Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004856.1 Kokia drynarioides strain JFW-HI SEQ_118518, 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, 720
Length: 1201
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Found at i:898 original size:39 final size:39
Alignment explanation
Indices: 829--1153 Score: 197
Period size: 39 Copynumber: 8.4 Consensus size: 39
819 TATGCCTCAT
* *
829 GCTCAGGGTAAAAGATCGAATGGCTACAATCTGTCCCAA
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAA
* *
868 GCTCGGGGTGAAAGATCGAATGGCTGCAATCTGCCCCAA
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAA
* * *
907 GCTCGGGGTAAGAGATTGGCTG-ATGG-T--GATCTGCCCCAT
1 GCTCGGGGTAAAAGA-T--C-GAATGGCTACAATCTGCCCCAA
* * * * *
946 GCTTGAGGTAAAAAATTGAATGGCTACAATCTGCCCCAG
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAA
* * * * * * *
985 GCTTGGGGTAAGAGATTGTTGATGG-T--GATTTGCCTCAA
1 GCTCGGGGTAAAAGATCG--AATGGCTACAATCTGCCCCAA
* *
1023 GCTCGGGGT--AAGATCGAATGGCTACAATATACCCCAA
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAA
** * * * * *
1060 GCTCAAGGTAAGAGATTGGGTGATGG-T--GATCTACCCCAA
1 GCTCGGGGTAAAAGA-T-CG-AATGGCTACAATCTGCCCCAA
* * *
1099 GCTCAGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAG
1 GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAA
*
1138 GCTCGGGGTAAGAGAT
1 GCTCGGGGTAAAAGAT
1154 TGGTTAATGG
Statistics
Matches: 218, Mismatches: 47, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
34 4 0.02
35 2 0.01
36 13 0.06
37 18 0.08
38 18 0.08
39 143 0.66
40 3 0.01
41 7 0.03
42 9 0.04
43 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAA
Found at i:916 original size:78 final size:77
Alignment explanation
Indices: 857--1201 Score: 333
Period size: 78 Copynumber: 4.5 Consensus size: 77
847 AATGGCTACA
* * *
857 ATCTGTCCCAAGCTCGGGGTGAAAGATCGAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
922 TTG-GCTGATGGTG
66 -TGCG-TGATGGTG
* * * * * * *
935 ATCTGCCCCATGCTTGAGGTAAAAAATTGAATGGCTACAATCTGCCCCAGGCTTGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
*
1000 TTG-TTGATGGTG
66 -TGCGTGATGGTG
* * * * **
1012 ATTTGCCTCAAGCTCGGGGT--AAGATCGAATGGCTACAATATACCCCAAGCTCAAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
*
1075 TTGGGTGATGGTG
66 -TGCGTGATGGTG
* * * *
1088 ATCTACCCCAAGCTCAGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
*
1153 TTG-GTTAATGGTG
66 -TGCG-TGATGGTG
* ** * *
1166 ATCTACCTTAGGCTCGAGGTAAAAGATC-AGATGGCT
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGA-ATGGCT
Statistics
Matches: 221, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
75 38 0.17
76 24 0.11
77 25 0.11
78 134 0.61
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (77 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGA
TGCGTGATGGTG
Found at i:993 original size:117 final size:117
Alignment explanation
Indices: 778--1167 Score: 327
Period size: 117 Copynumber: 3.4 Consensus size: 117
768 GGATGGTTGT
** * * *
778 AATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGATGGTGATATGCCTCATGCTCAGGGTAAAAG
1 AATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATATGCCCCATGCTCAGGGTAAAAA
*
843 ATCGAATGGCTACAATCTGTCCCAAGCTCGGGGTGAAAGATCGAATGGCTGC
66 ATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTGAAAGATCGAATGGCTGC
* *
895 AATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCATGCT-TGAGGTAAAA
1 AATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATATGCCCCATGCTCAG-GGTAAAA
* * * * *
959 AATTGAATGGCTACAATCTGCCCCAGGCTTGGGGT-AAGAGATTGTTGATGG-TG-
65 AATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTGAA-AGATCG--AATGGCTGC
* * * ** * * *
1012 -ATTTGCCTCAAGCTCGGGGTAAGATCGAATGGCT-A---CAATATACCCCAAGCTCAAGGTAAG
1 AATCTGCCCCAAGCTCGGGGTAAGA--GATTGGCTGATGGTGATATGCCCCATGCTCAGGGTAA-
* * * * * * * *
1072 AGATTGGGTGATGG-T--GATCTACCCCAAGCTCAGGGTAAAAGATCGAATGGCTGC
63 AAAAT-CG-AATGGCTACAATCTGCCCCAAGCTCGGGGTGAAAGATCGAATGGCTGC
* * *
1126 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTAATGGTGAT
1 AATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGAT
1168 CTACCTTAGG
Statistics
Matches: 214, Mismatches: 41, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
112 4 0.02
113 8 0.04
114 38 0.18
115 26 0.12
116 27 0.13
117 98 0.46
118 9 0.04
119 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (117 bp):
AATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATATGCCCCATGCTCAGGGTAAAAA
ATCGAATGGCTACAATCTGCCCCAAGCTCGGGGTGAAAGATCGAATGGCTGC
Found at i:1073 original size:153 final size:155
Alignment explanation
Indices: 865--1167 Score: 441
Period size: 153 Copynumber: 2.0 Consensus size: 155
855 CAATCTGTCC
* * * **
865 CAAGCTCGGGGTGAAAGATCGAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGA
1 CAAGCTCGGGGT-AAAGATCGAATGGCTACAATATACCCCAAGCTCAAGGTAAGAGATTGGCTGA
* * * * *
930 TGGTGATCTGCCCCATGCT-TGAGGTAAAAAATTGAATGGCTACAATCTGCCCCAGGCTTGGGGT
65 TGGTGATCTACCCCAAGCTCAG-GGTAAAAAATCGAATGGCTACAATCTGCCCCAGGCTCGGGGT
*
994 AAGAGATT-GTTGATGGTGATTTGCCT
129 AAGAGATTGGTTAATGGTGATTTGCCT
*
1020 CAAGCTCGGGGT-AAGATCGAATGGCTACAATATACCCCAAGCTCAAGGTAAGAGATTGGGTGAT
1 CAAGCTCGGGGTAAAGATCGAATGGCTACAATATACCCCAAGCTCAAGGTAAGAGATTGGCTGAT
* *
1084 GGTGATCTACCCCAAGCTCAGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAGGCTCGGGGTAA
66 GGTGATCTACCCCAAGCTCAGGGTAAAAAATCGAATGGCTACAATCTGCCCCAGGCTCGGGGTAA
1149 GAGATTGGTTAATGGTGAT
131 GAGATTGGTTAATGGTGAT
1168 CTACCTTAGG
Statistics
Matches: 132, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
153 108 0.82
154 12 0.09
155 12 0.09
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (155 bp):
CAAGCTCGGGGTAAAGATCGAATGGCTACAATATACCCCAAGCTCAAGGTAAGAGATTGGCTGAT
GGTGATCTACCCCAAGCTCAGGGTAAAAAATCGAATGGCTACAATCTGCCCCAGGCTCGGGGTAA
GAGATTGGTTAATGGTGATTTGCCT
Done.