Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010361.1 Kokia drynarioides strain JFW-HI SEQ_125232, 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, 805
Length: 1343
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.34
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:123 original size:6 final size:6
Alignment explanation
Indices: 112--173 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
102 AATTTTGAAG
*
112 TTAAAT TTAAA- TTAAAT TTAAAT TTAAGA- TT-AAT TTAAAT TTAATT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT
*
158 TTAAA- TCAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
174 ATAAATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
4 1 0.02
5 12 0.26
6 33 0.70
7 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:128 original size:11 final size:12
Alignment explanation
Indices: 112--173 Score: 69
Period size: 11 Copynumber: 5.4 Consensus size: 12
102 AATTTTGAAG
112 TTAAATTTAAA-
1 TTAAATTTAAAT
123 TTAAATTTAAAT
1 TTAAATTTAAAT
135 TTAAGA-TT-AAT
1 TTAA-ATTTAAAT
*
146 TTAAATTTAATT
1 TTAAATTTAAAT
*
158 TTAAA-TCAAAT
1 TTAAATTTAAAT
169 TTAAA
1 TTAAA
174 ATAAATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
10 1 0.02
11 29 0.66
12 13 0.30
13 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:161 original size:17 final size:17
Alignment explanation
Indices: 99--172 Score: 76
Period size: 17 Copynumber: 4.3 Consensus size: 17
89 TTTTGGACTG
*
99 TTTAATTTTGAAGTTAAA
1 TTTAATTTT-AATTTAAA
* *
117 TTTAAATTAAATTTAAA
1 TTTAATTTTAATTTAAA
**
134 TTTAAGATTAATTTAAA
1 TTTAATTTTAATTTAAA
* *
151 TTTAATTTTAAATCAAA
1 TTTAATTTTAATTTAAA
168 TTTAA
1 TTTAA
173 AATAAATTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
17 39 0.85
18 7 0.15
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTAATTTTAATTTAAA
Found at i:1154 original size:201 final size:203
Alignment explanation
Indices: 659--1191 Score: 881
Period size: 204 Copynumber: 2.6 Consensus size: 203
649 NNNNNNNNNN
*
659 AGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGACC
1 AGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACC
* * *
724 TGCTTCTCAGTGTCTCATCAGGAAGCTGAGGTTTGAAGATTTTGCTTGTTTTGAGCCTCGTCTGG
66 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCGTTTTGAGCCTCGTTTGG
*
789 GTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCTG
131 GTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATC-CTATTTGTTTCAATTCGCTCCTCTG
854 TACCACATC
195 TACCACATC
*
863 AAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACC
1 AGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACC
* * *
928 TGCTTCTCAGTGTCTCATTAGGAAGCTGGGGTTTGAAGATTTTTCTCGTTTTGAACCTCGTTTGG
66 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCGTTTTGAGCCTCGTTTGG
* * *
993 GTTTTCTTCTTAGTGTCTCATCAGGAAGATGATCACGT-C-ATTTGTTTCAATTCGCTCCTCTGT
131 GTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCCTATTTGTTTCAATTCGCTCCTCTGT
* *
1056 ATCTCATC
196 ACCACATC
* *
1064 AGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGGTTCGACC
1 AGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACC
* *
1129 TGCTTCACAGTGTTTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCGTTTTGAGCCTCGTTT
66 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCGTTTTGAGCCTCGTTT
1192 TGAAGAAGAG
Statistics
Matches: 307, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
201 149 0.49
202 1 0.00
204 157 0.51
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (203 bp):
AGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACC
TGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTTGCTCGTTTTGAGCCTCGTTTGG
GTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCCTATTTGTTTCAATTCGCTCCTCTGT
ACCACATC
Done.