Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003347.1 Kokia drynarioides strain JFW-HI SEQ_116057, 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: 47614
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:2237 original size:28 final size:27
Alignment explanation
Indices: 2185--2238 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
2175 TTCTAAACTT
* * *
2185 TAAACTTTAAATTTATATGTTAAACCC
1 TAAAATTTAAATCTATATCTTAAACCC
2212 TAAAATTTAAATCCTATATCTTAAACC
1 TAAAATTTAAAT-CTATATCTTAAACC
2239 TTACATCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAATTTAAATCTATATCTTAAACCC
Found at i:3409 original size:20 final size:21
Alignment explanation
Indices: 3384--3423 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3374 CATCGTCCGG
*
3384 TTTTCTTTTTCTTTT-TTTGC
1 TTTTCTGTTTCTTTTCTTTGC
*
3404 TTTTCTGTTTGTTTTCTTTG
1 TTTTCTGTTTCTTTTCTTTG
3424 TTTCCGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (21 bp):
TTTTCTGTTTCTTTTCTTTGC
Found at i:10315 original size:55 final size:56
Alignment explanation
Indices: 10246--10363 Score: 202
Period size: 55 Copynumber: 2.1 Consensus size: 56
10236 TAAAATCATT
10246 TCAATTTGTCTAACAAGTGTAGTCGACGAGATACTATCCAAATGAACATTTATCAAA
1 TCAA-TTGTCTAACAAGTGTAGTCGACGAGATACTATCCAAATGAACATTTATCAAA
* *
10303 TCAATTG-CTAACAAGTGTAGTCGACGAGATACTATCCGAATGAATATTTATCAAA
1 TCAATTGTCTAACAAGTGTAGTCGACGAGATACTATCCAAATGAACATTTATCAAA
10358 TCAATT
1 TCAATT
10364 ACTACCTTGC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
55 52 0.88
56 3 0.05
57 4 0.07
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (56 bp):
TCAATTGTCTAACAAGTGTAGTCGACGAGATACTATCCAAATGAACATTTATCAAA
Found at i:11074 original size:25 final size:26
Alignment explanation
Indices: 11022--11082 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
11012 GGGAGGGTTT
* *
11022 TTTTTAATTTAATAGTAATATAATTA
1 TTTTTAATTTAATAATAACATAATTA
11048 TTTTT-ATTTAATAATAACATTAA-TA
1 TTTTTAATTTAATAATAACA-TAATTA
11073 --TTTAATTTAA
1 TTTTTAATTTAA
11083 ATTTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
23 3 0.10
24 6 0.19
25 14 0.45
26 8 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
TTTTTAATTTAATAATAACATAATTA
Found at i:20357 original size:33 final size:33
Alignment explanation
Indices: 20292--20354 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
20282 AGACTCGTCC
*
20292 ATATTATTTTTAATTTTTTAAAATATTTATATT
1 ATATTATTTTTAATTATTTAAAATATTTATATT
20325 ATATTA-TTTTAA-TATTTAATAAT-TTTATAT
1 ATATTATTTTTAATTATTTAA-AATATTTATAT
20355 ATTTTTACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 13 0.46
32 9 0.32
33 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
ATATTATTTTTAATTATTTAAAATATTTATATT
Found at i:24727 original size:13 final size:13
Alignment explanation
Indices: 24709--24735 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24699 TATGATATTC
24709 AAATAATAACAAT
1 AAATAATAACAAT
24722 AAATAATAACAAT
1 AAATAATAACAAT
24735 A
1 A
24736 TAACAGTAAA
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:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAATAACAAT
Found at i:25867 original size:17 final size:17
Alignment explanation
Indices: 25820--25868 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 17
25810 AAAGACATAA
*
25820 AATATTTTATTG-TTA-
1 AATATTTAATTGTTTAT
25835 AATATTTAATTGTTTAT
1 AATATTTAATTGTTTAT
25852 AATACTTTAATT-TTTAT
1 AATA-TTTAATTGTTTAT
25869 TAGATGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 11 0.37
16 3 0.10
17 9 0.30
18 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
AATATTTAATTGTTTAT
Found at i:25913 original size:22 final size:22
Alignment explanation
Indices: 25887--25928 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25877 ATTATTGAAA
*
25887 TAAAATATT-ATTATCAAAAAAT
1 TAAAACATTCATTAT-AAAAAAT
25909 TAAAACATTCATTATAAAAA
1 TAAAACATTCATTATAAAAA
25929 TTACTTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAACATTCATTATAAAAAAT
Found at i:36859 original size:16 final size:16
Alignment explanation
Indices: 36834--36868 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
36824 TTAGTTTAAA
36834 GTTTTATTTA-AAATT
1 GTTTTATTTATAAATT
36849 GTTTATATTTATAAATT
1 GTTT-TATTTATAAATT
36866 GTT
1 GTT
36869 AGTTCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 6 0.33
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (16 bp):
GTTTTATTTATAAATT
Found at i:40199 original size:27 final size:26
Alignment explanation
Indices: 40167--40288 Score: 95
Period size: 27 Copynumber: 4.5 Consensus size: 26
40157 CTGCTGCCGT
*
40167 TGAAGTTCCAACTGTCGTTGATGCTGC
1 TGAAGCTCCAACTG-CGTTGATGCTGC
* * *
40194 TGAAGTTCCAACTGC--TGCTGCCGC
1 TGAAGCTCCAACTGCGTTGATGCTGC
* *
40218 CGAAGCTCCAACAGACGTTGATGCTGC
1 TGAAGCTCCAACTG-CGTTGATGCTGC
* * *
40245 TGAAGCTCCAGCTGCTGATGTCGCTGCCGC
1 TGAAGCTCCAACTGC-G-T-T-GATGCTGC
40275 TGAAGCTCCAACTG
1 TGAAGCTCCAACTG
40289 ATGCTGCTGC
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
24 18 0.24
25 1 0.01
26 2 0.03
27 33 0.44
28 1 0.01
29 1 0.01
30 19 0.25
ACGTcount: A:0.20, C:0.30, G:0.26, T:0.25
Consensus pattern (26 bp):
TGAAGCTCCAACTGCGTTGATGCTGC
Found at i:40237 original size:51 final size:51
Alignment explanation
Indices: 40157--40261 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 51
40147 GACGAAGCTC
** * * * *
40157 CTGCTGCCGTTGAAGTTCCAACTGTCGTTGATGCTGCTGAAGTTCCAACTG
1 CTGCTGCCGCCGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
*
40208 CTGCTGCCGCCGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAGCTG
1 CTGCTGCCGCCGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
40259 CTG
1 CTG
40262 ATGTCGCTGC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.26
Consensus pattern (51 bp):
CTGCTGCCGCCGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
Found at i:40312 original size:27 final size:27
Alignment explanation
Indices: 40159--40300 Score: 78
Period size: 27 Copynumber: 5.3 Consensus size: 27
40149 CGAAGCTCCT
* * *
40159 GCTGCCGTTGAAGTTCCAACTG-TCGTT
1 GCTGCCGCTGAAGCTCCAACTGAT-GTC
* * * *
40186 GATGCTGCTGAAGTTCCAACTG--CT-
1 GCTGCCGCTGAAGCTCCAACTGATGTC
* * * *
40210 GCTGCCGCCGAAGCTCCAACAGACGTT
1 GCTGCCGCTGAAGCTCCAACTGATGTC
* * *
40237 GATGCTGCTGAAGCTCCAGCTGCTGATGTC
1 GCTGCCGCTGAAGCTCCA---ACTGATGTC
40267 GCTGCCGCTGAAGCTCCAACTGATG-C
1 GCTGCCGCTGAAGCTCCAACTGATGTC
40293 TGCTGCCG
1 -GCTGCCG
40301 TTGTAGTTCC
Statistics
Matches: 88, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
24 17 0.19
25 1 0.01
26 2 0.02
27 47 0.53
30 21 0.24
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (27 bp):
GCTGCCGCTGAAGCTCCAACTGATGTC
Done.