Locus 6416

Sequence ID	3L_DroMel_CAF1
Location	17,191,630 – 17,191,749
Length	119
Max. P	0.837357

overview

Window 4

Location	17,191,630 – 17,191,735
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	83.71
Mean single sequence MFE	-19.52
Consensus MFE	-13.48
Energy contribution	-13.88
Covariance contribution	0.40
Combinations/Pair	1.25
Mean z-score	-2.02
Structure conservation index	0.69
SVM decision value	0.60
SVM RNA-class probability	0.795225
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17191630 105 + 23771897
CGCACGCCUCUUGUUCGGCUUACAACUCCCCUAAAACUCCCAUUCCCAACCUACACUGGGAACAAAUUCACACAACAACAGAAGUCGAAAAAGGGUAAAGAUUUC
.....(((.(((.((((((((.....................((((((........)))))).............(....))))))))).))))))......... ( -20.50)
>DroSec_CAF1 76134 105 + 1
CGCACGCCUCUUGUUCGGCUUACAACUCCCCUAAAACUCCCAUUCCCAGCCUACACUGGGAACAAAUUCACACAACUAUAGAAGUCGAAAAAGGGUUAAAAUUUC
.....(((.(((.((((((((.....................(((((((......))))))).............(....))))))))).))))))......... ( -23.00)
>DroSim_CAF1 68479 105 + 1
CGCACGCCCCUUGUUCGGCUUACAACUCCCCUAAAACUCCCAUUCCCAGCCUACACUGGCAACAAAUUCACACAACAAAAGAAGCCGAAAAGAAUAUAUAUAUUU
.........(((.((((((((...........................(((......)))...............(....))))))))))))............. ( -15.60)
>DroEre_CAF1 78304 105 + 1
CGCACGCCUCUUGUUCGGCUUACAACUCCCCUAAAUCUCCCCUACGCUGCCUACACAGAGAACAAAUUCACAGAGCAACAGAAGUCGAUUAAAGUUUAAGAUUUC
.........(((..(((((((....(((..................(((......))).(((....)))...)))......)))))))...)))........... ( -12.30)
>DroYak_CAF1 79960 104 + 1
CGCACGCCUCUUGUUCGGCUUACAACUCUCCUAAAUCUCCUCUUCUCUGC-UACACAGAGAAUAAAUUUAAACAGCUACAGAAGUCGAAAGAGGCUUAGGAUUUC
.....(((((((..(((((((......((..(((((......(((((((.-....)))))))...)))))...))......)))))))))))))).......... ( -26.20)
>consensus
CGCACGCCUCUUGUUCGGCUUACAACUCCCCUAAAACUCCCAUUCCCAGCCUACACUGGGAACAAAUUCACACAACAACAGAAGUCGAAAAAGGGUUAAGAUUUC
........((((.((((((((.....................(((((((......))))))).............(....))))))))).))))........... (-13.48 = -13.88 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	17,191,655 – 17,191,749
Length	94
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	69.36
Mean single sequence MFE	-17.30
Consensus MFE	-9.69
Energy contribution	-9.95
Covariance contribution	0.25
Combinations/Pair	1.15
Mean z-score	-1.66
Structure conservation index	0.56
SVM decision value	0.74
SVM RNA-class probability	0.837357
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17191655 94 + 23771897
CUCCCCUAAAACUCCCAUUCCCAACCUACACUGGGAACAAAUUCACACAACAACAGAAGUCGAAAAAGGGUAAAGAUUUCAAAGCA---AGAA-------------AUUU----------
...((((..........((((((........))))))....(((((............)).)))..))))...(((((((......---.)))-------------))))---------- ( -14.50)
>DroSec_CAF1 76159 94 + 1
CUCCCCUAAAACUCCCAUUCCCAGCCUACACUGGGAACAAAUUCACACAACUAUAGAAGUCGAAAAAGGGUUAAAAUUUCAAAGAA---AGAA-------------AUUU----------
...((((..........(((((((......)))))))..........(.(((.....))).)....))))...(((((((......---.)))-------------))))---------- ( -17.80)
>DroEre_CAF1 78329 101 + 1
CUCCCCUAAAUCUCCCCUACGCUGCCUACACAGAGAACAAAUUCACAGAGCAACAGAAGUCGAUUAAAGUUUAAGAUUUCAAAGUUACGGGAA-------------AUUAGUAG------
.....((((...((((..(((((..((....)).(((....)))....)))....((((((.............))))))...))...)))).-------------.))))...------ ( -14.12)
>DroYak_CAF1 79985 119 + 1
CUCUCCUAAAUCUCCUCUUCUCUGC-UACACAGAGAAUAAAUUUAAACAGCUACAGAAGUCGAAAGAGGCUUAGGAUUUCAAAGUUUAUUUAAUUUGAACAAGCUUUUUAGUAGUAUUUU
...((((((..(((...(((((((.-....)))))))..........(.(((.....))).)...)))..))))))....(((((((.(((.....))).)))))))............. ( -22.80)
>consensus
CUCCCCUAAAACUCCCAUUCCCAGCCUACACAGAGAACAAAUUCACACAACAACAGAAGUCGAAAAAGGGUUAAGAUUUCAAAGUA___AGAA_____________AUUA__________
.................(((((((......)))))))..................((((((.............))))))........................................ ( -9.69 =  -9.95 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:53 2006