Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006280.1 Kokia drynarioides strain JFW-HI SEQ_120852, 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: 30162
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Found at i:2816 original size:17 final size:18
Alignment explanation
Indices: 2794--2840 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
2784 ATCCCTTTAA
*
2794 AAAAATATAAAAACTT-T
1 AAAAATATAAAAAATTAT
2811 AAAAAT-TCAAAAAATTAT
1 AAAAATAT-AAAAAATTAT
2829 AAAAATA-AAAAA
1 AAAAATATAAAAA
2841 TATATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 18 0.69
18 7 0.27
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATATAAAAAATTAT
Found at i:3521 original size:19 final size:20
Alignment explanation
Indices: 3499--3536 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3489 TTGATTTTTT
3499 TAAAAAAATTT-AACTCAAA
1 TAAAAAAATTTCAACTCAAA
* *
3518 TAAATATATTTCAACTCAA
1 TAAAAAAATTTCAACTCAA
3537 CTCAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAAAATTTCAACTCAAA
Found at i:6301 original size:51 final size:51
Alignment explanation
Indices: 6227--6354 Score: 186
Period size: 51 Copynumber: 2.5 Consensus size: 51
6217 TTTCATTTAA
* * * *
6227 TACTCACGATGACATATTA-TCATCGGACCTTTAATTCGTCACGAATTCATT
1 TACTCACGATGACA-CTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATT
* *
6278 TACTCACAATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATT
6329 TACTCACGATGACACTTAGTCATCGG
1 TACTCACGATGACACTTAGTCATCGG
6355 GCCCTTTCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 3 0.04
51 66 0.96
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATT
Found at i:13372 original size:51 final size:51
Alignment explanation
Indices: 13275--13372 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
13265 TTTCATTTAA
* * * *
13275 TACTCACGATGACATATTATCATCGGGCCTTTAATTCGTTACGGATTCATT
1 TACTCACGATGACATATTATCATCGGACCTTTAATCCGTAAAGGATTCATT
*
13326 TACTCACGATGACA-CTTACTCATCGGACCTTTAATCCGTAAAGGATT
1 TACTCACGATGACATATTA-TCATCGGACCTTTAATCCGTAAAGGATT
13373 AAATCTAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 3 0.07
51 38 0.93
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACATATTATCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:13448 original size:17 final size:17
Alignment explanation
Indices: 13382--13460 Score: 52
Period size: 17 Copynumber: 4.6 Consensus size: 17
13372 TAAATCTAAC
*
13382 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
* * * *
13399 CAAGTTTAAATTTAAAT
1 TAAATTTAAACTTAAAA
* *
13416 TCAGAA-ATAAATTTAAAA
1 T-A-AATTTAAACTTAAAA
* *
13434 TTAATTTAAACTTAATA
1 TAAATTTAAACTTAAAA
13451 TAAATTTAAA
1 TAAATTTAAA
13461 AGTTGGATCT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
16 2 0.04
17 32 0.68
18 12 0.26
19 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:14920 original size:21 final size:22
Alignment explanation
Indices: 14894--15023 Score: 102
Period size: 23 Copynumber: 5.7 Consensus size: 22
14884 ATACGGAACA
*
14894 AACAGAGAGTAC-CAAAGTACT
1 AACAGAGAGCACACAAAGTACT
* *
14915 AACAGAGAGCACA-TAAGTGCTGGGT
1 AACAGAGAGCACACAAAGTAC----T
* * *
14940 AATAGAGAGCACACACAGTGCT
1 AACAGAGAGCACACAAAGTACT
*
14962 AAACAGAGAGTACACAAAGTACT
1 -AACAGAGAGCACACAAAGTACT
*
14985 AATCAGAGAGCACACAAAGTGCT
1 AA-CAGAGAGCACACAAAGTACT
*
15008 AGTCAGAGAGCACACA
1 A-ACAGAGAGCACACA
15024 CAATGCTAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
21 16 0.18
22 3 0.03
23 50 0.57
25 13 0.15
26 5 0.06
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (22 bp):
AACAGAGAGCACACAAAGTACT
Found at i:14976 original size:23 final size:23
Alignment explanation
Indices: 14943--15066 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
14933 GCTGGGTAAT
14943 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACACAGTGCTAAAC
* * * *
14966 AGAGAGTACACAAAGTACTAATC
1 AGAGAGCACACACAGTGCTAAAC
* **
14989 AGAGAGCACACAAAGTGCTAGTC
1 AGAGAGCACACACAGTGCTAAAC
*
15012 AGAGAGCACACACAATGCTAATCAC
1 AGAGAGCACACACAGTGCTAA--AC
*
15037 AGAGAGCACGAGAC-GTGCTAAAC
1 AGAGAGCAC-ACACAGTGCTAAAC
15060 AGAGAGC
1 AGAGAGC
15067 GCGCTAGTGT
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 66 0.78
25 16 0.19
26 3 0.04
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAAAC
Found at i:15016 original size:69 final size:68
Alignment explanation
Indices: 14893--15042 Score: 196
Period size: 69 Copynumber: 2.1 Consensus size: 68
14883 TATACGGAAC
* * * *
14893 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGTAATAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAGT-ACAGAGAGCACACACAA
14958 TGCT
65 TGCT
14962 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AGT-CAGAGAGCACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAGTACAGAGAGCACACAC
15025 AATGCT
63 AATGCT
15031 AATCACAGAGAG
1 AA--ACAGAGAG
15043 CACGAGACGT
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
69 33 0.46
70 11 0.15
71 21 0.29
72 7 0.10
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAGTACAGAGAGCACACACAAT
GCT
Found at i:26250 original size:30 final size:28
Alignment explanation
Indices: 26202--26264 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
26192 TTCATTAAAA
*
26202 ATTT-AAATTTTTTGTTCATGTTTGTTT
1 ATTTAAAATTTTTTGTTCATGTTCGTTT
26229 ATTTAAAATTTTGTGTGTTCATGTTCGTTT
1 ATTTAAAATTTT-T-TGTTCATGTTCGTTT
*
26259 GTTTAA
1 ATTTAA
26265 TGTTCACGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 4 0.13
28 7 0.23
29 1 0.03
30 19 0.61
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.60
Consensus pattern (28 bp):
ATTTAAAATTTTTTGTTCATGTTCGTTT
Found at i:26338 original size:24 final size:23
Alignment explanation
Indices: 26302--26362 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
26292 ATTGAACATG
* *
26302 TTGAACATGTTCACGAACATATAA
1 TTGAATATATTCACGAACA-ATAA
26326 TTGAATATATTCACGAACAATAA
1 TTGAATATATTCACGAACAATAA
* * *
26349 ATAAATACATTCAC
1 TTGAATATATTCAC
26363 ACAAATATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (23 bp):
TTGAATATATTCACGAACAATAA
Found at i:26355 original size:23 final size:24
Alignment explanation
Indices: 26311--26362 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
26301 GTTGAACATG
* * *
26311 TTCACGAACATATAATTGAATATA
1 TTCACGAACATATAAATAAATACA
26335 TTCACGAACA-ATAAATAAATACA
1 TTCACGAACATATAAATAAATACA
26358 TTCAC
1 TTCAC
26363 ACAAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (24 bp):
TTCACGAACATATAAATAAATACA
Found at i:29736 original size:37 final size:37
Alignment explanation
Indices: 29694--29804 Score: 222
Period size: 37 Copynumber: 3.0 Consensus size: 37
29684 GACATACGCA
29694 TAAAATCATTTCTTTTAAGTTGATTTGGTATGATTGT
1 TAAAATCATTTCTTTTAAGTTGATTTGGTATGATTGT
29731 TAAAATCATTTCTTTTAAGTTGATTTGGTATGATTGT
1 TAAAATCATTTCTTTTAAGTTGATTTGGTATGATTGT
29768 TAAAATCATTTCTTTTAAGTTGATTTGGTATGATTGT
1 TAAAATCATTTCTTTTAAGTTGATTTGGTATGATTGT
29805 CCATGCCTCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (37 bp):
TAAAATCATTTCTTTTAAGTTGATTTGGTATGATTGT
Done.