Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001721.1 Kokia drynarioides strain JFW-HI SEQ_113419, 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: 41103
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:4194 original size:13 final size:13
Alignment explanation
Indices: 4176--4219 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
4166 ATTAGTTTTG
4176 AAAAGTGTTGTGA
1 AAAAGTGTTGTGA
*
4189 AAAAGTGATTTTG-
1 AAAAGTG-TTGTGA
4202 AAAAGTGTTGTGA
1 AAAAGTGTTGTGA
4215 AAAAG
1 AAAAG
4220 GGATTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 19 0.70
14 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (13 bp):
AAAAGTGTTGTGA
Found at i:4200 original size:26 final size:26
Alignment explanation
Indices: 4171--4231 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
4161 TTAGCATTAG
*
4171 TTTTGAAAAGTGTTGTGAAAAAGTGA
1 TTTTGAAAAGTGTTGTGAAAAAGGGA
4197 TTTTGAAAAGTGTTGTGAAAAAGGGA
1 TTTTGAAAAGTGTTGTGAAAAAGGGA
4223 TTTTGAAAA
1 TTTTGAAAA
4232 ATACTTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (26 bp):
TTTTGAAAAGTGTTGTGAAAAAGGGA
Found at i:4231 original size:13 final size:12
Alignment explanation
Indices: 4170--4231 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 12
4160 TTTAGCATTA
4170 GTTTTGAAAAGT
1 GTTTTGAAAAGT
*
4182 GTTGTGAAAAAGT
1 GTTTTG-AAAAGT
4195 GATTTTGAAAAGT
1 G-TTTTGAAAAGT
* *
4208 GTTGTGAAAAAGG
1 GTTTTG-AAAAGT
4221 GATTTTGAAAA
1 G-TTTTGAAAA
4232 ATACTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
12 9 0.22
13 24 0.59
14 8 0.20
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (12 bp):
GTTTTGAAAAGT
Found at i:4243 original size:26 final size:26
Alignment explanation
Indices: 4171--4244 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
4161 TTAGCATTAG
* * * *
4171 TTTTGAAAAGTGTTGTGAAAAAGTGA
1 TTTTGAAAAATCTTGTAAAAAAGGGA
* * *
4197 TTTTGAAAAGTGTTGTGAAAAAGGGA
1 TTTTGAAAAATCTTGTAAAAAAGGGA
4223 TTTTGAAAAATACTT-TAAAAAA
1 TTTTGAAAAAT-CTTGTAAAAAA
4245 TTTTGGTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 41 0.95
27 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.34
Consensus pattern (26 bp):
TTTTGAAAAATCTTGTAAAAAAGGGA
Found at i:11810 original size:21 final size:20
Alignment explanation
Indices: 11786--11825 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
11776 CGATCAGTTG
11786 AACTGATAATCGAAAAGACTT
1 AACTGATAATC-AAAAGACTT
*
11807 AACTGATAATCAAGAGACT
1 AACTGATAATCAAAAGACT
11826 CGATTGGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (20 bp):
AACTGATAATCAAAAGACTT
Found at i:12514 original size:12 final size:12
Alignment explanation
Indices: 12497--12539 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12487 AATATGTTCA
12497 TGAACATATAAT
1 TGAACATATAAT
* *
12509 TGAACATGTTCA-
1 TGAACAT-ATAAT
12521 TGAACATATAAT
1 TGAACATATAAT
12533 TGAACAT
1 TGAACAT
12540 GTTCACGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (12 bp):
TGAACATATAAT
Found at i:12519 original size:24 final size:23
Alignment explanation
Indices: 12439--12550 Score: 118
Period size: 24 Copynumber: 4.8 Consensus size: 23
12429 TTAATGTTCA
*
12439 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
* * *
12462 CGAACATGTTCACGAATATTAAA
1 CGAACATGTTCATGAACATTAAT
*
12485 CGAATATGTTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
*
12509 TGAACATGTTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
* *
12533 TGAACATGTTCACGAACA
1 CGAACATGTTCATGAACA
12551 ATATTAATGA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
22 2 0.03
23 32 0.42
24 42 0.55
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:31134 original size:30 final size:29
Alignment explanation
Indices: 31072--31134 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
31062 TTTAATATAC
*
31072 AATTTTATATATAAATTTTAATTGTATGT
1 AATTTTATATATAAATTTTAATTGTATCT
* *
31101 AATTTTATATGTGAAATTCTTATTTG-ATCT
1 AATTTTATATAT-AAATT-TTAATTGTATCT
31131 AATT
1 AATT
31135 CTCATAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (29 bp):
AATTTTATATATAAATTTTAATTGTATCT
Found at i:36074 original size:4 final size:4
Alignment explanation
Indices: 36067--36097 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
36057 TATATATCAA
36067 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
36098 AGTGAGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Done.