Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002902.1 Kokia drynarioides strain JFW-HI SEQ_115319, 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: 2063
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Found at i:164 original size:23 final size:23
Alignment explanation
Indices: 131--199 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
121 TTGGGACATC
*
131 ATTTA-AATAAATTTAAATCTAA
1 ATTTACAATAAATTTAAATTTAA
**
153 ATTTATGATAAATTTAAATTTAA
1 ATTTACAATAAATTTAAATTTAA
*
176 ATTTCCAATAAATTTAAATTTAA
1 ATTTACAATAAATTTAAATTTAA
199 A
1 A
200 ATAAATTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 5 0.12
23 36 0.88
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (23 bp):
ATTTACAATAAATTTAAATTTAA
Found at i:170 original size:6 final size:6
Alignment explanation
Indices: 138--212 Score: 52
Period size: 6 Copynumber: 13.0 Consensus size: 6
128 ATCATTTAAA
* * *
138 TAAATT TAAATC TAAATT T--ATGA TAAATT TAAATT TAAATT TCCAA--
1 TAAATT TAAATT TAAATT TAAAT-T TAAATT TAAATT TAAATT T-AAATT
* *
184 TAAATT TAAATT TAAA-A TAAATT CAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT
213 ATGTTAGGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
4 4 0.08
5 6 0.11
6 39 0.74
7 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:187 original size:17 final size:17
Alignment explanation
Indices: 167--212 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
157 ATGATAAATT
**
167 TAAATTTAAATTTCCAA
1 TAAATTTAAATTTAAAA
184 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
201 TAAATTCAAATT
1 TAAATTTAAATT
213 ATGTTAGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:792 original size:98 final size:97
Alignment explanation
Indices: 645--1061 Score: 462
Period size: 98 Copynumber: 4.3 Consensus size: 97
635 CCCCGTTACG
* *
645 GCTTAAATTTTTCCTTTCATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCT
1 GCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCT
* *
710 TTGTGTCTTCGTGGTACTGGATTCGCTGTTGC
66 TTATGTCTTCGTGGTACTGGATTCGCCGTTGC
* *
742 AGCTTAAATCTTTCCCTTCATG-TCTCTGAGGTATTAGGTTCGTCATTGCGACTTAAACCTTACC
1 -GCTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCC
* *
806 ATTTATGTCTTCATGGTACTGGATTCGCCGTTGC
64 CTTTATGTCTTCGTGGTACTGGATTCGCCGTTGC
* * ** *
840 GGCTTAAATATTTCCCTTCACGCTTCTGAGGTACGAGGTTCG-CGATTGCGACTTAAAGCTTTCC
1 -GCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGTC-ATTGCGACTTAAACCTTTCC
** * ** *
904 CTCCATATCTTCGTGGTACTGGATTTACCGTTAC
64 CTTTATGTCTTCGTGGTACTGGATTCGCCGTTGC
* * *
938 GACTTAAATCTTTCCCTTCATG-TCTCTGAGGTATAAGGTTTGCCATTACGACTTAAACCTTTCC
1 G-CTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCC
** * * * * * * **
1002 CTCCATATATTTGGGGTACTAGATTCACCACTGC
64 CTTTATGTCTTCGTGGTACTGGATTCGCCGTTGC
1036 GGCTTAAATCTTTCCCTTCATGCTTC
1 -GCTTAAATCTTTCCCTTCATGCTTC
1062 GTGGTACTGA
Statistics
Matches: 273, Mismatches: 38, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
97 4 0.01
98 265 0.97
99 4 0.01
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (97 bp):
GCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCT
TTATGTCTTCGTGGTACTGGATTCGCCGTTGC
Found at i:955 original size:196 final size:196
Alignment explanation
Indices: 621--998 Score: 526
Period size: 196 Copynumber: 1.9 Consensus size: 196
611 CTTTAATCTG
* * * *
621 CATGGTACTAAATTCCCCGTTACGGCTTAAATTTTTCCTTTCATGCTTCTGAGGTATAAGGTTCG
1 CATGGTACTAAATTCCCCGTTACGGCTTAAATATTTCCCTTCACGCTTCTGAGGTACAAGGTTCG
*** * * * *
686 TCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCTGTTGCAGCTTAAAT
66 TCATTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCACCGTTACAGCTTAAAT
* * *
751 CTTTCCCTTCATGTCTCTGAGGTATTAGGTTCGTCATTGCGACTTAAACCTTACCATTTATGTCT
131 CTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTACGACTTAAACCTTACCATTTATGTCT
816 T
196 T
** * * *
817 CATGGTACTGGATTCGCCGTTGCGGCTTAAATATTTCCCTTCACGCTTCTGAGGTACGAGGTTCG
1 CATGGTACTAAATTCCCCGTTACGGCTTAAATATTTCCCTTCACGCTTCTGAGGTACAAGGTTCG
* *
882 -CGATTGCGACTTAAAGCTTTCCCTCCATATCTTCGTGGTACTGGATTTACCGTTAC-GACTTAA
66 TC-ATTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCACCGTTACAG-CTTAA
*
945 ATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCCATTACGACTTAAACCTT
129 ATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTACGACTTAAACCTT
999 TCCCTCCATA
Statistics
Matches: 158, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
195 2 0.01
196 156 0.99
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.38
Consensus pattern (196 bp):
CATGGTACTAAATTCCCCGTTACGGCTTAAATATTTCCCTTCACGCTTCTGAGGTACAAGGTTCG
TCATTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCACCGTTACAGCTTAAAT
CTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTACGACTTAAACCTTACCATTTATGTCT
T
Found at i:987 original size:49 final size:48
Alignment explanation
Indices: 646--1057 Score: 239
Period size: 49 Copynumber: 8.4 Consensus size: 48
636 CCCGTTACGG
* * *
646 CTTAAATTTTTCCTTTCATG-CTTCTGAGGTATAAGGTTCGTCATTGCGA
1 CTTAAATCTTTCCCTTCATGTC-TCTGAGGTAT-AGGTTCGCCATTGCGA
* ** * **
695 CTTAAACCTTTCCCTTTGTGTCT-TCGTGGTACT-GGATTCGCTGTTGC-A
1 CTTAAATCTTTCCCTTCATGTCTCT-GAGGTA-TAGG-TTCGCCATTGCGA
*
743 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTATTAGGTTCGTCATTGCGA
1 -CTTAAATCTTTCCCTTCATGTCTCTGAGGTA-TAGGTTCGCCATTGCGA
* * * * * * *
793 CTTAAACCTTACCATTTATGTCT-TCATGGTACT-GGATTCGCCGTTGCGG
1 CTTAAATCTTTCCCTTCATGTCTCTGA-GGTA-TAGG-TTCGCCATTGCGA
* * * *
842 CTTAAATATTTCCCTTCACG-CTTCTGAGGTACGAGGTTCGCGATTGCGA
1 CTTAAATCTTTCCCTTCATGTC-TCTGAGGTA-TAGGTTCGCCATTGCGA
* * * * ** * *
891 CTTAAAGCTTTCCCTCCATATCT-TCGTGGTACT-GGATTTACCGTTACGA
1 CTTAAATCTTTCCCTTCATGTCTCT-GAGGTA-TAGG-TTCGCCATTGCGA
* *
940 CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTTGCCATTACGA
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTAT-AGGTTCGCCATTGCGA
* * * * * * * * * *
989 CTTAAACCTTTCCCTCCATATATTTGGGGTACTAGATTCACCACTGCGG
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTA-TAGGTTCGCCATTGCGA
1038 CTTAAATCTTTCCCTTCATG
1 CTTAAATCTTTCCCTTCATG
1058 CTTCGTGGTA
Statistics
Matches: 273, Mismatches: 70, Indels: 40
0.71 0.18 0.10
Matches are distributed among these distances:
48 13 0.05
49 245 0.90
50 15 0.05
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (48 bp):
CTTAAATCTTTCCCTTCATGTCTCTGAGGTATAGGTTCGCCATTGCGA
Found at i:1039 original size:196 final size:196
Alignment explanation
Indices: 643--1061 Score: 518
Period size: 196 Copynumber: 2.1 Consensus size: 196
633 TTCCCCGTTA
* * *
643 CGGCTTAAATTTTTCCTTTCATGCTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCC
1 CGGCTTAAATATTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCC
*** * * * *
708 CTTTGTGTCTTCGTGGTACTGGATTCGCTGTTGCAGCTTAAATCTTTCCCTTCATGTCTCTGAGG
66 CTCCATATCTTCGTGGTACTGGATTCACCGTTACAGCTTAAATCTTTCCCTTCATGTCTCTGAGG
* * * ** * * * * * **
773 TATTAGGTTCGTCATTGCGACTTAAACCTTACCATTTATGTCTTCATGGTACTGGATTCGCCGTT
131 TATAAGGTTCGCCATTACGACTTAAACCTTACCATCCATATATTCAGGGTACTAGATTCACCACT
838 G
196 G
* * *
839 CGGCTTAAATATTTCCCTTCACGCTTCTGAGGTACGAGGTTCG-CGATTGCGACTTAAAGCTTTC
1 CGGCTTAAATATTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTC-ATTGCGACTTAAACCTTTC
*
903 CCTCCATATCTTCGTGGTACTGGATTTACCGTTAC-GACTTAAATCTTTCCCTTCATGTCTCTGA
65 CCTCCATATCTTCGTGGTACTGGATTCACCGTTACAG-CTTAAATCTTTCCCTTCATGTCTCTGA
* * * **
967 GGTATAAGGTTTGCCATTACGACTTAAACCTTTCCCTCCATATATTTGGGGTACTAGATTCACCA
129 GGTATAAGGTTCGCCATTACGACTTAAACCTTACCATCCATATATTCAGGGTACTAGATTCACCA
1032 CTG
194 CTG
*
1035 CGGCTTAAATCTTTCCCTTCATGCTTC
1 CGGCTTAAATATTTCCCTTCATGCTTC
1062 GTGGTACTGA
Statistics
Matches: 188, Mismatches: 33, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
195 2 0.01
196 186 0.99
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (196 bp):
CGGCTTAAATATTTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCC
CTCCATATCTTCGTGGTACTGGATTCACCGTTACAGCTTAAATCTTTCCCTTCATGTCTCTGAGG
TATAAGGTTCGCCATTACGACTTAAACCTTACCATCCATATATTCAGGGTACTAGATTCACCACT
G
Done.