Locus 923

Sequence ID 2R_DroMel_CAF1
Location 4,064,938 – 4,065,116
Length 178
Max. P 0.963420
window1628 window1629 window1630

overview

Window 8

Location 4,064,938 – 4,065,036
Length 98
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 85.24
Mean single sequence MFE -22.17
Consensus MFE -17.01
Energy contribution -18.07
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -1.42
Structure conservation index 0.77
SVM decision value -0.02
SVM RNA-class probability 0.522986
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4064938 98 + 20766785
GCUAAUGGCGGCUGACUUUAUUUGGCUUUAAAGCAGAAAGCGCUCCACAUGAAAGGAAAUAG-----AAAGAAAAGAAUGGACGCGGAAAGCAAACAGCCACC
......((.(((((..(((((((..((((...((.....))..(((........))).....-----))))....))))))).((.....))...))))).)) ( -21.40)
>DroSec_CAF1 47540 98 + 1
GCUAAUGGCGGCUGACUUUAUUUGGCUUUAAAGCAGAACGCGCUCCAAAUACUAAGAAAUAG-----AAUGAAAAGAAUGGACGCGGAAAGCAAACAGCCAGC
((.....))(((((..........(((....)))....((((.((((....(((.....)))-----..(....)...)))))))).........)))))... ( -22.90)
>DroSim_CAF1 54105 98 + 1
GCUAAUGGCGGCUGACUUUAUUUGGCUUUAAAGCAGAACGCGCACCAAAUAAAAGGAAAUAG-----AAUGAAAAGAAUGGACGCGGAAAGCAAACAGCCAGC
((.....))(((((..(((((((((.......((.....))...))))))))).........-----................((.....))...)))))... ( -20.90)
>DroEre_CAF1 48832 99 + 1
GCUAAUGGCGGCUGACUUUAUUUGGCUUUAAAGCCGCAACCGCUCAAAAUAAAAAGAACAAGAGAAA----AAGGAAAUAGACGCGGAAAGCACACAGCCACC
......((.(((((.........((((....))))((..((((((......................----.........)).))))...))...))))).)) ( -23.48)
>consensus
GCUAAUGGCGGCUGACUUUAUUUGGCUUUAAAGCAGAAAGCGCUCCAAAUAAAAAGAAAUAG_____AAUGAAAAGAAUGGACGCGGAAAGCAAACAGCCACC
((.....))(((((..(((((((((......(((.......))))))))))))..............................((.....))...)))))... (-17.01 = -18.07 +   1.06) 

alignment

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secondary structure

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dotplot

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Window 9

Location 4,064,938 – 4,065,036
Length 98
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 85.24
Mean single sequence MFE -25.15
Consensus MFE -18.50
Energy contribution -19.51
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.74
SVM decision value 1.09
SVM RNA-class probability 0.913812
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4064938 98 - 20766785
GGUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCUUU-----CUAUUUCCUUUCAUGUGGAGCGCUUUCUGCUUUAAAGCCAAAUAAAGUCAGCCGCCAUUAGC
((((((((...((.((((((((..............-----............)))))))).)).....((((((........))))))))))))))...... ( -27.17)
>DroSec_CAF1 47540 98 - 1
GCUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCAUU-----CUAUUUCUUAGUAUUUGGAGCGCGUUCUGCUUUAAAGCCAAAUAAAGUCAGCCGCCAUUAGC
((((((((((((.....((((((((...........-----(((.....)))....)))).))))....(((....))))))))..))))))).......... ( -22.06)
>DroSim_CAF1 54105 98 - 1
GCUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCAUU-----CUAUUUCCUUUUAUUUGGUGCGCGUUCUGCUUUAAAGCCAAAUAAAGUCAGCCGCCAUUAGC
((((((((..(((.....)))..))...........-----.........((((((((((..((.....))......)))))))))))))))).......... ( -21.70)
>DroEre_CAF1 48832 99 - 1
GGUGGCUGUGUGCUUUCCGCGUCUAUUUCCUU----UUUCUCUUGUUCUUUUUAUUUUGAGCGGUUGCGGCUUUAAAGCCAAAUAAAGUCAGCCGCCAUUAGC
((((((((...((...((((.((.........----......................))))))..))((((....)))).........))))))))...... ( -29.68)
>consensus
GCUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCAUU_____CUAUUUCCUUUUAUUUGGAGCGCGUUCUGCUUUAAAGCCAAAUAAAGUCAGCCGCCAUUAGC
((((((((...(((((..(((((((...............................))).)))).....(((....))).....)))))))))))))...... (-18.50 = -19.51 +   1.00) 

alignment

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secondary structure

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dotplot

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Window 0

Location 4,065,000 – 4,065,116
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.97
Mean single sequence MFE -38.54
Consensus MFE -34.60
Energy contribution -35.04
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -1.71
Structure conservation index 0.90
SVM decision value 1.55
SVM RNA-class probability 0.963420
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4065000 116 - 20766785
UGGCCGUAAUGAAGACUAUCAGAUGGUCAUAAGGAUCGGGGGAGGCCAUUGUGGCUUUUGUUCAGCCUACAAUGGGAGUUGGUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCUUU----
(((((((..(((......))).)))))))...(((.((.(((((((((((((((((.......)))).))))))..(((.....)))....))))))).)))))............---- ( -38.50)
>DroSec_CAF1 47602 116 - 1
UGGCCGUAAUGAAGACUAUCAGAUGGUCAUAAGGAUCGGGGGAGGCCAUUGUGGCUUUUGUUCAGCCUUCAAUGGGUGUUGCUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCAUU----
(((((((..(((......))).)))))))...(((.((.(((((((....(..(((...((...((((.....))))...)).)))..)..))))))).)))))............---- ( -38.40)
>DroSim_CAF1 54167 116 - 1
UGGCCGUAAUGAAGACUAUCAGAUGGUCAUAAGGAUCGGGGGAGGCCAUUGUGGCUUUUGUUCAGCCUUCAAUGGGUGUUGCUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCAUU----
(((((((..(((......))).)))))))...(((.((.(((((((....(..(((...((...((((.....))))...)).)))..)..))))))).)))))............---- ( -38.40)
>DroEre_CAF1 48899 112 - 1
UGGCCGUAAUGAAGACUAUCAGAUGGUCAUAAGGAUCGGGGGAGGCCAUUGUGGCUGUUGUUCUGCCUUCAAUGAGAGUUGGUGGCUGUGUGCUUUCCGCGUCUAUUUCCUU--------
(((((((..(((......))).))))))).(((((.((.((((((((((.(((((.........))).(((((....)))))..)).))).))))))).))......)))))-------- ( -37.00)
>DroYak_CAF1 51722 117 - 1
UGGCCGUAAUGAAGACUAUCAGAUGGCCAUAAGGAUCGGGGGAGGCCAUUGUGGCCUUUGUUGUGCCUUCAAUGGGAGUUG---GCUGCGUGCUUUCCGCGUCUAUUCUCUUCUUUUUAU
(((((((..(((......))).))))))).((((..(((.(((((((.....))))))).)))..))))....((((((.(---((.(((.......)))))).)))))).......... ( -40.40)
>consensus
UGGCCGUAAUGAAGACUAUCAGAUGGUCAUAAGGAUCGGGGGAGGCCAUUGUGGCUUUUGUUCAGCCUUCAAUGGGAGUUGCUGGCUGUUUGCUUUCCGCGUCCAUUCUUUUCAUU____
(((((((..(((......))).)))))))...(((((((((((((((.....)))))))((.(((((..((((....))))..)))))...))..)))).))))................ (-34.60 = -35.04 +   0.44) 

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 09:51:29 2006