Locus 2080

Sequence ID X_DroMel_CAF1
Location 5,675,663 – 5,675,756
Length 93
Max. P 0.972988
window3380 window3381

overview

Window 0

Location 5,675,663 – 5,675,756
Length 93
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.42
Mean single sequence MFE -26.60
Consensus MFE -16.60
Energy contribution -15.85
Covariance contribution -0.75
Combinations/Pair 1.16
Mean z-score -1.91
Structure conservation index 0.62
SVM decision value 0.55
SVM RNA-class probability 0.779126
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5675663 93 + 22224390
AUAAUCGCUCGAGUACU-UGGUAAAAAGCCAAUAAAGAAGAGGAAAAUGAAAAUACUUUCCUUUGAGCGCAGGUG-----------------AGCGG-GGCACGGAGAAUGG--------
....(((((((.(..((-((((.....)))........((((((((((....))..)))))))))))..)...))-----------------)))))-..............-------- ( -21.60)
>DroSec_CAF1 14617 95 + 1
AUAAUCGCUCGAGUACU-UGGUAAAAAGCCAAUAAAGAAGAGGAAAAUGAAAAUACUUUCCUUUGAGCUCAGGUG----------------GAGCGGGGGCACGGAGAAUGG--------
....((((((((((..(-((((.....)))))......((((((((((....))..))))))))..)))).....----------------))))))...............-------- ( -21.80)
>DroAna_CAF1 18784 120 + 1
AUAAUCGCUCGAAUACAACGGCAAAAAGCCAAUAAAGGAGAGGAAAAUGAAAAUAUUUUCCUUUGAGCUCAGUCCAGGGAGGUGCUGGCUGGAGGGAGGUCCUGGUGGGCGGGAGGUCCU
......((((.........(((.....)))........(((((((((((....)))))))))))))))((((.((((.......)))))))).((((..(((((.....)))))..)))) ( -40.30)
>DroSim_CAF1 15187 94 + 1
AUAAUCGCUCGAGUACU-UGGUAAAAAGCCAAUAAAGAAGAGGAAAAUGAAAAUACUUUCCUUUGAGCUCAGGUG-----------------AGCGGGGGCACGGAGAAUGG--------
....((((..((((..(-((((.....)))))......((((((((((....))..))))))))..))))..)))-----------------)((....))...........-------- ( -22.70)
>consensus
AUAAUCGCUCGAGUACU_UGGUAAAAAGCCAAUAAAGAAGAGGAAAAUGAAAAUACUUUCCUUUGAGCUCAGGUG_________________AGCGGGGGCACGGAGAAUGG________
....((((((.........(((.....)))........((((((((..........)))))))))))).........................((....)).....))............ (-16.60 = -15.85 +  -0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 5,675,663 – 5,675,756
Length 93
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.42
Mean single sequence MFE -21.48
Consensus MFE -14.93
Energy contribution -14.42
Covariance contribution -0.50
Combinations/Pair 1.17
Mean z-score -2.21
Structure conservation index 0.69
SVM decision value 1.70
SVM RNA-class probability 0.972988
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5675663 93 - 22224390
--------CCAUUCUCCGUGCC-CCGCU-----------------CACCUGCGCUCAAAGGAAAGUAUUUUCAUUUUCCUCUUCUUUAUUGGCUUUUUACCA-AGUACUCGAGCGAUUAU
--------..............-.((((-----------------(...(((......((((((((......))))))))........((((.......)))-))))...)))))..... ( -18.30)
>DroSec_CAF1 14617 95 - 1
--------CCAUUCUCCGUGCCCCCGCUC----------------CACCUGAGCUCAAAGGAAAGUAUUUUCAUUUUCCUCUUCUUUAUUGGCUUUUUACCA-AGUACUCGAGCGAUUAU
--------.....(((.((((....((((----------------.....))))....((((((((......))))))))........((((.......)))-)))))..)))....... ( -17.90)
>DroAna_CAF1 18784 120 - 1
AGGACCUCCCGCCCACCAGGACCUCCCUCCAGCCAGCACCUCCCUGGACUGAGCUCAAAGGAAAAUAUUUUCAUUUUCCUCUCCUUUAUUGGCUUUUUGCCGUUGUAUUCGAGCGAUUAU
.(((..(((.(.....).)))..)))...(((((((.......)))).))).((((..((((((((......))))))))..........(((.....))).........))))...... ( -30.80)
>DroSim_CAF1 15187 94 - 1
--------CCAUUCUCCGUGCCCCCGCU-----------------CACCUGAGCUCAAAGGAAAGUAUUUUCAUUUUCCUCUUCUUUAUUGGCUUUUUACCA-AGUACUCGAGCGAUUAU
--------.....(((.((((....(((-----------------(....))))....((((((((......))))))))........((((.......)))-)))))..)))....... ( -18.90)
>consensus
________CCAUUCUCCGUGCCCCCGCU_________________CACCUGAGCUCAAAGGAAAGUAUUUUCAUUUUCCUCUUCUUUAUUGGCUUUUUACCA_AGUACUCGAGCGAUUAU
.................(((....))).........................((((..((((((((......)))))))).........(((.......)))........))))...... (-14.93 = -14.42 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:44 2006