Locus 4996

Sequence ID 3L_DroMel_CAF1
Location 13,753,900 – 13,754,108
Length 208
Max. P 0.974807
window7893 window7894 window7895 window7896

overview

Window 3

Location 13,753,900 – 13,754,003
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 94.82
Mean single sequence MFE -38.33
Consensus MFE -32.95
Energy contribution -34.20
Covariance contribution 1.25
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.86
SVM decision value 0.55
SVM RNA-class probability 0.776981
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13753900 103 + 23771897
CUUAAAUUCCUCUUGGCCAGGAGAAGGACACGGGGCAAUCUCACUUUCCCGCUUACACUCUCUGCUGGUUAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUC
..............(((((((.(((((....(((.....))).)))))))((((.((((((((((..(...)..))))))))))...)))).)))))...... ( -38.60)
>DroSim_CAF1 172883 103 + 1
CUUAAAUUCCUCUUGGCCAGGAGAAGGACACGGGGCAAUCUCACUUGCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUC
.........(((((....)))))..((.(((.((((((......))))))((((.((((((((((..(...)..))))))))))...))))))).))...... ( -42.30)
>DroEre_CAF1 167461 103 + 1
CUUAAAUUCCUCUUGGCCAGCAAAAGGACACGGGUCCAUCUGACUUUCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUC
..............(((((......((((....))))............(((((.((((((((((..(...)..))))))))))...))))))))))...... ( -39.40)
>DroYak_CAF1 171869 103 + 1
CUUAAAUUCCUCUUGGCCAGCAGAAGGACACGGGGCCAUCUCACUUUCCCGCUUACACUCUCGACUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUC
.......((((..((.....))..)))).(((((((((...((((((...((...(((((((.....(((...))).)))))))))))))))))))).)))). ( -33.00)
>consensus
CUUAAAUUCCUCUUGGCCAGCAGAAGGACACGGGGCAAUCUCACUUUCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUC
..............(((((.((((.((........)).)))).......(((((.((((((((((..(...)..))))))))))...))))))))))...... (-32.95 = -34.20 +   1.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,753,900 – 13,754,003
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 94.82
Mean single sequence MFE -36.27
Consensus MFE -31.88
Energy contribution -32.75
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.88
SVM decision value 0.43
SVM RNA-class probability 0.732764
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13753900 103 - 23771897
GACAACGGCCACACUCUGCCACUCUCUGCCAAUAACCAGCAGAGAGUGUAAGCGGGAAAGUGAGAUUGCCCCGUGUCCUUCUCCUGGCCAAGAGGAAUUUAAG
......(((((......((((((((((((.........))))))))))...))((..(((.((.((......)).)))))..))))))).............. ( -34.30)
>DroSim_CAF1 172883 103 - 1
GACAACGGCCACACUCUGCCACUCUCUGCCAAUGGCCAGCAGAGAGUGUAAGCGGGCAAGUGAGAUUGCCCCGUGUCCUUCUCCUGGCCAAGAGGAAUUUAAG
......((((((((...((((((((((((.........))))))))))...))((((((......)))))).)))).........)))).............. ( -37.30)
>DroEre_CAF1 167461 103 - 1
GACAACGGCCACACUCUGCCACUCUCUGCCAAUGGCCAGCAGAGAGUGUAAGCGGGAAAGUCAGAUGGACCCGUGUCCUUUUGCUGGCCAAGAGGAAUUUAAG
......((((....(((((((((((((((.........))))))))))...)))))..((.((((.((((....)))).)))))))))).............. ( -38.40)
>DroYak_CAF1 171869 103 - 1
GACAACGGCCACACUCUGCCACUCUCUGCCAAUGGCCAGUCGAGAGUGUAAGCGGGAAAGUGAGAUGGCCCCGUGUCCUUCUGCUGGCCAAGAGGAAUUUAAG
((((..((((((((((((((((((((.(((...))).....)))))))...))))...))))...)))))...))))(((((........)))))........ ( -35.10)
>consensus
GACAACGGCCACACUCUGCCACUCUCUGCCAAUGGCCAGCAGAGAGUGUAAGCGGGAAAGUGAGAUGGCCCCGUGUCCUUCUCCUGGCCAAGAGGAAUUUAAG
((((..(((((((((((((((((((((((.........))))))))))...))))...))))...)))))...))))(((((........)))))........ (-31.88 = -32.75 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,753,926 – 13,754,043
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 96.44
Mean single sequence MFE -43.13
Consensus MFE -40.44
Energy contribution -40.95
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.64
Structure conservation index 0.94
SVM decision value 1.74
SVM RNA-class probability 0.974807
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13753926 117 + 23771897
GACACGGGGCAAUCUCACUUUCCCGCUUACACUCUCUGCUGGUUAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUU
....(((((...........)))))....((((((((((..(...)..))))))))))...(((((((((.(.((((...(((((.....))))).)))).).))).)))))).... ( -43.40)
>DroSim_CAF1 172909 117 + 1
GACACGGGGCAAUCUCACUUGCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUU
......((((((......))))))((...((((((((((..(...)..)))))))))))).(((((((((.(.((((...(((((.....))))).)))).).))).)))))).... ( -48.40)
>DroEre_CAF1 167487 117 + 1
GACACGGGUCCAUCUGACUUUCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUU
....((((.............))))....((((((((((..(...)..))))))))))...(((((((((.(.((((...(((((.....))))).)))).).))).)))))).... ( -43.02)
>DroYak_CAF1 171895 117 + 1
GACACGGGGCCAUCUCACUUUCCCGCUUACACUCUCGACUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUU
....(((((...........)))))....(((((((.....(((...))).)))))))...(((((((((.(.((((...(((((.....))))).)))).).))).)))))).... ( -37.70)
>consensus
GACACGGGGCAAUCUCACUUUCCCGCUUACACUCUCUGCUGGCCAUUGGCAGAGAGUGGCAGAGUGUGGCCGUUGUCCUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUU
....((((.............))))....((((((((((..(...)..))))))))))...(((((((((.(.((((...(((((.....))))).)))).).))).)))))).... (-40.44 = -40.95 +   0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,754,003 – 13,754,108
Length 105
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 96.21
Mean single sequence MFE -28.30
Consensus MFE -26.35
Energy contribution -26.47
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.69
Structure conservation index 0.93
SVM decision value 1.50
SVM RNA-class probability 0.959464
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13754003 105 + 23771897
CUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUCCGGGCGAGGCAGAAAAAAUCCUGAGCGGCCCAACAUGCCAACACCCAUCCCCAA-
...........(((....((((....))))..............((((((..((((....(((........)))....))))...))))))..........))).- ( -26.20)
>DroSim_CAF1 172986 105 + 1
CUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUCCGGCCGAGGCAGAAAAAAUCCUGAGCGGCCCAACAUGCCAACACCCACCCCCAA-
...........(((....((((....))))..............((((((..(((((...(((........)))..)))))....))))))..........))).- ( -29.00)
>DroEre_CAF1 167564 106 + 1
CUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUCCGGCCGAGGCGGAAAAAAUCCUGAGCGGCCCAACAUGCCAACAACCACCUCCAAC
...........((((...((((....))))..............((((((..(((((...(((........)))..)))))....)))))).........)))).. ( -29.70)
>consensus
CUUGUUUUUCCUGGAAACUGGCAUCCGCCAACACUUAAUUAAAAUGGCAUCCGGCCGAGGCAGAAAAAAUCCUGAGCGGCCCAACAUGCCAACACCCACCCCCAA_
...........(((....((((....))))..............((((((..(((((...(((........)))..)))))....))))))..........))).. (-26.35 = -26.47 +   0.11)

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 11:39:03 2006