Locus 9381

Sequence ID	3R_DroMel_CAF1
Location	24,903,382 – 24,903,542
Length	160
Max. P	0.939410

overview

Window 6

Location	24,903,382 – 24,903,502
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-33.82
Consensus MFE	-29.90
Energy contribution	-30.06
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.79
Structure conservation index	0.88
SVM decision value	1.30
SVM RNA-class probability	0.939410
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24903382 120 - 27905053
GCGGACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUGUAAGAAUUGAUGGCAAACAAUGCGCGAAUGGGCGGAGCAA
((....((((((((((....)))))))))).(((.(((..((((((...(((.(((((....))))).))).))))))..)))...)))...))......(.(((......))).).... ( -33.20)
>DroSec_CAF1 16418 120 - 1
GCGUACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUGUAAGAAUUGAUGGCAAACAAUGCGCGAAUGGGCGGAGCAA
(((((.((((((((((....)))))))))).(((.(((..((((((...(((.(((((....))))).))).))))))..)))...)))...........)))))............... ( -34.10)
>DroSim_CAF1 15752 120 - 1
GCGUACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUGUAAGAAUUGAUGGCAAACAAUGCGCGAAUGGGCGGAGCAA
(((((.((((((((((....)))))))))).(((.(((..((((((...(((.(((((....))))).))).))))))..)))...)))...........)))))............... ( -34.10)
>DroEre_CAF1 16487 120 - 1
GCGGACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUCUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUGUAAGAAUUGAUGGCAAACAAUGCGCGAAUGGGCAGAGCAA
((....((((((((((....))))))))))......((((((((((...(((.(((((....))))).))).)))))(((((....(((....)))....)))))......))))))).. ( -33.40)
>DroYak_CAF1 16631 120 - 1
UCGAACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUGUAAGAAUUGAUGGCAAACAAUGCGCGAAUGGGCAGUGCAA
((((..((((((((((....)))))))))).....(((..((((((...(((.(((((....))))).))).))))))..)))...))))..(((.....(((.(....).))).))).. ( -34.30)
>consensus
GCGGACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUGUAAGAAUUGAUGGCAAACAAUGCGCGAAUGGGCGGAGCAA
((....((((((((((....)))))))))).(((.(((..((((((...(((.(((((....))))).))).))))))..)))...)))...))......(((.(....).)))...... (-29.90 = -30.06 +   0.16)

alignment

secondary structure

dotplot

Window 7

Location	24,903,422 – 24,903,542
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.00
Mean single sequence MFE	-37.58
Consensus MFE	-30.94
Energy contribution	-31.66
Covariance contribution	0.72
Combinations/Pair	1.03
Mean z-score	-1.93
Structure conservation index	0.82
SVM decision value	0.82
SVM RNA-class probability	0.858568
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24903422 120 - 27905053
CAAGUGGCAAGAAGCAGCGGUAGGAGGCCAAGUGCGAGGGGCGGACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUG
......((((.((((((((((.....)))...((((((..(((.((.....))))).))))))))))))).....)))).((((((...(((.(((((....))))).))).)))))).. ( -38.60)
>DroSec_CAF1 16458 120 - 1
CAAGUGGCAAGAAGCAGCGGCAGGAGGCGGAAUGCGAGGGGCGUACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUG
......((((.(((((((.((.....))....((((((..(((.((.....))))).))))))))))))).....)))).((((((...(((.(((((....))))).))).)))))).. ( -36.80)
>DroSim_CAF1 15792 120 - 1
CAAGUGGCAAGAAGCAGCGGCAGGAGGCGGAGUGCGAGGGGCGUACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUG
((..((.(..(((((((..((((.((((((..((((((..(((.((.....))))).)))))).)))))).....))))..))))))).(((.(((((....))))).))).).))..)) ( -37.40)
>DroEre_CAF1 16527 120 - 1
CAAGUGGCAAGAAGCAGCGGAAGGAGGCGGAGUGCGAGGGGCGGACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUCUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUG
((..((.(..((((((((((((.(((((((..((((((..(((.((.....))))).)))))).)))))).)...))))).))))))).(((.(((((....))))).))).).))..)) ( -40.70)
>DroYak_CAF1 16671 120 - 1
CAAGUGGCAAGAAGCAGCGGAAGGAGGCGGAGUGCGAGGGUCGAACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUG
......((((.(((((((........(((.(((((((...((....))....)))))))))).))))))).....)))).((((((...(((.(((((....))))).))).)))))).. ( -34.40)
>consensus
CAAGUGGCAAGAAGCAGCGGAAGGAGGCGGAGUGCGAGGGGCGGACGAAUAGUUGCACUCGCAGCUGUUUACAAAUUGUGUUUGCUUUAGCAUAAUAUUUAGAUAUUUUGCGGGCAAGUG
......((((.(((((((.((.....))....((((((..(((.((.....))))).))))))))))))).....)))).((((((...(((.(((((....))))).))).)))))).. (-30.94 = -31.66 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:33:12 2006