Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014988.1 Kokia drynarioides strain JFW-HI SEQ_130032, 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: 19227
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:1978 original size:5 final size:5
Alignment explanation
Indices: 1968--2006 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
1958 ATTTTTAGTG
1968 AAATA AAATA AAATA AAATA TTAAATAA AAATA AAATA A
1 AAATA AAATA AAATA AAATA --AAAT-A AAATA AAATA A
2007 TTATTAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 22 0.71
6 4 0.13
7 4 0.13
8 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:1995 original size:22 final size:22
Alignment explanation
Indices: 1968--2014 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1958 ATTTTTAGTG
1968 AAAT-AAAATAAAATAAAATATT
1 AAATAAAAATAAAAT-AAATATT
*
1990 AAATAAAAATAAAATAATTATT
1 AAATAAAAATAAAATAAATATT
2012 AAA
1 AAA
2015 CACGTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAAAATAAAATAAATATT
Found at i:5109 original size:12 final size:12
Alignment explanation
Indices: 5070--5157 Score: 72
Period size: 12 Copynumber: 7.4 Consensus size: 12
5060 ATTTTTACTG
5070 TTTTGATTGTTG-
1 TTTTG-TTGTTGT
*
5082 TTTTGGTGTTGT
1 TTTTGTTGTTGT
* *
5094 TTTTATTGTTAT
1 TTTTGTTGTTGT
*
5106 TTTTGTTGATGT
1 TTTTGTTGTTGT
* * *
5118 TTTTTTTGCTAT
1 TTTTGTTGTTGT
5130 TTTTGTTGTTG-
1 TTTTGTTGTTGT
* *
5141 TTTTGCTGTTAT
1 TTTTGTTGTTGT
5153 TTTTG
1 TTTTG
5158 CTACTGTTTT
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
11 14 0.24
12 45 0.76
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.70
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:5109 original size:24 final size:24
Alignment explanation
Indices: 5068--5157 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
5058 TTATTTTTAC
* * *
5068 TGTTTTGATTGTT-GTTTTGGTGT
1 TGTTTTTATTGTTATTTTTGTTGT
*
5091 TGTTTTTATTGTTATTTTTGTTGA
1 TGTTTTTATTGTTATTTTTGTTGT
* *
5115 TGTTTTTTTTGCTATTTTTGTTGT
1 TGTTTTTATTGTTATTTTTGTTGT
**
5139 TG-TTTTGCTGTTATTTTTG
1 TGTTTTTATTGTTATTTTTG
5158 CTACTGTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 26 0.46
24 30 0.54
ACGTcount: A:0.07, C:0.02, G:0.21, T:0.70
Consensus pattern (24 bp):
TGTTTTTATTGTTATTTTTGTTGT
Found at i:7410 original size:19 final size:19
Alignment explanation
Indices: 7386--7430 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
7376 TATTCAACTA
7386 TCAATTTTTGTTCCAGTTC
1 TCAATTTTTGTTCCAGTTC
7405 TCAATTTTTGTTCCAGTTC
1 TCAATTTTTGTTCCAGTTC
7424 TCAATTT
1 TCAATTT
7431 ATACCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.53
Consensus pattern (19 bp):
TCAATTTTTGTTCCAGTTC
Found at i:11155 original size:20 final size:19
Alignment explanation
Indices: 11130--11170 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
11120 TTGTCAAAGA
11130 AAAGTCAAC-AGTCAATAGTC
1 AAAGTCAACTA-TCAA-AGTC
11150 AAAGTCAACTATCAAAGTC
1 AAAGTCAACTATCAAAGTC
11169 AA
1 AA
11171 TAGATCAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 13 0.65
21 1 0.05
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.20
Consensus pattern (19 bp):
AAAGTCAACTATCAAAGTC
Found at i:11157 original size:13 final size:13
Alignment explanation
Indices: 11132--11178 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
11122 GTCAAAGAAA
11132 AGTCAACAGTCAAT
1 AGTCAA-AGTCAAT
11146 AGTCAAAGTCAACT
1 AGTCAAAGTCAA-T
11160 A-TCAAAGTCAAT
1 AGTCAAAGTCAAT
11172 AGATCAA
1 AG-TCAA
11179 CGGGTCGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.07
13 16 0.53
14 12 0.40
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (13 bp):
AGTCAAAGTCAAT
Found at i:12237 original size:22 final size:22
Alignment explanation
Indices: 12209--12254 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12199 CTTTGTACAA
12209 GTTCTTTCCTCTAAGTAAGATG
1 GTTCTTTCCTCTAAGTAAGATG
12231 GTTCTTTCCTCTAAGTAAGATG
1 GTTCTTTCCTCTAAGTAAGATG
12253 GT
1 GT
12255 CCACTTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (22 bp):
GTTCTTTCCTCTAAGTAAGATG
Found at i:13326 original size:17 final size:17
Alignment explanation
Indices: 13277--13327 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
13267 ATTATACAAA
*
13277 AATAAATATATAATTTT
1 AATAAATATATAAATTT
*
13294 AAGT-TATATA-ATAATTT
1 AA-TAAATATATA-AATTT
13311 AATAAATATATAAATTT
1 AATAAATATATAAATTT
13328 GGTTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AATAAATATATAAATTT
Found at i:13338 original size:34 final size:33
Alignment explanation
Indices: 13277--13343 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
13267 ATTATACAAA
*
13277 AATAAATATATAATTTTAAGTTATATAATAATTT
1 AATAAATATATAAATTTAAGTTATATAA-AATTT
*
13311 AATAAATATATAAATTT-GGTTATTATAAAATTT
1 AATAAATATATAAATTTAAGTTA-TATAAAATTT
13344 TATATGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 9 0.30
34 21 0.70
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (33 bp):
AATAAATATATAAATTTAAGTTATATAAAATTT
Found at i:17355 original size:34 final size:34
Alignment explanation
Indices: 17300--17367 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
17290 GAAAATATAT
*
17300 GATAAGATTTATTTCCTAAAAA-AAATATATATGA
1 GATAAGATTTATTTCCAAAAAAGAAATAT-TATGA
*
17334 GATAAGATTTGTTAT-CAAAAAAGAAATATTATGA
1 GATAAGATTTATT-TCCAAAAAAGAAATATTATGA
17368 AATGGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 23 0.77
35 7 0.23
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (34 bp):
GATAAGATTTATTTCCAAAAAAGAAATATTATGA
Found at i:17694 original size:18 final size:18
Alignment explanation
Indices: 17659--17693 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
17649 CCATATAATT
17659 TTTAAAATAATTATAAAA
1 TTTAAAATAATTATAAAA
17677 TTTAAAA-AATTATAAAA
1 TTTAAAATAATTATAAAA
17694 AAATTTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTAAAATAATTATAAAA
Found at i:17806 original size:17 final size:18
Alignment explanation
Indices: 17770--17813 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
17760 GAAACAAATC
*
17770 TTATCTCATGAGATAAGAT
1 TTATTTCATGAGA-AAGAT
17789 TTATTTCATGAG-AAGAT
1 TTATTTCATGAGAAAGAT
*
17806 TTGTTTCA
1 TTATTTCA
17814 AAAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (18 bp):
TTATTTCATGAGAAAGAT
Found at i:18003 original size:26 final size:27
Alignment explanation
Indices: 17974--18028 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
17964 AATGAATACA
17974 ATTTTTAATAAAAAT-AATTATATTTT
1 ATTTTTAATAAAAATAAATTATATTTT
** *
18000 A-TTTTAATTTATATAAATTATATTTT
1 ATTTTTAATAAAAATAAATTATATTTT
18026 ATT
1 ATT
18029 CCTGATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
25 10 0.42
26 13 0.54
27 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTTAATAAAAATAAATTATATTTT
Found at i:18285 original size:40 final size:43
Alignment explanation
Indices: 18241--18321 Score: 98
Period size: 40 Copynumber: 2.0 Consensus size: 43
18231 GGTGTTTAAA
*
18241 AATTAAACATAATAA-ATAAT-AAA-ATGTATAAT-TTAAAAAT
1 AATTAAACATAATAACA-AATGAAATATATATAATATTAAAAAT
**
18281 AATTAATTATAATAACAAATGAAATATATATAATATTAAAA
1 AATTAAACATAATAACAAATGAAATATATATAATATTAAAA
18322 TAAAAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 16 0.47
41 4 0.12
42 8 0.24
43 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (43 bp):
AATTAAACATAATAACAAATGAAATATATATAATATTAAAAAT
Done.