********************************************************************************
STREME - Sensitive, Thorough, Rapid, Enriched Motif Elicitation
********************************************************************************
MEME version 5.4.0 (Release date: Mon Aug 16 16:18:19 2021 -0700)

For further information on how to interpret these results please access https://meme-suite.org/meme.
To get a copy of the MEME Suite software please access https://meme-suite.org.

********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey,
"STREME: accurate and versatile sequence motif discovery",
Bioinformatics, Mar. 24, 2021.
********************************************************************************


********************************************************************************
ALPHABET "DNA with covalent modifications" DNA-LIKE
********************************************************************************
A "Adenine" 8510A8 ~ T "Thymine" A89610
C "Cytosine" A50026 ~ G "Guanine" 313695
c "5-Carboxylcytosine" FEE090 ~ 4 "Guanine:5-Carboxylcytosine" E0F3F8
f "5-Formylcytosine" FDAE61 ~ 3 "Guanine:5-Formylcytosine" ABD9E9
h "5-Hydroxymethylcytosine" F46D43 ~ 2 "Guanine:5-Hydroxymethylcytosine" 74ADD1
m "5-Methylcytosine" D73027 ~ 1 "Guanine:5-Methylcytosine" 4575B4
? = ACGTcfhm1234
z = Ccfhm
9 = G1234
N = ACGT
V = ACG
H = ACT
D = AGT
B = CGT
y = Ccf
8 = G34
M = AC
R = AG
W = AT
S = CG
Y = CT
K = GT
x = hm
7 = 12
********************************************************************************

strands: + -

Background letter frequencies
A 0.24 C 0.244 G 0.244 T 0.24 c 4.3e-08 f 4.3e-08 h 0.000222 m 0.0156 1 0.0156 2 0.000222 3 4.3e-08 4 4.3e-08 

MOTIF 1-1CCATCTTRKWW STREME-1
letter-probability matrix: alength= 12 w= 12 nsites= 222 E= 1.5e-010
 0.167896 0.000184 0.278310 0.018064 0.000000 0.000000 0.000000 0.000012 0.530297 0.005236 0.000000 0.000000
 0.000181 0.978485 0.000184 0.010653 0.000000 0.000000 0.000000 0.000012 0.010484 0.000000 0.000000 0.000000
 0.005417 0.973249 0.000184 0.015889 0.000000 0.000000 0.000000 0.000012 0.005248 0.000000 0.000000 0.000000
 0.999426 0.000184 0.000184 0.000181 0.000000 0.000000 0.000000 0.000012 0.000012 0.000000 0.000000 0.000000
 0.000181 0.000184 0.000184 0.988954 0.000000 0.000000 0.000000 0.000012 0.010484 0.000000 0.000000 0.000000
 0.015889 0.952305 0.000184 0.031598 0.000000 0.000000 0.000000 0.000012 0.000012 0.000000 0.000000 0.000000
 0.000181 0.000184 0.000184 0.999426 0.000000 0.000000 0.000000 0.000012 0.000012 0.000000 0.000000 0.000000
 0.000181 0.000184 0.057872 0.931266 0.000000 0.000000 0.000000 0.000012 0.010484 0.000000 0.000000 0.000000
 0.336210 0.000184 0.595318 0.068263 0.000000 0.000000 0.000000 0.000012 0.000012 0.000000 0.000000 0.000000
 0.005417 0.031620 0.409759 0.547944 0.000000 0.000000 0.000000 0.000012 0.005248 0.000000 0.000000 0.000000
 0.516520 0.005421 0.120655 0.352144 0.000000 0.000000 0.000000 0.000012 0.005248 0.000000 0.000000 0.000000
 0.568900 0.010657 0.031612 0.388808 0.000000 0.000000 0.000000 0.000012 0.000012 0.000000 0.000000 0.000000

MOTIF 2-AAKAWAWAD STREME-2
letter-probability matrix: alength= 12 w= 9 nsites= 1040 E= 8.3e-010
 0.882351 0.000084 0.000084 0.117471 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000
 0.992599 0.000084 0.000084 0.002462 0.000000 0.000000 0.000000 0.000005 0.004765 0.000000 0.000000 0.000000
 0.063218 0.082321 0.358054 0.496396 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000
 0.987102 0.000084 0.000084 0.003199 0.000000 0.000000 0.000000 0.000005 0.009525 0.000000 0.000000 0.000000
 0.607711 0.000084 0.000084 0.392110 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000
 0.714681 0.000084 0.255787 0.029437 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000
 0.549554 0.000084 0.000084 0.447887 0.000000 0.000000 0.000000 0.000005 0.002385 0.000000 0.000000 0.000000
 0.872296 0.000084 0.000084 0.127525 0.000000 0.000000 0.000000 0.000005 0.000005 0.000000 0.000000 0.000000
 0.425626 0.059751 0.255518 0.225772 0.000000 0.000000 0.000000 0.030948 0.002385 0.000000 0.000000 0.000000

********************************************************************************
Stopped because maximum number of motifs (2) reached.
********************************************************************************
COMMAND:	streme -p common/dna_with_covalent.fa -oc results/streme8 -objfun de -order 1 -nmotifs 2 -alph common/dna_with_covalent.alph -nmotifs 2 -hofract 0.2 -verbosity 1
********************************************************************************
CPU:		Timothys-Mac-Mini.local
********************************************************************************
FINALTIME:	24.03 seconds
********************************************************************************