chr18_4

cmsearch-Rfam

Family :

KCNQ1OT1_2

Id:

RF01947

Type:

Gene; lncRNA;

Taxonomy:

Eukaryota;

Ontology:

GO:0006342 chromatin silencingRF01947

Description:

not description

Score:

20.3

E-value:

0.0088

From sequence:

113723

To sequence:

113891

Alignments:

                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::.......:::::::::........:::::::::::::::: CS
  RF01947     27 GCuGGGGCCACCCAGuGuGGGCuCaGGAAGGGaAGGAAUGuGaCuGAGGcuGGGUG.......uGGCuGgGg........aGaGcgCAGCcAGuuG 107   
                    G G CC CC A  GuGGGCuCa    G GaAGGAA G        G +GGG G        GGC G+          aGaG +C GC A    
    chr18 113723 AUCGCGCCCGCCGAAAGUGGGCUCACCUGGAGAAGGAAAGAA-----AGGCGGGCGaucagaaAGGCAGAAAcaaauccaAGAGAACCGCGAAGAA 113813
                 445667789999999********9987777777777776642.....2334444331111111566665432111111115566666677777777 PP

                 :::::::::::::...:::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::: CS
  RF01947    108 UGGGUUUUUCuUG...GGGCCcAGAgAGacguGAGCaGAGauGGAGGCCCc.UCUCuCcCaGCCCCCagCaCaCACACUa 183   
                   GGU    C  G   G GCCcAGAgAGa   G   aGAGa  GA GCCC   C C CcCa CC     CaCaCACAC  
    chr18 113814 AAGGUCCACCCGGcaaGAGCCCAGAGAGAGAGGGAGAGAGAGAGAAGCCCAcACCCACCCACCC--ACACACACACACAC 113891
                 7788877766544444789***************99*****99999996540333333333332..23344444444433 PP



Internal HMM-only pipeline statistics summary: (run for model(s) with zero basepairs)
--------------------------------------------------------------------------------------
Query model(s):                                          1  (196 consensus positions)
Target sequences:                                       34  (57702516 residues searched)
Windows passing local HMM SSV      filter:           27526  (0.1812); expected (0.02)
Windows passing local HMM MSV bias filter:            9356  (0.06187); expected (0.02)
Windows passing local HMM Viterbi  filter:             664  (0.004647); expected (0.001)
Windows passing local HMM Forward  filter:             268  (0.002076); expected (1e-05)
Total HMM hits reported:                                 1  (2.929e-06)

# CPU time: 3.54u 0.00s 00:00:03.54 Elapsed: 00:00:00.86
//

RNAfold
>chr18_4
UAAAGGGAGGCCCAUCGCGCCCGCCGAAAGUGGGCUCACCUGGAGAAGGA
AAGAAAGGCGGGCGAUCAGAAAGGCAGAAACAAAUCCAAGAGAACCGCGA
AGAAAAGGUCCACCCGGCAAGAGCCCAGAGAGAGAGGGAGAGAGAGAGAA
GCCCACACCCACCCACCCACACACACACACACACACCUCCAGAAGG
.....(((((.......((((((((.........((..(((.....)))..))...))))))))........(((.........((.......(((..........)))...((((((....)))..........))).)).........)))................................)))))...... (-38.50)

Length sequence

: 196

Length match:

167