Locus 7293

Sequence ID 2L_DroMel_CAF1
Location 20,443,856 – 20,443,987
Length 131
Max. P 0.937616
window11674 window11675 window11676

overview

Window 4

Location 20,443,856 – 20,443,960
Length 104
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -14.43
Consensus MFE -10.80
Energy contribution -10.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.06
Structure conservation index 0.75
SVM decision value 0.31
SVM RNA-class probability 0.681166
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20443856 104 + 22407834
CAC--GCAGCAACAUGAAAUCAAAUAUAUACUAAAUAUAUAAACAUUUAUGUAUAUAUUUAGCAGACGAGUAAAUAAACCACACCCGCGCACAAAUCGCUUACAUA
...--..(((...........(((((((((((((((........))))).)))))))))).((.(.((.((...........)).))))).......)))...... ( -13.20)
>DroSim_CAF1 6987 104 + 1
CAC--ACAGCAACAUGAAAUCAAAUAUAUACUAAAUAUAUAAACAUUUAUGUAUAUAUUUAGCAGACGAGUAAAUAAACCACACCCGCGCACAAAUCGCUCACAUA
...--..(((...........(((((((((((((((........))))).)))))))))).((.(.((.((...........)).))))).......)))...... ( -13.20)
>DroEre_CAF1 5893 104 + 1
CACGUGCAGCAACAUAAAAUCAAAUAUAUACUAAAUAUAUAAACAUUUAUGUAUAUAUUUAGCAAACGAGUAAAUAAACCACACCCG--CACAAAUCGCUCACAUA
...(((.(((...........(((((((((((((((........))))).)))))))))).((.......................)--).......))))))... ( -16.10)
>DroYak_CAF1 6932 104 + 1
CACGUGCAGCAACAUAAAAUCAAAUAUAUACUAAAUAUAUAAACAUUUAUGUAUAUAUUUAGCAAAUGAGUAAAUAAACCACACCCG--CACAAAUCGCUCUCAAA
...((((..............(((((((((((((((........))))).))))))))))......((.((......)))).....)--))).............. ( -15.20)
>consensus
CAC__GCAGCAACAUAAAAUCAAAUAUAUACUAAAUAUAUAAACAUUUAUGUAUAUAUUUAGCAAACGAGUAAAUAAACCACACCCG__CACAAAUCGCUCACAUA
.......(((...........(((((((((((((((........))))).)))))))))).((......))..........................)))...... (-10.80 = -10.80 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,443,856 – 20,443,960
Length 104
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -28.42
Consensus MFE -23.58
Energy contribution -24.32
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -3.76
Structure conservation index 0.83
SVM decision value 1.26
SVM RNA-class probability 0.937616
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20443856 104 - 22407834
UAUGUAAGCGAUUUGUGCGCGGGUGUGGUUUAUUUACUCGUCUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUAUAUAUUUGAUUUCAUGUUGCUGC--GUG
((((((.(((((.((...((((..(.(((......))))..))))(((((((((((.(((((((....))))))))))))))))))....)).))))))))--))) ( -30.00)
>DroSim_CAF1 6987 104 - 1
UAUGUGAGCGAUUUGUGCGCGGGUGUGGUUUAUUUACUCGUCUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUAUAUAUUUGAUUUCAUGUUGCUGU--GUG
......((((((.((...((((..(.(((......))))..))))(((((((((((.(((((((....))))))))))))))))))....)).))))))..--... ( -27.60)
>DroEre_CAF1 5893 104 - 1
UAUGUGAGCGAUUUGUG--CGGGUGUGGUUUAUUUACUCGUUUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUAUAUAUUUGAUUUUAUGUUGCUGCACGUG
((((((((((((..(((--((((((.........)))))))..))(((((((((((.(((((((....)))))))))))))))))).......)))))).)))))) ( -30.00)
>DroYak_CAF1 6932 104 - 1
UUUGAGAGCGAUUUGUG--CGGGUGUGGUUUAUUUACUCAUUUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUAUAUAUUUGAUUUUAUGUUGCUGCACGUG
..((..((((((....(--((((((.(((......))))))))))(((((((((((.(((((((....)))))))))))))))))).......)))))).)).... ( -26.10)
>consensus
UAUGUGAGCGAUUUGUG__CGGGUGUGGUUUAUUUACUCGUCUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUAUAUAUUUGAUUUCAUGUUGCUGC__GUG
......((((((..(((.(((((((.........))))))).)))(((((((((((.(((((((....)))))))))))))))))).......))))))....... (-23.58 = -24.32 +   0.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,443,882 – 20,443,987
Length 105
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 91.79
Mean single sequence MFE -24.61
Consensus MFE -18.16
Energy contribution -17.98
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.13
Structure conservation index 0.74
SVM decision value 0.28
SVM RNA-class probability 0.664314
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20443882 105 - 22407834
CAAAGCAU---AGUUAAUUCGU-------AAUUCGUUUAUGUAAGCGAUUUGUGCGCGGGUGUGGUUUAUUUACUCGUCUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUA
....((((---((.........-------...((((((....)))))).))))))(((((((.........))))))).(((((((((((((.((....)).))))))))))))) ( -24.72)
>DroSim_CAF1 7013 105 - 1
CAAAGCAU---AGUUAAUUCGU-------AAUUCGUUUAUGUGAGCGAUUUGUGCGCGGGUGUGGUUUAUUUACUCGUCUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUA
....((((---((.........-------...((((((....)))))).))))))(((((((.........))))))).(((((((((((((.((....)).))))))))))))) ( -25.12)
>DroEre_CAF1 5921 103 - 1
CAAAGCAU---AGUUAAUUCGU-------AAUUCGUUUAUGUGAGCGAUUUGUG--CGGGUGUGGUUUAUUUACUCGUUUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUA
..((((..---.....((((((-------(..((((((....))))))....))--)))))((((.....))))..))))((((((((((((.((....)).)))))))))))). ( -23.50)
>DroYak_CAF1 6960 113 - 1
CAAAGCAUAAUAGUUAAUUCGUAAUUGGUAAUUCGUUUUUGAGAGCGAUUUGUG--CGGGUGUGGUUUAUUUACUCAUUUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUA
....((((((((((((.....)))))).....((((((....)))))).)))))--)(((((.........)))))...(((((((((((((.((....)).))))))))))))) ( -25.10)
>consensus
CAAAGCAU___AGUUAAUUCGU_______AAUUCGUUUAUGUGAGCGAUUUGUG__CGGGUGUGGUUUAUUUACUCGUCUGCUAAAUAUAUACAUAAAUGUUUAUAUAUUUAGUA
................................((((((....)))))).........(((((.........)))))...(((((((((((((.((....)).))))))))))))) (-18.16 = -17.98 +  -0.19)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:35 2006