Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006958.1 Kokia drynarioides strain JFW-HI SEQ_121563, 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: 6509
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:57 original size:14 final size:16
Alignment explanation
Indices: 34--76 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
24 TAATTTAGTG
34 ATTAAAATATAATATT
1 ATTAAAATATAATATT
50 -TT-AAATATAA-ATT
1 ATTAAAATATAATATT
63 ATTAAAATATAATA
1 ATTAAAATATAATA
77 GAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 10 0.42
16 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAAAATATAATATT
Found at i:2519 original size:30 final size:30
Alignment explanation
Indices: 2457--2521 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2447 AACTTATTTA
* * * *
2457 TTGTTAATTTTGTTATTGTTTTAGAGGTAT
1 TTGTTAATTTTGTTACTATTTTAAAAGTAT
2487 TTGTTAATTTTGTTACTATTTTAAATAG-AT
1 TTGTTAATTTTGTTACTATTTTAAA-AGTAT
2517 TTGTT
1 TTGTT
2522 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.15, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAAGTAT
Found at i:3987 original size:33 final size:33
Alignment explanation
Indices: 3920--4035 Score: 89
Period size: 33 Copynumber: 3.6 Consensus size: 33
3910 GTCAAAATAA
* *
3920 TAAAAGTTG--AAAAAAA-AAATTTAGATCTCC-
1 TAAAAGTTGTAAAAAAAATAAATTTGGAGC-CCT
3950 TAAAAGTTGGTAAAAAAAATAAATTTGGA-CCCT
1 TAAAAGTT-GTAAAAAAAATAAATTTGGAGCCCT
** ** * * *
3983 TAAAAACTAAAAAAAAAAAAAAATTGGAGCTCT
1 TAAAAGTTGTAAAAAAAATAAATTTGGAGCCCT
4016 TAAAAGTTAGTAAAAAAAAT
1 TAAAAGTT-GTAAAAAAAAT
4036 GTTAACCTCT
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
30 8 0.12
31 1 0.02
32 18 0.27
33 23 0.35
34 16 0.24
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (33 bp):
TAAAAGTTGTAAAAAAAATAAATTTGGAGCCCT
Found at i:4797 original size:9 final size:9
Alignment explanation
Indices: 4760--4797 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
4750 CACCAATCTG
*
4760 TTATTTGAG
1 TTATTTGAA
4769 TTATTTGAA
1 TTATTTGAA
4778 TTATTCT-AA
1 TTATT-TGAA
4787 TTATTTGAA
1 TTATTTGAA
4796 TT
1 TT
4798 GTAAAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.58
Consensus pattern (9 bp):
TTATTTGAA
Found at i:5163 original size:35 final size:35
Alignment explanation
Indices: 5124--5227 Score: 140
Period size: 35 Copynumber: 3.0 Consensus size: 35
5114 CCAAATTCCT
* *
5124 TTTAAATTTATTTTAAAATTAAAATTGTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAAATTATTTAAAAA
* *
5159 TTTAAATTTATTTTAAATTTAAATTTAATTT--AAG
1 TTTAAATTTATTTTAAATTTAAAATT-ATTTAAAAA
5193 TTTAAATTTATTTTCAAATTTAAAATTATTTAAAA
1 TTTAAATTTATTTT-AAATTTAAAATTATTTAAAA
5228 TAAATAAAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
34 20 0.33
35 35 0.58
36 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAAATTATTTAAAAA
Found at i:5165 original size:6 final size:6
Alignment explanation
Indices: 5156--5216 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
5146 AATTGTTTAA
* *
5156 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
5202 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
5217 ATTATTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 13 0.29
6 28 0.62
7 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:5173 original size:11 final size:11
Alignment explanation
Indices: 5159--5214 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
5149 TGTTTAAAAA
5159 TTTAAATTTAT
1 TTTAAATTTAT
*
5170 TTTAAATTTAAA
1 TTTAAATTT-AT
*
5182 TTT-AATTTAAG
1 TTTAAATTT-AT
5193 TTTAAATTTAT
1 TTTAAATTTAT
5204 TTTCAAATTTA
1 TTT-AAATTTA
5215 AAATTATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:5176 original size:17 final size:17
Alignment explanation
Indices: 5124--5228 Score: 120
Period size: 17 Copynumber: 6.1 Consensus size: 17
5114 CCAAATTCCT
5124 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * * *
5141 ATTAAAATTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
5159 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
5176 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
5193 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
5211 TTTAAAATTATTTAAAA
1 TTTAAATTTATTTTAAA
5228 T
1 T
5229 AAATAAAACT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
17 45 0.62
18 27 0.38
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5191 original size:52 final size:52
Alignment explanation
Indices: 5124--5228 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
5114 CCAAATTCCT
* * * *
5124 TTTAAATTTATTTTAAAATTAAAATTGTTTAAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATTTAAAA
** * **
5176 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAATTATTTAAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATTTAAAA
5228 T
1 T
5229 AAATAAAACT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (52 bp):
TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATTTAAAA
Done.