Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011461.1 Kokia drynarioides strain JFW-HI SEQ_126445, 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: 57486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6608 original size:11 final size:11
Alignment explanation
Indices: 6575--6609 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
6565 TCTTAGGTTG
6575 TGTACTAATTT
1 TGTACTAATTT
*
6586 TGTATCTTATTT
1 TGTA-CTAATTT
6598 TGTACTAATTT
1 TGTACTAATTT
6609 T
1 T
6610 ATTTTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (11 bp):
TGTACTAATTT
Found at i:11523 original size:21 final size:21
Alignment explanation
Indices: 11497--11546 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
11487 AACAAGTCAA
11497 ATTAAAAACATTAAATTTAAAT
1 ATTAAAAACA-TAAATTTAAAT
** *
11519 -TTAAAATGATATATTTAAAT
1 ATTAAAAACATAAATTTAAAT
11539 ATTAAAAA
1 ATTAAAAA
11547 AATACCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTAAAAACATAAATTTAAAT
Found at i:16882 original size:23 final size:22
Alignment explanation
Indices: 16856--16899 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
16846 TGTTGTAATG
16856 TATT-ATACAATATTGAGATAAAT
1 TATTAATA-AATATTGAG-TAAAT
*
16879 TATTAATAATTATTGAGTAAA
1 TATTAATAAATATTGAGTAAA
16900 ATGTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 12 0.63
24 3 0.16
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (22 bp):
TATTAATAAATATTGAGTAAAT
Found at i:18110 original size:18 final size:17
Alignment explanation
Indices: 18087--18120 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18077 AAATAAGAAT
18087 TTTATTTAATTTTTTAAG
1 TTTATTT-ATTTTTTAAG
*
18105 TTTATTTTTTTTTTAA
1 TTTATTTATTTTTTAA
18121 ATGAAAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATTTATTTTTTAAG
Found at i:26186 original size:16 final size:17
Alignment explanation
Indices: 26165--26201 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
26155 TCATACCATG
26165 GTTTTATTTATTATTA-
1 GTTTTATTTATTATTAT
26181 GTTTTATTTATTATTAT
1 GTTTTATTTATTATTAT
26198 GTTT
1 GTTT
26202 CTTTACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (17 bp):
GTTTTATTTATTATTAT
Found at i:27850 original size:55 final size:57
Alignment explanation
Indices: 27771--27893 Score: 169
Period size: 55 Copynumber: 2.2 Consensus size: 57
27761 TAAACATGCT
* *
27771 ACATAACAATCAATTTAAACATATAAACAATCGATTCAAAAGAAGCAG-A-ATTCCA
1 ACATAACAATCAATATAAACATATAAACAATCGATTCAAAAGAAGAAGAATATTCCA
* * *
27826 ACATAACAATCGATATAAATATATAAACAATCGATTTAAAAGAAGAAGTAATATTCCA
1 ACATAACAATCAATATAAACATATAAACAATCGATTCAAAAGAAGAAG-AATATTCCA
*
27884 CCATAACAAT
1 ACATAACAAT
27894 AGATTTTTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 43 0.73
57 1 0.02
58 15 0.25
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (57 bp):
ACATAACAATCAATATAAACATATAAACAATCGATTCAAAAGAAGAAGAATATTCCA
Found at i:30815 original size:55 final size:55
Alignment explanation
Indices: 30742--30985 Score: 181
Period size: 55 Copynumber: 4.7 Consensus size: 55
30732 TGCAAAAATT
* * * * *
30742 TTACTTTTTTTGGATCGATTGTTTTTATGTTTAAATTAATTACCGTGTTGGAATA
1 TTACTTCTTTTGAATCGATTGTTTATATGTTTAAATTAATTATCATGTTGGAATA
* * * * * *
30797 TTGCTTCTTTTGAATCGATTG--T-TATG-CTAAAAT-ACT-TC-TGCT-G---C
1 TTACTTCTTTTGAATCGATTGTTTATATGTTTAAATTAATTATCATGTTGGAATA
** * * *
30841 TT-CTTCTTTTGAATCGATTGTTTATATGTTTAAATTGGTTGTTATGTTGAAATA
1 TTACTTCTTTTGAATCGATTGTTTATATGTTTAAATTAATTATCATGTTGGAATA
** * * *
30895 CCATTTCTTTTGAATCGATTGTTTATA-GTTTAAATTTATTATTATGTTGGAATA
1 TTACTTCTTTTGAATCGATTGTTTATATGTTTAAATTAATTATCATGTTGGAATA
* * *
30949 TTACTTCTTTTAAATCAATTGTTTGTATGTTTAAATT
1 TTACTTCTTTTGAATCGATTGTTTATATGTTTAAATT
30986 TATTGTTATG
Statistics
Matches: 146, Mismatches: 30, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
43 18 0.12
44 2 0.01
45 1 0.01
46 4 0.03
47 6 0.04
48 4 0.03
49 2 0.01
50 5 0.03
51 5 0.03
52 4 0.03
53 1 0.01
54 44 0.30
55 50 0.34
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (55 bp):
TTACTTCTTTTGAATCGATTGTTTATATGTTTAAATTAATTATCATGTTGGAATA
Found at i:30957 original size:54 final size:55
Alignment explanation
Indices: 30843--30996 Score: 211
Period size: 54 Copynumber: 2.8 Consensus size: 55
30833 TCTGCTGCTT
**
30843 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTGGTTGTTATGTTGAAATACCA
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTTATTGTTATGTTGAAATACCA
* * * **
30898 TTTCTTTTGAATCGATTGTTTATA-GTTTAAATTTATTATTATGTTGGAATATTA
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTTATTGTTATGTTGAAATACCA
* * *
30952 CTTCTTTTAAATCAATTGTTTGTATGTTTAAATTTATTGTTATGT
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATTTATTGTTATGT
30997 AACACATTTA
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 44 0.51
55 42 0.49
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (55 bp):
CTTCTTTTGAATCGATTGTTTATATGTTTAAATTTATTGTTATGTTGAAATACCA
Found at i:30990 original size:21 final size:22
Alignment explanation
Indices: 30957--30997 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
30947 TATTACTTCT
30957 TTTAAATCAATTGTT-TGTATG
1 TTTAAATCAATTGTTATGTATG
**
30978 TTTAAATTTATTGTTATGTA
1 TTTAAATCAATTGTTATGTA
30998 ACACATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.56
Consensus pattern (22 bp):
TTTAAATCAATTGTTATGTATG
Found at i:34721 original size:18 final size:20
Alignment explanation
Indices: 34683--34722 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
34673 TTTTTAAAAA
*
34683 TTAAAAATCATTAAAATTAT
1 TTAAAAATCATTAAAAATAT
34703 TTAAAAAT-A-TAAAAATAT
1 TTAAAAATCATTAAAAATAT
34721 TT
1 TT
34723 TTAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAAAATCATTAAAAATAT
Found at i:34737 original size:20 final size:19
Alignment explanation
Indices: 34683--34747 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
34673 TTTTTAAAAA
34683 TTAAAAATCATTAAAATTAT
1 TTAAAAAT-ATTAAAATTAT
* *
34703 TTAAAAATATAAAAATATTT
1 TTAAAAATATTAAAAT-TAT
* *
34723 TTAAAAATTTTAAAAATTAA
1 TTAAAAATATT-AAAATTAT
34743 TTAAA
1 TTAAA
34748 TTCTGACATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 7 0.19
20 25 0.68
21 5 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAATATTAAAATTAT
Found at i:45918 original size:2 final size:2
Alignment explanation
Indices: 45911--45945 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
45901 TTTCAGGTTT
* *
45911 AC AC AC AC GC GC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
45946 TATGCACAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.49, G:0.06, T:0.00
Consensus pattern (2 bp):
AC
Found at i:50972 original size:25 final size:25
Alignment explanation
Indices: 50943--50997 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
50933 AAGTGTTAAA
50943 TACCTTAACCAAATGAACTTAAACC
1 TACCTTAACCAAATGAACTTAAACC
*
50968 TACCTTAACCAAATGAACTTAAATC
1 TACCTTAACCAAATGAACTTAAACC
50993 TACCT
1 TACCT
50998 AAAACTTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (25 bp):
TACCTTAACCAAATGAACTTAAACC
Done.