Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000138.1 Kokia drynarioides strain JFW-HI SEQ_110790, 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: 8313
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Found at i:730 original size:12 final size:12
Alignment explanation
Indices: 713--737 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
703 CAAATATACT
713 AAATTTATAAAA
1 AAATTTATAAAA
725 AAATTTATAAAA
1 AAATTTATAAAA
737 A
1 A
738 CTATATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTTATAAAA
Found at i:747 original size:20 final size:18
Alignment explanation
Indices: 724--762 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
714 AATTTATAAA
724 AAAATTTATAAAAACTATAT
1 AAAA-TTATAAAAA-TATAT
744 AAAATTATAAAAATATAT
1 AAAATTATAAAAATATAT
762 A
1 A
763 TAAGGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTATAAAAATATAT
Found at i:763 original size:20 final size:20
Alignment explanation
Indices: 724--765 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
714 AATTTATAAA
*
724 AAAATTTATAAAAACTATAT
1 AAAATTTATAAAAAATATAT
744 AAAA-TTATAAAAATATATAT
1 AAAATTTATAAAAA-ATATAT
764 AA
1 AA
766 GGATGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTTATAAAAAATATAT
Found at i:883 original size:17 final size:18
Alignment explanation
Indices: 863--988 Score: 55
Period size: 19 Copynumber: 6.8 Consensus size: 18
853 AATTTTAGAT
863 ATTTTT-TTATTTTTATA
1 ATTTTTATTATTTTTATA
* * * *
880 ATTTTTGTAATTTTATGTT
1 ATTTTTATTATTTT-TATA
*
899 ATTGTTT-TTATATTTTTTA
1 ATT-TTTATTAT-TTTTATA
918 ATTTTCTATTATTTTTA-A
1 ATTTT-TATTATTTTTATA
* *
936 ATGATTTTAATA-TTATAT-
1 AT--TTTTATTATTTTTATA
**
954 ATTTTTACAATTTTCTATA
1 ATTTTTATTATTTT-TATA
*
973 ATTTGTTATAATTTTT
1 ATTT-TTATTATTTTT
989 TTTTGCACTT
Statistics
Matches: 83, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
16 6 0.07
17 8 0.10
18 20 0.24
19 27 0.33
20 22 0.27
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTTTTATTATTTTTATA
Found at i:929 original size:29 final size:31
Alignment explanation
Indices: 872--930 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
862 TATTTTTTTA
*
872 TTTTTATAATTTTTGTAATTTTATGTTATTG
1 TTTTTATAATTTTTGTAATTTTATATTATTG
*
903 TTTTTAT-ATTTTT-TAATTTTCTATTATT
1 TTTTTATAATTTTTGTAATTTTATATTATT
931 TTTAAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 13 0.50
30 6 0.23
31 7 0.27
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (31 bp):
TTTTTATAATTTTTGTAATTTTATATTATTG
Found at i:985 original size:20 final size:20
Alignment explanation
Indices: 949--987 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
939 ATTTTAATAT
949 TATATATTTTTACAATTTTC
1 TATATATTTTTACAATTTTC
*
969 TATA-ATTTGTTATAATTTT
1 TATATATTT-TTACAATTTT
988 TTTTTGCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TATATATTTTTACAATTTTC
Found at i:5128 original size:20 final size:20
Alignment explanation
Indices: 5091--5129 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5081 CAAATACTTC
*
5091 GAATTATGTAGTTCATATTA
1 GAATTATGTAATTCATATTA
* *
5111 GAATTGTGTAATTTATATT
1 GAATTATGTAATTCATATT
5130 CAAATTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (20 bp):
GAATTATGTAATTCATATTA
Found at i:8220 original size:22 final size:19
Alignment explanation
Indices: 8193--8235 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
8183 AAAACGGGCA
8193 AGAAAGAAAG--GAAGGAG
1 AGAAAGAAAGAAGAAGGAG
8210 AGGAAAGAAAGAAGAAGGAG
1 A-GAAAGAAAGAAGAAGGAG
8230 AGAAAG
1 AGAAAG
8236 GTAATGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 9 0.39
19 5 0.22
20 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (19 bp):
AGAAAGAAAGAAGAAGGAG
Done.