Locus 235

Sequence ID X_DroMel_CAF1
Location 805,412 – 805,544
Length 132
Max. P 0.988512
window352 window353 window354 window355

overview

Window 2

Location 805,412 – 805,509
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 97.94
Mean single sequence MFE -20.42
Consensus MFE -19.15
Energy contribution -19.27
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.94
SVM decision value 0.20
SVM RNA-class probability 0.631593
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 805412 97 + 22224390
GCAGCAAAUGCAUUUUAUUUCUCCAAUCUUGUUUCCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGUAUUUGAUUCAGAUUUCUUUAAGUGCUAAG
(((((....))................((((........((.((((..(.((((((.....)))))).)..))))..)).......))))))).... ( -17.86)
>DroSec_CAF1 1873 97 + 1
GCAGCAAAUGCAUUUUAUUUCUCCAAUCUCGUUUCCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGGAUUCGAUUCAGAUUUCUUUAAGUGCUAAG
.........((((((....(((..((((.(((....))).........((((((((.....))))))))...)))).))).......)))))).... ( -21.70)
>DroSim_CAF1 1853 97 + 1
GCAGCAAAUGCAUUUUAUUUCUCCAAUCUCGUUUCCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGGAUUCGAUUCAGAUUUCUUUAAGUGCUAAG
.........((((((....(((..((((.(((....))).........((((((((.....))))))))...)))).))).......)))))).... ( -21.70)
>consensus
GCAGCAAAUGCAUUUUAUUUCUCCAAUCUCGUUUCCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGGAUUCGAUUCAGAUUUCUUUAAGUGCUAAG
.........((((((....(((..((((.(((....))).........((((((((.....))))))))...)))).))).......)))))).... (-19.15 = -19.27 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 805,412 – 805,509
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 97.94
Mean single sequence MFE -26.03
Consensus MFE -24.84
Energy contribution -24.73
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.30
Structure conservation index 0.95
SVM decision value 1.16
SVM RNA-class probability 0.924810
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 805412 97 - 22224390
CUUAGCACUUAAAGAAAUCUGAAUCAAAUACGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGGAAACAAGAUUGGAGAAAUAAAAUGCAUUUGCUGC
..(((((...............((((....((((((.....))))))....))))..((.((....))..(((..(....)..)))))...))))). ( -22.70)
>DroSec_CAF1 1873 97 - 1
CUUAGCACUUAAAGAAAUCUGAAUCGAAUCCGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGGAAACGAGAUUGGAGAAAUAAAAUGCAUUUGCUGC
....((((((.....(((((..((((..((((((((.....))))))))..))))...(((....)))))))).))).........((....))))) ( -27.70)
>DroSim_CAF1 1853 97 - 1
CUUAGCACUUAAAGAAAUCUGAAUCGAAUCCGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGGAAACGAGAUUGGAGAAAUAAAAUGCAUUUGCUGC
....((((((.....(((((..((((..((((((((.....))))))))..))))...(((....)))))))).))).........((....))))) ( -27.70)
>consensus
CUUAGCACUUAAAGAAAUCUGAAUCGAAUCCGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGGAAACGAGAUUGGAGAAAUAAAAUGCAUUUGCUGC
....((((((.....(((((..((((..((((((((.....))))))))..)))).....((....))))))).))).........((....))))) (-24.84 = -24.73 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 805,446 – 805,544
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 97.96
Mean single sequence MFE -25.50
Consensus MFE -23.30
Energy contribution -23.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.91
SVM decision value 0.96
SVM RNA-class probability 0.889477
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 805446 98 + 22224390
CCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGUAUUUGAUUCAGAUUUCUUUAAGUGCUAAGAUGGAAAUGAUUUGUUUUGCGAUCUUAAUGAUUUU
...(((.(((((((((((((((.....)))))((((((((...........))))))))......))))))))..))....))).............. ( -27.10)
>DroSec_CAF1 1907 98 + 1
CCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGGAUUCGAUUCAGAUUUCUUUAAGUGCUAAGAUGGAAAUGAUUUGUUUUGCGAUUUUAAUGAUUUU
...(((.(((((((((((((((.....)))))(((.((......)).)))...............))))))))..))....))).............. ( -24.70)
>DroSim_CAF1 1887 98 + 1
CCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGGAUUCGAUUCAGAUUUCUUUAAGUGCUAAGAUGGAAAUGAUUUGUUUUGCGAUUUUAAUGAUUUU
...(((.(((((((((((((((.....)))))(((.((......)).)))...............))))))))..))....))).............. ( -24.70)
>consensus
CCACGCUCAUCAUUUCCGCCAGCUAAACUGGCGGAUUCGAUUCAGAUUUCUUUAAGUGCUAAGAUGGAAAUGAUUUGUUUUGCGAUUUUAAUGAUUUU
...(((.(((((((((((((((.....)))))................((((........)))).))))))))..))....))).............. (-23.30 = -23.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 805,446 – 805,544
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 97.96
Mean single sequence MFE -24.00
Consensus MFE -24.00
Energy contribution -24.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.80
Structure conservation index 1.00
SVM decision value 2.12
SVM RNA-class probability 0.988512
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 805446 98 - 22224390
AAAAUCAUUAAGAUCGCAAAACAAAUCAUUUCCAUCUUAGCACUUAAAGAAAUCUGAAUCAAAUACGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGG
..............(((.......(((((((((.((((........))))................(((((.....))))))))))))))..)))... ( -24.00)
>DroSec_CAF1 1907 98 - 1
AAAAUCAUUAAAAUCGCAAAACAAAUCAUUUCCAUCUUAGCACUUAAAGAAAUCUGAAUCGAAUCCGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGG
..............(((.......(((((((((.((((........))))................(((((.....))))))))))))))..)))... ( -24.00)
>DroSim_CAF1 1887 98 - 1
AAAAUCAUUAAAAUCGCAAAACAAAUCAUUUCCAUCUUAGCACUUAAAGAAAUCUGAAUCGAAUCCGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGG
..............(((.......(((((((((.((((........))))................(((((.....))))))))))))))..)))... ( -24.00)
>consensus
AAAAUCAUUAAAAUCGCAAAACAAAUCAUUUCCAUCUUAGCACUUAAAGAAAUCUGAAUCGAAUCCGCCAGUUUAGCUGGCGGAAAUGAUGAGCGUGG
..............(((.......(((((((((.((((........))))................(((((.....))))))))))))))..)))... (-24.00 = -24.00 +   0.00)

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 09:39:37 2006