Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003845.1 Kokia drynarioides strain JFW-HI SEQ_116864, 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: 22011
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:357 original size:20 final size:20
Alignment explanation
Indices: 332--370 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
322 GGAAGTCGCA
332 TCATTTGGTATAA-AAGTTTG
1 TCATTTGGTA-AACAAGTTTG
*
352 TCATTTTGTAAACAAGTTT
1 TCATTTGGTAAACAAGTTT
371 TGGCCTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (20 bp):
TCATTTGGTAAACAAGTTTG
Found at i:7828 original size:43 final size:43
Alignment explanation
Indices: 7772--7905 Score: 144
Period size: 43 Copynumber: 3.1 Consensus size: 43
7762 ATCTGTTAAT
* *
7772 TTTAGCGGCATTTGTTAGAAAAGAGCCGTTGAAA-ACCATGTTA
1 TTTAGCGGCATTTGTGAGAAAAGAGCCGCT-AAAGACCATGTTA
* *
7815 TTTAGCGGCATTTGTGAGAAAAGTGCCGCTAAAGACCATGTTC
1 TTTAGCGGCATTTGTGAGAAAAGAGCCGCTAAAGACCATGTTA
* * * * * * * *
7858 TTTAGTGGCGTTTATGGGAAAAGCGTCGCTAAAGACCTTGTTC
1 TTTAGCGGCATTTGTGAGAAAAGAGCCGCTAAAGACCATGTTA
7901 TTTAG
1 TTTAG
7906 TGGCGTTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 3 0.04
43 76 0.96
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCATTTGTGAGAAAAGAGCCGCTAAAGACCATGTTA
Found at i:8561 original size:17 final size:17
Alignment explanation
Indices: 8547--8586 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
8537 ATTATTCATA
8547 TGGTAAGTGTATTCACT
1 TGGTAAGTGTATTCACT
8564 TGGTAAGTGTATTCACT
1 TGGTAAGTGTATTCACT
8581 TGGTAA
1 TGGTAA
8587 TTTAATCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (17 bp):
TGGTAAGTGTATTCACT
Found at i:16283 original size:17 final size:17
Alignment explanation
Indices: 16261--16299 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
16251 AGGTGGAGAA
* *
16261 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
16278 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
16295 CTTGT
1 CTTGT
16300 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:16346 original size:41 final size:41
Alignment explanation
Indices: 16289--16382 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
16279 TTGTTCGTAG
*
16289 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTAGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAGGTGACT
*
16330 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAGGTGACT
16371 AGAATTCTTGTT
1 AGAATTCTTGTT
16383 CAAATAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.28, C:0.06, G:0.29, T:0.37
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTAGGTGACT
Found at i:18080 original size:27 final size:28
Alignment explanation
Indices: 18039--18095 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
18029 AACATCTACA
18039 TTTCTATTTCAAAAAAAAAGCTAAAAGT
1 TTTCTATTTCAAAAAAAAAGCTAAAAGT
* ** *
18067 TTTCT-TTTCTAAAATGAAGTTAAAAGT
1 TTTCTATTTCAAAAAAAAAGCTAAAAGT
18094 TT
1 TT
18096 AGAGCTATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (28 bp):
TTTCTATTTCAAAAAAAAAGCTAAAAGT
Found at i:18246 original size:19 final size:19
Alignment explanation
Indices: 18222--18263 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18212 TTTTTAAATT
*
18222 TATATACATATATATAAAA
1 TATATACATAAATATAAAA
* *
18241 TATATATATAAATATTAAA
1 TATATACATAAATATAAAA
18260 TATA
1 TATA
18264 AAATGCTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATACATAAATATAAAA
Found at i:18247 original size:13 final size:13
Alignment explanation
Indices: 18229--18267 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
18219 ATTTATATAC
18229 ATATATATAAAAT
1 ATATATATAAAAT
18242 ATATATAT-AAAT
1 ATATATATAAAAT
*
18254 ATTAAATATAAAAT
1 A-TATATATAAAAT
18268 GCTCAGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 5 0.22
13 14 0.61
14 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATATAAAAT
Found at i:18255 original size:21 final size:19
Alignment explanation
Indices: 18215--18263 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
18205 TTTTTTTTTT
*
18215 TTAAATTTATATACATATATA
1 TTAAATATATATACA-A-ATA
* *
18236 TAAAATATATATATAAATA
1 TTAAATATATATACAAATA
18255 TTAAATATA
1 TTAAATATA
18264 AAATGCTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 11 0.46
20 1 0.04
21 12 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATATATATACAAATA
Found at i:21789 original size:14 final size:13
Alignment explanation
Indices: 21760--21786 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21750 CTAGTTTAGC
21760 ATTACTTTTAAAA
1 ATTACTTTTAAAA
21773 ATTACTTTTAAAA
1 ATTACTTTTAAAA
21786 A
1 A
21787 ATTTTGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTACTTTTAAAA
Done.