Locus 6185

Sequence ID 2R_DroMel_CAF1
Location 19,470,086 – 19,470,218
Length 132
Max. P 0.725905
window9904 window9905

overview

Window 4

Location 19,470,086 – 19,470,199
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.17
Mean single sequence MFE -32.38
Consensus MFE -15.32
Energy contribution -17.77
Covariance contribution 2.45
Combinations/Pair 1.13
Mean z-score -1.77
Structure conservation index 0.47
SVM decision value -0.02
SVM RNA-class probability 0.525731
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19470086 113 - 20766785
CUAUUAUGGACUAUGGG---CCAUG-AGGCCAACUUCUUU---GAGUUCGUCUUUUCCCACGCUAAACUGCGAAAUUGAAUGUGAGAAAAUUUGCAUGGGUCAGGCGGAUUCGGAACGUA
....((((.......((---((...-.))))......(((---((((((((((...(((.(((......))).......(((..((....))..))))))..))))))))))))).)))) ( -35.70)
>DroSec_CAF1 4768 113 - 1
CUAUUAUGGACUAUGGG---CCAUG-GGCCCAACUUCUUU---GAGUUCGUCUUUUCGCACGCUAAACUGCGAAACCGAAUGUGAGAAAAUUUGCAUGGGUCAGGCGGAUUCGGAACGUA
....((((.....((((---((...-)))))).....(((---((((((((((.((((((........))))))(((..(((..((....))..))).))).))))))))))))).)))) ( -37.90)
>DroSim_CAF1 6015 113 - 1
CUAUUAUGGGCUAUGGG---CCAUG-AGGCCAACUUCUUU---GAGUUCGUCUUUUCCCACGCUAAACUGCGAAACCGAAUGUGAGAAAAUUUGCAUGGGUCAGGCGGAUUCGGAACGUA
....((((..((...((---((...-.)))).........---((((((((((...(((.(((......))).......(((..((....))..))))))..))))))))))))..)))) ( -36.50)
>DroPer_CAF1 7083 97 - 1
-----------UAUAGUCAACAAUGCUAACCAACUUCUUACUCGCAUGUUACUUGUCCCACACUCAAUGG---ACAUAAAUGUGGGAAAAGUAACACGGGUUC---------CACUUGCA
-----------..((((.......))))..(((......(((((..((((((((.(((((((........---.......))))))).)))))))))))))..---------...))).. ( -23.96)
>DroEre_CAF1 4692 111 - 1
CAAUUAUUGGCA--GAA---CCAUG-AGGCCAACUUCUUU---GAGUUCGUCUUUUCCCACGCUAAACUGCGAAAUCAAAUGUGAGAAAAUUUGCAUGGGUCAGGCGGAUUCGGAACGUA
......(((((.--...---.....-..)))))....(((---((((((((((...(((.(((......))).......(((..((....))..))))))..)))))))))))))..... ( -31.90)
>DroYak_CAF1 5128 110 - 1
UAAUAAUGGGCA--GAA---CCGUG-AGGCCAACUUCUUU---GAGUUUGUCUU-UCCCACGCUAAACUGCGAAACCAAAUGUGAGAAAAUUUGCAUGGGUCAGGCGGAUUGGGAACGUA
.....((((...--...---))))(-(((....))))(((---.(((((((((.-.(((.(((......))).......(((..((....))..))))))..))))))))).)))..... ( -28.30)
>consensus
CUAUUAUGGGCUAUGGG___CCAUG_AGGCCAACUUCUUU___GAGUUCGUCUUUUCCCACGCUAAACUGCGAAACCAAAUGUGAGAAAAUUUGCAUGGGUCAGGCGGAUUCGGAACGUA
...........................................((((((((((...(((.(((......))).......(((((((....))))))))))..))))))))))........ (-15.32 = -17.77 +   2.45)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,470,126 – 19,470,218
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 88.16
Mean single sequence MFE -26.86
Consensus MFE -19.94
Energy contribution -20.34
Covariance contribution 0.40
Combinations/Pair 1.17
Mean z-score -1.84
Structure conservation index 0.74
SVM decision value 0.41
SVM RNA-class probability 0.725905
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19470126 92 - 20766785
AGCAGUUCAAGGUUUUGGGCUAUUAUGGACUAUGGGCCAUGAGGCCAACUUCUUUGAGUUCGUCUUUUCCCACGCUAAACUGCGAAAUUGAA
.((((((...(((..((((..(..(((((((...((((....))))..(......))))))))..)..)))).))).))))))......... ( -27.30)
>DroSec_CAF1 4808 91 - 1
AGCAGUUCAAGGUU-UGGGCUAUUAUGGACUAUGGGCCAUGGGCCCAACUUCUUUGAGUUCGUCUUUUCGCACGCUAAACUGCGAAACCGAA
.....(((((((.(-((((((..(((((.(.....)))))))))))))...)))))))((((...(((((((........))))))).)))) ( -29.60)
>DroSim_CAF1 6055 91 - 1
AGCAGUUCAAGGUU-UGGGCUAUUAUGGGCUAUGGGCCAUGAGGCCAACUUCUUUGAGUUCGUCUUUUCCCACGCUAAACUGCGAAACCGAA
.((((((...(((.-((((...((((((.(....).))))))(((.(((((....))))).)))....)))).))).))))))......... ( -28.90)
>DroEre_CAF1 4732 89 - 1
UGCAGUUCAAGGUU-UGGGCAAUUAUUGGCA--GAACCAUGAGGCCAACUUCUUUGAGUUCGUCUUUUCCCACGCUAAACUGCGAAAUCAAA
.((((((...(((.-((((.((.....(((.--((((((.((((....))))..)).)))))))..)))))).))).))))))......... ( -24.70)
>DroYak_CAF1 5168 88 - 1
UGCAGUUCAAGGUU-UUGGUAAUAAUGGGCA--GAACCGUGAGGCCAACUUCUUUGAGUUUGUCUU-UCCCACGCUAAACUGCGAAACCAAA
.((((((...((((-(((.(.......).))--)))))(((((((.(((((....))))).)))).-...)))....))))))......... ( -23.80)
>consensus
AGCAGUUCAAGGUU_UGGGCUAUUAUGGGCUAUGGGCCAUGAGGCCAACUUCUUUGAGUUCGUCUUUUCCCACGCUAAACUGCGAAACCGAA
.(((((((((((.....((((.((((((........)))))))))).....))))))...(((........)))....)))))......... (-19.94 = -20.34 +   0.40)

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 12:04:56 2006