U3

Sequences

Descriptor 1st iteration

parms
wc += gu;
descr
ss (tag='S1', minlen=75, maxlen=75)
h5 (tag='H1', minlen=4, maxlen=4)
ss (tag='S2', minlen=14, maxlen=14)
h5 (tag='H2', minlen=12, maxlen=12)
ss (tag='S3', minlen=12, maxlen=12)
h5 (tag='H3', minlen=3, maxlen=4)
ss (tag='S4', minlen=2, maxlen=3)
h5 (tag='H4', minlen=3, maxlen=4)
h5 (tag='H5', minlen=5, maxlen=5, mispair=1)
ss (tag='S5', minlen=4, maxlen=6)
h3 (tag='H5')
ss (tag='S6', minlen=1, maxlen=2)
h3 (tag='H4')
ss (tag='S7', minlen=2, maxlen=3)
h3 (tag='H3')
ss (tag='S8', minlen=12, maxlen=12)
h5 (tag='H6', minlen=4, maxlen=5)
ss (tag='S9', minlen=1, maxlen=2)
h5 (tag='H7', minlen=5, maxlen=6)
ss (tag='S10', minlen=3, maxlen=5)
h3 (tag='H7')
ss (tag='S11', minlen=0, maxlen=3)
h3 (tag='H6')
h3 (tag='H2')
ss (tag='S12', minlen=7, maxlen=7, seq="CUGA$")
h3 (tag='H1')

Descriptor 2nd iteration

parms
wc += gu;
descr
ss (tag='S1', minlen=75, maxlen=75)
h5 (tag='H1', minlen=4, maxlen=4)
ss (tag='S2', minlen=12, maxlen=16, seq="GAGGAGGA", mismatch=2)
h5 (tag='H2', minlen=12, maxlen=12)
ss (tag='S3', minlen=10, maxlen=14)
h5 (tag='H3', minlen=3, maxlen=4)
ss (tag='S4', minlen=2, maxlen=3)
h5 (tag='H4', minlen=3, maxlen=4)
h5 (tag='H5', minlen=5, maxlen=5, mispair=1)
ss (tag='S5', minlen=2, maxlen=8)
h3 (tag='H5')
ss (tag='S6', minlen=1, maxlen=2)
h3 (tag='H4')
ss (tag='S7', minlen=2, maxlen=3)
h3 (tag='H3')
ss (tag='S8', minlen=10, maxlen=14)
h5 (tag='H6', minlen=4, maxlen=5)
ss (tag='S9', minlen=1, maxlen=3)
h5 (tag='H7', minlen=4, maxlen=6)
ss (tag='S10', minlen=3, maxlen=5)
h3 (tag='H7')
ss (tag='S11', minlen=0, maxlen=3)
h3 (tag='H6')
h3 (tag='H2')
ss (tag='S12', minlen=5, maxlen=9, seq="CUGA$")
h3 (tag='H1')

Descriptor 3rd iteration

parms
wc += gu;
descr
ss (tag='S1', minlen=75, maxlen=75)
h5 (tag='H1', minlen=4, maxlen=4)
ss (tag='S2', minlen=12, maxlen=16, seq="GAGGAGGA", mismatch=2) 
h5 (tag='H2', minlen=10, maxlen=12, mispair=2)
ss (tag='S3', minlen=10, maxlen=14)
h5 (tag='H3', minlen=3, maxlen=4)
ss (tag='S4', minlen=2, maxlen=3)
h5 (tag='H4', minlen=3, maxlen=4)
h5 (tag='H5', minlen=5, maxlen=5, mispair=1)
ss (tag='S5', minlen=2, maxlen=8) 
h3 (tag='H5')
ss (tag='S6', minlen=1, maxlen=2)
h3 (tag='H4')
ss (tag='S7', minlen=2, maxlen=3)
h3 (tag='H3')
ss (tag='S8', minlen=10, maxlen=14)
h5 (tag='H6', minlen=4, maxlen=5)
ss (tag='S9', minlen=0, maxlen=3)
h5 (tag='H7', minlen=4, maxlen=6)
ss (tag='S10', minlen=3, maxlen=5)
h3 (tag='H7')
ss (tag='S11', minlen=0, maxlen=3)
h3 (tag='H6')
h3 (tag='H2')
ss (tag='S12', minlen=5, maxlen=9, seq="CUGA$")
h3 (tag='H1')

Result table

SpeciesRNAMotif 1RNAMotif 2RNAMotif 3BLASTBlast RankBlast E-ValuesERPINERPIN RankRaveNnARaveNnA Rank
homo sapiens (1)2 hits2 hits47 hits58 hits | top hits(1) 9e-69 30 hits(1)   
pan troglodytes (1)1 hits1 hits36 hits50 hits | top hits(1) 8e-60 27 hits(1)   
macaca mulatta (1) 2 hits27 hits47 hits | top hits(1) 9e-53 17 hits(1)   
rattus norvegicus (1) 2 hits37 hits15 hits | top hits(1) 8e-65 24 hits(1)   
mus musculus (2)5 hits5 hits33 hits17 hits | top hits(1) 7e-68 20 hits(2)   
bos taurus (1)4 hits5 hits39 hits22 hits | top hits(1) 4e-67 21 hits(2)   
canis familiaris (1)2 hits2 hits26 hits11 hits | top hits(1) 1e-49 18 hits(1)   
monodelphis domestica (1)8 hits8 hits41 hits10 hits | top hits(1) 9e-42 17 hits(1)   
ornithorhynchus anatinus  25 hits7 hits | top hits(1) new candidate
(aln with mon.dom.)
4e-16 6 hits(3) new cand.  
gallus gallus (1)  11 hits1 hits | top hits(1) 3e-31 2 hits(1)   
anolis carolinensis1 hits1 hits29 hits1 hits | top hits(1) new candidate
(aln with xen.tro.)
8e-27 3 hits(1) new cand.  
xenopus tropicalis (1) 1 hits13 hits30 hits | top hits(3) 1e-23 94 hits(7)  
danio rerio (1)  21 hits29 hits | top hits(22) 1e-16 110 hits 2847 hits(8)
takifugu rubripes (1)  11 hits4 hits | top hits(3) 3e-17 50 hits 24 hits(2)
branchiostoma floridae  10 hits7 hits | top hits(1-7) new candidates
(aln with seed)
2e-25 - 1e-222 hits(1,2) new cand.49 hits(1-7) new cand.
ciona intestinalis (1) 1 hits3 hits24 hits | top hits(8) 7e-12 4 hits 64 hits(14)
strongylocentrotus purpuratus1 hits1 hits12 hits9 hits | top hits(1-9) new candidates
(aln with known seq.)
2e-20 - 2e-173 hits(3) new cand.171 hits(1-9) new cand.
drosophila melanogaster (2)  1 hits3 hits | top hits(1-3) 8e-06 - 1e-04 9 hits 17 hits(1,3)
apis mellifera   3 hits | top hits(1-3) new candidates
(aln with known seq.)
2e-12 - 1e-78 hits 2291 hits(1-3) new cand.
caenorhabditis elegans (2)      5 hits 75 hits(3,6)
trichinella spiralis   1 hits | top hits(1) new cand.
(aln with known seq)
2e-83 hits 34 hits(1) new cand.
schmidtea mediterannea  7 hits   50 hits 3858 hits 
capitella capitata  4 hits11 hits | top hits(1-12) new candidates
(aln with known seq.)
2e-18 - 3e-1224 hits 96 hits(1-11) new cand.
hydra magnipapillata 21 hits31 hits78 hits | top hits(1,6,7,14,..) new candidates
(aln with known seq.)
9e-08 - 6e-0427 hits   
nematostella vectensis  3 hits17 hits | top hits(1-14) new candidates
(aln with known seq.)
3e-13 - 1e-0712 hits 164 hits(1-17) new cand.
trichoplax adhaerens (1)  2 hits1 hits | top hits(1)6e-171 hits(1)14 hits(1)
monosiga brevicollis  2 hits1 hits | top hits(1) new cand.
(aln with seed CM)
3e-067 hits 1 hits(1) new cand.

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.