Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000609.1 Kokia drynarioides strain JFW-HI SEQ_111560, 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: 23148
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Warning! 14 characters in sequence are not A, C, G, or T
Found at i:26 original size:14 final size:14
Alignment explanation
Indices: 7--82 Score: 59
Period size: 14 Copynumber: 5.4 Consensus size: 14
1 AGCCCC
7 GAACCCCAAACCCT
1 GAACCCCAAACCCT
*
21 GAA-CCCAAACCCC
1 GAACCCCAAACCCT
*
34 G-ACCCCTGAACCCT
1 GAACCCC-AAACCCT
*
48 TAACCCCTAAA-CCT
1 GAACCCC-AAACCCT
*
62 CGAACTCCAAACCCT
1 -GAACCCCAAACCCT
*
77 AAACCC
1 GAACCC
83 AAAAAGTGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.02
13 13 0.27
14 18 0.38
15 16 0.33
ACGTcount: A:0.34, C:0.49, G:0.07, T:0.11
Consensus pattern (14 bp):
GAACCCCAAACCCT
Found at i:965 original size:22 final size:22
Alignment explanation
Indices: 916--979 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
906 AATTATTAGA
*
916 TATTATATAAAAATTATATATT
1 TATTATATAAAAATTAAATATT
*
938 TA-TATACTTAAAATTAAAT-TT
1 TATTATA-TAAAAATTAAATATT
*
959 TATTATAAAATAGAATTAAAT
1 TATTATATAA-A-AATTAAAT
980 TAATAATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 9 0.26
22 17 0.50
23 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTATATAAAAATTAAATATT
Found at i:1774 original size:31 final size:31
Alignment explanation
Indices: 1738--1796 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1728 AAAAACCATA
*
1738 AAAATGTGAAGTAAGATGATATGGTTAGTAT
1 AAAATGTGAAATAAGATGATATGGTTAGTAT
1769 AAAATGTGAAATAAGATGATATGGTTAG
1 AAAATGTGAAATAAGATGATATGGTTAG
1797 GAAGAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (31 bp):
AAAATGTGAAATAAGATGATATGGTTAGTAT
Found at i:5317 original size:22 final size:23
Alignment explanation
Indices: 5283--5326 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5273 ATGTAAAAGT
5283 AATTAATAAAATGAGAAAAAAAA
1 AATTAATAAAATGAGAAAAAAAA
* *
5306 AATTAA-ACAATGATAAAAAAA
1 AATTAATAAAATGAGAAAAAAA
5327 TGTATGGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (23 bp):
AATTAATAAAATGAGAAAAAAAA
Found at i:9309 original size:10 final size:10
Alignment explanation
Indices: 9294--9321 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
9284 CTGATCCTTC
9294 GACTATGTAT
1 GACTATGTAT
9304 GACTATGTAT
1 GACTATGTAT
9314 GACTATGT
1 GACTATGT
9322 TAAACCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (10 bp):
GACTATGTAT
Found at i:12957 original size:21 final size:22
Alignment explanation
Indices: 12907--12955 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
12897 AAGAAATGTC
**
12907 AAATTTAAGTATTAAATTAAAA
1 AAATTTAAGTACCAAATTAAAA
12929 AAATTTAAGTACCAAATTAAAA
1 AAATTTAAGTACCAAATTAAAA
12951 AAATT
1 AAATT
12956 AAATTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATTTAAGTACCAAATTAAAA
Found at i:13506 original size:15 final size:15
Alignment explanation
Indices: 13469--13497 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13459 AGAAGAAGCA
13469 GACGAAGAGGAGGAC
1 GACGAAGAGGAGGAC
13484 GACGAAGAGGAGGA
1 GACGAAGAGGAGGA
13498 GGAGGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.48, T:0.00
Consensus pattern (15 bp):
GACGAAGAGGAGGAC
Found at i:13508 original size:18 final size:18
Alignment explanation
Indices: 13472--13512 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
13462 AGAAGCAGAC
*
13472 GAAGAGGAGGACGACGAA
1 GAAGAGGAGGAGGACGAA
* *
13490 GAGGAGGAGGAGGAAGAA
1 GAAGAGGAGGAGGACGAA
13508 GAAGA
1 GAAGA
13513 AGAAGGGAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.49, T:0.00
Consensus pattern (18 bp):
GAAGAGGAGGAGGACGAA
Found at i:21965 original size:194 final size:194
Alignment explanation
Indices: 21636--22023 Score: 722
Period size: 194 Copynumber: 2.0 Consensus size: 194
21626 AACTCTGATC
*
21636 CTACCACATGTTTATTTCTTTTTGTATTCTATATGAGGTGTGTATTATCAGGTGCCATCTCTTTA
1 CTACCACATGTTTATTTCTTTTTGTATTCTATACGAGGTGTGTATTATCAGGTGCCATCTCTTTA
21701 TACACTTTATTAAATAAAGCATTTTCATCAGACATCATTCAAATTCATTGTAGCTGGTGTCTTAA
66 TACACTTTATTAAATAAAGCATTTTCATCAGACATCATTCAAATTCATTGTAGCTGGTGTCTTAA
*
21766 GTCTTTAATCTAGATGGTTCCCTAGGGTGGTCTTTTTGAATGAGGACAGCGCAAATGGAAACTT
131 GTCTTTAATCTAGATGGTTCCCTAGGGTGGTCTTTCTGAATGAGGACAGCGCAAATGGAAACTT
*
21830 CTACCACATGTTTATTTCTTTTTGTATTCTATACGTGGTGTGTATTATCAGGTGCCATCTCTTTA
1 CTACCACATGTTTATTTCTTTTTGTATTCTATACGAGGTGTGTATTATCAGGTGCCATCTCTTTA
* *
21895 TACACTTTATTATATAAAGCATTTTCATCAGACATCATTCAAATTCGTTGTAGCTGGTGTCTTAA
66 TACACTTTATTAAATAAAGCATTTTCATCAGACATCATTCAAATTCATTGTAGCTGGTGTCTTAA
*
21960 GTCTTTAATCTAGATGGTTCCCTAGGGTGGTCTTTCTGAATGAGGATAGCGCAAATGGAAACTT
131 GTCTTTAATCTAGATGGTTCCCTAGGGTGGTCTTTCTGAATGAGGACAGCGCAAATGGAAACTT
22024 GTGCATTGAA
Statistics
Matches: 188, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
194 188 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (194 bp):
CTACCACATGTTTATTTCTTTTTGTATTCTATACGAGGTGTGTATTATCAGGTGCCATCTCTTTA
TACACTTTATTAAATAAAGCATTTTCATCAGACATCATTCAAATTCATTGTAGCTGGTGTCTTAA
GTCTTTAATCTAGATGGTTCCCTAGGGTGGTCTTTCTGAATGAGGACAGCGCAAATGGAAACTT
Done.