Locus 6001

Sequence ID 3L_DroMel_CAF1
Location 16,024,133 – 16,024,266
Length 133
Max. P 0.906406
window9598 window9599

overview

Window 8

Location 16,024,133 – 16,024,233
Length 100
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 92.36
Mean single sequence MFE -23.27
Consensus MFE -20.87
Energy contribution -21.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.90
SVM decision value 1.05
SVM RNA-class probability 0.906406
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16024133 100 - 23771897
UCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGAGAGAAGUGUGAAAAAUCAUGAACACAAGCUAUUCCACAGUGAAA-------AAUAAACAAGCCGAAAGA
..(((..(((.(((((((....))))))).)))...(((((..((((............))))...)).)))....)))...-------...........(....). ( -23.40)
>DroSec_CAF1 23909 100 - 1
UCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGAGAGAAGUGUGAAAAAUCAUGAACACCAGCUAUUCCACAAUGAAA-------AAUAAACAAACCGAAAGA
.......(((.(((((((....))))))).)))...(((((..((((............))))...)).)))..........-------...........(....). ( -21.30)
>DroSim_CAF1 32536 107 - 1
UCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGCUAGAAGUGUGAAAAAUCAUGAACACCAGCUAUUCCACAGUGAAAAAAAAAAAAUAAACAAACCGAAAGA
..(((..(((.(((((((....))))))).)))..((((....((((............)))).))))........))).....................(....). ( -25.10)
>consensus
UCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGAGAGAAGUGUGAAAAAUCAUGAACACCAGCUAUUCCACAGUGAAA_______AAUAAACAAACCGAAAGA
..(((..(((.(((((((....))))))).)))......((..((((............))))...))........))).....................(....). (-20.87 = -21.20 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 16,024,161 – 16,024,266
Length 105
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 92.86
Mean single sequence MFE -30.50
Consensus MFE -25.80
Energy contribution -27.13
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.85
SVM decision value 0.80
SVM RNA-class probability 0.853784
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16024161 105 - 23771897
AAUAUAUUUUUAUUUCUAAUUUCUUUCGACUAG-------UCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGAGAGAAGUGUGAAAAAUCAUGAACACAAGCUAUUC
............((((..(((((((((...(((-------((((((((((((.....).))))))).)))))))..)))))))))..))))..................... ( -33.20)
>DroSec_CAF1 23937 112 - 1
AAUGUAUUUUUAUUUCUAAUUUCUUUCGAGUAGUCAGUCGUCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGAGAGAAGUGUGAAAAAUCAUGAACACCAGCUAUUC
.(((.((((((.......(((((((((...(((((......((....))..(((((((....))))))))))))..)))))))))...)))))))))............... ( -31.60)
>DroSim_CAF1 32571 112 - 1
AAUAUAUUUUUAUUUCUAAUUUCUUUCGAGUAGUCAGUCGUCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGCUAGAAGUGUGAAAAAUCAUGAACACCAGCUAUUC
...........................(((((((.....(((((((((((((.....).))))))).)))))...........((((............))))..))))))) ( -26.70)
>consensus
AAUAUAUUUUUAUUUCUAAUUUCUUUCGAGUAGUCAGUCGUCCACCAGGUGCGGCCAGACAUCUGGCUGGACUAAAGAGAGAAGUGUGAAAAAUCAUGAACACCAGCUAUUC
............((((..(((((((((...(((((......((....))..(((((((....))))))))))))..)))))))))..))))..................... (-25.80 = -27.13 +   1.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:27 2006