Locus 4588

Sequence ID 2R_DroMel_CAF1
Location 14,972,154 – 14,972,474
Length 320
Max. P 0.926257
window7366 window7367 window7368 window7369

overview

Window 6

Location 14,972,154 – 14,972,274
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -24.10
Consensus MFE -21.79
Energy contribution -21.60
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.90
SVM decision value 0.69
SVM RNA-class probability 0.825107
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14972154 120 - 20766785
UUAUAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUAUACCAUCGAAAUGAAAAUUCCCUUUCGGUGAAAACAACUGUUUUUUAAAAAUUUAAGCACGCACACUAGUUGCAAAUGAA
............(((....)))((.((((..............((((((((.(.......).))))))))(((((....)))))...........)))).)).................. ( -22.10)
>DroSim_CAF1 2887 120 - 1
UUAAAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUAUACCAUCGAAAUGAAAAUUCCCUUUCGGUGAAAACAACUGUUUUUAAAAAAUUUAAGCACGCACACUAGUGGCAAAUGAA
(((((........((((((((((((....))))..........(((....))).......))))))))(((((((....))))))).....)))))((.(((......)))))....... ( -24.40)
>DroEre_CAF1 2489 120 - 1
UUAUAAAUAAUUUCCGAAAGGAGCUUGCUGUCUAAAAAUAUACCAUCGAAAUGAAAAUUCCCUUUCGGUGAAAACAACUGUUUUUUAAAAAUUUAAGCACGCACACUAGUGGCAGCAGAA
...........((((....)))).((((((((...........((((((((.(.......).))))))))(((((....)))))..........................)))))))).. ( -26.00)
>DroYak_CAF1 2186 120 - 1
UUAUAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUAUACCAUUGAAAUGAAAAUUCCCUUUCGGUGAAAACAACUGUUUUUUAAAAAUUUAAGCACGCACACUAGUGGCAGCCGAA
.......(((.((((....)))).))).(((((..........((((((((.(.......).))))))))(((((....)))))............((.(((......)))))))))).. ( -23.90)
>consensus
UUAUAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUAUACCAUCGAAAUGAAAAUUCCCUUUCGGUGAAAACAACUGUUUUUUAAAAAUUUAAGCACGCACACUAGUGGCAAAUGAA
............(((....)))((.((((..............((((((((.(.......).))))))))(((((....)))))...........)))).)).................. (-21.79 = -21.60 +  -0.19)

alignment

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secondary structure

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Window 7

Location 14,972,234 – 14,972,354
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.50
Mean single sequence MFE -33.92
Consensus MFE -31.12
Energy contribution -32.38
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.41
Structure conservation index 0.92
SVM decision value 1.08
SVM RNA-class probability 0.911937
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14972234 120 - 20766785
AGUGGUCUUUGCACUUACUUAUAUCUGAUUUUGUAAAAGUUUAUCGCGUAAAUCGUUGCGUGGAAACAUUUCGAGGGGGGUUAUAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUA
..(((((...(((.(((.(((((.((..(((((.(((.((((.((((((((....)))))))))))).))))))))..)).))))).))).((((....))))..))).)))))...... ( -30.50)
>DroSim_CAF1 2967 120 - 1
AGUGGGCUUUGCACAUACUUAUAUCUGCUUUUGUAAAAGUUUAUCGCGUAAAUCGGUGCGUGGAAACAUUUCGAGGGGGGUUAAAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUA
(((.(((...((.........((.((.((((((.(((.((((.(((((((......))))))))))).))))))))).)).)).........(((....)))))..))).)))....... ( -33.20)
>DroEre_CAF1 2569 120 - 1
AGUGGGCUUUGCACAUACUUAUAUCUGCUUUUGUAAAAGUUUAUCGCGUAAAUCGUUGCGUGGAAACAUUUCGAGGGGGGUUAUAAAUAAUUUCCGAAAGGAGCUUGCUGUCUAAAAAUA
((..(((...........(((((.((.((((((.(((.((((.((((((((....)))))))))))).))))))))).)).)))))......(((....))))))..))........... ( -35.00)
>DroYak_CAF1 2266 120 - 1
AGUGGGCUUUGCACAUACUUAUAUCUGCUUUUGUAAAAGUUUAUCGCGUAAAUCGUUGCGUGGAAACAUUUCGAGGGGGGUUAUAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUA
(((.(((...((......(((((.((.((((((.(((.((((.((((((((....)))))))))))).))))))))).)).)))))......(((....)))))..))).)))....... ( -37.00)
>consensus
AGUGGGCUUUGCACAUACUUAUAUCUGCUUUUGUAAAAGUUUAUCGCGUAAAUCGUUGCGUGGAAACAUUUCGAGGGGGGUUAUAAAUAAUUUCCGAAAGGAGCUUGCUGGCUAAAAAUA
(((.(((...((......(((((.((.((((((.(((.((((.((((((((....)))))))))))).))))))))).)).)))))......(((....)))))..))).)))....... (-31.12 = -32.38 +   1.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,972,314 – 14,972,434
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.08
Mean single sequence MFE -33.60
Consensus MFE -31.01
Energy contribution -32.08
Covariance contribution 1.06
Combinations/Pair 1.02
Mean z-score -2.34
Structure conservation index 0.92
SVM decision value 1.17
SVM RNA-class probability 0.926257
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14972314 120 + 20766785
ACUUUUACAAAAUCAGAUAUAAGUAAGUGCAAAGACCACUUGAUUUUCGUAUAGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUU
............................(((....(((((.(((((.(((((((((.((((((.........))))))(((((.....)))))))))))))).))))))))))...))). ( -27.50)
>DroSim_CAF1 3047 120 + 1
ACUUUUACAAAAGCAGAUAUAAGUAUGUGCAAAGCCCACUUUAUUUUCGUAUGGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUU
.....(((....(((.(((....))).)))...(((((((....(((((((.(((((((((((.........))))))))))))))))))..((((.....))))...)))))))))).. ( -34.20)
>DroEre_CAF1 2649 120 + 1
ACUUUUACAAAAGCAGAUAUAAGUAUGUGCAAAGCCCACUUGAUUUUCGUAUGGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUU
.....(((....(((.(((....))).)))...(((((((.(((((.(((((((((.((((((.........))))))(((((.....)))))))))))))).))))))))))))))).. ( -37.70)
>DroYak_CAF1 2346 120 + 1
ACUUUUACAAAAGCAGAUAUAAGUAUGUGCAAAGCCCACUUGAUUUUCGUAUGCUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUA
.....((((...(((.(((....))).)))...(((((((.....(((((..(((.....)))..)))))..((((((((((.((........))..)))))))))).))))))).)))) ( -35.00)
>consensus
ACUUUUACAAAAGCAGAUAUAAGUAUGUGCAAAGCCCACUUGAUUUUCGUAUGGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUU
.....(((....(((.(((....))).)))...(((((((.(((((.(((((((((.((((((.........))))))(((((.....)))))))))))))).))))))))))))))).. (-31.01 = -32.08 +   1.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,972,354 – 14,972,474
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -31.87
Consensus MFE -31.34
Energy contribution -31.21
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -1.36
Structure conservation index 0.98
SVM decision value -0.01
SVM RNA-class probability 0.528141
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14972354 120 + 20766785
UGAUUUUCGUAUAGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUUUCAACGUUUUAGCCCACAGUUUUCACUCAUUUUCCUGCGG
(((((((((((.(((((((((((.........)))))))))))))))))).)))).....((((((...((((((................))))))(((....)))......)))))). ( -33.39)
>DroSim_CAF1 3087 120 + 1
UUAUUUUCGUAUGGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUUUCAACGUUUUAGCCCACAGUUUUCACUCAUUUUCCUGCGG
....(((((((.(((((((((((.........))))))))))))))))))..........((((((...((((((................))))))(((....)))......)))))). ( -32.79)
>DroEre_CAF1 2689 120 + 1
UGAUUUUCGUAUGGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUUUUAUCGUCUCAGCCCACAGUUUUCACUCAUUUUCCUGUGG
.(((((.(((((((((.((((((.........))))))(((((.....)))))))))))))).))))).((((((.((...........))))))))......(((..........))). ( -29.90)
>DroYak_CAF1 2386 120 + 1
UGAUUUUCGUAUGCUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUAUCAGCGUUUCAGCCCACAGUUUUCACUCAUUUUCCUGCGG
(((((((((((...(((((((((.........)))))))))..))))))).)))).....((((((...((((((.((...........))))))))(((....)))......)))))). ( -31.40)
>consensus
UGAUUUUCGUAUGGUAUGUAAGUCCACGAAUUGCUUACGUAUUUAUGAAAUAUUACUGUGCGUAGGUCGGUGGGCGUGUUUCAACGUUUCAGCCCACAGUUUUCACUCAUUUUCCUGCGG
....(((((((.(((((((((((.........))))))))))))))))))..........((((((...((((((................))))))(((....)))......)))))). (-31.34 = -31.21 +  -0.13)

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 11:24:02 2006