RegulonDB
CRP matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/CRP/CRP.EcolK12_2nt_upstream.20.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 /CRP.EcolK12_2nt_upstream.20.meme_quality_logo
; Input files
; input /CRP.EcolK12_2nt_upstream.20.meme_quality_matrix.tf
; prior /CRP.EcolK12_2nt_upstream.20.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /CRP.EcolK12_2nt_upstream.20.meme_quality_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Strand undef
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.29114
; c 0.20781
; g 0.20402
; t 0.29702
A 44 35 29 36 188 62 62 50 123 49 133 12 28 243 20 208 96 90 88 58
C 46 18 50 4 34 42 83 85 33 72 34 13 227 2 232 14 49 27 21 44
G 22 151 20 206 23 56 49 48 49 85 54 15 11 20 9 37 20 0 22 11
T 159 67 172 25 26 111 77 88 66 65 50 231 5 6 10 12 106 154 140 158
//
A 0.2 0.1 0.1 0.1 0.7 0.2 0.2 0.2 0.5 0.2 0.5 0.0 0.1 0.9 0.1 0.8 0.4 0.3 0.3 0.2
C 0.2 0.1 0.2 0.0 0.1 0.2 0.3 0.3 0.1 0.3 0.1 0.0 0.8 0.0 0.9 0.1 0.2 0.1 0.1 0.2
G 0.1 0.6 0.1 0.8 0.1 0.2 0.2 0.2 0.2 0.3 0.2 0.1 0.0 0.1 0.0 0.1 0.1 0.0 0.1 0.0
T 0.6 0.2 0.6 0.1 0.1 0.4 0.3 0.3 0.2 0.2 0.2 0.9 0.0 0.0 0.0 0.0 0.4 0.6 0.5 0.6
//
A -0.6 -0.8 -1.0 -0.8 0.9 -0.2 -0.2 -0.5 0.4 -0.5 0.5 -1.9 -1.0 1.1 -1.4 1.0 0.2 0.1 0.1 -0.3
C -0.2 -1.1 -0.1 -2.6 -0.5 -0.3 0.4 0.4 -0.5 0.2 -0.5 -1.5 1.4 -3.2 1.4 -1.4 -0.1 -0.7 -1.0 -0.2
G -0.9 1.0 -1.0 1.3 -0.9 0.0 -0.1 -0.1 -0.1 0.4 -0.0 -1.3 -1.6 -1.0 -1.8 -0.4 -1.0 -5.6 -0.9 -1.6
T 0.7 -0.2 0.8 -1.2 -1.1 0.3 -0.0 0.1 -0.2 -0.2 -0.5 1.1 -2.7 -2.6 -2.1 -1.9 0.3 0.6 0.6 0.7
//
A -0.1 -0.1 -0.1 -0.1 0.6 -0.1 -0.1 -0.1 0.2 -0.1 0.3 -0.1 -0.1 1.0 -0.1 0.7 0.1 0.0 0.0 -0.1
C -0.0 -0.1 -0.0 -0.0 -0.1 -0.0 0.1 0.1 -0.1 0.1 -0.1 -0.1 1.2 -0.0 1.2 -0.1 -0.0 -0.1 -0.1 -0.0
G -0.1 0.6 -0.1 1.0 -0.1 0.0 -0.0 -0.0 -0.0 0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1
T 0.4 -0.0 0.5 -0.1 -0.1 0.1 -0.0 0.0 -0.0 -0.1 -0.1 0.9 -0.1 -0.1 -0.1 -0.1 0.1 0.4 0.3 0.4
//
; Sites 271
>site_0
TGTGATTCATATCACATATT
>site_1
TGTGATTGGTATCACATTTT
>site_2
TGTGATCGTCATCACAATTC
>site_3
TGTGAAGTTGATCACAAATT
>site_4
TGTGATCCAGATCACATCTA
>site_5
TGTTATCCACATCACAATTT
>site_6
AGTGATTTAGATCACATAAT
>site_7
TGTGATTTTCATCACGATTT
>site_8
TGTGATCTGCATCACGCATT
>site_9
TGTGAGTAGTGTCACATTTT
>site_10
TTTGATACCCATCACACTTT
>site_11
CGTGATCAAGATCACATTCT
>site_12
CGTGATCTTCATCACAAATA
>site_13
TGTGATTCAGATCACAAAGA
>site_14
TGTGATTTGCTTCACATCTT
>site_15
TCTGACTCACATCACACTTT
>site_16
TGTGATACAAATCACATAAA
>site_17
TGAGATTCAGATCACATATA
>site_18
CGTGATGATGTTCACAATTT
>site_19
TGTGATTCGATTCACATTTA
>site_20
TGTGATTAACAGCACATTTT
>site_21
TTCGATACACATCACAATTA
>site_22
GGTGATCTATTTCACAAATT
>site_23
TGTGATTGATATCACACAAA
>site_24
TGAGATTTTCATCACACATT
>site_25
AGTGACGTAGATCACACTTA
>site_26
TGTGTACGAAATCACATTTT
>site_27
TTTGATTTAGATCGCAATTT
>site_28
TTTGACATGTATCACAAATT
>site_29
TTTGAAGTTCATCACACTTC
>site_30
TTCGAGGTTGATCACATTTC
>site_31
TGTGAATCTTTTCACAGTTT
>site_32
TGTGATGCAAGCCACATTTT
>site_33
AGTGATCCACGCCACATTTT
>site_34
TGTGAGTGATTTCACAGTAT
>site_35
AGTGATGCAAATCACATAAA
>site_36
TGCGATTCCACTCACAATAT
>site_37
TTTGAAGTAGCTCACACTTA
>site_38
AGTGACCGAAATCACACTTA
>site_39
TTTGTTCCTCTTCACATTTT
>site_40
AGTGATCCAGGTCACGATAA
>site_41
CGTGACGTTCATCACAAAAC
>site_42
AGTGAAGCAGATCGCATTAT
>site_43
TGTGCGGCAATTCACATTTA
>site_44
TATGACCCTCTTCACATTTC
>site_45
TGCGATCTATATCACGCTGT
>site_46
TTTGCACGGCGTCACACTTT
>site_47
TGCGAGCCAGCTCAAACTTT
>site_48
AGTGAGCTAACTCACATTAA
>site_49
TGCGGGCGTGATCACAATTA
>site_50
TGTGAGCCAGCTCACCATAA
>site_51
TTTGAACCAGATCGCATTAC
>site_52
CGTGATGCATCTCACCTTTT
>site_53
CGTGAACTACGGCACACTTT
>site_54
TGTGAGCGAGATCAAATTCT
>site_55
TGTGAAATAAATCAAAATTT
>site_56
TGTGAGCTTGCTCGCACTTC
>site_57
TGCGATCAAAATAACACTTT
>site_58
TGCGGGTCGCGTCACATTTA
>site_59
TGTGCGACCACTCACAAATT
>site_60
AGAGATCTACTTCACAAATC
>site_61
TGTGATGGCTCTCACCTTTT
>site_62
TGTTAAATTGATCACGTTTT
>site_63
TTTGCACTGTGTCACAATTC
>site_64
TGTGAGTTTTGTCACCAAAT
>site_65
TTAAATATAGATCACAATTT
>site_66
TGCAATTCGTGTCACAAAAT
>site_67
ATAGATCTCCGTCACATTTT
>site_68
TTCAATATTCATCACACTTT
>site_69
TGCGAGTCTGCTCGCATAAT
>site_70
TGCGAAGCGCGTCACTATTT
>site_71
TGTTATTAGTCTCACACTTT
>site_72
GGTGATTTGCTTCACATCTC
>site_73
AGTGATATGTATAACATTAT
>site_74
TGCGAAATCCGTCACAGTTC
>site_75
TGCGATGAATGTCACATCCT
>site_76
TGTAACAGAGATCACACAAA
>site_77
TGTGAATCAGATCAGAAAAC
>site_78
ATTGTCCCCGATCACACTTT
>site_79
TATGACGGCGGTCACACTTA
>site_80
TGCGCGACGCATCGCAAATT
>site_81
TGAGATCGAGCACACATTTT
>site_82
TGAGGGGTTGATCACGTTTT
>site_83
CGTGATCAAAATCACCTCTT
>site_84
TTTGAATCCCATCACAAACC
>site_85
AGTGATGGTAGTCACATAAA
>site_86
GGTGACCGGTTTCACAAATA
>site_87
TATGACGCTCTTCACACTCT
>site_88
TGCAAGCAACATCACGAAAT
>site_89
TGCGAGCATGGTCATATTTT
>site_90
TGCAAAGGACGTCACATTAC
>site_91
TGTGGTTGCCATCACAGATA
>site_92
TTTGACGGCTATCACGTTTC
>site_93
TTTATTCCATGTCACACTTT
>site_94
AGTGATCGAGTTAACATTGT
>site_95
TGTGCGCTCGCTCGCAAAAT
>site_96
TGTGATGGTTGTCATATTAT
>site_97
CATGATCCGCGCCACACTTT
>site_98
TTTGCGCGAGGTCACTATTT
>site_99
CGTGATTCCTGTCACGAAAC
>site_100
TGTGACTCGATTCACGAAGT
>site_101
GGTGACGGAGTTCACCCTTT
>site_102
TATGACGGTGTTCACAAAGT
>site_103
CTTGAGCCGCAGCACAATGT
>site_104
GTTGCTTTTGATCACAATAA
>site_105
TATGAAGCCCTTCACAGAAT
>site_106
CGCGACTTTTATCACTTTTT
>site_107
GGTGAGGAACTTAACAATAT
>site_108
TGCGGTGAGCATCACATCAC
>site_109
ATTTAAACAGATCACAAAAT
>site_110
TTTGCGCTAAAGCACATTTC
>site_111
TGTGGCCTGCTTCAAACTTT
>site_112
AGTGAACCATATCTCAATTC
>site_113
TACAAGGCACATCACGTTAT
>site_114
CGTGATACTCATCACCATGA
>site_115
TGAGGCATAAATCACATTAC
>site_116
GTTGCACTCTCTCACATTTT
>site_117
TTTAATTCGTATCGCAAATT
>site_118
TGTGATGTGGTTAACCAATT
>site_119
CAGGATTTAGCTCACACTTA
>site_120
TTTGAGTAAGTTCTCAATTT
>site_121
TGTGATCGTTATCTCGATAT
>site_122
CGCAGCGAAGATCACAATTT
>site_123
TTTGACATGCATCGCAGAAT
>site_124
CATGAGCAACCGCACATATT
>site_125
TTTGAAAATGATGACACTAT
>site_126
TGCGAGTGGGAGCACGGTTT
>site_127
TGGGCGACAGATCACGCAAA
>site_128
TGGAATATCCATCACATAAC
>site_129
TTTGAAGCAGTTAACGCTAT
>site_130
TGAGAGGTTGGTCATATTAT
>site_131
CGTGCCAGTTTTCACATTCT
>site_132
TGTGTGTCAGATCTCGTTTT
>site_133
TGTGCGCATCTCCACATTAC
>site_134
TACGACAGCTATCACGAATT
>site_135
CTTGCTTACCGTCACATTCT
>site_136
TATGATAAATATCAAACAAT
>site_137
CATGAAACTGTGCACATTTT
>site_138
TGTGTGCCTCGTCATAAAAT
>site_139
ATTGATCTAACTCACGAAAA
>site_140
TGTGACCGTGGTCGCAGTTG
>site_141
TGTATGACAGATCACTATTT
>site_142
ACGGATCTTCATCACATAAA
>site_143
CGTGATATTGCTCACGCCAA
>site_144
TGTAAGCTGTGCCACGTTTT
>site_145
CGTGAACGATCCCACGAATT
>site_146
CGTGAAAGCGATCACAAAGG
>site_147
TGTGATCTACAGCATGTTAT
>site_148
TGCAGGCTTGATCACAACTC
>site_149
AGTGACAGATTTCACGAAAA
>site_150
AGCGACATCTGTCACATTCC
>site_151
TGCGTGTGTTTTCACAAAAA
>site_152
GGTGATCCATAAAACAATAT
>site_153
TGTTAATTTCCTCACATCGT
>site_154
TTAGAAACCGATCACATACA
>site_155
TCCTACATAGATCACATTAC
>site_156
CCTGACGGAGTTCACACTTG
>site_157
TATGTTTCGTTTCACAGTTC
>site_158
TGAGATTCAACTCTCAAATT
>site_159
CATGCTCAATCTCACAAAGT
>site_160
TCTAATAGCCATCACAAAAC
>site_161
TGTTGATATGATCACGTTAT
>site_162
ATTGAACCAAATCATAAAAT
>site_163
AACGCTTTGGCTCACAGTTT
>site_164
ATCGATTGCGTTCACGTTTA
>site_165
TTAGAGGCAGGTAACAAAAC
>site_166
ATTGATTTAAATCAAAGATT
>site_167
TGTGCTGCGCATAATACTTT
>site_168
TTGAACCCCGATCACACCAT
>site_169
TGTGAGGTAGATAAGAAAAA
>site_170
CAGGAAGCACATCACAAAGA
>site_171
TCTGAGATGGATCAAAGAAT
>site_172
ATTGACCGATGCCACGTTTT
>site_173
TGTGGATAAAATCACGGTCT
>site_174
TTTGCCACAGGTAACAAAAA
>site_175
TATGCGCGAAATCAAACAAT
>site_176
GGAGAGCAATATCACATCGC
>site_177
CAGGCGTTAAATCACGTTTT
>site_178
TCATCTCTATGTCACATTTT
>site_179
TGCGTTTCAGTTAACGTTTC
>site_180
AATGAAAAGGATGACATATT
>site_181
ATTGATATAGATCATATCTC
>site_182
TTTGAATCGTGTCTCATTCT
>site_183
CTTAATTTAAATAACAAAAT
>site_184
CCTGTCACAAATCACAAAAA
>site_185
CGTTTTATCTGTCACATAAT
>site_186
GCAGATACAACTCACACAAT
>site_187
TTCGTAACGCCTCGCAAATT
>site_188
TGTGCGCGCAACGACATTTT
>site_189
ATTGATGTAAATCAAATTCA
>site_190
TTAGATGTAAATCACTCCAT
>site_191
ACCTCTTTGCGTCACATTTT
>site_192
TGTGACAAGCTCCGCAAATC
>site_193
CAAAACATATGTCACAATAT
>site_194
ATTGACGCACAGCACATTGG
>site_195
TGGGATGAAAGTGACATTTG
>site_196
TAATAATCTAATCACATCTT
>site_197
CGACGAATAGATCACAATTT
>site_198
TTCGACAAAGCGCACAATCC
>site_199
CACAATTAAGATCACAGAAA
>site_200
GGTGCGCATGATAACGCCTT
>site_201
TACAAAATTGTTAACAATTT
>site_202
CTTGCGTGACTACACATTCT
>site_203
GACGCATGAAATCACGTTTC
>site_204
TTTGTAACAATTCAAACTTC
>site_205
TTAGTAAGTTATCACCATTT
>site_206
ATTGTTTTATTTCACATTGG
>site_207
ATCGGGTTTGATCACAGTCA
>site_208
TTAAATTGATGTAACATAAT
>site_209
AGTGCTCAGCGACACTATTT
>site_210
GTTGCTGACCTTCAAAAATT
>site_211
TGACTTTCTCATCACATCAT
>site_212
TGGAACGCTTTTCGCATTCT
>site_213
CTCGGTTTAGTTCACAGAAG
>site_214
CATGACCCAGGTCGCCTTCC
>site_215
CGGAAAGAGCCTCGCAAATT
>site_216
CATGAAACGGAACACGAAAA
>site_217
GGTGTTTATCCGCACAACAT
>site_218
TGTAAACAGATTAACACCTC
>site_219
TTTACTTTTGGTTACATATT
>site_220
TGTCATCTTTCTGACACCTT
>site_221
GGTAATTCGAATGACATTGC
>site_222
AGTAAGTGAGAGAACAATGT
>site_223
CGTTATATATGTCAAGTTGT
>site_224
TTGTTATCCGCTCACAATTC
>site_225
CATGAATTTTATTACATAAA
>site_226
TGTTAAACATGTAACTAAAT
>site_227
ATCGATTTAACACACCATTT
>site_228
CTTTATCTTTGTAGCACTTT
>site_229
TCTGGGTAGCATCACAGCAG
>site_230
AGTTATTTTTAACAAATTTT
>site_231
CGCGCACTATGTCAACTCTT
>site_232
CCCATGGCAGATGACATTTT
>site_233
TCGGCAATGTCTCACAAAGC
>site_234
GGGTATTAGCACCACATATA
>site_235
AATGAAAAATTGCACAGTAA
>site_236
TGCAAAATCAAAAACAATTT
>site_237
TGAGTCATAAATAACCTTTA
>site_238
TGCATATTAATTGACATTTC
>site_239
CCCGCTTTAAAACACGCTAT
>site_240
TTTGTGCATAGTTACAACTT
>site_241
GGTGGCGCAGGAAACACATA
>site_242
TCTTGAAATAATCACATTGA
>site_243
AGTGAACCCCTTCCCAACCA
>site_244
AACGAGAAATATCGAACTTA
>site_245
TGGGAGCAGGCTCGATTTAT
>site_246
TTTAATCATGTTTACAGTAA
>site_247
TTGGGTTGTTATCAAATCGT
>site_248
AATGCTAATCATCAGAAATG
>site_249
TGTAAGTCGGGTAATAACAA
>site_250
GTGGAAATTAATCCCACTAT
>site_251
TCATACCACCATCACAACCA
>site_252
GTAAATCTGCATCGGAATTT
>site_253
AAATATCCTTGTCACATTCG
>site_254
GGTGAATCGCGCCAGCAAAT
>site_255
TGAGACTAGTACGACTTTTT
>site_256
TCGTGTTTAAATAACAAAAT
>site_257
CATGATAAATTTGACGAAGA
>site_258
TGCAACCATCTACAAATAAC
>site_259
AGCGTGAATTTTCAGGAAAT
>site_260
ATTTAACGCCGTCAGAAATG
>site_261
TAGCAAATACCTCACAGTGA
>site_262
CTATGAGCAAAACACATTTA
>site_263
CGTGAGCGTTGTAAGTAAAA
>site_264
AGGTGACTATACCACACTCA
>site_265
GGTTGACCAATTTACATAAC
>site_266
TGCGTGAAGCAGCAGTAAAT
>site_267
GCAAGTGGTATTCGCACTTT
>site_268
TACGTTTGCAGTGAAATAAC
>site_269
CAGGCACCTGATAAAGCCAT
>site_270
TTTAATGAAGAGAATTTTTT
;
; Matrix parameters
; Number of sites 271
; Columns 20
; Rows 4
; Alphabet A|C|G|T
; Prior A:0.291144263562772|C:0.207810681831126|G:0.204024081631615|T:0.297020972974487|a:0.291144263562772|c:0.207810681831126|g:0.204024081631615|t:0.297020972974487
; program transfac
; matrix.nb 1
; accession TGTGADNNWNATCACAWWWT
; AC TGTGADNNWNATCACAWWWT
; id TGTGADNNWNATCACAWWWT
; name TGTGADNNWNATCACAWWWT
; description tGtGakcyasaTCACawwwt
; statistical_basis 271 sequences
; sites 271
; nb_sites 271
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 6.97553
; information.per.column 0.348777
; max.possible.info.per.col 1.58952
; consensus.strict tGtGatccagaTCACatttt
; consensus.strict.rc AAAATGTGATCTGGATCACA
; consensus.IUPAC tGtGakcyasaTCACawwwt
; consensus.IUPAC.rc AWWWTGTGATSTRGMTCACA
; consensus.regexp tGtGa[gt]c[ct]a[cg]aTCACa[at][at][at]t
; consensus.regexp.rc A[AT][AT][AT]TGTGAT[CG]T[AG]G[AC]TCACA
; residues.content.crude.freq a:0.3052|c:0.2085|g:0.1675|t:0.3188
; G+C.content.crude.freq 0.376015
; residues.content.corrected.freq a:0.3051|c:0.2085|g:0.1677|t:0.3187
; G+C.content.corrected.freq 0.376146
; min(P(S|M)) 1.44988e-26
; max(P(S|M)) 8.45769e-06
; proba_range 8.45769e-06
; Wmin -30.3
; Wmax 15.3
; Wrange 45.6
; logo file:/CRP.EcolK12_2nt_upstream.20.meme_quality_logo_m1.png
; logo file:/CRP.EcolK12_2nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.67
; user 0.67
; system 0.07
; cuser 0.49
; csystem 0.06