Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014536.1 Kokia drynarioides strain JFW-HI SEQ_129575, 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: 69782
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 187 characters in sequence are not A, C, G, or T
Found at i:5862 original size:20 final size:20
Alignment explanation
Indices: 5837--5890 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
5827 TTAATTAAAA
*
5837 AAATTTATAATTTTTTTTAT
1 AAATTTATAATTTTTTTAAT
*
5857 AAATTTTATGA-TTTTTTAAT
1 AAA-TTTATAATTTTTTTAAT
5877 AAA-TTATATATTTT
1 AAATTTATA-ATTTT
5891 AAAAGGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
19 1 0.04
20 17 0.61
21 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
AAATTTATAATTTTTTTAAT
Found at i:5873 original size:19 final size:19
Alignment explanation
Indices: 5848--5890 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5838 AATTTATAAT
* *
5848 TTTTTTTATAAATTTTATGA
1 TTTTTTAATAAATTATAT-A
5868 TTTTTTAATAAATTATATA
1 TTTTTTAATAAATTATATA
5887 TTTT
1 TTTT
5891 AAAAGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTTAATAAATTATATA
Found at i:16697 original size:14 final size:14
Alignment explanation
Indices: 16678--16706 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16668 ACAGATGGAT
16678 TCGTATAATTCTTA
1 TCGTATAATTCTTA
16692 TCGTATAATTCTTA
1 TCGTATAATTCTTA
16706 T
1 T
16707 ATATATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TCGTATAATTCTTA
Found at i:21794 original size:12 final size:12
Alignment explanation
Indices: 21755--21850 Score: 59
Period size: 10 Copynumber: 8.8 Consensus size: 12
21745 AAAAATTATA
21755 TTATTGTTTTGG
1 TTATTGTTTTGG
*
21767 -TGTT-TTTT--
1 TTATTGTTTTGG
*
21775 TTACTGTTTTGG
1 TTATTGTTTTGG
21787 TTATTGTTTTGG
1 TTATTGTTTTGG
*
21799 -TATTATTTT--
1 TTATTGTTTTGG
* *
21808 TTACTATTTTGG
1 TTATTGTTTTGG
*
21820 TTGTTGTTTTGG
1 TTATTGTTTTGG
*
21832 -TATT-TTTT-T
1 TTATTGTTTTGG
21841 TTATTGTTTT
1 TTATTGTTTT
21851 CATGCTGTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
9 2 0.03
10 24 0.38
11 18 0.28
12 20 0.31
ACGTcount: A:0.09, C:0.02, G:0.18, T:0.71
Consensus pattern (12 bp):
TTATTGTTTTGG
Found at i:21818 original size:33 final size:32
Alignment explanation
Indices: 21755--21841 Score: 138
Period size: 33 Copynumber: 2.7 Consensus size: 32
21745 AAAAATTATA
* *
21755 TTATTGTTTTGGTGTTTTTTTTACTGTTTTGG
1 TTATTGTTTTGGTATTTTTTTTACTATTTTGG
21787 TTATTGTTTTGGTATTATTTTTTACTATTTTGG
1 TTATTGTTTTGGTATT-TTTTTTACTATTTTGG
*
21820 TTGTTGTTTTGGTATTTTTTTT
1 TTATTGTTTTGGTATTTTTTTT
21842 TATTGTTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 21 0.41
33 30 0.59
ACGTcount: A:0.09, C:0.02, G:0.18, T:0.70
Consensus pattern (32 bp):
TTATTGTTTTGGTATTTTTTTTACTATTTTGG
Found at i:21875 original size:12 final size:12
Alignment explanation
Indices: 21858--21915 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
21848 TTTCATGCTG
21858 TTATTTTTGTTA
1 TTATTTTTGTTA
*
21870 TTATTTTTGTTG
1 TTATTTTTGTTA
* * * *
21882 CTATTGTTGCTG
1 TTATTTTTGTTA
21894 TTATTTTTGTTA
1 TTATTTTTGTTA
*
21906 CTATTTTTGT
1 TTATTTTTGT
21916 ATTGCTGTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69
Consensus pattern (12 bp):
TTATTTTTGTTA
Found at i:21877 original size:36 final size:37
Alignment explanation
Indices: 21826--21921 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 37
21816 TTGGTTGTTG
* * *
21826 TTTTGGTATTTTTTTTTATTG-TTTTCATGCTGTTAT
1 TTTTGTTATTATTTTTTATTGCTATTCATGCTGTTAT
* **
21862 TTTTGTTATTA-TTTTTGTTGCTATTGTTGCTGTTAT
1 TTTTGTTATTATTTTTTATTGCTATTCATGCTGTTAT
*
21898 TTTTGTTACTATTTTTGTATTGCT
1 TTTTGTTATTATTTTT-TATTGCT
21922 GTTTTGGTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 8 0.16
36 31 0.63
37 4 0.08
38 6 0.12
ACGTcount: A:0.11, C:0.06, G:0.15, T:0.68
Consensus pattern (37 bp):
TTTTGTTATTATTTTTTATTGCTATTCATGCTGTTAT
Found at i:21886 original size:24 final size:24
Alignment explanation
Indices: 21859--21915 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
21849 TTCATGCTGT
*
21859 TATTTTTGTTATTATTTTTGTTGC
1 TATTTTTGTTATTATTTTTGTTAC
* * *
21883 TATTGTTGCTGTTATTTTTGTTAC
1 TATTTTTGTTATTATTTTTGTTAC
21907 TATTTTTGT
1 TATTTTTGT
21916 ATTGCTGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.68
Consensus pattern (24 bp):
TATTTTTGTTATTATTTTTGTTAC
Found at i:22143 original size:21 final size:21
Alignment explanation
Indices: 22101--22144 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
22091 ATTTATTTAT
* *
22101 TTTTTAATGTTTGTTTTAATA
1 TTTTTAATGTTTATTTGAATA
22122 TTTTTAA-GTTTATTTGATATA
1 TTTTTAATGTTTATTTGA-ATA
22143 TT
1 TT
22145 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTTTAATGTTTATTTGAATA
Found at i:33521 original size:6 final size:6
Alignment explanation
Indices: 33510--33536 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
33500 TAAAAATGGT
33510 GGTAAG GGTAAG GGTAAG GGTAAG GGT
1 GGTAAG GGTAAG GGTAAG GGTAAG GGT
33537 TTTCTTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.52, T:0.19
Consensus pattern (6 bp):
GGTAAG
Found at i:34520 original size:25 final size:25
Alignment explanation
Indices: 34483--34532 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
34473 TGCTTACTGG
* *
34483 TTCAGTGCAAGAGTAGCTACAACAA
1 TTCAGTGCAAGAGCAACTACAACAA
*
34508 TTCAGTGCGAGAGCAACTACAACAA
1 TTCAGTGCAAGAGCAACTACAACAA
34533 AGAAGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (25 bp):
TTCAGTGCAAGAGCAACTACAACAA
Found at i:35090 original size:23 final size:23
Alignment explanation
Indices: 35047--35091 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35037 AAAAAAATTC
**
35047 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
35070 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
35092 ATTCAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:50225 original size:28 final size:28
Alignment explanation
Indices: 50162--50225 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 28
50152 ACTAATCTAA
* * * *
50162 AAAAATTAATTAATTATGTAAATAATTT
1 AAAATTTAATTAAATACGAAAATAATTT
***
50190 ATTTTTTAATTAAATACGAAAATAATTT
1 AAAATTTAATTAAATACGAAAATAATTT
50218 AAAATTTA
1 AAAATTTA
50226 TAGTGAAAAT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (28 bp):
AAAATTTAATTAAATACGAAAATAATTT
Found at i:52663 original size:2 final size:2
Alignment explanation
Indices: 52656--52681 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52646 NNNNNNNNNN
52656 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
52682 TAATTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.