RegulonDB
Fis matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/Fis/Fis.EcolK12_1nt_upstream.17.meme
Figures
Matrix logo
Decreasing cumulative distributions (dCDF)
Decreasing cumulative distributions (dCDF), logarithmic Y axis
ROC curve (logarithmic X axis)
Matrix information
; convert-matrix -v 1 -from transfac -i /Fis.EcolK12_1nt_upstream.17.meme_quality_logo
; Input files
; input /Fis.EcolK12_1nt_upstream.17.meme_quality_matrix.tf
; prior /Fis.EcolK12_1nt_upstream.17.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /Fis.EcolK12_1nt_upstream.17.meme_quality_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Bernoulli model (order=0)
; Strand undef
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.29093
; c 0.20756
; g 0.20418
; t 0.29732
A 6 46 43 21 125 79 48 56 43 50 14 85 98 47 8 133 110
C 14 52 61 80 7 30 29 15 29 21 37 67 41 51 193 13 32
G 162 54 31 42 60 12 20 0 13 13 13 46 37 68 3 51 29
T 37 67 84 76 27 98 122 148 134 135 155 21 43 53 15 22 48
//
A 0.0 0.2 0.2 0.1 0.6 0.4 0.2 0.3 0.2 0.2 0.1 0.4 0.4 0.2 0.0 0.6 0.5
C 0.1 0.2 0.3 0.4 0.0 0.1 0.1 0.1 0.1 0.1 0.2 0.3 0.2 0.2 0.9 0.1 0.1
G 0.7 0.2 0.1 0.2 0.3 0.1 0.1 0.0 0.1 0.1 0.1 0.2 0.2 0.3 0.0 0.2 0.1
T 0.2 0.3 0.4 0.3 0.1 0.4 0.6 0.7 0.6 0.6 0.7 0.1 0.2 0.2 0.1 0.1 0.2
//
A -2.3 -0.3 -0.4 -1.1 0.7 0.2 -0.3 -0.1 -0.4 -0.2 -1.5 0.3 0.4 -0.3 -2.0 0.7 0.5
C -1.2 0.1 0.3 0.6 -1.8 -0.4 -0.4 -1.1 -0.4 -0.8 -0.2 0.4 -0.1 0.1 1.4 -1.2 -0.3
G 1.3 0.2 -0.4 -0.1 0.3 -1.3 -0.8 -5.4 -1.2 -1.2 -1.2 0.0 -0.2 0.4 -2.6 0.1 -0.4
T -0.6 0.0 0.3 0.2 -0.9 0.4 0.6 0.8 0.7 0.7 0.9 -1.1 -0.4 -0.2 -1.5 -1.1 -0.3
//
A -0.1 -0.1 -0.1 -0.1 0.4 0.1 -0.1 -0.0 -0.1 -0.1 -0.1 0.1 0.2 -0.1 -0.1 0.4 0.3
C -0.1 0.0 0.1 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.1 -0.0 0.0 1.3 -0.1 -0.1
G 0.9 0.0 -0.1 -0.0 0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 0.0 -0.0 0.1 -0.0 0.0 -0.1
T -0.1 0.0 0.1 0.1 -0.1 0.2 0.3 0.6 0.4 0.4 0.6 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1
//
; Sites 219
>site_0
GCGCATTTTTTCAGCAA
>site_1
GTATAATTTTTCAGCAA
>site_2
GCCTATCTTTTCAGCAA
>site_3
GCCTGATTTTTCAGCGA
>site_4
GGACATTTTTCCAGCAA
>site_5
GCCGATTATTTACGCAA
>site_6
GTCTATTTTTTGCACAA
>site_7
GGCTGTTTTTCAGGCAA
>site_8
GCTGAAATTTTCAGCAT
>site_9
GCTCACTTTTCAGGCAA
>site_10
GTTCATTTTTCAACCAC
>site_11
GTTTATTATTTGAGCGA
>site_12
GGCGATTTTTGCAGCAA
>site_13
GCTCATCTTTTAATCAT
>site_14
GTTCACTTGTTCAGCAA
>site_15
GCACACTTTTTCAACAT
>site_16
GGTCGTTTCCTCAGCAA
>site_17
GGTCATATTTTTATCAA
>site_18
GGTCACATTTTATGCGA
>site_19
GTAGGATTTATCCGCAA
>site_20
GGCCAAACTTTGACCAA
>site_21
GTTCAAGTTTTGTTCAA
>site_22
GGCTGTTTCTTCATCGT
>site_23
GCTCATTTTTGCCTCGA
>site_24
GCTCATTTTTTAGACTT
>site_25
GAGAGTTTTTTGACCAA
>site_26
GAACATATTTTAAACAG
>site_27
GGCGATTATTTGTGCGT
>site_28
TAACAATTTTTAAACAA
>site_29
GCTCATTTTAAATGCAA
>site_30
GACCATTTTTTTTCCAG
>site_31
GCTGATTAATTCGCCAT
>site_32
GTCTAACTTATAGACAA
>site_33
GTCGTAAATTTAAGCAA
>site_34
GTCTGCTTTTTAATCCA
>site_35
GGCGATTTTATGTGCGC
>site_36
GCGCAACATTCAACCAA
>site_37
GCTGACTTTCTCGCCGA
>site_38
GCGCAATTTGTCAACGA
>site_39
GTTCTACTTTTCATCAT
>site_40
GATTATATTCTATCCAA
>site_41
GCCCATTTAACCGACAA
>site_42
GACCGTTTTCCAACCGA
>site_43
GTGTAAATTTTAGTCAC
>site_44
GGCTATTTAACACCCAA
>site_45
GGTTATTTGTTACACAT
>site_46
GCCCAAATACTAAACAA
>site_47
GGTCGAATGTCAAGCAA
>site_48
GCCGTTTATTTGCACAA
>site_49
GGCGATTTATCGCGCAG
>site_50
GTTTTTATTTCATGCAA
>site_51
GGCGATTTCTTGAACGG
>site_52
GGTCATTAACTGCCCAA
>site_53
GCGCATTTTTTATTCTT
>site_54
GCATATTTTTAACACAA
>site_55
GGCGAAATCTTCGCCAG
>site_56
GCATGTTTTACAGGCAT
>site_57
GGCTACTTTTGCATCAC
>site_58
GGGCGTATTATGTGCGA
>site_59
GCCAGTTTTTCGAGCGT
>site_60
TTCTATTTTTTAGCCGG
>site_61
TCTTGATTTATGACCGA
>site_62
GGTAGATTTTCACTCGA
>site_63
TGCTATTTTCTCTGCAC
>site_64
GCACAATCTATCATCAC
>site_65
TTTTGTTATTTAAACAC
>site_66
GTTTAAATTTTGACTAA
>site_67
GAACAATTATTGCCCGT
>site_68
GTGTGAAATTTTACCAA
>site_69
GGTTGTTTTCTATTCGG
>site_70
GTGCGATAATTACTCAT
>site_71
GGCCGAAATTTGCTCGT
>site_72
TTTCGAATTATGAGCGA
>site_73
GTGCGAATCATAAGCAG
>site_74
GCTTAAGATTGCGGCAA
>site_75
TGTTGTTTTTTCACCCT
>site_76
TCACATTTTTACAACAA
>site_77
GTGAAACTTTTGCACAA
>site_78
TTCTGTATTTTGCCCAC
>site_79
GTCTGTTTTGCGATCAT
>site_80
GGCTGTTAATTATCCTA
>site_81
GAACAGTTATTAAGCGG
>site_82
GTATATATACTCCTCAA
>site_83
CCAGAATTTTTCGTCAT
>site_84
GTACATTCCTTAACCGG
>site_85
GGCTATGTGTTCCGCTA
>site_86
GTCTATCTCTTTAGCTA
>site_87
GGTATATTTGTCTGCAA
>site_88
GCTGATTTTTCGTTCTC
>site_89
GTTTGGGTGTTCACCAA
>site_90
GATCGCATTATAAGCTT
>site_91
GGTGGTTAATCATGCGT
>site_92
TAGCATGTTTTGCACAA
>site_93
GTTCGCTATATAGGCTT
>site_94
TCTCAATTGATCGACAA
>site_95
GCACGCCATATCGCCGA
>site_96
GTACGCGTACTAACCAA
>site_97
GCTTGTCTGATAAACGA
>site_98
CAATATTTATTAACCAC
>site_99
GATTAATTATAAATCAG
>site_100
GCCGGTTTTTGCTGCTT
>site_101
GCTTACTTTATCGATAA
>site_102
CTTTATTTATTACACAG
>site_103
GAGTAATTATTGTTCGG
>site_104
GGCAAATTGTTAGCCGC
>site_105
GTTGTTATTTTGCACGG
>site_106
GAATGTTTTCTTAACAT
>site_107
TATGACGTTTTAACCAC
>site_108
GAATAATATTTTTTCAT
>site_109
GTGAATTATTTGAACCA
>site_110
GGTCATTTCTTAACTCA
>site_111
GATGATCTTTTTGTCGC
>site_112
GGCAATATCTCGACCAG
>site_113
GTGGATTTTTTATTTAC
>site_114
GGTCGCGAAATGAGCGA
>site_115
GAACACGTTATAGACAT
>site_116
GGCGATTTTTATTACGA
>site_117
TTTTATAATATAAACAT
>site_118
GTGTGCGATTGCAGCAA
>site_119
GATCAATTAAGCAACAC
>site_120
GGACGTAAAATCTGCAG
>site_121
GTTCATCTTTCATTCCC
>site_122
GATGGCTTATTAATCTT
>site_123
GGACGGAATATGAACAA
>site_124
GATTGTCATTCTACCGA
>site_125
TGCCATAAAACAAGCAA
>site_126
TTTTACCATTTAGCCAT
>site_127
GCTGCATTCCCCAGCAA
>site_128
GTCAAAATTGTGATCAC
>site_129
TGGCGAATTTCGCCCGA
>site_130
GCCGTTTTTGCAACCGT
>site_131
GCCGTTTAATTCTTCGT
>site_132
TGATAAATATCAAACAA
>site_133
GATCTATATTTAACAAA
>site_134
GGCGTTATCATGCGCAC
>site_135
GGCGCTTTTTCAAGCCC
>site_136
GATTAACACCTCGTCAA
>site_137
GTCTTATTTATGATTAA
>site_138
GCACAAACCGTAACCAA
>site_139
TAAGAAAATTTATACAA
>site_140
GGCCAATAATGCCCCCA
>site_141
CTCTATTATTACCTCAA
>site_142
GTTTGAGATTACTACAA
>site_143
GAACGATTATTCTTTAA
>site_144
GGGTACTTACTATTCGT
>site_145
GTCCCATTCTTGCTCTA
>site_146
AATCATCATTTCCACAA
>site_147
GCTTATTTCAGCGTCGG
>site_148
GCACATTCCTTTAACGC
>site_149
GGAAGGTTTATCAACGT
>site_150
GGGGTTGATATCCGCAG
>site_151
TGTGACGCTTTCGTCAA
>site_152
GAGCGCCTTACTGGCAA
>site_153
GACGGTTCATTTTGCAG
>site_154
GTTTTTATTTTCATAAT
>site_155
GTTTTTAATATTATCAT
>site_156
TGCTAAAAAGTAACCAA
>site_157
GTTTGATTTACATCAAA
>site_158
GACGAAGCATTCCGCGG
>site_159
CTCCAAAATATATTCAC
>site_160
TTTTATTATTTGTACCT
>site_161
CTTTATTTTTCATCCCC
>site_162
GTGCTATACTTAATCTC
>site_163
GCGTCGCTTTTAAGCGG
>site_164
GTCTATTCCATCAACTG
>site_165
GTTTTATTAATAAATAA
>site_166
GTTTTACTTTAGACCTA
>site_167
TGGTATTTAAAATGCAA
>site_168
CGCAACTTTATTAGCAT
>site_169
GCTATGTTAATAACCAT
>site_170
GTTTATTCAAACTTCAA
>site_171
ACTTGCTTCTTATCCAT
>site_172
GTTGCACATTTTGACAA
>site_173
GATTGTTACTTATTAAA
>site_174
GATAAATTTGTAACAAA
>site_175
TACCTTTTTACGCACAG
>site_176
GGACGTCACATTACCGT
>site_177
GCTGAAGACCGCATCAA
>site_178
GTACTGCATGTATGCAA
>site_179
TTCTTTATTTTGTGCCG
>site_180
CACAGAGTTATCCACAA
>site_181
GACTGTCTGGTCAGCTT
>site_182
GTATCAGTTGTGGTCAA
>site_183
GAAAACAATCTGAACAT
>site_184
CAGGAAGTTTTAACCTC
>site_185
GTAAAGTTCACCGCCGA
>site_186
GGTCACTATTTTGCAGT
>site_187
GGTAAACCTATACGCTT
>site_188
CAGTCACTTTCGAGCAA
>site_189
GTAAAATAATTCAGTGC
>site_190
TTACAACTATTAATAAA
>site_191
TATCGCGTTCTTCGCAC
>site_192
GTACAGTTGATAGCCCC
>site_193
TTGCGCATTCCAATCGC
>site_194
CCTCGCCATTTATGCCG
>site_195
AGTCAGAACTTCCTCAA
>site_196
TAACAAATTTTTCTCTT
>site_197
GCTGAATCGTTAAGGAT
>site_198
GTAATTTTCATCCGTAA
>site_199
ACGTGGTTATTCACCGC
>site_200
TAACAAAAACGCAGCAA
>site_201
TTGTAAATCTTATTTAA
>site_202
GGTTTACCCGTACGCAC
>site_203
CCTGAATTTTCGTGAAC
>site_204
TCGGATTTTATCAGGTA
>site_205
GATGAATTCCTATTTGT
>site_206
GACTATATTTAAGATGT
>site_207
CGCGTCTTTTCTGGCTA
>site_208
GTCTGTACGTCAAACCG
>site_209
CTAAAAGACTTGCACAA
>site_210
TCTGTATAATGCCGCGG
>site_211
TAACAGCTTTACGACAG
>site_212
TACCGATATGGACTCGC
>site_213
ACCTTATTTATGGCTAA
>site_214
TAGCGCCTGTAGGCCAA
>site_215
TCTCGTAAACACAACTA
>site_216
AATCATTTATTGCTGAG
>site_217
TTGCTATCATTCGTTAT
>site_218
GCAAAAATAACTGGTTA
;
; Matrix parameters
; Number of sites 219
; Columns 17
; Rows 4
; Alphabet A|C|G|T
; Prior A:0.290929484294843|C:0.207560750607506|G:0.204184816848168|T:0.297324948249482|a:0.290929484294843|c:0.207560750607506|g:0.204184816848168|t:0.297324948249482
; program transfac
; matrix.nb 1
; accession GNHBAWTTTTTVANCAA
; AC GNHBAWTTTTTVANCAA
; id GNHBAWTTTTTVANCAA
; name GNHBAWTTTTTVANCAA
; description GbyyrwtttttvasCra
; statistical_basis 219 sequences
; sites 219
; nb_sites 219
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 4.47944
; information.per.column 0.263497
; max.possible.info.per.col 1.58873
; consensus.strict GgccattttttcagCaa
; consensus.strict.rc TTGCTGAAAAAATGGCC
; consensus.IUPAC GbyyrwtttttvasCra
; consensus.IUPAC.rc TYGSTBAAAAAWYRRVC
; consensus.regexp G[cgt][ct][ct][ag][at]ttttt[acg]a[cg]C[ag]a
; consensus.regexp.rc T[CT]G[CG]T[CGT]AAAAA[AT][CT][AG][AG][ACG]C
; residues.content.crude.freq a:0.2718|c:0.2074|g:0.1757|t:0.3452
; G+C.content.crude.freq 0.383024
; residues.content.corrected.freq a:0.2719|c:0.2074|g:0.1758|t:0.3449
; G+C.content.corrected.freq 0.383155
; min(P(S|M)) 1.12982e-21
; max(P(S|M)) 1.14032e-05
; proba_range 1.14032e-05
; Wmin -23.6
; Wmax 11.2
; Wrange 34.8
; logo file:/Fis.EcolK12_1nt_upstream.17.meme_quality_logo_m1.png
; logo file:/Fis.EcolK12_1nt_upstream.17.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.64
; user 0.64
; system 0.05
; cuser 0.45
; csystem 0.04