Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013139.1 Kokia drynarioides strain JFW-HI SEQ_128158, 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: 30781
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Warning! 75 characters in sequence are not A, C, G, or T
Found at i:882 original size:23 final size:23
Alignment explanation
Indices: 856--976 Score: 109
Period size: 23 Copynumber: 5.2 Consensus size: 23
846 TCCTGGGCAG
* * *
856 CAGAGAGCACTCACAGTGCCAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
879 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
*
902 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
925 CAAAGAGCACACACAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
* *
950 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
973 CAGA
1 CAGA
977 AAGCGCGCTA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
23 62 0.77
24 2 0.03
25 15 0.19
26 1 0.01
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:957 original size:25 final size:23
Alignment explanation
Indices: 856--959 Score: 118
Period size: 23 Copynumber: 4.4 Consensus size: 23
846 TCCTGGGCAG
* * * *
856 CAGAGAGCACTCACAGTGCCAAA
1 CAGAGAGCACACAAAGTGCTAAT
* *
879 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
902 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
925 CAAAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
948 AACAGAGAGCAC
1 --CAGAGAGCAC
960 GAGACGTGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 59 0.87
25 9 0.13
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:3040 original size:24 final size:24
Alignment explanation
Indices: 3010--3056 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3000 ATAATCTTTA
3010 AATTAAA-TTATGTTTAATTGTTTC
1 AATTAAACTT-TGTTTAATTGTTTC
*
3034 AATTAAACTTTGTTTATTTGTTT
1 AATTAAACTTTGTTTAATTGTTT
3057 GAGTCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (24 bp):
AATTAAACTTTGTTTAATTGTTTC
Found at i:3065 original size:24 final size:24
Alignment explanation
Indices: 3020--3068 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3010 AATTAAATTA
*
3020 TGTTTAATTGTTTCAATTAAACTT
1 TGTTTAATTGTTTCAATCAAACTT
* * *
3044 TGTTTATTTGTTTGAGTCAAACTT
1 TGTTTAATTGTTTCAATCAAACTT
3068 T
1 T
3069 TATTAGTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.55
Consensus pattern (24 bp):
TGTTTAATTGTTTCAATCAAACTT
Found at i:8990 original size:2 final size:2
Alignment explanation
Indices: 8985--9020 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
8975 TATATAGAAT
8985 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9021 TATTATGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25748 original size:25 final size:26
Alignment explanation
Indices: 25720--25768 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
25710 ATTCTTCTTT
25720 AATAAAT-TGCT-CATTTGATTAAAAA
1 AATAAATATGCTGC-TTTGATTAAAAA
*
25745 AATAAATATGTTGCTTTGATTAAA
1 AATAAATATGCTGCTTTGATTAAA
25769 TAATCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (26 bp):
AATAAATATGCTGCTTTGATTAAAAA
Done.