Locus 488

Sequence ID 2R_DroMel_CAF1
Location 2,702,422 – 2,702,582
Length 160
Max. P 0.996540
window925 window926 window927

overview

Window 5

Location 2,702,422 – 2,702,516
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 78.66
Mean single sequence MFE -31.28
Consensus MFE -24.33
Energy contribution -24.25
Covariance contribution -0.08
Combinations/Pair 1.16
Mean z-score -2.72
Structure conservation index 0.78
SVM decision value 2.71
SVM RNA-class probability 0.996540
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702422 94 + 20766785
AUCGCAGUUAAGAGCAAUGCAAUACAGCAAUGGCAACUUCUGCAUUUGCCUAGGCUGAGGCGUGUGCAAACGCGCAUACGCCCCGUUGGCCUAG
...((((......((..(((......)))...)).....))))......((((((..((((((((((......)))))))))...)..)))))) ( -37.90)
>DroSec_CAF1 17329 75 + 1
AUCGCAGUUAGCA-------------------ACAACUUCUGCAUUUGCCUCGGCUGAGGCGUGUGCAAACGCGCAUACGCCCCGUUGGCCUAG
...((((..((..-------------------....)).))))....(((.(((....(((((((((......))))))))))))..))).... ( -29.10)
>DroSim_CAF1 14734 75 + 1
AUCGCAGUUAGCA-------------------GCAACUUCUGCAUUUGUCUCGGCUGAGGCGUGUGCAAACGCGCAUACGCCCCGUUGGCCUAG
...((((...(((-------------------(......))))..))))...(((..((((((((((......)))))))))...)..)))... ( -28.80)
>DroEre_CAF1 14767 80 + 1
AUCGCAGUCAACAGCACUGC--------AAUGGCAACUUCUGUAUUUU------CCGAGGCGUGUGCGAACGCGCAUACGCCCCAUUGGCCUAG
...((((((....).)))))--------...(((.((....)).....------..(.((((((((((....)))))))))).)....)))... ( -29.40)
>DroYak_CAF1 14439 86 + 1
AUUGCAGUUAACAGCAAUUC--------AAUGCCAACUUCUGCAGUUGCUUCGGCUGAGGUGUGUGCAAACGCGCAUACGCCCCGUUGGCCUAG
(((((........)))))..--------...((((((..........((....)).(.(((((((((......))))))))).))))))).... ( -31.20)
>consensus
AUCGCAGUUAACAGCA_U_C________AAUGGCAACUUCUGCAUUUGCCUCGGCUGAGGCGUGUGCAAACGCGCAUACGCCCCGUUGGCCUAG
...((((................................)))).........(((((((((((((((......)))))))))...))))))... (-24.33 = -24.25 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,702,422 – 2,702,516
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 78.66
Mean single sequence MFE -29.38
Consensus MFE -18.79
Energy contribution -19.27
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -1.86
Structure conservation index 0.64
SVM decision value 0.66
SVM RNA-class probability 0.814814
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702422 94 - 20766785
CUAGGCCAACGGGGCGUAUGCGCGUUUGCACACGCCUCAGCCUAGGCAAAUGCAGAAGUUGCCAUUGCUGUAUUGCAUUGCUCUUAACUGCGAU
((((((....(((((((.((((....)))).))))))).))))))((((.(((((.(((....))).)))))))))(((((........))))) ( -36.80)
>DroSec_CAF1 17329 75 - 1
CUAGGCCAACGGGGCGUAUGCGCGUUUGCACACGCCUCAGCCGAGGCAAAUGCAGAAGUUGU-------------------UGCUAACUGCGAU
((.(((....(((((((.((((....)))).))))))).))).)).....(((((.(((...-------------------.)))..))))).. ( -26.60)
>DroSim_CAF1 14734 75 - 1
CUAGGCCAACGGGGCGUAUGCGCGUUUGCACACGCCUCAGCCGAGACAAAUGCAGAAGUUGC-------------------UGCUAACUGCGAU
((.(((....(((((((.((((....)))).))))))).))).)).....(((((.(((...-------------------.)))..))))).. ( -26.40)
>DroEre_CAF1 14767 80 - 1
CUAGGCCAAUGGGGCGUAUGCGCGUUCGCACACGCCUCGG------AAAAUACAGAAGUUGCCAUU--------GCAGUGCUGUUGACUGCGAU
...(((.((((((((((.((((....)))).)))))))(.------......)....))))))(((--------(((((.(....))))))))) ( -29.70)
>DroYak_CAF1 14439 86 - 1
CUAGGCCAACGGGGCGUAUGCGCGUUUGCACACACCUCAGCCGAAGCAACUGCAGAAGUUGGCAUU--------GAAUUGCUGUUAACUGCAAU
....((((((((((.((.((((....)))).)).)))).......((....))....))))))...--------..(((((........))))) ( -27.40)
>consensus
CUAGGCCAACGGGGCGUAUGCGCGUUUGCACACGCCUCAGCCGAGGCAAAUGCAGAAGUUGCCAUU________G_A_UGCUGUUAACUGCGAU
...(((....(((((((.((((....)))).))))))).)))........(((((................................))))).. (-18.79 = -19.27 +   0.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,702,491 – 2,702,582
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 96.48
Mean single sequence MFE -28.22
Consensus MFE -26.68
Energy contribution -26.72
Covariance contribution 0.04
Combinations/Pair 1.10
Mean z-score -1.33
Structure conservation index 0.95
SVM decision value 0.90
SVM RNA-class probability 0.878471
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702491 91 + 20766785
ACGCGCAUACGCCCCGUUGGCCUAGUGCGAUUUCAAUCAGCCGCUGCCAAUGGGUCAGGCAUUAUCAGAUAUUAACGCCGGCAAUUUGGCA
..((.((...(((((((((((..((((((((....))).).))))))))))))....(((.(((........))).))))))....)))). ( -29.20)
>DroSec_CAF1 17379 91 + 1
ACGCGCAUACGCCCCGUUGGCCUAGUGCGAUUUCAAUCAGCCACUUUCAAUGGGUCAGGCAUUAUCAGAUAUUAACGCCGGCAAUUUGGCA
.(((((.((.(((.....))).)))))))..........((((((......))(((.(((.(((........))).))))))....)))). ( -24.90)
>DroSim_CAF1 14784 91 + 1
ACGCGCAUACGCCCCGUUGGCCUAGUGCGAUUUCAAUCAGCCACUUCCAAUGGGUCAGGCAUUAUCAGAUAUUAACGCCGGCAAUUUGGCA
..((.((...((((((((((...((((((((....))).).)))).)))))))....(((.(((........))).))))))....)))). ( -26.80)
>DroEre_CAF1 14822 91 + 1
ACGCGCAUACGCCCCAUUGGCCUAGUGCGAUUUCAAUCAGCCGCUGCCAAUGGGUCAGGCAUUAUCAGAUAUUAACGCCGGCAAUUUGGCU
..((.((...(((((((((((..((((((((....))).).))))))))))))....(((.(((........))).))))))....)))). ( -29.10)
>DroYak_CAF1 14500 91 + 1
ACGCGCAUACGCCCCGUUGGCCUAGUGCGAUUGCAAGCAGCCGCUGCCAAUGGGUCAGGCAUUAUCAGAUAUUAACGCCGGCAAUUUGGCA
..((.((...(((((((((((.....(((..((....))..))).))))))))....(((.(((........))).))))))....)))). ( -31.10)
>consensus
ACGCGCAUACGCCCCGUUGGCCUAGUGCGAUUUCAAUCAGCCGCUGCCAAUGGGUCAGGCAUUAUCAGAUAUUAACGCCGGCAAUUUGGCA
..((.((...(((((((((((..((((((((....))).).))))))))))))....(((.(((........))).))))))....)))). (-26.68 = -26.72 +   0.04)

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 09:39:55 2006