Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013838.1 Kokia drynarioides strain JFW-HI SEQ_128866, 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: 26163
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1839 original size:17 final size:17
Alignment explanation
Indices: 1819--1852 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1809 TTTTACATGA
*
1819 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
1836 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
1853 GAATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:2281 original size:27 final size:26
Alignment explanation
Indices: 2226--2288 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
2216 TCATATCAGT
* *
2226 ATTTTTTTTAATTTATTATTTAAATA
1 ATTTTTTTTAATTTAATATTTAAAAA
*
2252 ATTTTTTATTTATTTAATA-TTAATAAA
1 ATTTTTT-TTAATTTAATATTTAA-AAA
*
2279 ATTATTTTTA
1 ATTTTTTTTA
2289 TGTCAGAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTTTTTTAATTTAATATTTAAAAA
Found at i:8409 original size:22 final size:22
Alignment explanation
Indices: 8377--8418 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8367 TTTTAAAACA
8377 ACAATTAATCCAATCCAAATAG
1 ACAATTAATCCAATCCAAATAG
* *
8399 ACAATTGATCCAATCTAAAT
1 ACAATTAATCCAATCCAAAT
8419 TGACTCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.26
Consensus pattern (22 bp):
ACAATTAATCCAATCCAAATAG
Found at i:10367 original size:25 final size:27
Alignment explanation
Indices: 10318--10368 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
10308 AATTGTATTA
* *
10318 TATTTTTATTTAATTTATAATTAAATT
1 TATTTTTATTTAATTTAGAAATAAATT
10345 TATTTTTA-TT-ATTTAGAAATAAAT
1 TATTTTTATTTAATTTAGAAATAAAT
10369 ATTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
26 2 0.09
27 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TATTTTTATTTAATTTAGAAATAAATT
Found at i:10518 original size:22 final size:21
Alignment explanation
Indices: 10477--10521 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
10467 GTTATTAATT
10477 TTTATTTATTTTTTAGAAATA
1 TTTATTTATTTTTTAGAAATA
*
10498 TTTATCTT-TTTTTTTGAAA-A
1 TTTAT-TTATTTTTTAGAAATA
10518 TTTA
1 TTTA
10522 CTAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTATTTATTTTTTAGAAATA
Found at i:12218 original size:30 final size:30
Alignment explanation
Indices: 12154--12219 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
12144 AAAAATTTGG
*
12154 AATTTAGTCCTTATACTTTTTATTTTGAGG
1 AATTTAGTCCTTATACTTTTTATTTTGAGA
* *
12184 AATTTAGT-CTTTTCACTTTTTATATTTTA-A
1 AATTTAGTCCTTAT-ACTTTTTAT-TTTGAGA
12214 AATTTA
1 AATTTA
12220 TGTTCGCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 4 0.13
30 23 0.74
31 4 0.13
ACGTcount: A:0.27, C:0.09, G:0.08, T:0.56
Consensus pattern (30 bp):
AATTTAGTCCTTATACTTTTTATTTTGAGA
Found at i:12930 original size:17 final size:18
Alignment explanation
Indices: 12883--12931 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
12873 AATTTATATT
* *
12883 AAATTATAAAAATTTAAA
1 AAATTATAATAATTGAAA
12901 AAATATATCAATAA-TGAAA
1 AAAT-TAT-AATAATTGAAA
12920 AAATTATAATAA
1 AAATTATAATAA
12932 AAGTTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 7 0.26
19 11 0.41
20 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTATAATAATTGAAA
Found at i:13616 original size:22 final size:22
Alignment explanation
Indices: 13588--13653 Score: 109
Period size: 22 Copynumber: 3.1 Consensus size: 22
13578 TTAAAACATG
13588 ATTGGATTGATCAATTGAACCA
1 ATTGGATTGATCAATTGAACCA
13610 ATTGGATTGATCAATTGAACCA
1 ATTGGATTGATCAATTGAACCA
*
13632 ATTGGATTGA-GAATTG-ACCA
1 ATTGGATTGATCAATTGAACCA
13652 AT
1 AT
13654 ATACTAATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
20 6 0.14
21 5 0.12
22 32 0.74
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (22 bp):
ATTGGATTGATCAATTGAACCA
Found at i:19011 original size:18 final size:17
Alignment explanation
Indices: 18984--19017 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
18974 AGTTCGATCA
18984 TGTGTTATATTTATAAT
1 TGTGTTATATTTATAAT
19001 TGTGATTATATTTATAA
1 TGTG-TTATATTTATAA
19018 ATTTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
TGTGTTATATTTATAAT
Found at i:21194 original size:16 final size:15
Alignment explanation
Indices: 21147--21194 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
21137 GATGAACCAG
*
21147 TTTAAATTTTTTATT
1 TTTATATTTTTTATT
21162 TTTAT-TTTTTTACATT
1 TTTATATTTTTT--ATT
21178 TTTATGATTTTTTATT
1 TTTAT-ATTTTTTATT
21194 T
1 T
21195 AGTTATCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 6 0.21
15 4 0.14
16 12 0.43
18 6 0.21
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTATATTTTTTATT
Found at i:21818 original size:15 final size:15
Alignment explanation
Indices: 21772--21824 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
21762 TTAAAATGTA
*
21772 AATTTATTTTTATATT
1 AATTTA-TTATATATT
21788 AATTTA-TA-AT-TT
1 AATTTATTATATATT
21800 -ATTTATTATATATT
1 AATTTATTATATATT
*
21814 AATTTCTTATA
1 AATTTATTATA
21825 AAATTAGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 5 0.16
12 4 0.13
13 4 0.13
14 3 0.10
15 9 0.29
16 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTATTATATATT
Done.