Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004095.1 Kokia drynarioides strain JFW-HI SEQ_117266, 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: 7655
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2865 original size:10 final size:10
Alignment explanation
Indices: 2850--2879 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2840 AAAGAAAAAG
2850 ATTAATATAA
1 ATTAATATAA
2860 ATTAATAT-A
1 ATTAATATAA
2869 ATTAATATAA
1 ATTAATATAA
2879 A
1 A
2880 AAATATAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTAATATAA
Found at i:2873 original size:9 final size:9
Alignment explanation
Indices: 2850--2888 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2840 AAAGAAAAAG
2850 ATTAATATAA
1 ATTAATAT-A
2860 ATTAATATA
1 ATTAATATA
2869 ATTAATATA
1 ATTAATATA
**
2878 AAAAATATA
1 ATTAATATA
2887 AT
1 AT
2889 CTATAATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAATATA
Found at i:2874 original size:19 final size:18
Alignment explanation
Indices: 2850--2888 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
2840 AAAGAAAAAG
*
2850 ATTAATATAAATTAATATA
1 ATTAATATAAA-AAATATA
2869 ATTAATATAAAAAATATA
1 ATTAATATAAAAAATATA
2887 AT
1 AT
2889 CTATAATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAATATAAAAAATATA
Found at i:3206 original size:20 final size:20
Alignment explanation
Indices: 3169--3213 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3159 GATCTGATTA
* * *
3169 TAAAATAATTATTTAACTGT
1 TAAAATAATCACTCAACTGT
*
3189 TAAAATAATCACTCAACTTT
1 TAAAATAATCACTCAACTGT
3209 TAAAA
1 TAAAA
3214 AATAATAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAATAATCACTCAACTGT
Found at i:3739 original size:39 final size:37
Alignment explanation
Indices: 3657--3742 Score: 102
Period size: 39 Copynumber: 2.3 Consensus size: 37
3647 TTTTGATGCC
3657 TGTGATAACTCAAAGCAAAAGAAAATCAGAAGATTCA
1 TGTGATAACTCAAAGCAAAAGAAAATCAGAAGATTCA
* * * *
3694 TCTGATATCTCAGAAGC-AAAGCAAAAATTAGAAGATTCT
1 TGTGATAACTCA-AAGCAAAAG--AAAATCAGAAGATTCA
3733 TGTGATAACT
1 TGTGATAACT
3743 TAGGGTCACA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 14 0.35
38 4 0.10
39 22 0.55
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.24
Consensus pattern (37 bp):
TGTGATAACTCAAAGCAAAAGAAAATCAGAAGATTCA
Found at i:6214 original size:102 final size:103
Alignment explanation
Indices: 6022--6213 Score: 293
Period size: 102 Copynumber: 1.9 Consensus size: 103
6012 TCGACACCCC
*
6022 TTTTTTTATCTGGTAAAAAATCAATTTTTTTTTGTGTTGGCCATTGCATGACTGACACCCTCTTT
1 TTTTTTTATCTGATAAAAAATCAATTTTTTTTTGTGTTGGCCATTGCATGACTGACACCCTCTTT
6087 TTGTCAAATAAAAAATTAAAATTTTTTGGTGTTGGCCA
66 TTGTCAAATAAAAAATTAAAATTTTTTGGTGTTGGCCA
* * *
6125 TTTTTTTATTTGATAAAAAATCAA-TTTTTTTTGTGTTGGCCATTGCAT-AGTTGATACCC-CTT
1 TTTTTTTATCTGATAAAAAATCAATTTTTTTTTGTGTTGGCCATTGCATGA-CTGACACCCTCTT
* *
6187 TTTGTCAGAT-AAAAATTCAAATTTTTT
65 TTTGTCAAATAAAAAATTAAAATTTTTT
6214 TGTATTGGTC
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
100 16 0.20
101 13 0.16
102 31 0.38
103 22 0.27
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (103 bp):
TTTTTTTATCTGATAAAAAATCAATTTTTTTTTGTGTTGGCCATTGCATGACTGACACCCTCTTT
TTGTCAAATAAAAAATTAAAATTTTTTGGTGTTGGCCA
Found at i:6269 original size:61 final size:60
Alignment explanation
Indices: 6127--6428 Score: 283
Period size: 61 Copynumber: 5.0 Consensus size: 60
6117 GTTGGCCATT
* * * * *
6127 TTTTTATTTGAT-AAAAAATCAATTTTTTTTGTGTTGGCCATTGCAT-AGTTGATACC-CC
1 TTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATTACATGA-TCGACACCACC
* * * * * *
6185 TTTTTGTCAGAT-AAAAATTCAAATTTTTTTGTATTGGTCATTGCATGATCGACACCACC
1 TTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATTACATGATCGACACCACC
* *
6244 TTTTTAATCTGATAAAAAATTCAAATTTTTTTGTGTTGGCCA-TACATCAGTCGACACCACC
1 TTTTT-ATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATTACATGA-TCGACACCACC
* * **
6305 TATTTTATCTGA-AAAAAAATCAAATTTTTTGGTGTTGGCCATTACGTGGCCGACACCACC
1 T-TTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATTACATGATCGACACCACC
* * * * * * ** *
6365 TTATTATTTGATTAAAAAAATCAAAATTTTTTATGTTGGTCATTTCATGGCCGACACCAAC
1 TTTTTATCTGA-TAAAAAAATCAAATTTTTTTGTGTTGGCCATTACATGATCGACACCACC
6426 TTT
1 TTT
6429 CCTTCATTTC
Statistics
Matches: 204, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
58 45 0.22
59 16 0.08
60 48 0.24
61 91 0.45
62 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (60 bp):
TTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATTACATGATCGACACCACC
Found at i:6381 original size:121 final size:117
Alignment explanation
Indices: 6130--6422 Score: 309
Period size: 121 Copynumber: 2.5 Consensus size: 117
6120 GGCCATTTTT
* * * * *
6130 TTATTTGATAAAAAATCAATTTTTTTTGTGTTGGCCATTGCATAGTTGATACCCCTTTTTGTCAG
1 TTATTTGATAAAAAATCAAATTTTTTTGTGTTGGCCATTACATAGTCGACACCCCTTTTTATCAG
* * * * * * *
6195 ATAAAAATTCAAATTTTTTTGTATTGGTCATTGCATGATCGACACCACCTTT
66 AAAAAAAATCAAATTTTTTGGTATTGGCCATTACATGACCGACACCACCTTA
*
6247 TTAATCTGATAAAAAATTCAAATTTTTTTGTGTTGGCCA-TACATCAGTCGACACCACCTATTTT
1 TT-ATTTGATAAAAAA-TCAAATTTTTTTGTGTTGGCCATTACAT-AGTCGACACC-CCT-TTTT
* * * *
6311 ATCTGAAAAAAAATCAAATTTTTTGGTGTTGGCCATTACGTGGCCGACACCACCTTA
61 ATCAGAAAAAAAATCAAATTTTTTGGTATTGGCCATTACATGACCGACACCACCTTA
* * * * * *
6368 TTATTTGATTAAAAAAATCAAAATTTTTTATGTTGGTCATTTCATGGCCGACACC
1 TTATTTGA-T-AAAAAATCAAATTTTTTTGTGTTGGCCATTACATAGTCGACACC
6423 AACTTTCCTT
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
117 2 0.01
118 16 0.11
119 29 0.20
120 8 0.06
121 79 0.55
122 10 0.07
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (117 bp):
TTATTTGATAAAAAATCAAATTTTTTTGTGTTGGCCATTACATAGTCGACACCCCTTTTTATCAG
AAAAAAAATCAAATTTTTTGGTATTGGCCATTACATGACCGACACCACCTTA
Found at i:7306 original size:30 final size:30
Alignment explanation
Indices: 7272--7375 Score: 138
Period size: 30 Copynumber: 3.5 Consensus size: 30
7262 GAAAAGAAAT
*
7272 TTAAAATATAAATGAAATTACAAATTAAAA
1 TTAAAATATAAACGAAATTACAAATTAAAA
* * * *
7302 TTAAAATATACAGGAAATTAGAAATTAAAT
1 TTAAAATATAAACGAAATTACAAATTAAAA
7332 TTAAAATATAAACGAAATTACAAATT-AAA
1 TTAAAATATAAACGAAATTACAAATTAAAA
*
7361 TTAAAAAAATAAACG
1 TT-AAAATATAAACG
7376 GAAAAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 4 0.06
30 60 0.94
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.28
Consensus pattern (30 bp):
TTAAAATATAAACGAAATTACAAATTAAAA
Done.