Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004686.1 Kokia drynarioides strain JFW-HI SEQ_118238, 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: 35981
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:75 original size:32 final size:31
Alignment explanation
Indices: 9--93 Score: 82
Period size: 32 Copynumber: 2.6 Consensus size: 31
1 TTAATTTT
* *
9 ATAATTTTTATAAT-TTAATTTTTATTAAATAA
1 ATAATTTTTA-AATATT-ATTTATATCAAATAA
*
41 ATAATTTTTAAATATTATTTATGTCAAATAAA
1 ATAATTTTTAAATATTATTTATATCAAAT-AA
**
73 ATAATTATTTTTATATTATTT
1 ATAATT-TTTAAATATTATTT
94 TACTAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
31 13 0.29
32 20 0.44
33 12 0.27
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
ATAATTTTTAAATATTATTTATATCAAATAA
Found at i:102 original size:32 final size:31
Alignment explanation
Indices: 9--103 Score: 79
Period size: 32 Copynumber: 3.0 Consensus size: 31
1 TTAATTTT
*
9 ATAATTTTTATAAT-TTAATTTTTATTAAAT-AA
1 ATAATTTTTA-AATATT-A-TTTTACTAAATAAA
*
41 ATAATTTTTAAATATTA-TTTATGTCAAATAAA
1 ATAATTTTTAAATATTATTTTA-CT-AAATAAA
**
73 ATAATTATTTTTATATTATTTTACTAAATAA
1 ATAATT-TTTAAATATTATTTTACTAAATAA
104 TCTTAACAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
29 4 0.08
30 1 0.02
31 8 0.15
32 26 0.49
33 10 0.19
34 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (31 bp):
ATAATTTTTAAATATTATTTTACTAAATAAA
Found at i:1185 original size:20 final size:20
Alignment explanation
Indices: 1154--1203 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1144 AGAAATTTCC
1154 ATTAATTTAAAAATAAATTAA
1 ATTAA-TTAAAAATAAATTAA
* *
1175 ATTAATT-AAAATTAATTCA
1 ATTAATTAAAAATAAATTAA
1194 ATTAAATTAA
1 ATT-AATTAA
1204 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 13 0.52
20 6 0.24
21 6 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAATTAAAAATAAATTAA
Found at i:1188 original size:15 final size:15
Alignment explanation
Indices: 1167--1203 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1157 AATTTAAAAA
1167 TAAATTAAATT-AAT
1 TAAATTAAATTCAAT
1181 TAAAATT-AATTCAAT
1 T-AAATTAAATTCAAT
1196 TAAATTAA
1 TAAATTAA
1204 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTAAATTCAAT
Found at i:11366 original size:31 final size:33
Alignment explanation
Indices: 11330--11406 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 33
11320 AAAATACAAT
11330 TAAATTAAAATTAAAATTTCATATATAT-A-TA
1 TAAATTAAAATTAAAATTTCATATATATAATTA
* * * * *
11361 TAAATTATAATTTAAATTTTATGTTTATAATTA
1 TAAATTAAAATTAAAATTTCATATATATAATTA
11394 TACAATTAAAATT
1 TA-AATTAAAATT
11407 TATATATCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 23 0.62
32 1 0.03
33 4 0.11
34 9 0.24
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (33 bp):
TAAATTAAAATTAAAATTTCATATATATAATTA
Found at i:11419 original size:27 final size:25
Alignment explanation
Indices: 11355--11420 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 25
11345 ATTTCATATA
* *
11355 TATATATAAATTATAATTTAAATTT
1 TATATATAAATTATAAATTAAAATT
* *
11380 TATGTTTATAATTATACAATTAAAATT
1 TATATATA-AATTATA-AATTAAAATT
11407 TATATATCAAATTA
1 TATATAT-AAATTA
11421 CACATAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 6 0.19
26 7 0.22
27 18 0.56
28 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (25 bp):
TATATATAAATTATAAATTAAAATT
Found at i:18750 original size:40 final size:40
Alignment explanation
Indices: 18698--18776 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
18688 AAAAATTGAA
18698 AAAAAAAGTATTTGAGTTGATTTGATATTACAATAAATTT
1 AAAAAAAGTATTTGAGTTGATTTGATATTACAATAAATTT
18738 AAAAAAAGTATTTGAGTTGATTTGATATTACAATAAATT
1 AAAAAAAGTATTTGAGTTGATTTGATATTACAATAAATT
18777 ATTTAGTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.39
Consensus pattern (40 bp):
AAAAAAAGTATTTGAGTTGATTTGATATTACAATAAATTT
Done.