Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005387.1 Kokia drynarioides strain JFW-HI SEQ_119383, 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: 8658
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Found at i:229 original size:14 final size:16
Alignment explanation
Indices: 205--236 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
195 ACAACCGAAT
205 GATGCGAGTAC-CTCC
1 GATGCGAGTACACTCC
220 GATG-GAGTACACTCC
1 GATGCGAGTACACTCC
235 GA
1 GA
237 ATTTACAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (16 bp):
GATGCGAGTACACTCC
Found at i:538 original size:45 final size:45
Alignment explanation
Indices: 474--610 Score: 195
Period size: 45 Copynumber: 3.0 Consensus size: 45
464 GCATAGCTTA
474 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* *
519 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACTGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * * * *
564 TCAAAG-GAAGGATATCAGGCTGAGTTTGACGAGCCATCGCGATAC
1 TC-AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
609 TC
1 TC
611 TATTCCTCTC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 79 0.96
46 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:638 original size:21 final size:20
Alignment explanation
Indices: 605--643 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
595 AGCCATCGCG
*
605 ATACTCTATTCCTCTCGGGCA
1 ATACTCTACTCCTC-CGGGCA
*
626 ATACTTTACTCCTCCGGG
1 ATACTCTACTCCTCCGGG
644 GCAAATGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (20 bp):
ATACTCTACTCCTCCGGGCA
Found at i:3879 original size:20 final size:18
Alignment explanation
Indices: 3854--3908 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 18
3844 ATCCATATTC
3854 AATAAATCTGTTAAAAATAA
1 AATAAAT-T-TTAAAAATAA
*
3874 AATAAAATTTAATAAATAA
1 AATAAATTTTAA-AAATAA
3893 AATATAATTTTAAAAA
1 AATA-AATTTTAAAAA
3909 GATATCATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 4 0.13
19 14 0.45
20 13 0.42
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAAATTTTAAAAATAA
Found at i:3970 original size:4 final size:4
Alignment explanation
Indices: 3948--4015 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
3938 AACACATTAC
* * * * *
3948 CTTT CTTT CCTCT CCTT CTTT CTTT CTTCT CCTT CTTC CTTT CTTT CCTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTT-T CTTT CTTT CTTT CTTT CTTT
3998 CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT CTTT C
4016 CCGTTTATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
4 42 0.82
5 9 0.18
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:3974 original size:21 final size:21
Alignment explanation
Indices: 3948--4016 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
3938 AACACATTAC
3948 CTTTCTTTCCTCTCCTTCTTT
1 CTTTCTTTCCTCTCCTTCTTT
*
3969 CTTTC--T--TCTCCTTCTTC
1 CTTTCTTTCCTCTCCTTCTTT
*
3986 CTTTCTTTCCT-TCTTTTCTTT
1 CTTTCTTTCCTCTC-CTTCTTT
4007 CTTTCTTTCC
1 CTTTCTTTCC
4017 CGTTTATTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 15 0.38
19 2 0.05
20 2 0.05
21 21 0.52
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (21 bp):
CTTTCTTTCCTCTCCTTCTTT
Found at i:3983 original size:13 final size:12
Alignment explanation
Indices: 3948--4015 Score: 64
Period size: 13 Copynumber: 5.4 Consensus size: 12
3938 AACACATTAC
*
3948 CTTTCTTTCCTCT
1 CTTTCTTT-CTTT
*
3961 CCTTCTTTCTTT
1 CTTTCTTTCTTT
* *
3973 CTTCTCCTTCTTC
1 CTT-TCTTTCTTT
*
3986 CTTTCTTTCCTT
1 CTTTCTTTCTTT
3998 CTTTTCTTTCTTT
1 C-TTTCTTTCTTT
4011 CTTTC
1 CTTTC
4016 CCGTTTATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
12 16 0.36
13 28 0.64
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (12 bp):
CTTTCTTTCTTT
Found at i:3999 original size:25 final size:25
Alignment explanation
Indices: 3963--4015 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3953 TTTCCTCTCC
*
3963 TTCTTTCTTTCTTCTCCTTCTTCCT
1 TTCTTTCCTTCTTCTCCTTCTTCCT
* * *
3988 TTCTTTCCTTCTTTTCTTTCTTTCT
1 TTCTTTCCTTCTTCTCCTTCTTCCT
4013 TTC
1 TTC
4016 CCGTTTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (25 bp):
TTCTTTCCTTCTTCTCCTTCTTCCT
Found at i:4008 original size:17 final size:16
Alignment explanation
Indices: 3948--4011 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 16
3938 AACACATTAC
*
3948 CTTTCTTTCCTCTCCTT
1 CTTTCTTT-CTTTCCTT
3965 CTTTCTTTCTTCTCCTT
1 CTTTCTTTCTT-TCCTT
*
3982 CTTCCTTTCTTTCCTT
1 CTTTCTTTCTTTCCTT
3998 CTTTTCTTTCTTTC
1 C-TTTCTTTCTTTC
4012 TTTCCCGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
16 8 0.19
17 34 0.81
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
CTTTCTTTCTTTCCTT
Done.