Locus 4654

Sequence ID 2R_DroMel_CAF1
Location 15,185,052 – 15,185,148
Length 96
Max. P 0.839173
window7483 window7484

overview

Window 3

Location 15,185,052 – 15,185,148
Length 96
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 82.49
Mean single sequence MFE -23.47
Consensus MFE -13.94
Energy contribution -15.75
Covariance contribution 1.81
Combinations/Pair 1.09
Mean z-score -2.27
Structure conservation index 0.59
SVM decision value 0.59
SVM RNA-class probability 0.791647
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15185052 96 + 20766785
UAAAUUCAAAACCCAAU-UUUCUUACCUGAAAUUUGAAAACCCAUUUCAAACUGGGAUUUCAAGUAUG---UUUGGGUUUUAUAUGACGGGUCUAACCAG
.......(((((((((.-.(((......)))((((((((.((((........)))).))))))))...---.))))))))).......((......)).. ( -25.40)
>DroSim_CAF1 15468 95 + 1
UAAAUUCAAAACCCAAU-UUUCUUACCUGUAAU-UGAAAACCCAUUUCAAACGGGGAUUUUAAGUAAG---UUUGGGUUUUAUAUGACGGGUCUUACCAG
.......(((((((((.-((((((((((((..(-(((((.....))))))))))).....)))).)))---.))))))))).......((......)).. ( -22.60)
>DroEre_CAF1 15528 98 + 1
UAAAUUCAAGGCCCAAAGUUUUAUACCUGAACUUUGAAAACCCACUUCAAACUGG--UUUCAAGUAAGUGUUUUGGGUUUUAUGUGUUGGGCUUAACCAG
........(((((((((((((.......))))))).((((((((...((.(((..--.....)))...))...)))))))).......))))))...... ( -25.10)
>DroYak_CAF1 15518 98 + 1
UAAAUUGCAUACCCAAAGUUUUGUACCUGAACUUCGAAAACCCAGUUCAAACUGG--UUUCAAGUAAGUAGUUUGGGUUUUAUAUGAUGGGCUUAAACAG
...........((((..((.....(((..((((.(((((..(((((....)))))--))))......).))))..))).....))..))))......... ( -20.80)
>consensus
UAAAUUCAAAACCCAAA_UUUCUUACCUGAAAUUUGAAAACCCAUUUCAAACUGG__UUUCAAGUAAG___UUUGGGUUUUAUAUGACGGGCCUAACCAG
..........((((..........(((((((((((((((.((((........)))).))))))))......)))))))..........))))........ (-13.94 = -15.75 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 15,185,052 – 15,185,148
Length 96
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 82.49
Mean single sequence MFE -21.50
Consensus MFE -15.04
Energy contribution -17.98
Covariance contribution 2.94
Combinations/Pair 1.07
Mean z-score -1.96
Structure conservation index 0.70
SVM decision value 0.74
SVM RNA-class probability 0.839173
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15185052 96 - 20766785
CUGGUUAGACCCGUCAUAUAAAACCCAAA---CAUACUUGAAAUCCCAGUUUGAAAUGGGUUUUCAAAUUUCAGGUAAGAAA-AUUGGGUUUUGAAUUUA
..((......))......((((((((((.---.....((((((.((((........)))).)))))).((((......))))-.))))))))))...... ( -24.40)
>DroSim_CAF1 15468 95 - 1
CUGGUAAGACCCGUCAUAUAAAACCCAAA---CUUACUUAAAAUCCCCGUUUGAAAUGGGUUUUCA-AUUACAGGUAAGAAA-AUUGGGUUUUGAAUUUA
..((......))......((((((((((.---(((((((..((..(((((.....)))))..))..-.....)))))))...-.))))))))))...... ( -20.80)
>DroEre_CAF1 15528 98 - 1
CUGGUUAAGCCCAACACAUAAAACCCAAAACACUUACUUGAAA--CCAGUUUGAAGUGGGUUUUCAAAGUUCAGGUAUAAAACUUUGGGCCUUGAAUUUA
....((((((((((........(((...(((((((((((.(((--....))).)))))))).......)))..)))........))))).)))))..... ( -20.20)
>DroYak_CAF1 15518 98 - 1
CUGUUUAAGCCCAUCAUAUAAAACCCAAACUACUUACUUGAAA--CCAGUUUGAACUGGGUUUUCGAAGUUCAGGUACAAAACUUUGGGUAUGCAAUUUA
......................(((((((.....((((((((.--(((((....)))))..........))))))))......))))))).......... ( -20.60)
>consensus
CUGGUUAAACCCAUCAUAUAAAACCCAAA___CUUACUUGAAA__CCAGUUUGAAAUGGGUUUUCAAAGUUCAGGUAAAAAA_AUUGGGUUUUGAAUUUA
..................(((((((((((.....((((((((......((((((((.....))))))))))))))))......)))))))))))...... (-15.04 = -17.98 +   2.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:50 2006