Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013380.1 Kokia drynarioides strain JFW-HI SEQ_128403, 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: 29725
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Warning! 332 characters in sequence are not A, C, G, or T
Found at i:2555 original size:17 final size:17
Alignment explanation
Indices: 2512--2559 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
2502 TATTAAAATT
2512 TATAAATATTTTATAAAAA
1 TATAAATA-TTT-TAAAAA
* *
2531 TATGAATATTTTAATAA
1 TATAAATATTTTAAAAA
2548 TATAAATATTTT
1 TATAAATATTTT
2560 TATTTGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 16 0.62
18 3 0.12
19 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TATAAATATTTTAAAAA
Found at i:8014 original size:12 final size:12
Alignment explanation
Indices: 7990--8023 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7980 TACATAAGAA
7990 GTACATATATAT
1 GTACATATATAT
* *
8002 GTATATATTTAT
1 GTACATATATAT
8014 GTACATATAT
1 GTACATATAT
8024 GGATATTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (12 bp):
GTACATATATAT
Found at i:11858 original size:20 final size:20
Alignment explanation
Indices: 11833--11870 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11823 ATAGTTGACC
*
11833 GTTGACTTTTGACTTTTTAG
1 GTTGACTATTGACTTTTTAG
11853 GTTGACTATTGACTTTTT
1 GTTGACTATTGACTTTTT
11871 TAGGGAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (20 bp):
GTTGACTATTGACTTTTTAG
Found at i:12960 original size:18 final size:18
Alignment explanation
Indices: 12937--12981 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
12927 TATAAACGTG
12937 TTTTATTTTAACTTATTA
1 TTTTATTTTAACTTATTA
*
12955 TTTTATTTTATCTTATTA
1 TTTTATTTTAACTTATTA
12973 TTTTATTTT
1 TTTTATTTT
12982 CAGGTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTATTTTAACTTATTA
Found at i:13102 original size:4 final size:4
Alignment explanation
Indices: 13095--13119 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
13085 TAAGTATATA
13095 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
13120 GAATAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:18229 original size:23 final size:23
Alignment explanation
Indices: 18203--18322 Score: 120
Period size: 23 Copynumber: 5.1 Consensus size: 23
18193 CATTAGTGCA
18203 CTCTCTGATTAGCACTGTGTGTG
1 CTCTCTGATTAGCACTGTGTGTG
* *
18226 CTCTCT-ATTCAGTACTGTATGTG
1 CTCTCTGATT-AGCACTGTGTGTG
* * *
18249 CTCTCTGTTTAGCAC-GTCTCATG
1 CTCTCTGATTAGCACTGTGT-GTG
18272 CTCTCTGTTATTAGCACT-TCGTGTG
1 CTCTCTG--ATTAGCACTGT-GTGTG
*
18297 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGATTAGCACTGTGTGTG
18320 CTC
1 CTC
18323 AGTACTTTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
22 6 0.08
23 53 0.66
24 3 0.04
25 17 0.21
26 1 0.01
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (23 bp):
CTCTCTGATTAGCACTGTGTGTG
Found at i:18322 original size:48 final size:46
Alignment explanation
Indices: 18203--18322 Score: 111
Period size: 48 Copynumber: 2.6 Consensus size: 46
18193 CATTAGTGCA
* *
18203 CTCTCTGATTAGCACTGTGTGTGCTCTCTATTCAGTACTGTATGTG
1 CTCTCTGATTAGCACTCTGTGTGCTCTCTATTCAGCACTGTATGTG
* * * *
18249 CTCTCTGTTTAGCACGTCTCATGCT-CTCTGTTATT-AGCACT-TCGTGTG
1 CTCTCTGATTAGCAC-TCT-GTG-TGCTCT-CTATTCAGCACTGT-ATGTG
*
18297 CTCTCTGATTAGCACTTTGTGTGCTC
1 CTCTCTGATTAGCACTCTGTGTGCTC
18323 AGTACTTTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
45 1 0.02
46 19 0.32
47 5 0.08
48 29 0.49
49 5 0.08
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (46 bp):
CTCTCTGATTAGCACTCTGTGTGCTCTCTATTCAGCACTGTATGTG
Done.