Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006027.1 Kokia drynarioides strain JFW-HI SEQ_120472, 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: 21455
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:4330 original size:62 final size:62
Alignment explanation
Indices: 4246--4380 Score: 155
Period size: 62 Copynumber: 2.2 Consensus size: 62
4236 TACTTCGGTA
* * * ** * *
4246 CATCATCGGAAAGTCTAAAGTAATATGTGCTTAGTGCTATCAAATCATACTAG-CACTTAATG
1 CATCATTGAAAAGACTAAAGTAATATACGCTTAGCGCTATCAAATCATA-TAGACACATAATG
* * * *
4308 CATCATTGAAAAGACTAAAGTAATTTACGCTTAGCGCTATTATATCATATTGACACATAATG
1 CATCATTGAAAAGACTAAAGTAATATACGCTTAGCGCTATCAAATCATATAGACACATAATG
4370 CATCATTGAAA
1 CATCATTGAAA
4381 TATAACTGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 2 0.03
62 59 0.97
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (62 bp):
CATCATTGAAAAGACTAAAGTAATATACGCTTAGCGCTATCAAATCATATAGACACATAATG
Found at i:6625 original size:2 final size:2
Alignment explanation
Indices: 6618--6650 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6608 TTTAAATGTA
6618 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6651 ATTAATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:11941 original size:12 final size:12
Alignment explanation
Indices: 11924--11949 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11914 TTTTAAAGTA
11924 AAAAAAAAAAAG
1 AAAAAAAAAAAG
11936 AAAAAAAAAAAG
1 AAAAAAAAAAAG
11948 AA
1 AA
11950 GATTTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:11941 original size:13 final size:14
Alignment explanation
Indices: 11918--11946 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
11908 ATAATGTTTT
11918 AAAGTAAAAAAAAA
1 AAAGTAAAAAAAAA
11932 AAAG-AAAAAAAAA
1 AAAGTAAAAAAAAA
11945 AA
1 AA
11947 GAAGATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (14 bp):
AAAGTAAAAAAAAA
Done.