Locus 8680

Sequence ID	X_DroMel_CAF1
Location	21,996,962 – 21,997,078
Length	116
Max. P	0.790193

overview

Window 1

Location	21,996,962 – 21,997,078
Length	116
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	81.78
Mean single sequence MFE	-35.60
Consensus MFE	-24.68
Energy contribution	-24.59
Covariance contribution	-0.09
Combinations/Pair	1.40
Mean z-score	-2.05
Structure conservation index	0.69
SVM decision value	0.58
SVM RNA-class probability	0.790193
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21996962 116 + 22224390
CGGGUAUUAAAAGUUACCCAACAAGUUUGGCCUGACAAAAA-GGAUCAGGACAAAUGUUUUCCGCUGCUUCGCUGAUAAAAGCUGCAUGCAUGCAUGCACAGGCAAAUGCGGUGGGG
.(((((........))))).....(((((.((((((.....-.).))))).)))))....((((((((...(((......)))((((((....)))))).........)))))))). ( -40.70)
>DroGri_CAF1 20171 102 + 1
-----------AGUUG-CCAGCAAACUUGGCACUCCAAAAA-CGACCAAGACAAAUAUUUU-CGUUGCCUGUGUGAUAAAAACUGCAUGCGAGUGUGCAUUG-UAUGUGUGUAUGUG
-----------(((((-((((.....)))))..((((....-((((.((((......))))-.))))....)).))....))))(((((((.(..(((...)-))..).))))))). ( -19.80)
>DroSec_CAF1 57542 116 + 1
CGGGUAUUAAAAGUUACCCAACAAGUUUGGCCUGACAAAAA-GGAUCAGGACAAAUGUUUUCCGCUGCUCCGUUGAUAAAAGCUGCAUGCAUGCAUGCACAGGCAAAUGCGGAGGGG
.(((((........))))).....(((((.((((((.....-.).))))).))))).((((((((((((..(((......)))((((((....))))))..))))...)))))))). ( -38.40)
>DroSim_CAF1 57567 116 + 1
CGGGUAUUAAAAGUUACCCAACAAGUUUGGCCUGACAAAAA-GGAUCAGGACAAAUGUUUUCCGCUGCUCCGCUGAUAAAAGCUGCAUGCAUGCAUGCACAGGCAAAUGCGGAGGGG
.(((((........))))).....(((((.((((((.....-.).))))).))))).((((((((((((..(((......)))((((((....))))))..))))...)))))))). ( -40.80)
>DroEre_CAF1 37863 114 + 1
CGGGUAUUAAAAGUUGCCCAACAAGUUUGGCCUGGCAAAA--GGAUCAGGACAAAUGUUUUCCGCUGCUUCGCUGAUAAAAAUUGCAUGCGUGCGUGCACU-GAAAAUGCGGUGGGG
.(((((........))))).....(((((.(((((.....--...))))).)))))....((((((((...............((((((....)))))).(-....).)))))))). ( -34.10)
>DroYak_CAF1 46313 117 + 1
CGGGUAUUAAAAGUUACCCAACAAGUUUGGCCUGGCAAAAAGGGAUCAGGACAAAUGUUUUCCGCUGCUUCUCUGAUUAGAAUUGCAUGCAUGCAUGCAGAGGGAAAUGCGGAGGAG
.(((((........))))).....(((((.((((((.......).))))).))))).((((((((...((((((........(((((((....)))))))))))))..)))))))). ( -39.80)
>consensus
CGGGUAUUAAAAGUUACCCAACAAGUUUGGCCUGACAAAAA_GGAUCAGGACAAAUGUUUUCCGCUGCUUCGCUGAUAAAAACUGCAUGCAUGCAUGCACAGGCAAAUGCGGAGGGG
.(((((........))))).....(((((.((((((.......).))))).)))))...........((((((((........((((((....))))))..........)))))))) (-24.68 = -24.59 +  -0.09)

alignment

secondary structure

dotplot

Window 2

Location	21,996,962 – 21,997,078
Length	116
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	81.78
Mean single sequence MFE	-31.45
Consensus MFE	-19.90
Energy contribution	-21.97
Covariance contribution	2.07
Combinations/Pair	1.19
Mean z-score	-2.03
Structure conservation index	0.63
SVM decision value	0.34
SVM RNA-class probability	0.696825
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21996962 116 - 22224390
CCCCACCGCAUUUGCCUGUGCAUGCAUGCAUGCAGCUUUUAUCAGCGAAGCAGCGGAAAACAUUUGUCCUGAUCC-UUUUUGUCAGGCCAAACUUGUUGGGUAACUUUUAAUACCCG
.....((((.........((((((....))))))(((((.......))))).))))..((((((((.((((((..-.....)))))).))))..))))(((((........))))). ( -37.20)
>DroGri_CAF1 20171 102 - 1
CACAUACACACAUA-CAAUGCACACUCGCAUGCAGUUUUUAUCACACAGGCAACG-AAAAUAUUUGUCUUGGUCG-UUUUUGGAGUGCCAAGUUUGCUGG-CAACU-----------
..............-...(((.((...(((.((.((.......))...((((.((-((((((((......))).)-))))))...))))..)).))))))-))...----------- ( -16.70)
>DroSec_CAF1 57542 116 - 1
CCCCUCCGCAUUUGCCUGUGCAUGCAUGCAUGCAGCUUUUAUCAACGGAGCAGCGGAAAACAUUUGUCCUGAUCC-UUUUUGUCAGGCCAAACUUGUUGGGUAACUUUUAAUACCCG
....(((((.........((((((....))))))(((((.......))))).))))).((((((((.((((((..-.....)))))).))))..))))(((((........))))). ( -38.00)
>DroSim_CAF1 57567 116 - 1
CCCCUCCGCAUUUGCCUGUGCAUGCAUGCAUGCAGCUUUUAUCAGCGGAGCAGCGGAAAACAUUUGUCCUGAUCC-UUUUUGUCAGGCCAAACUUGUUGGGUAACUUUUAAUACCCG
....(((((...(((((.((((((....))))))(((......))))).)))))))).((((((((.((((((..-.....)))))).))))..))))(((((........))))). ( -38.70)
>DroEre_CAF1 37863 114 - 1
CCCCACCGCAUUUUC-AGUGCACGCACGCAUGCAAUUUUUAUCAGCGAAGCAGCGGAAAACAUUUGUCCUGAUCC--UUUUGCCAGGCCAAACUUGUUGGGCAACUUUUAAUACCCG
.(((.((((..((((-.((((......))))((...........))))))..))))..((((((((.((((....--......)))).))))..)))))))................ ( -25.50)
>DroYak_CAF1 46313 117 - 1
CUCCUCCGCAUUUCCCUCUGCAUGCAUGCAUGCAAUUCUAAUCAGAGAAGCAGCGGAAAACAUUUGUCCUGAUCCCUUUUUGCCAGGCCAAACUUGUUGGGUAACUUUUAAUACCCG
....(((((.........((((((....)))))).((((......))))...))))).((((((((.((((............)))).))))..))))(((((........))))). ( -32.60)
>consensus
CCCCUCCGCAUUUGCCUGUGCAUGCAUGCAUGCAGCUUUUAUCAGCGAAGCAGCGGAAAACAUUUGUCCUGAUCC_UUUUUGUCAGGCCAAACUUGUUGGGUAACUUUUAAUACCCG
.....((((.........((((((....))))))(((((.......))))).))))..((((((((.((((............)))).))))..))))(((((........))))). (-19.90 = -21.97 +   2.07)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:12 2006