Locus 4435

Sequence ID 3R_DroMel_CAF1
Location 11,707,879 – 11,707,969
Length 90
Max. P 0.796859
window7249

overview

Window 9

Location 11,707,879 – 11,707,969
Length 90
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 77.66
Mean single sequence MFE -15.83
Consensus MFE -8.94
Energy contribution -9.83
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -1.88
Structure conservation index 0.56
SVM decision value 0.60
SVM RNA-class probability 0.796859
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11707879 90 - 27905053
GUGCAGCG--------------AAAUGGCA-AAAAUCGUGACUGGGCGACCAGUAACAAAAAUCAAAUGAAA----UUCACUUCAGAAUUUGAAACAAUCAAACCAUUA
........--------------.(((((..-......((.(((((....))))).))..........(.(((----(((......)))))).)..........))))). ( -18.00)
>DroPse_CAF1 49941 104 - 1
GCGAA---AAAUUGCUUGGCUAAAAUACCAGAAAAUCGUGACUGUAAAUCCAU-A-AAAAAAUCAACGCAUUUUCCUUCCUUUCAAUUUCUGAAACAAUCAAACCAUCA
((((.---...)))).(((...........(((((((((..............-.-.........))).)))))).....(((((.....)))))........)))... (  -9.66)
>DroSec_CAF1 45204 90 - 1
GUGCAGCG--------------AAAUGGCA-AAAAUCGUGACUGGGCGACCAGUAACAAUAAUCAAAUGAAA----UUCACUUCAGAAUUUGAAACAAUCAAACCAUUA
........--------------.(((((..-......((.(((((....))))).))..........(.(((----(((......)))))).)..........))))). ( -18.00)
>DroSim_CAF1 46856 90 - 1
GUGCAGCG--------------AAAUGGCA-AAAAUCGUGACUGGGCGACCAGUAACAAAAAUCAAAUGAAA----UUCACUUCAGAAUUUGAAACAAUCAAACCAUUA
........--------------.(((((..-......((.(((((....))))).))..........(.(((----(((......)))))).)..........))))). ( -18.00)
>DroEre_CAF1 45164 82 - 1
GUGCAGCG--------------A---------GAAUCGUGACUGGGAGACCAGUAACAAUAAUCAAAUGAAA----UUCACUUCAAAAUUUGAAACAAUCAAACCAUUA
.......(--------------(---------.....((.(((((....))))).)).....(((((((((.----.....))))...))))).....))......... ( -15.60)
>DroYak_CAF1 45498 82 - 1
GUGCAGCG--------------A---------GAAUCGUGACUGGGAAACCAGUAACAAAAAUCAAAUGAAA----UUCACUUCAGAAUUUGAAACAAUCAAACCAUUA
.......(--------------(---------.....((.(((((....))))).))..........(.(((----(((......)))))).).....))......... ( -15.70)
>consensus
GUGCAGCG______________AAAUGGCA_AAAAUCGUGACUGGGAGACCAGUAACAAAAAUCAAAUGAAA____UUCACUUCAGAAUUUGAAACAAUCAAACCAUUA
.....................................((.(((((....))))).)).....((((((...................))))))................ ( -8.94 =  -9.83 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:11 2006