Locus 2838

Sequence ID 3L_DroMel_CAF1
Location 8,090,948 – 8,091,068
Length 120
Max. P 0.994910
window4435 window4436 window4437

overview

Window 5

Location 8,090,948 – 8,091,042
Length 94
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 93.24
Mean single sequence MFE -31.82
Consensus MFE -29.86
Energy contribution -30.17
Covariance contribution 0.31
Combinations/Pair 1.10
Mean z-score -1.86
Structure conservation index 0.94
SVM decision value 2.52
SVM RNA-class probability 0.994910
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8090948 94 - 23771897
GCGAUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUCUACAGUGGGGCCAAAGCAAUUGGUUAGUGG--GGUGG
.(.((((..((((((((((...((((((...((((...))))..)))))))))))))))).)))).)((((((.....)))))).....--..... ( -32.10)
>DroSec_CAF1 1963 94 - 1
GCGAUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUCUACAGUGGGGCCAAAGCAAUUGGUUAGUGG--GGUGG
.(.((((..((((((((((...((((((...((((...))))..)))))))))))))))).)))).)((((((.....)))))).....--..... ( -32.10)
>DroSim_CAF1 3003 94 - 1
GCGAUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUCUACAGUGGGGCCAAAGCAAUUGGUUAGUGG--GGUGG
.(.((((..((((((((((...((((((...((((...))))..)))))))))))))))).)))).)((((((.....)))))).....--..... ( -32.10)
>DroEre_CAF1 1964 94 - 1
UUGAUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCAUAAUGAGCAUGCCUCUACAGUGGGGCCAAAGCAAAUGGUCAGUGG--GGUGG
.(.((((..((((((((((...((((((...((((...))))..)))))))))))))))).)))).)(((((.......))))).....--..... ( -32.50)
>DroYak_CAF1 2138 94 - 1
GUGAUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUCUACAGUGGGGCCAAAUCCAUUGGUCAGUGG--GGUGG
.(.(((((.((((((((((...((((((...((((...))))..)))))))))))))))).(((((((......))))))).))))).)--..... ( -33.40)
>DroAna_CAF1 2160 95 - 1
GCGA-UGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUGGACAGUGGUGCCGAAGCAAUUGGUUAAUUGCGGCCGG
....-......((((((((...((((((...((((...))))..))))))))))))))((...(..(((((((.....)))))..))..)..)).. ( -28.70)
>consensus
GCGAUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUCUACAGUGGGGCCAAAGCAAUUGGUUAGUGG__GGUGG
.(.((((..((((((((((...((((((...((((...))))..)))))))))))))))).)))).)((((((.....))))))............ (-29.86 = -30.17 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,090,975 – 8,091,068
Length 93
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 80.08
Mean single sequence MFE -19.62
Consensus MFE -12.98
Energy contribution -14.98
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.66
SVM decision value 0.78
SVM RNA-class probability 0.848067
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8090975 93 + 23771897
CCACUGUA---GAGGCAUGCUCAUUACGACUGAGUCAGCAUCUAACGAUUUGCAUGCCCCUCCCAAU-C---GCCUCCCACC-AACCCCCCUGUUGUCAAU
........---(((((..(((((.......)))))..(((((....))..)))..............-.---)))))....(-(((......))))..... ( -18.20)
>DroPse_CAF1 2907 99 + 1
CCACUGUACCAUGGGCAUGCUCAUUACGACUGAGUCAGCAUCUAACGAUUUGCAUGCCCGUCUCCCUUCCAGGCCCCCCUCCUAAUUCUA--UUGGUUAAU
.......((((.((((((((.......(((...)))...(((....)))..))))))))((((.......))))................--.)))).... ( -23.60)
>DroEre_CAF1 1991 91 + 1
CCACUGUA---GAGGCAUGCUCAUUAUGACUGAGUCAGCAUCUAACGAUUUGCAUGCCCCUCCCAAU-C---AACACCCACC-AACCCUC--CUUGUCAGU
..((((.(---(.(((((((......((((...))))..(((....)))..))))))).))......-.---.........(-((.....--.))).)))) ( -17.40)
>DroYak_CAF1 2165 93 + 1
CCACUGUA---GAGGCAUGCUCAUUACGACUGAGUCAGCAUCUAACGAUUUGCAUGCCCCUCCCAAU-C---ACCUCCCACC-AACCCUCCCCUUGUCAAU
.......(---(.(((((((.......(((...)))...(((....)))..))))))).))......-.---..........-.................. ( -15.70)
>DroAna_CAF1 2189 85 + 1
CCACUGUC---CAGGCAUGCUCAUUACGACUGAGUCAGCAUCUAACGAUUUGCAUGCCCCUCCCA-U-C---GCCA--------CCCCUUCUUGGGUUAAU
........---..(((((((.......(((...)))...(((....)))..))))))).......-.-.---...(--------(((......)))).... ( -19.20)
>DroPer_CAF1 2897 99 + 1
CCACUGUACCAUGGGCAUGCUCAUUACGACUGAGUCAGCAUCUAACGAUUUGCAUGCCCGUCUCUCUUCCAGGCCCCCCUCCUAAUUCUA--UUGGUUAAU
.......((((.((((((((.......(((...)))...(((....)))..))))))))((((.......))))................--.)))).... ( -23.60)
>consensus
CCACUGUA___GAGGCAUGCUCAUUACGACUGAGUCAGCAUCUAACGAUUUGCAUGCCCCUCCCAAU_C___GCCACCCACC_AACCCUC__UUGGUCAAU
.............(((((((.......(((...)))...(((....)))..)))))))........................................... (-12.98 = -14.98 +   2.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,090,975 – 8,091,068
Length 93
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 80.08
Mean single sequence MFE -28.35
Consensus MFE -20.07
Energy contribution -19.85
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -1.71
Structure conservation index 0.71
SVM decision value 0.69
SVM RNA-class probability 0.824345
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8090975 93 - 23771897
AUUGACAACAGGGGGGUU-GGUGGGAGGC---G-AUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUC---UACAGUGG
.....((((......)))-)........(---.-((((..((((((((((...((((((...((((...))))..)))))))))))))))---).)))).) ( -29.20)
>DroPse_CAF1 2907 99 - 1
AUUAACCAA--UAGAAUUAGGAGGGGGGCCUGGAAGGGAGACGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCCAUGGUACAGUGG
....((((.--.....(((((.......)))))...(....)((((((((...((((((...((((...))))..)))))))))))))).))))....... ( -29.80)
>DroEre_CAF1 1991 91 - 1
ACUGACAAG--GAGGGUU-GGUGGGUGUU---G-AUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCAUAAUGAGCAUGCCUC---UACAGUGG
((..((...--....)).-.)).......---.-((((..((((((((((...((((((...((((...))))..)))))))))))))))---).)))).. ( -30.30)
>DroYak_CAF1 2165 93 - 1
AUUGACAAGGGGAGGGUU-GGUGGGAGGU---G-AUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUC---UACAGUGG
((..((.........)).-.)).......---.-((((..((((((((((...((((((...((((...))))..)))))))))))))))---).)))).. ( -27.30)
>DroAna_CAF1 2189 85 - 1
AUUAACCCAAGAAGGGG--------UGGC---G-A-UGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUG---GACAGUGG
....((((......)))--------)..(---(-.-((....((((((((...((((((...((((...))))..)))))))))))))).---..)).)). ( -24.80)
>DroPer_CAF1 2897 99 - 1
AUUAACCAA--UAGAAUUAGGAGGGGGGCCUGGAAGAGAGACGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCCAUGGUACAGUGG
....((((.--.....(((((.......))))).........((((((((...((((((...((((...))))..)))))))))))))).))))....... ( -28.70)
>consensus
AUUAACAAA__GAGGGUU_GGUGGGAGGC___G_AUUGGGAGGGGCAUGCAAAUCGUUAGAUGCUGACUCAGUCGUAAUGAGCAUGCCUC___UACAGUGG
..........................................((((((((...((((((...((((...))))..))))))))))))))............ (-20.07 = -19.85 +  -0.22)

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 10:43:03 2006