Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005536.1 Kokia drynarioides strain JFW-HI SEQ_119628, 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, 671
Length: 1119
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Found at i:608 original size:49 final size:49
Alignment explanation
Indices: 555--1029 Score: 312
Period size: 49 Copynumber: 9.7 Consensus size: 49
545 TGATATTGGA
* *
555 TTCACTGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGG
1 TTCACTGTTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACAAGG
* ** * *
604 TTCACTATTGCGACTTAAACCTTTCCCTTTGTGTCTGC-GTGGTAC-TGG
1 TTCACTGTTGCGACTTAAACCTTTCCCTTCATGTCT-CTGAGGTACAAGG
* * * *
652 ATTCACCGTTACGGCTTAAATCC-TTCCCTTCATG-CTTCTGAGGTAAAAGG
1 -TTCACTGTTGCGACTTAAA-CCTTTCCCTTCATGTC-TCTGAGGTACAAGG
* * * * **
702 TTCA-TCGTTGCGACTTAAACCTTTCCCTCCATATCT-TCGTGGTACCATA
1 TTCACT-GTTGCGACTTAAACCTTTCCCTTCATGTCTCT-GAGGTACAAGG
* * * *
751 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGG
1 TTCACTGTTGCGACTTAAACCTTTCCCTTCATGTC-TCTGAGGTACAAGG
* ** * *
800 TTCACCGTTGCGACTTAAACCTTTCCCTTTGTGTCT-TCGTGGTAC-TGG
1 TTCACTGTTGCGACTTAAACCTTTCCCTTCATGTCTCT-GAGGTACAAGG
** * * * * *
848 ATT-TGTCGTTGCGACTTTAATCTTTCCCTTTATG-CTTCTGAGTTACAAAG
1 -TTCACT-GTTGCGACTTAAACCTTTCCCTTCATGTC-TCTGAGGTACAAGG
** * * * * * *
898 TTTTCCGTTACGACTTAAACCTTTCCCTCCATATCT-TCATGGTAC-CGG
1 TTCACTGTTGCGACTTAAACCTTTCCCTTCATGTCTCTGA-GGTACAAGG
* * *
946 ATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGG
1 -TTCACTGTTGCGACTTAAACCTTTCCCTTCATGTC-TCTGAGGTACAAGG
* *
996 TTCGCTGTTGTGACTTAAACCTTTCCCTTCATGT
1 TTCACTGTTGCGACTTAAACCTTTCCCTTCATGT
1030 TTCGCGGTGC
Statistics
Matches: 320, Mismatches: 78, Indels: 55
0.71 0.17 0.12
Matches are distributed among these distances:
48 16 0.05
49 288 0.90
50 16 0.05
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (49 bp):
TTCACTGTTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACAAGG
Found at i:672 original size:98 final size:98
Alignment explanation
Indices: 455--1024 Score: 667
Period size: 98 Copynumber: 5.8 Consensus size: 98
445 CACGTACTAA
** * * * ** **
455 ATTCGCCGTTGCGGCTTAAAAATTTTCTTTCATGCTTCTGAGGTATAAGGTTTGCCCTTGCGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACTGTTGCGAC-
* * *
520 TTAAACCTTTCCCTTTGTATCTTTGTGATATTGG
65 TTAAACCTTTCCCTTTGTATCTTCGTGGTACTGG
* * *
554 ATTCACTGTTGCGGCTTAAATCTTTCCCTTCATG-TCTCTGAGGTACAAGGTTCACTATTGCGAC
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTACAAGGTTCACTGTTGCGAC
* *
618 TTAAACCTTTCCCTTTGTGTCTGCGTGGTACTGG
65 TTAAACCTTTCCCTTTGTATCTTCGTGGTACTGG
* * * *
652 ATTCACCGTTACGGCTTAAATCCTTCCCTTCATGCTTCTGAGGTAAAAGGTTCA-TCGTTGCGAC
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACT-GTTGCGAC
*** ***
716 TTAAACCTTTCCCTCCATATCTTCGTGGTACCAT
65 TTAAACCTTTCCCTTTGTATCTTCGTGGTACTGG
*
750 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACTGTTGCGACT
*
815 TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
66 TAAACCTTTCCCTTTGTATCTTCGTGGTACTGG
* * * * * * * ** * *
848 ATTTGTCGTTGCGACTTTAATCTTTCCCTTTATGCTTCTGAGTTACAAAGTTTTCCGTTACGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACTGTTGCGACT
*** * *
913 TAAACCTTTCCCTCCATATCTTCATGGTACCGG
66 TAAACCTTTCCCTTTGTATCTTCGTGGTACTGG
* * *
946 ATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCTGTTGTGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACTGTTGCGACT
1011 TAAACCTTTCCCTT
66 TAAACCTTTCCCTT
1025 CATGTTTCGC
Statistics
Matches: 396, Mismatches: 71, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
97 1 0.00
98 343 0.87
99 52 0.13
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACTGTTGCGACT
TAAACCTTTCCCTTTGTATCTTCGTGGTACTGG
Done.