Locus 3477

Sequence ID 3R_DroMel_CAF1
Location 9,401,263 – 9,401,353
Length 90
Max. P 0.705467
window5593 window5594

overview

Window 3

Location 9,401,263 – 9,401,353
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 90.19
Mean single sequence MFE -16.38
Consensus MFE -11.01
Energy contribution -11.07
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -2.19
Structure conservation index 0.67
SVM decision value 0.02
SVM RNA-class probability 0.545162
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9401263 90 + 27905053
ACAUAAUAACCUUCAGUAGCAAUAUUUUGUCUCUGUGCACUAAUACACACGUGCGCACACGCACACUUCCACGGCCACACCGAUGAAUUC
.(((.........(((..((((....))))..)))...............(((((....))))).......(((.....))))))..... ( -16.00)
>DroSec_CAF1 30842 90 + 1
ACUUGAUAUCCUUCGGUACCCAUUUUUUCUCUCUGUGCACUAAUACACACGUGCGCACACGCACACUUCCACGGCCACACCGACGAAUUC
..........(.(((((..((............((((........)))).(((((....)))))........))....))))).)..... ( -17.20)
>DroSim_CAF1 32945 90 + 1
ACUUGAUAUCCUUCAGUACCAAUAUUUUCUCUCUGUGCACUAAUACACACGUGCGCACACGCACACUUCCACGGACACACGGACAAAUUC
..((((......))))...............((((((.............(((((....)))))...((....))..))))))....... ( -15.10)
>DroEre_CAF1 31979 90 + 1
ACUUGUUAUGCAUCAGUAACAAUAUUUUUUUUCUGUGCACUAAUACACACGUGCGCACACGCACACUUCCACGGCCACACCGACAAAUUC
...(((((((((.(((.((.((....)).)).))))))).))))).....(((((....))))).......(((.....)))........ ( -17.20)
>consensus
ACUUGAUAUCCUUCAGUACCAAUAUUUUCUCUCUGUGCACUAAUACACACGUGCGCACACGCACACUUCCACGGCCACACCGACAAAUUC
..............(((................((((........)))).(((((....))))))))....(((.....)))........ (-11.01 = -11.07 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,401,263 – 9,401,353
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 90.19
Mean single sequence MFE -25.32
Consensus MFE -19.92
Energy contribution -20.30
Covariance contribution 0.38
Combinations/Pair 1.09
Mean z-score -1.72
Structure conservation index 0.79
SVM decision value 0.36
SVM RNA-class probability 0.705467
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9401263 90 - 27905053
GAAUUCAUCGGUGUGGCCGUGGAAGUGUGCGUGUGCGCACGUGUGUAUUAGUGCACAGAGACAAAAUAUUGCUACUGAAGGUUAUUAUGU
......(((...(((((.(((...((((((....)))))).((((((....)))))).........))).)))))....)))........ ( -22.30)
>DroSec_CAF1 30842 90 - 1
GAAUUCGUCGGUGUGGCCGUGGAAGUGUGCGUGUGCGCACGUGUGUAUUAGUGCACAGAGAGAAAAAAUGGGUACCGAAGGAUAUCAAGU
((((((.((((((...((((....((((((....)))))).((((((....))))))..........)))).)))))).)))).)).... ( -28.30)
>DroSim_CAF1 32945 90 - 1
GAAUUUGUCCGUGUGUCCGUGGAAGUGUGCGUGUGCGCACGUGUGUAUUAGUGCACAGAGAGAAAAUAUUGGUACUGAAGGAUAUCAAGU
.....(((((..(((.(((.....((((((....)))))).((((((....))))))............))))))....)))))...... ( -23.90)
>DroEre_CAF1 31979 90 - 1
GAAUUUGUCGGUGUGGCCGUGGAAGUGUGCGUGUGCGCACGUGUGUAUUAGUGCACAGAAAAAAAAUAUUGUUACUGAUGCAUAACAAGU
..(((((((((.....))).....((((((....)))))).((((((((((((.((((..........)))))))))))))))))))))) ( -26.80)
>consensus
GAAUUCGUCGGUGUGGCCGUGGAAGUGUGCGUGUGCGCACGUGUGUAUUAGUGCACAGAGAGAAAAUAUUGGUACUGAAGGAUAUCAAGU
..((((.((((((...........((((((....)))))).((((((....))))))...............)))))).))))....... (-19.92 = -20.30 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:11 2006