Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006512.1 Kokia drynarioides strain JFW-HI SEQ_121096, 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: 46597
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1915 original size:21 final size:20
Alignment explanation
Indices: 1872--1924 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1862 TTATGAGTTA
**
1872 TTTCGATAGAAGTACACTTG
1 TTTCGATAGAAGTACACAAG
* *
1892 TTTTGGTAGAAGTGACACAAG
1 TTTCGATAGAAGT-ACACAAG
1913 TTTCGATAGAAG
1 TTTCGATAGAAG
1925 ACTATACTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (20 bp):
TTTCGATAGAAGTACACAAG
Found at i:10205 original size:24 final size:24
Alignment explanation
Indices: 10174--10230 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
10164 ATTCATCACT
10174 CTCAAAGCAAACAATGATTTTCGA
1 CTCAAAGCAAACAATGATTTTCGA
10198 CTCAAAGCAAACAATGATTTTCGA
1 CTCAAAGCAAACAATGATTTTCGA
10222 CTCAAAGCA
1 CTCAAAGCA
10231 TCAACAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (24 bp):
CTCAAAGCAAACAATGATTTTCGA
Found at i:18100 original size:17 final size:17
Alignment explanation
Indices: 18078--18128 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
18068 CCTTTTTCAT
*
18078 TGCATTTTAATTGTGAC
1 TGCATTTTAATTGTCAC
* *
18095 TGCATTTTCATTGTCAT
1 TGCATTTTAATTGTCAC
*
18112 TGCATTTCTATTTGTCA
1 TGCATTT-TAATTGTCA
18129 TTGTAAATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.51
Consensus pattern (17 bp):
TGCATTTTAATTGTCAC
Found at i:19287 original size:26 final size:26
Alignment explanation
Indices: 19240--19301 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
19230 TTGCGCCCAA
*
19240 AATTGTCACTGTAGGAACTTGTTCAG
1 AATTGTCACTGTAGGAACTTGTCCAG
* *
19266 AATTATCACTGT-GTGAATTTGTCCAG
1 AATTGTCACTGTAG-GAACTTGTCCAG
*
19292 AGTTGTCACT
1 AATTGTCACT
19302 AAATAAGAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (26 bp):
AATTGTCACTGTAGGAACTTGTCCAG
Found at i:20580 original size:23 final size:23
Alignment explanation
Indices: 20548--20593 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20538 CCGATGGCTG
20548 AAAACAAAGCGAAAAACATGTTC
1 AAAACAAAGCGAAAAACATGTTC
*
20571 AAAACGAAGCGAAAAACATGTTC
1 AAAACAAAGCGAAAAACATGTTC
20594 TTTGGCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.13
Consensus pattern (23 bp):
AAAACAAAGCGAAAAACATGTTC
Found at i:24241 original size:18 final size:17
Alignment explanation
Indices: 24210--24243 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24200 ATGTTTTTTT
24210 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
24227 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
24244 TTCTTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:25555 original size:17 final size:18
Alignment explanation
Indices: 25534--25577 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
25524 GTAGCCTAAC
25534 CAGATGCAATCATA-AA-
1 CAGATGCAATCATATAAT
25550 CTAGATGCAATCATATAAT
1 C-AGATGCAATCATATAAT
25569 CAGATGCAA
1 CAGATGCAA
25578 CCACAAGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.04
17 13 0.52
18 10 0.40
19 1 0.04
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (18 bp):
CAGATGCAATCATATAAT
Found at i:33028 original size:25 final size:25
Alignment explanation
Indices: 32997--33160 Score: 141
Period size: 25 Copynumber: 6.6 Consensus size: 25
32987 TTCTGAAGTT
*
32997 TAGCTTGTAAGAGCGATATTCTGTC
1 TAGCTCGTAAGAGCGATATTCTGTC
* * *
33022 TTGCTTGTAAGAGCGATATTCTTTC
1 TAGCTCGTAAGAGCGATATTCTGTC
* *
33047 TAGATCGTAAGAGCGATATTCTGCC
1 TAGCTCGTAAGAGCGATATTCTGTC
* * * *
33072 TGGCTCGTGAGAGCGATATTCTATT
1 TAGCTCGTAAGAGCGATATTCTGTC
* * * *
33097 TGGCTCGTAAGAAC-AAATTTTGTC
1 TAGCTCGTAAGAGCGATATTCTGTC
* * * *
33121 TAGCACATAAGAGCGAAATTCTATC
1 TAGCTCGTAAGAGCGATATTCTGTC
*
33146 TGGCCTCGTAAGAGC
1 TAG-CTCGTAAGAGC
33161 TAAACTATGT
Statistics
Matches: 109, Mismatches: 28, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
24 16 0.15
25 84 0.77
26 9 0.08
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (25 bp):
TAGCTCGTAAGAGCGATATTCTGTC
Found at i:36135 original size:12 final size:11
Alignment explanation
Indices: 36103--36140 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
36093 TACACAACTC
36103 CTTTTTCT-TT
1 CTTTTTCTCTT
*
36113 CTTTCTCTCTT
1 CTTTTTCTCTT
36124 CTTTTTCTTCTT
1 CTTTTTC-TCTT
36136 CTTTT
1 CTTTT
36141 ATCAAGTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 7 0.29
11 8 0.33
12 9 0.38
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
CTTTTTCTCTT
Done.