chr5_30

cmsearch-Rfam

Family :

Six3os1_2

Id:

RF02247

Type:

Gene; lncRNA;

Taxonomy:

Eukaryota;

Ontology:

GO:0010468 regulation of gene expression

Description:

not description

Score:

21.9

E-value:

0.0028

From sequence:

294281

To sequence:

294074

Alignments:

                 ::::::::::::::::::::::::::::::::::::::::::....:::::::::::::::::......:::::::::::.......::::::::: CS
  RF02247     11 GGGCgAaaGgAgGGAgGGGAGaGGAUGGGGgaAcgCGCGCCC....CAaGAGcGAAgGCAAAC......AGCUGugGAGG.......CGCUGCCcG 89    
                 G G +Aa G  gG    GGA  G   GGGG+aAcg GCGCCC     A+GAG  AA GC AAC      AGC  ugG  G       C CUGCCc 
     chr5 294281 GAGAAAAUGACGGAGAUGGACUGAGGGGGGAAACGGGCGCCCacaaUAGGAGAAAACGCUAACaacgacAGCAAUGGUAGucuccgcCUCUGCCCU 294186
                 444444444444433445566666667788889999999887433347899999999999988433333555555553331111111233444443 PP

                 ::::::....:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: CS
  RF02247     90 cgGcUC....AGGCUUCCCAACAGGUUAGCUAgaCugGGAUCCAcCCGGcAUUUCGCAGGAagGGGuGGGGGGgaGacagAGcgAGAGGgGGaGaG 181   
                    cUC     G C UCCC  CA G U G  A aC  G  UCCAc C G     C CA GA   G +GGGGG gaGa ag G gAGAGGg GaG G
     chr5 294185 GCUCUCuccgUGACCUCCCGUCAUGAUGGGCACAC--GCCUCCACACCGA----CCCACGAUCAGAGGGGGGAGAGAGAGGGAGAGAGGGAGAGGG 294096
                 33333222223678899999999999998777665..5567887776654....445555555555555555556666666666777777777777 PP

                 :::::::::::::::::::::: CS
  RF02247    182 aGCCUcacaaGAGGACAGAGGG 203   
                 aG C  aca+   GACAGA  G
     chr5 294095 AGACGGACAGACAGACAGACAG 294074
                 7777777766666666665544 PP



Internal HMM-only pipeline statistics summary: (run for model(s) with zero basepairs)
--------------------------------------------------------------------------------------
Query model(s):                                          1  (217 consensus positions)
Target sequences:                                       34  (57702516 residues searched)
Windows passing local HMM SSV      filter:           24722  (0.1804); expected (0.02)
Windows passing local HMM MSV bias filter:            4323  (0.03081); expected (0.02)
Windows passing local HMM Viterbi  filter:             709  (0.005327); expected (0.001)
Windows passing local HMM Forward  filter:             211  (0.001754); expected (1e-05)
Total HMM hits reported:                                 1  (3.605e-06)

# CPU time: 3.22u 0.01s 00:00:03.23 Elapsed: 00:00:00.78
//

RNAfold
>chr5_30
ACGUCUGUCUGUCUGUCUGUCCGUCUCCCUCUCCCUCUCUCCCUCUCUCU
CCCCCCUCUGAUCGUGGGUCGGUGUGGAGGCGUGUGCCCAUCAUGACGGG
AGGUCACGGAGAGAGCAGGGCAGAGGCGGAGACUACCAUUGCUGUCGUUG
UUAGCGUUUUCUCCUAUUGUGGGCGCCCGUUUCCCCCCUCAGUCCAUCUC
CGUCAUUUUCUCAGGCU
..............(((((..........(((((.(((((((((((((((((..(((((..((((((((..((((....))))..))))))...))..)))))....)))))))).)))).))))).))))).......(((((.......)))))............((((((.................))))))..............))))). (-66.90)

Length sequence

: 217

Length match:

206