Locus 3613

Sequence ID 2R_DroMel_CAF1
Location 11,993,987 – 11,994,125
Length 138
Max. P 0.901329
window5884 window5885

overview

Window 4

Location 11,993,987 – 11,994,089
Length 102
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.32
Mean single sequence MFE -25.08
Consensus MFE -15.02
Energy contribution -14.85
Covariance contribution -0.17
Combinations/Pair 1.10
Mean z-score -1.79
Structure conservation index 0.60
SVM decision value 0.03
SVM RNA-class probability 0.550164
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11993987 102 - 20766785
------------AUGGACA---UAGGUAGAA-AGGCAAAUACGCCUUGACUCUCGGUCAGAUAUUCUGAUUUGUUUGAGUUUCUACUUUUCGAGCUUAACAAAUUAAGCGCUCAAUCU
------------.((..(.---.((((((((-((((......)))))(((((.(((((((.....)))).)))...)))))))))))).....((((((....)))))))..)).... ( -28.40)
>DroVir_CAF1 48318 102 - 1
AC------------ACAAA---CAAGGGCCA-AAGCAAACACACCUUGACUUCUGGUCAGAUAUUCUGAUUUGUUUGAGUUUCUACUUUUGCAGCUUAACAAAUUAAGCGCUCAAUCG
..------------.....---...((((..-..(((((........((((((..(((((.....)))))..)...)))))......))))).((((((....))))))))))..... ( -22.54)
>DroGri_CAF1 46528 115 - 1
ACACACUCACUAAUACAUA---CAGGGGCCAAAAGCAAACACACCUUGACUUCUGGCCAGAUAUUCUGAUUUGUUUGAGUUUCUACUUUUGUAGCUUAACAAAUUAAGCGCUCAAUCG
...................---(((((((((.((((((.......))).))).)))))......))))....(.((((((...(((....)))((((((....)))))))))))).). ( -24.30)
>DroEre_CAF1 45355 105 - 1
------------AUGGACAUUGUAGGUAGAA-AGGCAAAUACGCCUUGACUCUCGGCCAGAUAUUCUGAUUUGUUUGAGUUUCUACUUUUCCAGCUUAACAAAUUAAGCGCUCAAUCU
------------.((((......((((((((-(..((((((.(((.........)))(((.....)))...))))))..))))))))).))))((((((....))))))......... ( -27.30)
>DroAna_CAF1 48046 106 - 1
--------AUGUAUGCAUG---UAGGUGAAG-AGGCAAACACACCUUGACUCUUGGUCAGAUAUUCUGAUUUGUUUGAGUUUCUACUUUUCGAGCUUAACAAAUUAAGCGCUCAAUCU
--------.((...((..(---((((....(-(((........))))(((((..((((((.....)))))).....)))))))))).......((((((....)))))))).)).... ( -23.70)
>DroMoj_CAF1 55832 102 - 1
AC------------AGAGA---UGAGGGCCA-AAGCAAACACACCUUGACUUCUGGUCAGAUAUUCUGAUUUGUUUGAGUUUCUACUUUUGCAGCUUAACAAAUUAAGCGCUCAAUCG
..------------...((---(..((((..-..(((((........((((((..(((((.....)))))..)...)))))......))))).((((((....)))))))))).))). ( -24.24)
>consensus
____________AUACACA___UAGGGGCAA_AAGCAAACACACCUUGACUCCUGGUCAGAUAUUCUGAUUUGUUUGAGUUUCUACUUUUCCAGCUUAACAAAUUAAGCGCUCAAUCG
.................................(((...........(((((..((((((.....)))))).....)))))............((((((....)))))))))...... (-15.02 = -14.85 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,994,027 – 11,994,125
Length 98
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 76.24
Mean single sequence MFE -18.60
Consensus MFE -14.49
Energy contribution -14.27
Covariance contribution -0.22
Combinations/Pair 1.20
Mean z-score -1.30
Structure conservation index 0.78
SVM decision value 1.02
SVM RNA-class probability 0.901329
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11994027 98 - 20766785
AAAGCAAAAUGAAUACACACACACACACACAGCCCA----AUGGACA---UAGGUAGAAAGGCAAAUACGCCUU--GACUCUCGGUCAGAUAUUCUGAUUUGUUUGA
.(((((((..((((((.............((.....----.))(((.---.((((...(((((......)))))--.)).))..))).).)))))...))))))).. ( -19.40)
>DroSec_CAF1 49250 76 - 1
AAAGCAAAAUGAACACACA--------------------------CA---UAGGUAGAAAGGCAAAUACGCCUU--GACUCUCGGUCAGAUAUUCUGAUUUGUUUGA
.((((((............--------------------------..---..(((...(((((......)))))--.)))....(((((.....))))))))))).. ( -16.00)
>DroSim_CAF1 48798 76 - 1
AAAACAAAAUGAACACACA--------------------------CA---UAGGUAGAAAGGCAAAUACGCCUU--GACUCUCGGUCAGAUAUUCUGAUUUGUUUGA
.((((((............--------------------------..---..(((...(((((......)))))--.)))....(((((.....))))))))))).. ( -16.00)
>DroEre_CAF1 45395 91 - 1
AAAGCAAAAUGAACAC----------ACACAUCCCA----AUGGACAUUGUAGGUAGAAAGGCAAAUACGCCUU--GACUCUCGGCCAGAUAUUCUGAUUUGUUUGA
.(((((((..(((...----------(((..(((..----..)))...))).(((((((((((......)))))--...)))..))).....)))...))))))).. ( -17.10)
>DroYak_CAF1 47157 100 - 1
AAAGCAAAAUGAACACACA-GCACACACACAUCCCA---AAUGGACA---UAGGUAGAAAGGCAAAUACGCCUUGUGACUCUCGGUCAGAUAUUCUGAUUUGUUUGA
.((((((........(((.-....((.....(((..---...)))..---...))...(((((......)))))))).......(((((.....))))))))))).. ( -18.70)
>DroAna_CAF1 48086 100 - 1
AACAUAAAACGGACAUUCA--CAUACACACAUAUGUAUGUAUGCAUG---UAGGUGAAGAGGCAAACACACCUU--GACUCUUGGUCAGAUAUUCUGAUUUGUUUGA
.........((((((((((--(.((((..(((((....)))))..))---)).)))))(((.(((.......))--).)))..((((((.....)))))))))))). ( -24.40)
>consensus
AAAGCAAAAUGAACACACA_______ACACAUCCCA____AUGGACA___UAGGUAGAAAGGCAAAUACGCCUU__GACUCUCGGUCAGAUAUUCUGAUUUGUUUGA
.........((((((.....................................(((...(((((......)))))...)))...((((((.....)))))))))))). (-14.49 = -14.27 +  -0.22)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:55 2006