Locus 8243

Sequence ID X_DroMel_CAF1
Location 20,463,123 – 20,463,232
Length 109
Max. P 0.966275
window13541 window13542

overview

Window 1

Location 20,463,123 – 20,463,232
Length 109
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 74.22
Mean single sequence MFE -28.87
Consensus MFE -13.72
Energy contribution -15.15
Covariance contribution 1.44
Combinations/Pair 1.17
Mean z-score -2.65
Structure conservation index 0.48
SVM decision value 1.59
SVM RNA-class probability 0.966275
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20463123 109 + 22224390
UAUGACACUGAUCCUAUGUGAAGAUGAACG-----CUUUCACGCACGUCCUAUUUGCGCAUACAAAUUUGCGGACUUAGUCGUGCGUAUAAAGCACGAACG--UAUCUAAAAAUAA
((((.(((.........))).........(-----((((.(((((((..(((..(.((((........)))).)..))).)))))))..))))).....))--))........... ( -27.70)
>DroSec_CAF1 36487 109 + 1
UAUCACACUGAUCCUGUGUGAAGAUGAACG-----CUUUCACGCACGUCCUAUUUGCGCAUACAAAUUUGCGAGCUUAGUCGUGCGUAUAAAGCAGGAACG--UAUCUAAAAAUAA
..((((((.......))))))(((((..((-----((((.(((((((..(((....((((........))))....))).)))))))..))))).).....--)))))........ ( -33.40)
>DroSim_CAF1 41587 109 + 1
UAUCACACUGAUCCUGUGUGAAGAUGAACG-----CUUUCACGCACGUCCUAUUUGCGCAUACAAAUUUGCGAGCUUGGUCGUGCGUAUAAAGCACGAACG--UAUCUAAAAAUAA
..((((((.......))))))(((((...(-----((((.(((((((.((......((((........)))).....)).)))))))..))))).......--)))))........ ( -35.10)
>DroYak_CAF1 35319 95 + 1
UAUGACACUGAUCCUGUGUGAGUAUGCACAUCCUUUUUGCGCAUACAAAUUAUUAGUGCGCAUAAAU--------------GUAU-------CUAAGAGUGUUUAUCUAAAAAUAA
...((((((.....(((((......)))))...(((.(((((((...........))))))).))).--------------....-------.....))))))............. ( -19.30)
>consensus
UAUCACACUGAUCCUGUGUGAAGAUGAACG_____CUUUCACGCACGUCCUAUUUGCGCAUACAAAUUUGCGAGCUUAGUCGUGCGUAUAAAGCACGAACG__UAUCUAAAAAUAA
..((((((.......))))))(((((((.........)))(((((((.........((((........))))........))))))).................))))........ (-13.72 = -15.15 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,463,123 – 20,463,232
Length 109
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 74.22
Mean single sequence MFE -27.88
Consensus MFE -13.50
Energy contribution -14.00
Covariance contribution 0.50
Combinations/Pair 1.32
Mean z-score -1.99
Structure conservation index 0.48
SVM decision value -0.03
SVM RNA-class probability 0.517237
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20463123 109 - 22224390
UUAUUUUUAGAUA--CGUUCGUGCUUUAUACGCACGACUAAGUCCGCAAAUUUGUAUGCGCAAAUAGGACGUGCGUGAAAG-----CGUUCAUCUUCACAUAGGAUCAGUGUCAUA
.........((((--(......(((((.((((((((.(((..(.((((........)))).)..)))..))))))))))))-----)....(((((.....)))))..)))))... ( -31.30)
>DroSec_CAF1 36487 109 - 1
UUAUUUUUAGAUA--CGUUCCUGCUUUAUACGCACGACUAAGCUCGCAAAUUUGUAUGCGCAAAUAGGACGUGCGUGAAAG-----CGUUCAUCUUCACACAGGAUCAGUGUGAUA
.............--.......(((((.((((((((.(((....((((........))))....)))..))))))))))))-----)........((((((.......)))))).. ( -31.10)
>DroSim_CAF1 41587 109 - 1
UUAUUUUUAGAUA--CGUUCGUGCUUUAUACGCACGACCAAGCUCGCAAAUUUGUAUGCGCAAAUAGGACGUGCGUGAAAG-----CGUUCAUCUUCACACAGGAUCAGUGUGAUA
........(((((--(....))(((((.((((((((.((.....((((........))))......)).))))))))))))-----)....))))((((((.......)))))).. ( -31.40)
>DroYak_CAF1 35319 95 - 1
UUAUUUUUAGAUAAACACUCUUAG-------AUAC--------------AUUUAUGCGCACUAAUAAUUUGUAUGCGCAAAAAGGAUGUGCAUACUCACACAGGAUCAGUGUCAUA
.(((((..(((.......))).))-------))).--------------...((((.(((((........(((((((((.......)))))))))((......))..))))))))) ( -17.70)
>consensus
UUAUUUUUAGAUA__CGUUCGUGCUUUAUACGCACGACUAAGCUCGCAAAUUUGUAUGCGCAAAUAGGACGUGCGUGAAAG_____CGUUCAUCUUCACACAGGAUCAGUGUCAUA
..................((((((.......)))))).................(((((((.........)))))))..................((((((.......)))))).. (-13.50 = -14.00 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:14 2006