Locus 1904

Sequence ID X_DroMel_CAF1
Location 5,279,264 – 5,279,448
Length 184
Max. P 0.987580
window3099 window3100 window3101

overview

Window 9

Location 5,279,264 – 5,279,368
Length 104
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 82.02
Mean single sequence MFE -26.42
Consensus MFE -17.98
Energy contribution -19.46
Covariance contribution 1.48
Combinations/Pair 1.05
Mean z-score -2.84
Structure conservation index 0.68
SVM decision value 2.08
SVM RNA-class probability 0.987580
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5279264 104 + 22224390
AACUUG------CGAA-----AGGG---CGAAGGUAAGAGC-AAAAGUGUGGCUUGAAUAGCGUAAGCGGGCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGUAAAA
...(((------(...-----...(---(....))....))-))..(((((((..((((.((....)).(((....))).((((((....)))))).)))).))))))).......... ( -27.70)
>DroSec_CAF1 16322 101 + 1
AAGAAG------C--------AAGG---AGAAGGUAAGAGA-AAAAGUGUGGCUUGAAUAGCGAAAGCUGGCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGCAAAA
.....(------(--------.((.---(...(((((((..-.......(.(((..((.(((....)))(((....)))....))..))).)......)))))))...).)).)).... ( -26.36)
>DroSim_CAF1 10976 101 + 1
AAGAAG------C--------AAGG---AGAAGGUAAGGGA-AAAAGUGUGGCUUGAAUAGCGAAAGCUGGCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGCAAAA
.....(------(--------.((.---(...(((((((..-.......(.(((..((.(((....)))(((....)))....))..))).)......)))))))...).)).)).... ( -25.56)
>DroEre_CAF1 16011 119 + 1
GACUUGGUUUUGCGGAGGGGCAAAGUCAGAAAAAAAUGAGAGAAAAGUGUGGCUUGAAUAGCGAAAGGUGCCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGCAAAA
...(((..(((((......)))))..))).......((...((...(((((((..((((..(....).(((((((((....)))))).)))......)))).))))))).))..))... ( -27.00)
>DroYak_CAF1 11905 107 + 1
AACUUG------CGC---AGCAAAG---AAAAAAAAAGAGACGAAAGUGUGGCUUGAAUAGCGAAAGCUGCAGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGAAAAA
......------..(---((((...---............((....))(((((..((.((((....))))((((((.....))))))...........))..))))).)))))...... ( -25.50)
>consensus
AACUUG______CG_______AAGG___AGAAGGUAAGAGA_AAAAGUGUGGCUUGAAUAGCGAAAGCUGGCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGCAAAA
...................................................(((..((.(((....)))(((....)))....))..)))........((((((((.....)))))))) (-17.98 = -19.46 +   1.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,279,290 – 5,279,408
Length 118
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -24.75
Consensus MFE -16.77
Energy contribution -18.33
Covariance contribution 1.56
Combinations/Pair 1.11
Mean z-score -2.58
Structure conservation index 0.68
SVM decision value 1.94
SVM RNA-class probability 0.983360
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5279290 118 + 22224390
C-AAAAGUGUGGCUUGAAUAGCGUAAGCGGGCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGUAAAAUCAAAAAAAAAAAGUAAAAAAAUAAACACGAGGAGGGCAA
.-....((((.(((..((..((....)).(((....)))....))..))).......(((((((((.....)))))))))........................))))........... ( -27.40)
>DroEre_CAF1 16051 101 + 1
AGAAAAGUGUGGCUUGAAUAGCGAAAGGUGCCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGCAAAAUAAAAAACA------------------CCGACGAGGGCAA
...........(((.....)))......((((....((((((((((....)))))).(((((((((.....)))))))))........------------------.))))...)))). ( -24.60)
>DroYak_CAF1 11933 100 + 1
ACGAAAGUGUGGCUUGAAUAGCGAAAGCUGCAGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGAAAAAUAAAAAAAA-------------------CGAUGAAGGCAA
.(((((((.((((((...((((....))))....))))))))))))).............(((((.((((((..............))-------------------).)))..))))) ( -22.24)
>consensus
A_AAAAGUGUGGCUUGAAUAGCGAAAGCUGCCGGAAGUCGAUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGAAAAAUAAAAAAAA___________________CGACGAGGGCAA
...........((((...((((....))))......((((((((((....)))))).(((((((((.....)))))))))...........................))))..)))).. (-16.77 = -18.33 +   1.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,279,329 – 5,279,448
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -20.21
Consensus MFE -16.62
Energy contribution -16.84
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -2.05
Structure conservation index 0.82
SVM decision value 1.59
SVM RNA-class probability 0.965882
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5279329 119 + 22224390
AUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGUAAAAUCAAAAAAAAAAAGUAAAAAAAUAAACACGAGGAGGGCAAUUCUAAAACAAAGUCACGCGCAGAAAAUCAGGGUGAAAGA
.((((((.(((((....(((((((((.....))))))))).............................((((......)))).........)).))).)))))).............. ( -18.50)
>DroEre_CAF1 16091 101 + 1
AUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGCAAAAUAAAAAACA------------------CCGACGAGGGCAAUUCUAAAACAAAGUCACGCGCAGAAAAUCUGAGCGAAAGA
.((((((.(((......(((((((((.....)))))))))........------------------..(((...(............)...))).))).)))))).......(....). ( -22.70)
>DroYak_CAF1 11973 100 + 1
AUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGAAAAAUAAAAAAAA-------------------CGAUGAAGGCAAUACUAAAACAAAGUCACGCUCAGAAAAUGGGGCUGAAAGG
.((((((((((.........(((((.((((((..............))-------------------).)))..))))).(((.......)))..)))))))))).............. ( -19.44)
>consensus
AUUUUUGAGCGGAAAUAAUUUUGCCACAUGUUGGAAAAAUAAAAAAAA___________________CGACGAGGGCAAUUCUAAAACAAAGUCACGCGCAGAAAAUCAGGGUGAAAGA
.((((((.(((......(((((((((.....)))))))))..................................(((..............))).))).)))))).............. (-16.62 = -16.84 +   0.22)

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 10:21:34 2006