Locus 4022

Sequence ID	3L_DroMel_CAF1
Location	11,730,906 – 11,731,003
Length	97
Max. P	0.997663

overview

Window 6

Location	11,730,906 – 11,731,003
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	75.58
Mean single sequence MFE	-20.24
Consensus MFE	-5.92
Energy contribution	-6.96
Covariance contribution	1.04
Combinations/Pair	1.07
Mean z-score	-2.77
Structure conservation index	0.29
SVM decision value	2.90
SVM RNA-class probability	0.997663
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11730906 97 + 23771897
CAUCCUUUAUACACAUUUAUCUAUAUGUAUAUAUGUGUGUAGGCAAAUAUCUAUAUGCCUGAGUACACAUUUACUUGCGAAAGUAAGCGUUUGCAAG
.......((((((.((......)).)))))).(((((((((((((.((....)).))))))..)))))))...((((((((.(....).)))))))) ( -24.10)
>DroSec_CAF1 43776 95 + 1
CAGCCUUUAUACACAUUUAUCUAUAUGUGU--AUGUGUGUAGACAAAUAUCUAUAUGCCUGAGUACACAUUUACUUGCGAAAGUAAGCGUUUGCAAG
(((.....((((((((........))))))--))(((((((((......)))))))))))).(((.((.(((((((....))))))).)).)))... ( -25.00)
>DroSim_CAF1 38860 75 + 1
CAGCCUUUAUACACAUUUAUCUAUAUGUAU----------------------AUAUGCCUGAGUACACAUUUACUUGCGAAAGUAAGCGUUUGCAAG
(((.(..((((((.((......)).)))))----------------------)...).))).(((.((.(((((((....))))))).)).)))... ( -14.70)
>DroEre_CAF1 40127 87 + 1
CCUCCUUUAUACACAUUUAUUUGUAUAUGU----------AGGCAAAUAUCUAUAUGCCUGCGUACACAUUUACUUACGAAAGCCACCGUUCGCAAG
.................((..(((.(((((----------(((((.((....)).)))))))))).)))..))(((.((((........)))).))) ( -19.10)
>DroYak_CAF1 41001 83 + 1
ACCCCUUUAUACACAUAUAUUUAUAUAUGU--AUGUAUGAAGGCAAAUAUCU------------ACACAUUUACUUACGAAAGCAACCGUUUGCAAG
...((((((((((.((((((....))))))--.)))))))))).........------------..................((((....))))... ( -18.30)
>consensus
CAGCCUUUAUACACAUUUAUCUAUAUGUGU__AUGU_UG_AGGCAAAUAUCUAUAUGCCUGAGUACACAUUUACUUGCGAAAGUAAGCGUUUGCAAG
..........((((((........))))))...........................................((((((((.(....).)))))))) ( -5.92 =  -6.96 +   1.04)

alignment

secondary structure

dotplot

Window 7

Location	11,730,906 – 11,731,003
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	75.58
Mean single sequence MFE	-19.30
Consensus MFE	-8.24
Energy contribution	-7.72
Covariance contribution	-0.52
Combinations/Pair	1.17
Mean z-score	-1.81
Structure conservation index	0.43
SVM decision value	0.10
SVM RNA-class probability	0.582544
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11730906 97 - 23771897
CUUGCAAACGCUUACUUUCGCAAGUAAAUGUGUACUCAGGCAUAUAGAUAUUUGCCUACACACAUAUAUACAUAUAGAUAAAUGUGUAUAAAGGAUG
(((((..............)))))...((((((....(((((..........)))))..)))))).(((((((((......)))))))))....... ( -22.24)
>DroSec_CAF1 43776 95 - 1
CUUGCAAACGCUUACUUUCGCAAGUAAAUGUGUACUCAGGCAUAUAGAUAUUUGUCUACACACAU--ACACAUAUAGAUAAAUGUGUAUAAAGGCUG
.......((((((((((....))))))..)))).....(((.((((.(((((((((((.......--.......))))))))))).))))...))). ( -19.74)
>DroSim_CAF1 38860 75 - 1
CUUGCAAACGCUUACUUUCGCAAGUAAAUGUGUACUCAGGCAUAU----------------------AUACAUAUAGAUAAAUGUGUAUAAAGGCUG
.......((((((((((....))))))..)))).....(((...(----------------------((((((((......)))))))))...))). ( -16.20)
>DroEre_CAF1 40127 87 - 1
CUUGCGAACGGUGGCUUUCGUAAGUAAAUGUGUACGCAGGCAUAUAGAUAUUUGCCU----------ACAUAUACAAAUAAAUGUGUAUAAAGGAGG
((((((.(((...((((....))))...)))...))))))..............(((----------..(((((((......)))))))..)))... ( -19.70)
>DroYak_CAF1 41001 83 - 1
CUUGCAAACGGUUGCUUUCGUAAGUAAAUGUGU------------AGAUAUUUGCCUUCAUACAU--ACAUAUAUAAAUAUAUGUGUAUAAAGGGGU
.(((((.....((((((....))))))...)))------------)).......((((.((((((--(.((((....)))).))))))).))))... ( -18.60)
>consensus
CUUGCAAACGCUUACUUUCGCAAGUAAAUGUGUACUCAGGCAUAUAGAUAUUUGCCU_CA_ACAU__ACACAUAUAGAUAAAUGUGUAUAAAGGAUG
(((....(((.((((((....)))))).)))....................................((((((........))))))...))).... ( -8.24 =  -7.72 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:38 2006