Locus 6421

Sequence ID 3R_DroMel_CAF1
Location 16,809,603 – 16,809,739
Length 136
Max. P 0.837694
window10463 window10464

overview

Window 3

Location 16,809,603 – 16,809,716
Length 113
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 90.16
Mean single sequence MFE -34.68
Consensus MFE -26.20
Energy contribution -27.32
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -2.03
Structure conservation index 0.76
SVM decision value 0.74
SVM RNA-class probability 0.837694
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16809603 113 + 27905053
GUGUGUACCAACGUCCUCGAGUUGUUUUC--UCCAGUG--GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUGGCAGUAC-AUAG
((((((((((((((....(((.......)--))(((.(--((..((((((.....))))))....)))....))).((((((.....))))))....)))))))).))).)))-.... ( -35.40)
>DroSec_CAF1 10788 115 + 1
GUGUGUACCAACGUCCUCGAGUUGUUUUCUCUCUAGUU--GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUACCAGUAC-AUGG
.((.((((((((((......((..((..(((((((...--.)))))))((((....)))).))..)).........((((((.....))))))....))))))))))))....-.... ( -37.50)
>DroSim_CAF1 6576 115 + 1
GUGUGUACCAACGUCCUCGAGUUGUUUUCUCUCUAGUU--GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUGCCAGUAC-AUGG
.((.((((((((((......((..((..(((((((...--.)))))))((((....)))).))..)).........((((((.....))))))....))))))))))))....-.... ( -37.50)
>DroEre_CAF1 10914 113 + 1
GUGUAUACCAACGUCCUCGAGUUGUUUCC--CCCAGAU--GGAGAGAGGAGGAAAUCCUCUAAUGAGCUUUUCUGCGUGUAUUUCUAGUGCACAUAAACGU-UGUGCCAGUAAAAUAG
(.(((...((((((((((...(..(((..--...))).--.)...)))))(((((..(((....)))..)))))..((((((.....)))))).....)))-)))))).......... ( -26.90)
>DroYak_CAF1 12064 116 + 1
GUGUGUACCAACGUCCUCGAGUUGUUUCC--UCCAGAAGAGGAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAGUGCAGAUAAACGUUUGUACCACUACCAUAG
(((.((((.(((((..(((((.......)--))(((((((((..((((((.....)))))).....)))))))))..(((((.....)))))))...))))).)))))))........ ( -36.10)
>consensus
GUGUGUACCAACGUCCUCGAGUUGUUUUC__UCCAGUU__GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUGCCAGUAC_AUAG
.((.((((((((((..........................((((((((((((....)))))........)))))))((((((.....))))))....))))))))))))......... (-26.20 = -27.32 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 16,809,639 – 16,809,739
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 91.56
Mean single sequence MFE -26.77
Consensus MFE -19.72
Energy contribution -19.72
Covariance contribution 0.00
Combinations/Pair 1.19
Mean z-score -1.72
Structure conservation index 0.74
SVM decision value -0.01
SVM RNA-class probability 0.528320
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16809639 100 + 27905053
GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUGGCAGUAC-AUAGCGCAAUAUGAAUGGCAAAUGGCA
((((((((((((....)))))........)))))))((((((.....))))))......((((...((.((.(-(((......)))).)).))...)))). ( -24.90)
>DroSec_CAF1 10826 100 + 1
GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUACCAGUAC-AUGGUGCAAUAUGAAUGGCAAAUGGCA
((((((((((((....)))))........)))))))((((((.....)))))).....(((..((((((....-.))))))...)))....((.....)). ( -28.60)
>DroSim_CAF1 6614 100 + 1
GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUGCCAGUAC-AUGGUGCAAUAUGAAUGGCAAAUGGCA
((((((((((((....)))))........)))))))((((((.....))))))......(((..(((((...(-(((......))))..)))))...))). ( -29.00)
>DroEre_CAF1 10950 100 + 1
GGAGAGAGGAGGAAAUCCUCUAAUGAGCUUUUCUGCGUGUAUUUCUAGUGCACAUAAACGU-UGUGCCAGUAAAAUAGUAUAAUACAAAUGGCAAAUGGCA
((((((.(((((....)))))......)))))).((((((((.....)))))).....(((-(.(((((....................))))))))))). ( -25.85)
>DroYak_CAF1 12102 101 + 1
GGAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAGUGCAGAUAAACGUUUGUACCACUACCAUAGUGCAAUACAAAUGGCAAAUGGCA
((..((((((.....)))))).....))...((((((...........))))))....((((((((.(((((...)))))...))))))))((.....)). ( -25.50)
>consensus
GUAGAGAGGAGGAAAUCCUCUAAUGACCUUUUCUGCGUGUAUUUCUAAUGCACAUAAACGUUGGUGCCAGUAC_AUAGUGCAAUAUGAAUGGCAAAUGGCA
....((((((.....))))))............(((((((((.....)))))).....((((.(((...((((....))))..))).)))))))....... (-19.72 = -19.72 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:05 2006