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STREME - Sensitive, Thorough, Rapid, Enriched Motif Elicitation
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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.

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

Timothy L. Bailey,
"STREME: accurate and versatile sequence motif discovery",
Bioinformatics, Mar. 24, 2021.
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ALPHABET "DNA with covalent modifications" DNA-LIKE
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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
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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

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Stopped because maximum number of motifs (2) reached.
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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
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CPU:		Timothys-Mac-Mini.local
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FINALTIME:	24.03 seconds
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