Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006394.1 Kokia drynarioides strain JFW-HI SEQ_120971, 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: 41138
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:7064 original size:14 final size:14
Alignment explanation
Indices: 7034--7074 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
7024 TTATTTTGTT
7034 GATTAAACTCAAAATC
1 GATTAAACT--AAATC
*
7050 GATTTAACTAAATC
1 GATTAAACTAAATC
7064 GATTAAACTAA
1 GATTAAACTAA
7075 TTATAATCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 15 0.65
16 8 0.35
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (14 bp):
GATTAAACTAAATC
Found at i:8301 original size:23 final size:23
Alignment explanation
Indices: 8256--8304 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
8246 TTACATTTAA
8256 ATATTAAAAATTATAAAATTTTT
1 ATATTAAAAATTATAAAATTTTT
*
8279 ATATTAAAAATATTATAAATTTTTT
1 ATATT-AAAA-ATTATAAAATTTTT
8304 A
1 A
8305 ATTCAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 4 0.17
25 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTAAAAATTATAAAATTTTT
Found at i:12457 original size:35 final size:36
Alignment explanation
Indices: 12374--12529 Score: 164
Period size: 35 Copynumber: 4.5 Consensus size: 36
12364 GTGAGAAGTT
* * *
12374 GAAGTATGCCTTGAAGGCT--GTGTAT-AAGAAAAC
1 GAAGTATGCCTTGAAGGCTAAGTGTCTCGAGAAGAC
*
12407 -AAGTATGCCTTGAAGGCTAAGTGTCT-TAGAAGAC
1 GAAGTATGCCTTGAAGGCTAAGTGTCTCGAGAAGAC
* * *
12441 GAAGCATGCCTTGAAGGCTAAGTAT-TCGAGAAGAT
1 GAAGTATGCCTTGAAGGCTAAGTGTCTCGAGAAGAC
* * *
12476 GAAGTTTGCCTTAAAGGCTAAGTG-CTGGAGAAGAC
1 GAAGTATGCCTTGAAGGCTAAGTGTCTCGAGAAGAC
*
12511 GAAGTATACCTTGAAGGCT
1 GAAGTATGCCTTGAAGGCT
12530 GTGTCTAAGA
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
32 18 0.18
34 12 0.12
35 72 0.71
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.24
Consensus pattern (36 bp):
GAAGTATGCCTTGAAGGCTAAGTGTCTCGAGAAGAC
Found at i:18841 original size:15 final size:16
Alignment explanation
Indices: 18812--18844 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18802 GTTGTTATAC
18812 CCCAAACATTTTTTTA
1 CCCAAACATTTTTTTA
18828 CCCAAACATTTTTTTA
1 CCCAAACATTTTTTTA
18844 C
1 C
18845 TTGATTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (16 bp):
CCCAAACATTTTTTTA
Found at i:23364 original size:62 final size:62
Alignment explanation
Indices: 23267--23390 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
23257 CCTTGCGCTG
*
23267 AGTTTTGCTTGACCTCGTATTTAAATGAGATGCATAAGGATTATTGTCATCCCCTTCAACAA
1 AGTTTTGCTTGACCTCGTATTTAAATGAGATGCATAAGCATTATTGTCATCCCCTTCAACAA
23329 AGTTTTGCTTGACCTCGTATTTAAATGAGATGCATAAGCATTATTGTCATCCCCTTCAACAA
1 AGTTTTGCTTGACCTCGTATTTAAATGAGATGCATAAGCATTATTGTCATCCCCTTCAACAA
23391 CCCACCTCCC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (62 bp):
AGTTTTGCTTGACCTCGTATTTAAATGAGATGCATAAGCATTATTGTCATCCCCTTCAACAA
Found at i:26548 original size:23 final size:23
Alignment explanation
Indices: 26518--26568 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
26508 GTAGTTTGGA
26518 GAAATGGAAGAAAAATCAATCTC
1 GAAATGGAAGAAAAATCAATCTC
26541 GAAATGGAAGAAAAATCAATCTC
1 GAAATGGAAGAAAAATCAATCTC
*
26564 AAAAT
1 GAAAT
26569 CATCTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.18
Consensus pattern (23 bp):
GAAATGGAAGAAAAATCAATCTC
Found at i:32827 original size:19 final size:19
Alignment explanation
Indices: 32803--32856 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
32793 TATTTTGAAA
32803 TTTTGGTAAATCTTTTTTT
1 TTTTGGTAAATCTTTTTTT
32822 TTTTGGTAAATCTTTTTTT
1 TTTTGGTAAATCTTTTTTT
32841 TTTTGGTAAATCTTTT
1 TTTTGGTAAATCTTTT
32857 GTTTCATGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTTGGTAAATCTTTTTTT
Done.