Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014070.1 Kokia drynarioides strain JFW-HI SEQ_129101, 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: 26685
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:5049 original size:19 final size:20
Alignment explanation
Indices: 5025--5062 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5015 TTTATTATAA
5025 AAATGA-AAAAAAAAACACT
1 AAATGATAAAAAAAAACACT
*
5044 AAATGATAAAATAAAACAC
1 AAATGATAAAAAAAAACAC
5063 CCTTAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.71, C:0.11, G:0.05, T:0.13
Consensus pattern (20 bp):
AAATGATAAAAAAAAACACT
Found at i:5281 original size:14 final size:14
Alignment explanation
Indices: 5262--5323 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
5252 ATTAGCTCTT
5262 TTTTTTATATTTA-A
1 TTTTTTA-ATTTATA
5276 TTTTTTAATTTATA
1 TTTTTTAATTTATA
*
5290 TTTAAATTTAATATATA
1 TTT---TTTAATTTATA
5307 -TTTTTAATTTGATA
1 TTTTTTAATTT-ATA
5321 TTT
1 TTT
5324 AAGTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
13 12 0.30
14 14 0.35
15 2 0.05
16 2 0.05
17 10 0.25
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTTTAATTTATA
Found at i:5299 original size:17 final size:18
Alignment explanation
Indices: 5265--5309 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
5255 AGCTCTTTTT
*
5265 TTTATATTTAATTTTTTAA
1 TTTATATTTAA-TATTTAA
5284 TTTATATTTAA-ATTTAA
1 TTTATATTTAATATTTAA
*
5301 TATATATTT
1 TTTATATTT
5310 TTAATTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
19 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATTTAATATTTAA
Found at i:6823 original size:5 final size:5
Alignment explanation
Indices: 6815--6841 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6805 TTTTTAAATT
6815 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
6842 GTAATTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:14117 original size:25 final size:27
Alignment explanation
Indices: 14062--14117 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 27
14052 TTAACTTTTT
** * *
14062 TTTTATATATTTTTTAGAATTTCTAAT
1 TTTTATATATTTTTTAGAAAATATAAA
14089 TTTTATATA-TTTTTA-AAAATATAAA
1 TTTTATATATTTTTTAGAAAATATAAA
14114 TTTT
1 TTTT
14118 GGAATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 10 0.40
26 6 0.24
27 9 0.36
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTATATATTTTTTAGAAAATATAAA
Found at i:14142 original size:19 final size:19
Alignment explanation
Indices: 14120--14165 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
14110 TAAATTTTGG
14120 AATTTTTTAAATATTTTAA
1 AATTTTTTAAATATTTTAA
** **
14139 AATTTTAAAAATATTTTGT
1 AATTTTTTAAATATTTTAA
14158 AATTTTTT
1 AATTTTTT
14166 GTTGAGAGTG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTTTTAAATATTTTAA
Found at i:15925 original size:128 final size:128
Alignment explanation
Indices: 15697--15953 Score: 514
Period size: 128 Copynumber: 2.0 Consensus size: 128
15687 CATCCTGAAG
15697 AAGTCCTTGAAGATGTATTAGTGAAAGTCAACGAATTGATTTTTCTTGCAGATTTTTATGTAGTG
1 AAGTCCTTGAAGATGTATTAGTGAAAGTCAACGAATTGATTTTTCTTGCAGATTTTTATGTAGTG
15762 AAAATGGAAGAGGATAATACTCCTGGGACTTCCGACATCTTATTAGGGCGACCTTTCCTTAGT
66 AAAATGGAAGAGGATAATACTCCTGGGACTTCCGACATCTTATTAGGGCGACCTTTCCTTAGT
15825 AAGTCCTTGAAGATGTATTAGTGAAAGTCAACGAATTGATTTTTCTTGCAGATTTTTATGTAGTG
1 AAGTCCTTGAAGATGTATTAGTGAAAGTCAACGAATTGATTTTTCTTGCAGATTTTTATGTAGTG
15890 AAAATGGAAGAGGATAATACTCCTGGGACTTCCGACATCTTATTAGGGCGACCTTTCCTTAGT
66 AAAATGGAAGAGGATAATACTCCTGGGACTTCCGACATCTTATTAGGGCGACCTTTCCTTAGT
15953 A
1 A
15954 CCGCAAATAC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (128 bp):
AAGTCCTTGAAGATGTATTAGTGAAAGTCAACGAATTGATTTTTCTTGCAGATTTTTATGTAGTG
AAAATGGAAGAGGATAATACTCCTGGGACTTCCGACATCTTATTAGGGCGACCTTTCCTTAGT
Found at i:16378 original size:22 final size:23
Alignment explanation
Indices: 16350--16398 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
16340 AGGCAACCTA
16350 ATTTTTACTTTTT-AATTTTA-TT
1 ATTTTTA-TTTTTCAATTTTATTT
*
16372 ATTTTTATTTTTCTATTTTATTT
1 ATTTTTATTTTTCAATTTTATTT
16395 ATTT
1 ATTT
16399 ATTTTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 5 0.21
22 13 0.54
23 6 0.25
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTTTTATTTTTCAATTTTATTT
Found at i:23052 original size:23 final size:25
Alignment explanation
Indices: 23026--23071 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
23016 CCAATTAAGG
23026 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
23049 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
23072 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:24171 original size:15 final size:15
Alignment explanation
Indices: 24138--24183 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
24128 AGCCATTTTA
*
24138 TTATTATTATTA-TT
1 TTATTATTTTTAGTT
24152 ATTATTAATTTTT-GTT
1 -TTATT-ATTTTTAGTT
24168 TTATTATTTTTAGTT
1 TTATTATTTTTAGTT
24183 T
1 T
24184 AATTTTTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 14 0.52
16 7 0.26
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (15 bp):
TTATTATTTTTAGTT
Done.