SRP

Sequences

• Seed sequences
• Seed alignment
• Known sequences used for evaluating
• Erpin epn file, Erpin parameters: -32,08 -add 32 14 -pcw 101 -cutoff 20.17 ( resp. -cutoff 15.17 [marked with *])

Descriptor 1st iteration

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parms
wc += gu;
descr
h5 (tag='H1', minlen=3, maxlen=3)
h5 (tag='H2', minlen=7, maxlen=7, mispair=2)
ss (tag='S1', minlen=6, maxlen=6)
h3 (tag='H2')
ss (tag='S2', minlen=4, maxlen=4)
h5 (tag='H3', minlen=3, maxlen=4, seq="^UCC")
ss (tag='S3', minlen=8, maxlen=10)
h3 (tag='H3')
h3 (tag='H1')
ss (tag='S3.1', minlen=0, maxlen=1)
h5 (tag='H4', minlen=7, maxlen=11, mispair=2)
ss (tag='S4', minlen=2, maxlen=5)
h5 (tag='H5', minlen=5, maxlen=5, mispair=1)
ss (tag='S5', minlen=3, maxlen=3)
h5 (tag='H6', minlen=7, maxlen=7, mispair=1)
ss (tag='S6', minlen=4, maxlen=4)
h5 (tag='H7', minlen=4, maxlen=5)
ss (tag='S7', minlen=0, maxlen=2)
h5 (tag='H8', minlen=7, maxlen=7, mispair=1)
ss (tag='S8', minlen=1, maxlen=2)
h5 (tag='H9', minlen=4, maxlen=5, mispair=1)
ss (tag='S9', minlen=1, maxlen=1)
h5 (tag='H10', minlen=1, maxlen=1)
ss (tag='S10', minlen=4, maxlen=5)
h5 (tag='H11', minlen=6, maxlen=7)
ss (tag='S11.1', minlen=0, maxlen=1)
h5 (tag='H12', minlen=2, maxlen=2)
ss (tag='S11', minlen=1, maxlen=1)
h5 (tag='H13', minlen=5, maxlen=5, mispair=1)
ss (tag='S12', minlen=1, maxlen=1)
h5 (tag='H14', minlen=1, maxlen=1)
ss (tag='S13', minlen=1, maxlen=1)
h5 (tag='H15', minlen=7, maxlen=7)
ss (tag='S15.1', minlen=0,maxlen=1)
h5 (tag='H16', minlen=3, maxlen=4)
ss (tag='S14', minlen=1, maxlen=1)
h5 (tag='H17', minlen=5, maxlen=5, mispair=1)
ss (tag='S15', minlen=2, maxlen=2)
h5 (tag='H18', minlen=6, maxlen=6, mispair=1)
ss (tag='S16', minlen=4, maxlen=4)
h3 (tag='H18')
ss (tag='S17', minlen=2, maxlen=2)
h3 (tag='H17')
ss (tag='S18', minlen=1, maxlen=1)
h3 (tag='H16')
ss (tag='S16.1', minlen=0, maxlen=2)
h5 (tag='H19', minlen=1, maxlen=2)
ss (tag='S19', minlen=3, maxlen=3)
h3 (tag='H19')
ss (tag='S20', minlen=1, maxlen=2)
h5 (tag='H20', minlen=5, maxlen=5)
ss (tag='S21', minlen=5, maxlen=5)
h5 (tag='H21', minlen=3, maxlen=4)
ss (tag='S22', minlen=4, maxlen=5)
h5 (tag='H22', minlen=1, maxlen=3)
ss (tag='S23', minlen=4, maxlen=8)
h3 (tag='H22')
ss (tag='S24', minlen=4, maxlen=5)
h3 (tag='H21')
ss (tag='S25', minlen=3, maxlen=3)
h3 (tag='H20')
ss (tag='S26', minlen=1, maxlen=1)
h3 (tag='H15')
ss (tag='S27', minlen=1, maxlen=1)
h3 (tag='H14')
ss (tag='S28', minlen=2, maxlen=2)
h3 (tag='H13')
h3 (tag='H12')
ss (tag='S29', minlen=3, maxlen=4)
h3 (tag='H11')
ss (tag='S30', minlen=1, maxlen=2)
h3 (tag='H10')
ss (tag='S31', minlen=1, maxlen=2)
h3 (tag='H9')
ss (tag='S8.1', minlen=0, maxlen=1)
h3 (tag='H8')
ss (tag='S32', minlen=1, maxlen=2)
h3 (tag='H7')
h3 (tag='H6')
ss (tag='S33', minlen=5, maxlen=5)
h3 (tag='H5')
ss (tag='S34', minlen=1, maxlen=4)
h3 (tag='H4')

Descriptor 2nd iteration

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• Diff to desc1
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parms
wc += gu;
descr
h5 (tag='H1', minlen=3, maxlen=3)
h5 (tag='H2', minlen=7, maxlen=7, mispair=3) 
ss (tag='S1', minlen=4, maxlen=8) 
h3 (tag='H2', seq="U$")
ss (tag='S2', minlen=4, maxlen=4, seq="^GU")
h5 (tag='H3', minlen=3, maxlen=4, seq="^UCC")
ss (tag='S3', minlen=6, maxlen=12) 
h3 (tag='H3')
h3 (tag='H1')
ss (tag='S3.1', minlen=0, maxlen=1)
h5 (tag='H4', minlen=7, maxlen=11, mispair=3) 
ss (tag='S4', minlen=2, maxlen=5) 
h5 (tag='H5', minlen=5, maxlen=5, mispair=2) 
ss (tag='S5', minlen=3, maxlen=3) 
h5 (tag='H6', minlen=7, maxlen=7, mispair=2) 
ss (tag='S6', minlen=4, maxlen=4) 
h5 (tag='H7', minlen=4, maxlen=5, mispair=1) 
ss (tag='S7', minlen=0, maxlen=2) 
h5 (tag='H8', minlen=7, maxlen=7, mispair=2) 
ss (tag='S8', minlen=1, maxlen=2) 
h5 (tag='H9', minlen=4, maxlen=5, mispair=2)
ss (tag='S9', minlen=1, maxlen=1) 
h5 (tag='H10', minlen=1, maxlen=1) 
ss (tag='S10', minlen=4, maxlen=5) 
h5 (tag='H11', minlen=6, maxlen=7, mispair=1) 
ss (tag='S11.1', minlen=0, maxlen=1) 
h5 (tag='H12', minlen=2, maxlen=2) 
ss (tag='S11', minlen=1, maxlen=1) 
h5 (tag='H13', minlen=5, maxlen=5, mispair=2)
ss (tag='S12', minlen=1, maxlen=1) 
h5 (tag='H14', minlen=1, maxlen=1) 
ss (tag='S13', minlen=1, maxlen=1) 
h5 (tag='H15', minlen=7, maxlen=7, mispair=1) 
ss (tag='S15.1', minlen=0,maxlen=1) 
h5 (tag='H16', minlen=3, maxlen=4) 
ss (tag='S14', minlen=1, maxlen=1) 
h5 (tag='H17', minlen=5, maxlen=5, mispair=2)
ss (tag='S15', minlen=2, maxlen=2)
h5 (tag='H18', minlen=6, maxlen=6, mispair=2)
ss (tag='S16', minlen=3, maxlen=6) 
h3 (tag='H18')
ss (tag='S17', minlen=2, maxlen=2) 
h3 (tag='H17')
ss (tag='S18', minlen=1, maxlen=1) 
h3 (tag='H16')
ss (tag='S16.1', minlen=0, maxlen=2) 
h5 (tag='H19', minlen=1, maxlen=2) 
ss (tag='S19', minlen=3, maxlen=5) 
h3 (tag='H19')
ss (tag='S20', minlen=1, maxlen=2) 
h5 (tag='H20', minlen=5, maxlen=5, mispair=1) 
ss (tag='S21', minlen=5, maxlen=5) 
h5 (tag='H21', minlen=3, maxlen=4) 
ss (tag='S22', minlen=4, maxlen=5) 
h5 (tag='H22', minlen=1, maxlen=3) 
ss (tag='S23', minlen=3, maxlen=10) 
h3 (tag='H22')
ss (tag='S24', minlen=4, maxlen=5) 
h3 (tag='H21')
ss (tag='S25', minlen=3, maxlen=3) 
h3 (tag='H20')
ss (tag='S26', minlen=1, maxlen=1) 
h3 (tag='H15')
ss (tag='S27', minlen=1, maxlen=1) 
h3 (tag='H14')
ss (tag='S28', minlen=2, maxlen=2) 
h3 (tag='H13')
h3 (tag='H12')
ss (tag='S29', minlen=3, maxlen=4) 
h3 (tag='H11')
ss (tag='S30', minlen=1, maxlen=2) 
h3 (tag='H10')
ss (tag='S31', minlen=1, maxlen=2) 
h3 (tag='H9')
ss (tag='S8.1', minlen=0, maxlen=1) 
h3 (tag='H8')
ss (tag='S32', minlen=1, maxlen=2) 
h3 (tag='H7')
h3 (tag='H6')
ss (tag='S33', minlen=5, maxlen=5) 
h3 (tag='H5')
ss (tag='S34', minlen=1, maxlen=4) 
h3 (tag='H4')

Descriptor 3nd iteration

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• Diff to desc2
• Toggle view here

parms
wc += gu;
descr
h5 (tag='H1', minlen=3, maxlen=3, seq="GCC")
h5 (tag='H2', minlen=7, maxlen=7, mispair=3, ends='mm') 
ss (tag='S1', minlen=4, maxlen=8) 
h3 (tag='H2', seq="U$")
ss (tag='S2', minlen=4, maxlen=4, seq="^GU")
h5 (tag='H3', minlen=3, maxlen=4, seq="^UCC")
ss (tag='S3', minlen=6, maxlen=12) 
h3 (tag='H3')
h3 (tag='H1')
ss (tag='S3.1', minlen=0, maxlen=1)
h5 (tag='H4', minlen=7, maxlen=11, mispair=3, ends='mm') 
ss (tag='S4', minlen=2, maxlen=5) 
h5 (tag='H5', minlen=5, maxlen=5, mispair=2, ends='mm') 
ss (tag='S5', minlen=3, maxlen=3) 
h5 (tag='H6', minlen=7, maxlen=7, mispair=2, ends='mm') 
ss (tag='S6', minlen=4, maxlen=4) 
h5 (tag='H7', minlen=4, maxlen=5, mispair=1, ends='mm') 
ss (tag='S7', minlen=0, maxlen=2) 
h5 (tag='H8', minlen=7, maxlen=7, mispair=2, ends='mm') 
ss (tag='S8', minlen=1, maxlen=2) 
h5 (tag='H9', minlen=4, maxlen=5, mispair=2, ends='mm')
ss (tag='S9', minlen=1, maxlen=1) 
h5 (tag='H10', minlen=1, maxlen=1) 
ss (tag='S10', minlen=4, maxlen=5) 
h5 (tag='H11', minlen=6, maxlen=7, mispair=1, ends='mm') 
ss (tag='S11.1', minlen=0, maxlen=1) 
h5 (tag='H12', minlen=2, maxlen=2) 
ss (tag='S11', minlen=1, maxlen=1) 
h5 (tag='H13', minlen=5, maxlen=5, mispair=2, ends='mm')
ss (tag='S12', minlen=1, maxlen=1) 
h5 (tag='H14', minlen=1, maxlen=1) 
ss (tag='S13', minlen=1, maxlen=1) 
h5 (tag='H15', minlen=7, maxlen=7, mispair=2, ends='mm') 
ss (tag='S15.1', minlen=0,maxlen=1) 
h5 (tag='H16', minlen=3, maxlen=4) 
ss (tag='S14', minlen=1, maxlen=1) 
h5 (tag='H17', minlen=5, maxlen=5, mispair=2, ends='mm')
ss (tag='S15', minlen=2, maxlen=2)
h5 (tag='H18', minlen=6, maxlen=6, mispair=2, ends='mm')
ss (tag='S16', minlen=3, maxlen=6) 
h3 (tag='H18')
ss (tag='S17', minlen=2, maxlen=2) 
h3 (tag='H17')
ss (tag='S18', minlen=1, maxlen=1) 
h3 (tag='H16')
ss (tag='S16.1', minlen=0, maxlen=2) 
h5 (tag='H19', minlen=1, maxlen=2) 
ss (tag='S19', minlen=3, maxlen=5) 
h3 (tag='H19')
ss (tag='S20', minlen=1, maxlen=2) 
h5 (tag='H20', minlen=5, maxlen=5, mispair=2, ends='mm') 
ss (tag='S21', minlen=5, maxlen=5) 
h5 (tag='H21', minlen=3, maxlen=4) 
ss (tag='S22', minlen=4, maxlen=5) 
h5 (tag='H22', minlen=1, maxlen=3) 
ss (tag='S23', minlen=3, maxlen=10) 
h3 (tag='H22')
ss (tag='S24', minlen=4, maxlen=5) 
h3 (tag='H21')
ss (tag='S25', minlen=3, maxlen=3) 
h3 (tag='H20')
ss (tag='S26', minlen=1, maxlen=1) 
h3 (tag='H15')
ss (tag='S27', minlen=1, maxlen=1) 
h3 (tag='H14')
ss (tag='S28', minlen=2, maxlen=2) 
h3 (tag='H13')
h3 (tag='H12')
ss (tag='S29', minlen=3, maxlen=4) 
h3 (tag='H11')
ss (tag='S30', minlen=1, maxlen=2) 
h3 (tag='H10')
ss (tag='S31', minlen=1, maxlen=2) 
h3 (tag='H9')
ss (tag='S8.1', minlen=0, maxlen=1) 
h3 (tag='H8')
ss (tag='S32', minlen=1, maxlen=2) 
h3 (tag='H7')
h3 (tag='H6')
ss (tag='S33', minlen=5, maxlen=5) 
h3 (tag='H5')
ss (tag='S34', minlen=1, maxlen=4) 
h3 (tag='H4')

Result table

Species	RNAMotif 1	RNAMotif 2	RNAMotif 3	BLAST	Blast Rank	Blast E-Values	ERPIN	ERPIN Rank	RaveNnA	RaveNnA Rank
homo sapiens (2)	3 hits	4 hits	9 hits	2 hits | top hits	(1)	6e-76	56 hits	(13)
pan troglodytes (1)	4 hits	5 hits	7 hits	3 hits | top hits	(1)	1e-166	58 hits	(1)
macaca mulatta (1)	3 hits	3 hits	8 hits	3 hits | top hits	(1)	1e-161	56 hits	(1)
rattus norvegicus (1)	3 hits	3 hits	3 hits	3 hits | top hits	(3)	1e-152	4 hits	(4)
mus musculus (1)	2 hits	2 hits	2 hits	2 hits | top hits	(1)	1e-157	4 hits	(1)
bos taurus (1)	4 hits	4 hits	7 hits	12 hits | top hits	(1)	1e-93	12 hits	(6)
canis familiaris	3 hits	3 hits	3 hits	3 hits | top hits	(1,2,3) new candidates (aln with hom.sap.) rfam annot. 1 2 3	2e-94 - 1e-93	9 hits	(1, 2, 3) new cand
monodelphis domestica (1)	3 hits	3 hits	3 hits	5 hits | top hits	(1)	9e-86	4 hits	(1)
ornithorhynchus anatinus (1)	2 hits	2 hits	2 hits	2 hits | top hits	(1)	2e-82	2 hits	(1)
gallus gallus (1)		2 hits	3 hits	3 hits | top hits	(1)	6e-76	2 hits	(1)
anolis carolinensis			2 hits	3 hits | top hits	(1) new candidate (aln with hom.sap.)	5e-61	1 hits	(2)
xenopus tropicalis			21 hits	21 hits | top hits	(1) new candidate (aln with xen.lae.)	3e-68	56 hits	(17)
danio rerio (1)	1 hits	2 hits	41 hits	53 hits | top hits	(1)	2e-69	88 hits	(55)
takifugu rubripes			6 hits	4 hits | top hits	(1)	2e-67	5 hits		8 hits	(1)
branchiostoma floridae (1)				15 hits | top hits	(1)	2e-53	51 hits		35 hits	(3)
ciona intestinalis (1)				21 hits | top hits	(1)	2e-42	1 hits		12 hits	(1)
strongylocentrotus purpuratus (1)				8 hits | top hits	(4)	5e-43	8 hits		7 hits	(2)
drosophila melanogaster (1)				2 hits | top hits	(1)	5e-19	3 hits		2 hits	(1)
apis mellifera				1 hits | top hits	(1) new candidate (aln with dro.mel.)	1e-27	6 hits		1 hits	(1)
caenorhabditis elegans (4)				5 hits | top hits	(2,3,4,5)	1e-18 - 4e-16	2 hits		5 hits	(1-4)
trichinella spiralis (1)				1 hits | top hits	(1)	9e-31	4 hits		1 hits	(1)
schmidtea mediterannea (1)				12 hits | top hits	(11)	4e-23	11 hits		14 hits	(11)
capitella capitata				8 hits | top hits	(1) new candidate (aln with sch.med.)	2e-38	14 hits	(1) new cand	8 hits	(2)
hydra magnipapillata				20 hits | top hits	(1) new candidate (aln with nem.vec.)	2e-27	170 hits
nematostella vectensis (1)				23 hits | top hits	(1)	1e-37	4 hits		28 hits	(1)
trichoplax adhaerens				1 hits | top hits	(1) new candidate (aln with nem.vec.)	8e-28	3 hits		1 hits	(1)
monosiga brevicollis									1 hits

The numbers in the "Rank" columns denote the rank of the hit(s), that match the annotated sequence(s). If the Rank column is empty, none of the annotated sequences was among the hits. The E-values are the range from the highest to the lowest rank.