Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007497.1 Kokia drynarioides strain JFW-HI SEQ_122121, 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: 17686
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:449 original size:17 final size:17
Alignment explanation
Indices: 427--461 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
417 AAAGTCTCGA
427 CAACAACATAATTAGCG
1 CAACAACATAATTAGCG
*
444 CAACAACATGATTAGCG
1 CAACAACATAATTAGCG
461 C
1 C
462 GACTCGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (17 bp):
CAACAACATAATTAGCG
Found at i:4004 original size:39 final size:39
Alignment explanation
Indices: 3955--4031 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
3945 GCCATATTTC
3955 ATTTGGTTTATCATATAAAAACATATAACATTATATATT
1 ATTTGGTTTATCATATAAAAACATATAACATTATATATT
3994 ATTTGGTTTATCATATAAAAACATATAACATTATATAT
1 ATTTGGTTTATCATATAAAAACATATAACATTATATAT
4032 CATCATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (39 bp):
ATTTGGTTTATCATATAAAAACATATAACATTATATATT
Found at i:9178 original size:3 final size:3
Alignment explanation
Indices: 9170--9198 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9160 TGAGGCAGCT
9170 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
9199 TCATAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:11418 original size:32 final size:32
Alignment explanation
Indices: 11381--11460 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
11371 TTAAATAACG
11381 GTTGCTATATAGCGGTAGCGGTACCGTCTGAA
1 GTTGCTATATAGCGGTAGCGGTACCGTCTGAA
11413 GTTGCTATATAGCGGTAGCGGTACCGTCTGAA
1 GTTGCTATATAGCGGTAGCGGTACCGTCTGAA
** *
11445 ACTGCTATATAACGGT
1 GTTGCTATATAGCGGT
11461 GTGAAACGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (32 bp):
GTTGCTATATAGCGGTAGCGGTACCGTCTGAA
Found at i:13053 original size:17 final size:16
Alignment explanation
Indices: 13024--13059 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
13014 GTTTTGACTT
*
13024 TAATTATTTTTTTAAA
1 TAATTATTATTTTAAA
13040 TAATTAATTATTTTAAA
1 TAATT-ATTATTTTAAA
13057 TAA
1 TAA
13060 GTTGGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTATTATTTTAAA
Done.