Locus 3043

Sequence ID 3L_DroMel_CAF1
Location 8,748,584 – 8,748,690
Length 106
Max. P 0.935799
window4754

overview

Window 4

Location 8,748,584 – 8,748,690
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.01
Mean single sequence MFE -29.93
Consensus MFE -20.84
Energy contribution -22.90
Covariance contribution 2.06
Combinations/Pair 1.08
Mean z-score -2.37
Structure conservation index 0.70
SVM decision value 1.25
SVM RNA-class probability 0.935799
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8748584 106 + 23771897
AAA--------AAAAACCCAAAAAGAGGAGACCAGCAGCGUCAGCUAUAA------AAAAAAGAGUUUCCUUGAGCCAGCGGGCGGGUUUCAUUACCUGCCAGUUGUUACUGUAGCUGAC
...--------.............(.(....))......((((((((((.------........((((....))))((((.(((((((......))))))).))))....)))))))))) ( -31.90)
>DroPse_CAF1 16624 90 + 1
--------------------AAAAGAGAGAAGCAGCAGCAUG-GCUCCA-------AA-AAAUAGUUUCCUUGAGCCAGCGGGCGGGUUUCAUUACCUGCCAGUUGUUACUGUACC-GCC
--------------------.....(.((.((((((.((.((-((((..-------..-.............)))))))).(((((((......))))))).)))))).)).)...-... ( -31.03)
>DroSec_CAF1 15137 105 + 1
AAA--------AAAAACCCAAAAAGAGGAGACCAGCAGCGUCAGCUAUAA------AA-AAAGAGUUUCCUUGAGCCAGCGGGCGGGUUUCAUUACCUGCCAGUUGUUACUGUAGCUGAC
...--------.............(.(....))......((((((((((.------..-.....((((....))))((((.(((((((......))))))).))))....)))))))))) ( -31.90)
>DroEre_CAF1 15442 108 + 1
AAAAAA-----------CCAAAAAGAGGAGACCAGCAGCGUCAGUUAAAAAAAAAAAA-AAAGAGUUUCCUUGAGCCAGCGGGCGGGUUUCAUUACAUGCCAGUUGUUACUGUAGCUGAC
......-----------.......(.(....))..((((..((((.............-.....((((....))))((((.((((.((......)).)))).))))..))))..)))).. ( -20.90)
>DroYak_CAF1 15460 117 + 1
AAAAAACGCAAAAAAACCCAAAAAGAGGAGACCAGCAGCGUCAGCUAAAAGAA--AAA-AAAGAGUUUUCUUGAGCCAGCGGGCGGGUUUCAUUACCUGCCAGUUGUUACUGUAGCUGAC
........................(.(....))......((((((((.(((((--((.-......)))))))....((((.(((((((......))))))).))))......)))))))) ( -32.80)
>DroPer_CAF1 16174 90 + 1
--------------------AAAAGAGAGAAGCAGCAGCAUG-GCUCCA-------AA-AAAUAGUUUCCUUGAGCCAGCGGGCGGGUUUCAUUACCUGCCAGUUGUUACUGUACC-GCC
--------------------.....(.((.((((((.((.((-((((..-------..-.............)))))))).(((((((......))))))).)))))).)).)...-... ( -31.03)
>consensus
AAA______________CCAAAAAGAGGAGACCAGCAGCGUCAGCUAAAA______AA_AAAGAGUUUCCUUGAGCCAGCGGGCGGGUUUCAUUACCUGCCAGUUGUUACUGUAGCUGAC
.......................................((((((((((...............((((....))))((((.(((((((......))))))).))))....)))))))))) (-20.84 = -22.90 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:14 2006