RegulonDB
ArcA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/ArcA/ArcA.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 /ArcA.EcolK12_1nt_upstream.17.meme_quality_logo
; Input files
; input /ArcA.EcolK12_1nt_upstream.17.meme_quality_matrix.tf
; prior /ArcA.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 /ArcA.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 36 50 22 43 31 34 14 20 36 15 12 69 70 6 46 41 38
C 7 6 38 10 14 4 4 11 5 2 9 5 0 64 10 12 11
G 5 10 6 10 1 11 4 14 22 4 3 0 4 0 5 4 9
T 31 13 13 16 33 30 57 34 16 58 55 5 5 9 18 22 21
//
A 0.5 0.6 0.3 0.5 0.4 0.4 0.2 0.3 0.5 0.2 0.2 0.9 0.9 0.1 0.6 0.5 0.5
C 0.1 0.1 0.5 0.1 0.2 0.1 0.1 0.1 0.1 0.0 0.1 0.1 0.0 0.8 0.1 0.2 0.1
G 0.1 0.1 0.1 0.1 0.0 0.1 0.1 0.2 0.3 0.1 0.0 0.0 0.1 0.0 0.1 0.1 0.1
T 0.4 0.2 0.2 0.2 0.4 0.4 0.7 0.4 0.2 0.7 0.7 0.1 0.1 0.1 0.2 0.3 0.3
//
A 0.4 0.8 -0.0 0.6 0.3 0.4 -0.5 -0.1 0.4 -0.4 -0.6 1.1 1.1 -1.3 0.7 0.6 0.5
C -0.8 -1.0 0.8 -0.5 -0.2 -1.4 -1.4 -0.4 -1.2 -2.0 -0.6 -1.2 -4.4 1.4 -0.5 -0.3 -0.4
G -1.1 -0.5 -1.0 -0.5 -2.6 -0.4 -1.4 -0.1 0.3 -1.4 -1.6 -4.4 -1.4 -4.4 -1.1 -1.4 -0.6
T 0.3 -0.6 -0.6 -0.4 0.3 0.2 0.9 0.4 -0.4 0.9 0.8 -1.5 -1.5 -0.9 -0.3 -0.1 -0.1
//
A 0.2 0.5 -0.0 0.3 0.1 0.2 -0.1 -0.0 0.2 -0.1 -0.1 0.9 1.0 -0.1 0.4 0.3 0.2
C -0.1 -0.1 0.4 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 1.1 -0.1 -0.0 -0.1
G -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.0 0.1 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1
T 0.1 -0.1 -0.1 -0.1 0.1 0.1 0.6 0.2 -0.1 0.7 0.6 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0
//
; Sites 79
>site_0
TACAAATCATTAACAAA
>site_1
AACAATTATTTAACAAA
>site_2
TAAAAATTGTTAACAAT
>site_3
AACATTTAGTTAACTTA
>site_4
AACATTTAGTTAACCAT
>site_5
TACGCTTTATTAACAAT
>site_6
TGCATATTTTTAACACA
>site_7
AACATAATATTAACTCA
>site_8
TGCTTTTTATTAACATA
>site_9
AACAATTGGTTAATAAA
>site_10
ATCATTTAATTAACTAT
>site_11
AAAACTTGATTAACATC
>site_12
AACGATTTGATAACAAC
>site_13
AACAAGTGGTTCACAAA
>site_14
AACATTTTGTTAGCACT
>site_15
GAAACATGATTAACATA
>site_16
AGCTCTTAATTAACAAC
>site_17
TGCAAATCGATAACAAC
>site_18
AAAATATAATGAACAAT
>site_19
TACATAATATCAACACC
>site_20
TAATTATTATTAACCTC
>site_21
AACAATTATTTTACATA
>site_22
TTATTTTTGTTAACATT
>site_23
TACATAAATTTAACCAG
>site_24
ATTATATTGTAAACATA
>site_25
AATACATTGTTAATTAA
>site_26
AACATGTTAATAAAAAC
>site_27
AATTATAAGTTAACTAA
>site_28
ATATTATAATTAACTCA
>site_29
TAATTTTGATTAATAAT
>site_30
AATATTTGATTATCCAA
>site_31
CACCTAAGATTAACTTA
>site_32
TACATCAATTTAACATT
>site_33
ATCAAATTCGTAACAAT
>site_34
AACCATTTTTTTACATT
>site_35
TAACTGTCAATAACACA
>site_36
TGAAAATGATTATCAAT
>site_37
CACGTTTTTATAACCAT
>site_38
TTCACATCATTAACCGT
>site_39
TAACTATAATGAACCAA
>site_40
TAATGGTTATTAACATA
>site_41
ACTTTATAATTAACAGA
>site_42
TTATATTGATAAACTAA
>site_43
TACTATTTAAAATCAAA
>site_44
ATCCTGTAATTAAAACA
>site_45
ATAAATTAATTAAAATG
>site_46
AAAACTTCGTTAATTCG
>site_47
CACATTTTGACAAAACA
>site_48
GACGAGATACTAACAAA
>site_49
AACATACTTGCAACATT
>site_50
AACAAAGTTGTTACAAA
>site_51
CACAAACGGTTAATTAT
>site_52
TTAGTGTAATTAATTAA
>site_53
TTTAATAGATAAACACC
>site_54
CGGAAATATTTAACTTG
>site_55
GTCAAAATTTAAACTAC
>site_56
CACAAAATCATTACAAT
>site_57
CTGATATTTATAGCAAA
>site_58
TATAAATTGATCACCGT
>site_59
AACAAATCATTTAAGTT
>site_60
TGTTTTACATCAACTTA
>site_61
TAAATATCGGTAATTTG
>site_62
TATTCACCGAAAACAAA
>site_63
GGGCAATTTTTAACGTA
>site_64
ACCGTTTAGTCCACTTT
>site_65
AGACATTGTTACACAAC
>site_66
TCACCTTTCTCAACGAA
>site_67
TCTGTGTAATAAATAAA
>site_68
AAAACAATAAAATCCAT
>site_69
AAAGCAACATAAAAAAG
>site_70
TCCATTTTTATCGCTAA
>site_71
AATACGCCGTTAATGAA
>site_72
AAGGAGTTGTGATCAAG
>site_73
TATCCCTACACAACACA
>site_74
ACCGAGGTCACAACATA
>site_75
AGGTCCAGATTAACAGG
>site_76
GAATAAGTGTAAACGCG
>site_77
TATCACGTTTCAACTTC
>site_78
TAGTATTGACAAGCCAA
;
; Matrix parameters
; Number of sites 79
; 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 WAMAWWTWRTTAACAWW
; AC WAMAWWTWRTTAACAWW
; id WAMAWWTWRTTAACAWW
; name WAMAWWTWRTTAACAWW
; description wacawwttrttAACaaa
; statistical_basis 79 sequences
; sites 79
; nb_sites 79
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 5.31526
; information.per.column 0.312662
; max.possible.info.per.col 1.58873
; consensus.strict aacatattattAACaaa
; consensus.strict.rc TTTGTTAATAATATGTT
; consensus.IUPAC wacawwttrttAACaaa
; consensus.IUPAC.rc TTTGTTAAYAAWWTGTW
; consensus.regexp [at]aca[at][at]tt[ag]ttAACaaa
; consensus.regexp.rc TTTGTTAA[CT]AA[AT][AT]TGT[AT]
; residues.content.crude.freq a:0.4341|c:0.1579|g:0.0834|t:0.3246
; G+C.content.crude.freq 0.241251
; residues.content.corrected.freq a:0.4323|c:0.1585|g:0.0849|t:0.3243
; G+C.content.corrected.freq 0.243382
; min(P(S|M)) 1.39187e-25
; max(P(S|M)) 8.05465e-05
; proba_range 8.05465e-05
; Wmin -30.4
; Wmax 12.2
; Wrange 42.6
; logo file:/ArcA.EcolK12_1nt_upstream.17.meme_quality_logo_m1.png
; logo file:/ArcA.EcolK12_1nt_upstream.17.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.58
; user 0.58
; system 0.06
; cuser 0.47
; csystem 0.04