Locus 5652

Sequence ID X_DroMel_CAF1
Location 14,604,815 – 14,604,962
Length 147
Max. P 0.966145
window9180 window9181 window9182

overview

Window 0

Location 14,604,815 – 14,604,922
Length 107
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 82.00
Mean single sequence MFE -16.09
Consensus MFE -9.60
Energy contribution -9.82
Covariance contribution 0.23
Combinations/Pair 1.11
Mean z-score -2.78
Structure conservation index 0.60
SVM decision value 0.92
SVM RNA-class probability 0.880992
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14604815 107 + 22224390
AUAUAUAACCUUUAUAUAUAAUCCUUUAAAGAAAUAUUCUCAGUGCUCUUAUUUUCCUCACUGCACAUAUGUACAUACAUACAUAUGUAUGUACGUUGGCCCAUAUA
(((((((.....)))))))...((..................((((................))))..((((((((((((....)))))))))))).))........ ( -20.19)
>DroSec_CAF1 79310 86 + 1
-------------AUAUAUAAUCCUUUAAAGAAAUAUUCUCAGUGCUCUUAUUUUCCUCACCGCACAUAUGUACACGCAU--------AUGUACUUUGGCCCAUAUA
-------------............((((((...........((((................))))((((((....))))--------))...))))))........ (  -9.89)
>DroSim_CAF1 79368 86 + 1
-------------AUAUAUAAUCCUUUAAAGAAAUAUUCUCAGUGCUCUUAUUUUCCUCACCGCACAUAUGUACACGCAU--------AUGUGCGUUGGUCCAUAUA
-------------.(((((...((....((((.((.......))..))))...........(((((((((((....))))--------)))))))..))...))))) ( -18.20)
>consensus
_____________AUAUAUAAUCCUUUAAAGAAAUAUUCUCAGUGCUCUUAUUUUCCUCACCGCACAUAUGUACACGCAU________AUGUACGUUGGCCCAUAUA
..........................................((((................))))(((((..(((((((((....)))))))...))...))))). ( -9.60 =  -9.82 +   0.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,604,815 – 14,604,922
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 82.00
Mean single sequence MFE -23.09
Consensus MFE -14.83
Energy contribution -14.72
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.95
Structure conservation index 0.64
SVM decision value 1.59
SVM RNA-class probability 0.966145
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14604815 107 - 22224390
UAUAUGGGCCAACGUACAUACAUAUGUAUGUAUGUACAUAUGUGCAGUGAGGAAAAUAAGAGCACUGAGAAUAUUUCUUUAAAGGAUUAUAUAUAAAGGUUAUAUAU
(((((((.((...((((((((((....))))))))))((((((((((((.............))))).......((((....)))).)))))))...))))))))). ( -25.42)
>DroSec_CAF1 79310 86 - 1
UAUAUGGGCCAAAGUACAU--------AUGCGUGUACAUAUGUGCGGUGAGGAAAAUAAGAGCACUGAGAAUAUUUCUUUAAAGGAUUAUAUAU-------------
(((((((.((...((((((--------(((......)))))))))..((((((((..................))))))))..)).))))))).------------- ( -19.77)
>DroSim_CAF1 79368 86 - 1
UAUAUGGACCAACGCACAU--------AUGCGUGUACAUAUGUGCGGUGAGGAAAAUAAGAGCACUGAGAAUAUUUCUUUAAAGGAUUAUAUAU-------------
(((((((.((..(((((((--------(((......)))))))))).((((((((..................))))))))..)).))))))).------------- ( -24.07)
>consensus
UAUAUGGGCCAACGUACAU________AUGCGUGUACAUAUGUGCGGUGAGGAAAAUAAGAGCACUGAGAAUAUUUCUUUAAAGGAUUAUAUAU_____________
(((((((.((...((((((............))))))((((...(((((.............)))))...)))).........)).))))))).............. (-14.83 = -14.72 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,604,855 – 14,604,962
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.45
Mean single sequence MFE -26.04
Consensus MFE -10.58
Energy contribution -10.06
Covariance contribution -0.52
Combinations/Pair 1.20
Mean z-score -2.07
Structure conservation index 0.41
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14604855 107 - 22224390
GUCCUCCGGCUUUAUUAUUUCAUCAUUAUAACAUUUCCUC----UAUAUGGGCCAACGUACAUACAUAUGUAUGUAUGUAC------AUAUGUGCAGUG---AGGAAAAUAAGAGCACUG
........(((((.((((.........))))..(((((((----....((.((....((((((((((....))))))))))------....)).))..)---))))))...))))).... ( -27.50)
>DroSec_CAF1 79337 99 - 1
GUCCUCCGGCUUUAUUAUUUCAUCAUUAUAACAUUUCCUC----UAUAUGGGCCAAAGUACAU--------AUGCGUGUAC------AUAUGUGCGGUG---AGGAAAAUAAGAGCACUG
.(((((((((((...(((......................----.))).)))))...((((((--------(((......)------)))))))).).)---)))).............. ( -22.70)
>DroSim_CAF1 79395 99 - 1
GUCCUCCGGCUUUAUUAUUUCAUCAUUAUAACAUUUCCUC----UAUAUGGACCAACGCACAU--------AUGCGUGUAC------AUAUGUGCGGUG---AGGAAAAUAAGAGCACUG
........(((((....((((.((((.........(((..----.....)))....(((((((--------(((......)------))))))))))))---).))))...))))).... ( -26.70)
>DroEre_CAF1 74256 86 - 1
GUCCUCUGGCUUUAUUAUUUCAUCAUUAUAACAUUUCCC-----UAUUUGGGGCA-------------------CAUGUAC------AUAUGUGCGGUG----GGGAAAUAAGAGCGUUG
........((((((((.(..((((............(((-----.....)))(((-------------------((((...------.)))))))))))----..).))).))))).... ( -25.50)
>DroYak_CAF1 75555 112 - 1
GUCCUCGGGCUUUAUUAUUUCAUCAUUAUAACAUUUCCUUUAUAUAUAUGGGGCAACUUACAU--------AUGCGUGUAUAUAUUGAUAUGUGCCGUGCGAAGGAAAAUAAGAGCACCG
.....((((((((.((((.........))))..((((((((..((((.((((....)))).))--------))(((.(((((((....))))))))))..))))))))...))))).))) ( -27.80)
>consensus
GUCCUCCGGCUUUAUUAUUUCAUCAUUAUAACAUUUCCUC____UAUAUGGGCCAACGUACAU________AUGCGUGUAC______AUAUGUGCGGUG___AGGAAAAUAAGAGCACUG
........((((((((.((((..............(((...........))).....................(((..((........))..)))........))))))).))))).... (-10.58 = -10.06 +  -0.52)

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 11:53:15 2006