Locus 9579

Sequence ID 3R_DroMel_CAF1
Location 25,303,387 – 25,303,480
Length 93
Max. P 0.512185
window15314

overview

Window 4

Location 25,303,387 – 25,303,480
Length 93
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 77.37
Mean single sequence MFE -17.88
Consensus MFE -6.03
Energy contribution -6.67
Covariance contribution 0.64
Combinations/Pair 1.07
Mean z-score -1.82
Structure conservation index 0.34
SVM decision value -0.04
SVM RNA-class probability 0.512185
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25303387 93 + 27905053
AAAGGAA--AAAGCCCGAGAAAAGCGGUGGGAAAACAUGAAAAGAAGGGU-UUCGCGUUUUUUUUCUUUUCAGCUAGAGGGUGGGUGGAAAUCUUC
..((((.--...(((((.....(((.(((......)))(((((((((((.-.........))))))))))).)))......))))).....)))). ( -21.20)
>DroSec_CAF1 160247 75 + 1
AAGGAAA--AAAUCCCGAGAAAAGCGGUGGGAAAACAUGAAAAGAAGGGU-UUCGCG------------------AAAGGUUGGGUGAAUAUCUUC
.......--...(((((.(.....)..)))))...........(((((..-(((((.------------------.........)))))..))))) ( -12.70)
>DroSim_CAF1 161116 75 + 1
AAUGAAA--AAAACCCGAGAAAAACGGUGGGAAAACAUGAAAAGAAGGGU-UUCGCG------------------AAAGGUUGGGUGGAACUCUUC
.......--....((((.(.....)..))))............(((((((-(((((.------------------.........)))))))))))) ( -18.00)
>DroEre_CAF1 180097 84 + 1
AAAGGAAGGAAAUACCGAGGAAAGCGGUGGGAAAACAUGAAAAGAAGGGU-UUCGCGUUCUCU---------G--CGAGGGUCUGAAGAAAUCUUC
....(((((...(((((.......)))))................(((.(-((((((.....)---------)--))))).))).......))))) ( -17.70)
>DroYak_CAF1 166710 85 + 1
AAAGGAAGGAAAACCCGAGGAAAGCGGUGGGAAAACAUGAAAAGAAGGGUUUUCGCGUAUUCU---------G--CGUGGGUGAGAGGAAAUCUUC
............(((((.((((.(((.((..((..(..........)..))..))))).))))---------.--..)))))..((((....)))) ( -19.80)
>consensus
AAAGGAA__AAAACCCGAGAAAAGCGGUGGGAAAACAUGAAAAGAAGGGU_UUCGCGU__U_U_________G__AGAGGGUGGGUGGAAAUCUUC
.............((((.(.....)..))))............(((((...(((((............................)))))..))))) ( -6.03 =  -6.67 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:37:32 2006