Locus 3700

Sequence ID	3L_DroMel_CAF1
Location	10,766,536 – 10,766,734
Length	198
Max. P	0.509418

overview

Window 0

Location	10,766,536 – 10,766,654
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.82
Mean single sequence MFE	-30.10
Consensus MFE	-29.70
Energy contribution	-29.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.08
Structure conservation index	0.99
SVM decision value	-0.05
SVM RNA-class probability	0.507822
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10766536 118 + 23771897
AUGCUUCGCUGGUCUCGGGGGCCAGAAAUUGGCAAACAAUAAAAGCCGUCAAAAAGUGCAGCCAACAGCAAAUAGGAAAAGCAAUAGCCAGGGAAAAAU--GUAGGGGCGCCAAGUGGCA
..(((((.((((((.....))))))...(((((...........(((........).)).((.....)).................)))))........--...)))))(((....))). ( -29.80)
>DroSec_CAF1 100232 120 + 1
AUGCUUCGCUGGUCUCGGGGGCCAGAAAUUGGCAAACAAUAAAAGCCGUCAAAAAGUGCAGCCAACAGCAAAUAGGAAAAGCAAUAGCCAGGGAAAAAUGUGUAGGGGCGCCAAGUGGCA
..(((((.((((((.....))))))...(((((...........(((........).)).((.....)).................))))).............)))))(((....))). ( -29.80)
>DroSim_CAF1 103109 120 + 1
AUGCUUCGCUGGUCUCGGGGGCCAGAAAUUGGCAAACAAUAAAAGCCGUCAAAAAGUGCAGCCAACAGCAAAUAGGAAAAGCAAUAGCCAGGGAAAAAUGUGUAGGGGCGCCAAGUGGCA
..(((((.((((((.....))))))...(((((...........(((........).)).((.....)).................))))).............)))))(((....))). ( -29.80)
>DroEre_CAF1 105143 118 + 1
AUGCUUCGCUGGUCUCGGGGGCCAGAAAUUGGCAAACAAUAAGAGCCGUCAAAAAGUGCAGCCAACAGCAAAUAGGAAAAGCAAUAGCCAGGGAAAAAU--GAAGGGGCGCCAAGUGGCA
..(((((.((((((.....))))))...(((((...(.....).((..((......(((........))).....))...))....)))))........--...)))))(((....))). ( -30.80)
>DroYak_CAF1 116306 118 + 1
AUGCUUCGCUGGUCUCGGGGGCCAGAAAUUGGCAAACAAUAAGAGCCGUCAAAAAGUGCAGCCAACAGCAAAUAGGAAAAGCAAUAGCCAGGGAAAAAU--GUAGGGGCGCCAAGUGGCU
..(((((.((((((.....))))))...(((((...(.....).((..((......(((........))).....))...))....)))))........--...)))))(((....))). ( -30.30)
>consensus
AUGCUUCGCUGGUCUCGGGGGCCAGAAAUUGGCAAACAAUAAAAGCCGUCAAAAAGUGCAGCCAACAGCAAAUAGGAAAAGCAAUAGCCAGGGAAAAAU__GUAGGGGCGCCAAGUGGCA
..(((((.((((((.....))))))...(((((...........(((........).)).((.....)).................))))).............)))))(((....))). (-29.70 = -29.70 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	10,766,616 – 10,766,734
Length	118
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	89.69
Mean single sequence MFE	-22.98
Consensus MFE	-16.85
Energy contribution	-17.66
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-1.50
Structure conservation index	0.73
SVM decision value	-0.05
SVM RNA-class probability	0.509418
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10766616 118 + 23771897
GCAAUAGCCAGGGAAAAAUGUAGGGGCGCCAAGUGGCAGGAGGGGUGCUGCAAAAGAAAAAACAGUUUGAAAAGUUGAUUGUUUAGUUGGAGUUGGAGCAUAAAAAAUGUUAGCUACA
((....))..........(((((.((((((....))).......(((((.(((..((..((((((((.........))))))))..))....))).))))).......)))..))))) ( -26.00)
>DroEre_CAF1 105223 118 + 1
GCAAUAGCCAGGGAAAAAUGAAGGGGCGCCAAGUGGCAGGAGGGGGGCUGCGAAAGAAAAAACAGUUUGAAAAGUUGAUUGUUUAGUUGGAGUUGGAGCAUAAAAAAUGUUAGCUACA
(((((((((...............)))(((....))).........(((.(((..((..((((((((.........))))))))..))....))).)))........)))).)).... ( -22.06)
>DroYak_CAF1 116386 118 + 1
GCAAUAGCCAGGGAAAAAUGUAGGGGCGCCAAGUGGCUGGCGGGGGGCUGCGAAAGAAAAAACAGUUUGAAAAGUUGAUUGUUUAGUUGGAGUUGGAGCAUAAAAAAUGUUAGCUACA
......(((...............))).....((((((((((....(((.(((..((..((((((((.........))))))))..))....))).)))........)))))))))). ( -28.56)
>DroAna_CAF1 100779 106 + 1
GCAAUAGCCAGAGAAAAAUAGAGGGGCGA----------GAGCAGAGC--GAAAAGAAAAAACAGUUUGAAAAGUUGAUUGUUUAGUUGGAGUUGGAGCAUAAAAAAUGUUAGCUACA
.((((..((((.........(....((..----------..))....)--.........((((((((.........))))))))..)))).)))).(((((.....)))))....... ( -15.30)
>consensus
GCAAUAGCCAGGGAAAAAUGUAGGGGCGCCAAGUGGCAGGAGGGGGGCUGCAAAAGAAAAAACAGUUUGAAAAGUUGAUUGUUUAGUUGGAGUUGGAGCAUAAAAAAUGUUAGCUACA
(((((((((...............)))(((....))).........(((.(((..((..((((((((.........))))))))..))....))).)))........)))).)).... (-16.85 = -17.66 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:39 2006