Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003453.1 Kokia drynarioides strain JFW-HI SEQ_116243, 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, 937
Length: 1562
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Found at i:612 original size:29 final size:28
Alignment explanation
Indices: 551--748 Score: 130
Period size: 30 Copynumber: 6.8 Consensus size: 28
541 TTTTGACCTC
* * * *
551 TAAACTTTTCAAAAATTACATTTTAATCAT
1 TAAAC-TTCCAAAAATTACA-TTTCACCCT
581 TAAACTTTCCAAAAATTACATTTCACCCT
1 TAAAC-TTCCAAAAATTACATTTCACCCT
**
610 TAAACTTCTCAAAAATTACATTT-TGCCT
1 TAAACTTC-CAAAAATTACATTTCACCCT
*
638 CAAACTTCTCAAAAATTACATTTTTC-CCCT
1 TAAACTTC-CAAAAATTACA--TTTCACCCT
* ** *
668 TTAACTTCCAAAAATTACATATTTTCCCC
1 TAAACTTCCAAAAATTACAT-TTCACCCT
* * * * *
697 CAAACATCTCAAAAATTATATTTTTACCCC
1 TAAACTTC-CAAAAATTACA-TTTCACCCT
* *
727 CAAACTTCCAAAAAATACATTT
1 TAAACTTCCAAAAATTACATTT
749 TTATCCTCGA
Statistics
Matches: 140, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.01
28 30 0.21
29 53 0.38
30 55 0.39
31 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (28 bp):
TAAACTTCCAAAAATTACATTTCACCCT
Found at i:720 original size:59 final size:59
Alignment explanation
Indices: 590--750 Score: 190
Period size: 59 Copynumber: 2.8 Consensus size: 59
580 TTAAACTTTC
* * *
590 CAAAAATTACA--TTTCACCCTTAAACTTCTCAAAAATTAC--ATTTTGCCTCAAACTTCT
1 CAAAAATTACATTTTTC-CCCTTAAACTTC-CAAAAATTACATATTTTCCCCCAAACATCT
*
647 CAAAAATTACATTTTTCCCCTTTAACTTCCAAAAATTACATATTTTCCCCCAAACATCT
1 CAAAAATTACATTTTTCCCCTTAAACTTCCAAAAATTACATATTTTCCCCCAAACATCT
* * *
706 CAAAAATTATATTTTTACCCC-CAAACTTCCAAAAAATACAT-TTTT
1 CAAAAATTACATTTTT-CCCCTTAAACTTCCAAAAATTACATATTTT
751 ATCCTCGAAC
Statistics
Matches: 91, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
57 21 0.23
58 15 0.16
59 51 0.56
60 4 0.04
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.35
Consensus pattern (59 bp):
CAAAAATTACATTTTTCCCCTTAAACTTCCAAAAATTACATATTTTCCCCCAAACATCT
Found at i:749 original size:29 final size:29
Alignment explanation
Indices: 560--873 Score: 252
Period size: 29 Copynumber: 10.9 Consensus size: 29
550 CTAAACTTTT
* * * *
560 CAAAAATTACATTTTAATCATTAAACTTTC
1 CAAAAATTACATTTTTACCCTCAAAC-TTC
* *
590 CAAAAATTACA-TTTCACCCTTAAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
*
618 TCAAAAATTACA-TTTT-GCCTCAAACTTC
1 -CAAAAATTACATTTTTACCCTCAAACTTC
* **
646 TCAAAAATTACATTTTTCCCCTTTAACTTC
1 -CAAAAATTACATTTTTACCCTCAAACTTC
* *
676 CAAAAATTACATATTTT-CCCCCAAACATC
1 CAAAAATTACAT-TTTTACCCTCAAACTTC
* *
705 TCAAAAATTATATTTTTACCCCCAAACTTC
1 -CAAAAATTACATTTTTACCCTCAAACTTC
* * *
735 CAAAAAATACATTTTTATCCTCGAACTT-
1 CAAAAATTACATTTTTACCCTCAAACTTC
*
763 C---AATCACATTTTTACCCTCAAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
* * **
789 CAAAAATCACATTTTTACCCTGAATTTTC
1 CAAAAATTACATTTTTACCCTCAAACTTC
* * *
818 CTAAAATGACATTTTTACCCCTAAAACTTTC
1 CAAAAATTACATTTTTA-CCCTCAAAC-TTC
* *
849 C-AAAATTACGTTTTAACCCT-AAACT
1 CAAAAATTACATTTTTACCCTCAAACT
874 CTTCGAAACT
Statistics
Matches: 237, Mismatches: 35, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
25 20 0.08
26 1 0.00
27 1 0.00
28 30 0.13
29 117 0.49
30 64 0.27
31 4 0.02
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCAAACTTC
Done.