Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001735.1 Kokia drynarioides strain JFW-HI SEQ_113440, 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: 24148
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:3354 original size:17 final size:17
Alignment explanation
Indices: 3329--3373 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3319 ATGTGTGTTT
* *
3329 TTTTTTTTTTTTTTGGG
1 TTTTGTTTTTTTTGGGG
*
3346 TTTTNTTTTTTTTGGGG
1 TTTTGTTTTTTTTGGGG
3363 TTTTGTTTTTT
1 TTTTGTTTTTT
3374 ATAATCAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.80
Consensus pattern (17 bp):
TTTTGTTTTTTTTGGGG
Found at i:8905 original size:25 final size:25
Alignment explanation
Indices: 8852--8905 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
8842 TACTTCATAA
* * **
8852 TTTCTTTTCTTTTTTGAGGTTTTCT
1 TTTCTTTTCTTCTTTGAGGTTATAG
*
8877 TTTCTTTTCTTCTTTGGGGTTATAG
1 TTTCTTTTCTTCTTTGAGGTTATAG
8902 TTTC
1 TTTC
8906 AAATAAAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.06, C:0.13, G:0.15, T:0.67
Consensus pattern (25 bp):
TTTCTTTTCTTCTTTGAGGTTATAG
Found at i:10576 original size:13 final size:13
Alignment explanation
Indices: 10558--10585 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10548 GAGCATACTA
10558 TTAAGAAACTTTC
1 TTAAGAAACTTTC
10571 TTAAGAAACTTTC
1 TTAAGAAACTTTC
10584 TT
1 TT
10586 GACAGGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (13 bp):
TTAAGAAACTTTC
Found at i:17109 original size:67 final size:59
Alignment explanation
Indices: 17065--17179 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
17055 ACGCAATCAC
* * ** *
17065 ACAAAGCATTAACCGATTACACAAATTATTACAACTTACGTAATGTTTTGTGCAATTAT
1 ACAAAACATTAACCAATTACACAAATTATTACAACTTTTGTAATGTTTTGTGTAATTAT
* *
17124 ACAAAACATTATCCAATTACACAAATTATTACAGCTTTTGTAATGTTTTGTGTAAT
1 ACAAAACATTAACCAATTACACAAATTATTACAACTTTTGTAATGTTTTGTGTAAT
17180 ATTGTAGCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (59 bp):
ACAAAACATTAACCAATTACACAAATTATTACAACTTTTGTAATGTTTTGTGTAATTAT
Found at i:20003 original size:88 final size:88
Alignment explanation
Indices: 19848--20016 Score: 275
Period size: 88 Copynumber: 1.9 Consensus size: 88
19838 CAAAAAGATA
* * *
19848 ATCTGCAATGCAGTAAGGTTACCTTGTTAATTGTGATTATTTTCATCCTTCACTTAAAAGGAAAC
1 ATCTGCAAAGCAGTAAGGATACCTTGCTAATTGTGATTATTTTCATCCTTCACTTAAAAGGAAAC
19913 CCTAGATTTTTTTCATGCCTATC
66 CCTAGATTTTTTTCATGCCTATC
* * **
19936 ATCTGCAAAGCAGTAAGGATACCTTGCTAATTGTGATTATTTTCGTCCTTCACTTTAAAGGGGAC
1 ATCTGCAAAGCAGTAAGGATACCTTGCTAATTGTGATTATTTTCATCCTTCACTTAAAAGGAAAC
20001 CCTAGATTTTTTTCAT
66 CCTAGATTTTTTTCAT
20017 ACCTTTCCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (88 bp):
ATCTGCAAAGCAGTAAGGATACCTTGCTAATTGTGATTATTTTCATCCTTCACTTAAAAGGAAAC
CCTAGATTTTTTTCATGCCTATC
Found at i:24006 original size:18 final size:18
Alignment explanation
Indices: 23985--24020 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
23975 AAAGAGAACC
*
23985 ATTTTTATTAAGAAAAAT
1 ATTTTTATAAAGAAAAAT
*
24003 ATTTTTATAAAGAGAAAT
1 ATTTTTATAAAGAAAAAT
24021 TGATAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTTTTATAAAGAAAAAT
Done.