Locus 3679

Sequence ID 3R_DroMel_CAF1
Location 9,978,037 – 9,978,135
Length 98
Max. P 0.806801
window5902 window5903

overview

Window 2

Location 9,978,037 – 9,978,135
Length 98
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 70.11
Mean single sequence MFE -29.93
Consensus MFE -7.34
Energy contribution -8.70
Covariance contribution 1.36
Combinations/Pair 1.28
Mean z-score -1.92
Structure conservation index 0.25
SVM decision value 0.63
SVM RNA-class probability 0.806801
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9978037 98 + 27905053
AAGUUUUCAGCCAGAAUGACCAUGAACACCAU------------------GUCCCACAACUGGACCAUGGCCUACAACUGGACCAUGGCCUACAACUGGACCGUGUCC---AACAGGAC
..........((((...(((.(((.....)))------------------)))........((.((((((((.......)).)))))))).....)))).....((((---....)))) ( -27.40)
>DroSec_CAF1 60487 98 + 1
AAGUUUUUAGCCAGAAUGACCAUGAACACCAU------------------GUCCUACAACUGGACCAUGUCCUACAACUGGACCGUGUCCUACAUGUCCACCGUGUCC---UACAGGUC
.................((((..(.(((((((------------------((((.......))).)))).........(((((.(((.....))))))))..)))).)---....)))) ( -21.40)
>DroSim_CAF1 60432 98 + 1
AAGUUUUUAGCCAGAAUGACCAUGAACACCAU------------------GUCCUACAACUGGACCAUGGCCUACAACUGGACCGUGUCCUACAGGUCCACCGUGUCC---UACAGGUC
.................((((.((....((((------------------((((.......))).)))))...(((..((((((.((.....))))))))...)))..---..)))))) ( -26.50)
>DroEre_CAF1 64811 119 + 1
AAGUGUUUAGCCAGAACGGCCGUGACCACCAUGGUCUAGUGCUGGACCACGUCCUGCAACUGGACCAUGUCCUCCAACUGGACCAGGUCCUCCAACUGGACCACGUCCUCCAACUGGAC
..(((.((((((.....)))..))).)))(((((((((((((.((((...)))).)).)))))))))))(((.......((((..(((((.......)))))..)))).......))). ( -48.34)
>DroAna_CAF1 67160 94 + 1
GAG--CUUUACC--AAUGUCCACUACCGCCAU------------------GGCCCACAGAGCCACCAUGGCCAACAGGUCCUCCAUGGCCGACAGAGCCUCCACGGCC---GACAGGUC
...--....(((--..((((.....(.(((((------------------((.((.....(((.....))).....))....))))))).)...(.(((.....))))---))))))). ( -26.00)
>consensus
AAGUUUUUAGCCAGAAUGACCAUGAACACCAU__________________GUCCUACAACUGGACCAUGGCCUACAACUGGACCAUGUCCUACAACUCCACCGUGUCC___AACAGGUC
.................(((.(((..........................((((.......))))(((((.(((....))).)))))..............))))))............ ( -7.34 =  -8.70 +   1.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,978,037 – 9,978,135
Length 98
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 70.11
Mean single sequence MFE -38.28
Consensus MFE -13.00
Energy contribution -14.92
Covariance contribution 1.92
Combinations/Pair 1.29
Mean z-score -1.75
Structure conservation index 0.34
SVM decision value 0.12
SVM RNA-class probability 0.593860
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9978037 98 - 27905053
GUCCUGUU---GGACACGGUCCAGUUGUAGGCCAUGGUCCAGUUGUAGGCCAUGGUCCAGUUGUGGGAC------------------AUGGUGUUCAUGGUCAUUCUGGCUGAAAACUU
((((....---)))).(((.((((..((.((((((((.........(.((((((..(((....)))..)------------------))))).))))))))))).)))))))....... ( -37.20)
>DroSec_CAF1 60487 98 - 1
GACCUGUA---GGACACGGUGGACAUGUAGGACACGGUCCAGUUGUAGGACAUGGUCCAGUUGUAGGAC------------------AUGGUGUUCAUGGUCAUUCUGGCUAAAAACUU
((((....---((((((.(((.(((....((((...((((.......))))...))))...)))....)------------------)).))))))..))))................. ( -32.50)
>DroSim_CAF1 60432 98 - 1
GACCUGUA---GGACACGGUGGACCUGUAGGACACGGUCCAGUUGUAGGCCAUGGUCCAGUUGUAGGAC------------------AUGGUGUUCAUGGUCAUUCUGGCUAAAAACUU
((((....---((((((((((((((((.....)).)))))).))))..((((((.(((.......))))------------------)))))))))..))))................. ( -33.00)
>DroEre_CAF1 64811 119 - 1
GUCCAGUUGGAGGACGUGGUCCAGUUGGAGGACCUGGUCCAGUUGGAGGACAUGGUCCAGUUGCAGGACGUGGUCCAGCACUAGACCAUGGUGGUCACGGCCGUUCUGGCUAAACACUU
.(((....)))((((..(((((.......)))))..))))(((..(((..(((((((.(((.((.((((...)))).))))).)))))))..(((....))).)))..)))........ ( -49.90)
>DroAna_CAF1 67160 94 - 1
GACCUGUC---GGCCGUGGAGGCUCUGUCGGCCAUGGAGGACCUGUUGGCCAUGGUGGCUCUGUGGGCC------------------AUGGCGGUAGUGGACAUU--GGUAAAG--CUC
.(((((((---.(((((.(.(((((....((((((.(.((.((....)))).).))))))....)))))------------------.).)))))....))))..--)))....--... ( -38.80)
>consensus
GACCUGUA___GGACACGGUGGACCUGUAGGACAUGGUCCAGUUGUAGGCCAUGGUCCAGUUGUAGGAC__________________AUGGUGUUCAUGGUCAUUCUGGCUAAAAACUU
...........((((((.((............(((((((........)))))))((((.......))))..................)).)))))).(((((.....)))))....... (-13.00 = -14.92 +   1.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:10 2006