965 AAAAATACCATTTTTGACCCCGAAGC-TTCC
1 AAAATTA-CATTTTT-ACCCCCAAACTTTCC
**
995 AAAAATTACCGTTTTACCCCCAAAC-TTCC
1 -AAAATTACATTTTTACCCCCAAACTTTCC
* * * *
1024 AAAATTCCATTTTTAACCCCGATCTTTCCC
1 AAAATTACATTTTTACCCCCAAACTTT-CC
1054 AAAATTACCATTTTT
1 AAAATTA-CATTTTT
1069 CCCTTGGGTA
Statistics
Matches: 356, Mismatches: 67, Indels: 64
0.73 0.14 0.13
Matches are distributed among these distances:
27 27 0.08
28 50 0.14
29 97 0.27
30 123 0.35
31 50 0.14
32 9 0.03
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCCAAACTTTCC
Found at i:852 original size:58 final size:57
Alignment explanation
Indices: 583--1068 Score: 366
Period size: 58 Copynumber: 8.3 Consensus size: 57
573 TAAACTATCA
* * ** * ** *
583 AAAAATTACATTTTGACCTC-AAACTTCTCCAAAATTATATTTTTAACCCTAAACTTTCAA
1 AAAAATTACATTTTTACCCCTAAAC-T-TCCAAAATTCCATTTTTGACCC-CGACTTTC-C
* * *
643 AAAAATTACATTATTACCCCCAAACTTCTCCAAAATT--ATATTTTGACCCCCGAACTTTCT
1 AAAAATTACATTTTTACCCCTAAAC-T-TCCAAAATTCCAT-TTTTGA-CCCCG-ACTTTCC
* * *
703 AAAAATTACATTTTTACCCTTGAACTTTCCAAAATTCCA--TTTGACCCCAAACTTTCC
1 AAAAATTACATTTTTACCCCTAAAC-TTCCAAAATTCCATTTTTGACCCC-GACTTTCC
* * * *
760 -AAAATTACTTTTTTA-CCCTCGAACTTCCTAAAATTCCATTTTTGACCTCGATTTTCCC
1 AAAAATTACATTTTTACCCCT-AAACTTCC-AAAATTCCATTTTTGACCCCGACTTT-CC
* *
818 AAAAATTACATTTTTACCCCTAAACTTTCCAAATTTCCATTTTTGACCTCGA-TTTCACC
1 AAAAATTACATTTTTACCCCTAAAC-TTCCAAAATTCCATTTTTGACCCCGACTTT--CC
* * * * *
877 AAAAAATTTCCA-TTTTACCCCCAAACATCCAAAAATTCTATTTTTGACCCCAAAAC-TTCC
1 -AAAAA-TTACATTTTTACCCCTAAACTTCC-AAAATTCCATTTTTGACCCC--GACTTTCC
*
937 AAAAATTACA-TTTTACCCCTAAACTTCCAAAAATACCATTTTTGACCCCGAAGC-TTCC
1 AAAAATTACATTTTTACCCCTAAACTTCC-AAAATTCCATTTTTGACCCCG-A-CTTTCC
** * *
995 AAAAATTACCGTTTTACCCCCAAACTTCCAAAATTCCATTTTTAACCCCGATCTTTCC
1 AAAAATTACATTTTTACCCCTAAACTTCCAAAATTCCATTTTTGACCCCGA-CTTTCC
*
1053 CAAAATTACCATTTTT
1 AAAAATTA-CATTTTT
1069 CCCTTGGGTA
Statistics
Matches: 356, Mismatches: 43, Indels: 55
0.78 0.09 0.12
Matches are distributed among these distances:
55 7 0.02
56 27 0.08
57 17 0.05
58 101 0.28
59 81 0.23
60 90 0.25
61 30 0.08
62 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCCTAAACTTCCAAAATTCCATTTTTGACCCCGACTTTCC
Done.