Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006658.1 Kokia drynarioides strain JFW-HI SEQ_121250, 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: 10198
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2147 original size:15 final size:16
Alignment explanation
Indices: 2121--2152 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2111 ACTTTGCCAG
2121 AACTAGAACCAGAACC
1 AACTAGAACCAGAACC
2137 AACTA-AACCAGAACC
1 AACTAGAACCAGAACC
2152 A
1 A
2153 GGACCAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.53, C:0.31, G:0.09, T:0.06
Consensus pattern (16 bp):
AACTAGAACCAGAACC
Found at i:3158 original size:19 final size:19
Alignment explanation
Indices: 3134--3171 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3124 TTTATTTCAG
3134 TTTAATAAGTGT-TTGCATT
1 TTTAATAA-TGTCTTGCATT
*
3153 TTTAATTATGTCTTGCATT
1 TTTAATAATGTCTTGCATT
3172 AAATGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTAATAATGTCTTGCATT
Found at i:3423 original size:48 final size:49
Alignment explanation
Indices: 3273--3421 Score: 205
Period size: 48 Copynumber: 3.1 Consensus size: 49
3263 TGTTTAATTA
*
3273 TGCATCATTAAGTGTTTTGTTTATTAAATGCATCTTTGTTTAATAATC-
1 TGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCT
* * *
3321 TACATCATTAAGTGATTTGTTTGTTAAATGCATCTTTGTTTAGTAAT-T
1 TGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCT
* * * *
3369 TGCATTATTAAATGTTTTGTTTGTTAAATGCATCTTTGTTAAAT-GTCT
1 TGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCT
3417 TGCAT
1 TGCAT
3422 TAATACATCA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.01
48 87 0.99
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.50
Consensus pattern (49 bp):
TGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCT
Found at i:3939 original size:80 final size:78
Alignment explanation
Indices: 3822--3979 Score: 226
Period size: 80 Copynumber: 2.0 Consensus size: 78
3812 CAACCAATAA
* * * * *
3822 ACACATTAAGGTTACATAAGTCTTCATTAAGGAGAAATGCCATGTCTTTTCATCTACATCAGATC
1 ACACATTAAGGATACATAAGTCATCATTAAGGAGAAATGCCATGCCTTTTCAACCACATCAGATC
*
3887 CTAGTGAAGAGAC
66 CTAATGAAGAGAC
*
3900 ACACATTAAGGATACAATAAGTCATCATTTAAGGAGAAATGCCTTGCCTTTTCAACCACATCAGA
1 ACACATTAAGGATAC-ATAAGTCATCA-TTAAGGAGAAATGCCATGCCTTTTCAACCACATCAGA
*
3965 TCCTAATGAATAGAC
64 TCCTAATGAAGAGAC
3980 GTGACTCATT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
78 14 0.20
79 10 0.14
80 46 0.66
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (78 bp):
ACACATTAAGGATACATAAGTCATCATTAAGGAGAAATGCCATGCCTTTTCAACCACATCAGATC
CTAATGAAGAGAC
Found at i:5622 original size:21 final size:22
Alignment explanation
Indices: 5596--5636 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5586 AATTATATTG
5596 TTGTTTAGG-TGCTGTTTTTTA
1 TTGTTTAGGTTGCTGTTTTTTA
* *
5617 TTGTTTTGGTTGTTGTTTTT
1 TTGTTTAGGTTGCTGTTTTT
5637 GCTGTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.05, C:0.02, G:0.24, T:0.68
Consensus pattern (22 bp):
TTGTTTAGGTTGCTGTTTTTTA
Found at i:5642 original size:12 final size:12
Alignment explanation
Indices: 5620--5755 Score: 114
Period size: 12 Copynumber: 11.5 Consensus size: 12
5610 TTTTTTATTG
* *
5620 TTTTGGTTGTTG
1 TTTTTGTTGTTA
*
5632 TTTTTGCTGTTA
1 TTTTTGTTGTTA
*
5644 TTTTTGTTGCTA
1 TTTTTGTTGTTA
* *
5656 TTTTTGTTGCTG
1 TTTTTGTTGTTA
* *
5668 TTTTTGCTGCTA
1 TTTTTGTTGTTA
5680 TTTTTGTTGTTA
1 TTTTTGTTGTTA
** *
5692 TTTTTGTTACTG
1 TTTTTGTTGTTA
*
5704 TTTTTGTTGCTA
1 TTTTTGTTGTTA
*
5716 ATTTTGTTGTT-
1 TTTTTGTTGTTA
*
5727 TTGTTGTTGTT-
1 TTTTTGTTGTTA
* *
5738 GTTTTGTTATTA
1 TTTTTGTTGTTA
5750 TTTTTG
1 TTTTTG
5756 CTTCTATTTT
Statistics
Matches: 100, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
11 17 0.17
12 83 0.83
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:5652 original size:24 final size:24
Alignment explanation
Indices: 5620--5772 Score: 114
Period size: 24 Copynumber: 6.5 Consensus size: 24
5610 TTTTTTATTG
* * *
5620 TTTTGGTTGTTGTTTTTGCTGTTA
1 TTTTTGTTGTTATTTTTGTTGTTA
* * *
5644 TTTTTGTTGCTATTTTTGTTGCTG
1 TTTTTGTTGTTATTTTTGTTGTTA
* *
5668 TTTTTGCTGCTATTTTTGTTGTTA
1 TTTTTGTTGTTATTTTTGTTGTTA
** * *
5692 TTTTTGTTACTGTTTTTGTTGCTA
1 TTTTTGTTGTTATTTTTGTTGTTA
* *
5716 ATTTTGTTGTT-TTGTTGTTGTT-
1 TTTTTGTTGTTATTTTTGTTGTTA
* * *
5738 GTTTTGTTATTATTTTTGCTT-CTA
1 TTTTTGTTGTTATTTTTG-TTGTTA
*
5762 TTTTGGTTGTT
1 TTTTTGTTGTT
5773 TGGATGTTAT
Statistics
Matches: 101, Mismatches: 25, Indels: 6
0.77 0.19 0.05
Matches are distributed among these distances:
22 9 0.09
23 15 0.15
24 77 0.76
ACGTcount: A:0.07, C:0.06, G:0.20, T:0.68
Consensus pattern (24 bp):
TTTTTGTTGTTATTTTTGTTGTTA
Found at i:5676 original size:36 final size:36
Alignment explanation
Indices: 5620--5742 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
5610 TTTTTTATTG
* * *
5620 TTTTGGTTGTTGTTTTTGCTGTTATTTTTGTTGCTA
1 TTTTTGTTGCTGTTTTTGCTGCTATTTTTGTTGCTA
*
5656 TTTTTGTTGCTGTTTTTGCTGCTATTTTTGTTGTTA
1 TTTTTGTTGCTGTTTTTGCTGCTATTTTTGTTGCTA
* * *
5692 TTTTTGTTACTGTTTTTGTTGCTAATTTTGTTG-T-
1 TTTTTGTTGCTGTTTTTGCTGCTATTTTTGTTGCTA
*
5726 TTTGTTGTTGTTGTTTT
1 TTT-TTGTTGCTGTTTT
5743 GTTATTATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
34 3 0.04
35 12 0.16
36 62 0.81
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (36 bp):
TTTTTGTTGCTGTTTTTGCTGCTATTTTTGTTGCTA
Found at i:5738 original size:14 final size:14
Alignment explanation
Indices: 5719--5745 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5709 GTTGCTAATT
5719 TTGTTGTTTTGTTG
1 TTGTTGTTTTGTTG
5733 TTGTTGTTTTGTT
1 TTGTTGTTTTGTT
5746 ATTATTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (14 bp):
TTGTTGTTTTGTTG
Found at i:5771 original size:46 final size:47
Alignment explanation
Indices: 5626--5773 Score: 137
Period size: 48 Copynumber: 3.2 Consensus size: 47
5616 ATTGTTTTGG
* * * **
5626 TTGTTG-TTT-TTGCTGTTATTTTTGTTGCTATTTTTGTTGCTGTTT
1 TTGTTGTTTTGTTGTTGTTAGTTTTGTTACTATTTTTGTTGCTAATT
* * *
5671 TTGCTGCTATTT-TTGTTGTTATTTTTGTTACTGTTTTTGTTGCTAATT
1 TTGTTG-T-TTTGTTGTTGTTAGTTTTGTTACTATTTTTGTTGCTAATT
*
5719 TTGTTGTTTTGTTGTTGTT-GTTTTGTTATTATTTTTGCTT-CT-ATT
1 TTGTTGTTTTGTTGTTGTTAGTTTTGTTACTATTTTTG-TTGCTAATT
5764 TTGGTTGTTT
1 TT-GTTGTTT
5774 GGATGTTATT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
45 10 0.11
46 27 0.31
47 11 0.13
48 39 0.45
ACGTcount: A:0.07, C:0.06, G:0.19, T:0.68
Consensus pattern (47 bp):
TTGTTGTTTTGTTGTTGTTAGTTTTGTTACTATTTTTGTTGCTAATT
Found at i:6487 original size:18 final size:21
Alignment explanation
Indices: 6447--6500 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
6437 TGGGAAGGTC
6447 CTACCGATACAAGTATGACTA
1 CTACCGATACAAGTATGACTA
* * *
6468 CTACCGATACAATTATTACTT
1 CTACCGATACAAGTATGACTA
*
6489 CTACTGATACAA
1 CTACCGATACAA
6501 CAAACTCCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (21 bp):
CTACCGATACAAGTATGACTA
Found at i:8886 original size:84 final size:84
Alignment explanation
Indices: 8789--8944 Score: 231
Period size: 84 Copynumber: 1.9 Consensus size: 84
8779 ATTTGTACAG
* * * *
8789 ATACCGTACCGATGGCTGAGATACCGCATATGTTACGAGTCCTTGTCATCTTAGTGTGAGCAGCA
1 ATACCGTACCGATGACTAAGATACCGCATATGTTACGAGTCCTCGTCAGCTTAGTGTGAGCAGCA
*
8854 TCGTATATTTGTAATAGTT
66 TCATATATTTGTAATAGTT
* * * *
8873 ATACCGTATCGATGACTAAGGTACCGCATATGTTGCGAGTCCTCGTCAGCTTAGTGTGAGTAGCA
1 ATACCGTACCGATGACTAAGATACCGCATATGTTACGAGTCCTCGTCAGCTTAGTGTGAGCAGCA
8938 TCATATA
66 TCATATA
8945 CTAGTAAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (84 bp):
ATACCGTACCGATGACTAAGATACCGCATATGTTACGAGTCCTCGTCAGCTTAGTGTGAGCAGCA
TCATATATTTGTAATAGTT
Done.