Locus 5608

Sequence ID	X_DroMel_CAF1
Location	14,469,279 – 14,469,454
Length	175
Max. P	0.901187

overview

Window 9

Location	14,469,279 – 14,469,376
Length	97
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	83.38
Mean single sequence MFE	-23.67
Consensus MFE	-21.22
Energy contribution	-21.00
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.17
Structure conservation index	0.90
SVM decision value	0.33
SVM RNA-class probability	0.689452
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14469279 97 + 22224390
--------------------AAAAGGCUUUGAUUUCAAAUCAAUGUUGUUGGAUCUUGUAGAACGAAGAUUAGUAGGAGUUUCUUUUGACACGGGUCUUACGAUACUUGAUCCG---CUU
--------------------...((((.(((((.....))))).......(((((..(((...((((((((..((((((...)))))).....)))))).)).)))..))))))---))) ( -22.00)
>DroSim_CAF1 6433 116 + 1
NNNNNNNNNNNNNNNNNNNNAAAAGGCUUUGAUUUCUAAUCAAUGUU-UUGGAUCGUGUAGAACGAAGAUUAGUAGGAGUUUUUUUUGACACGGGUCUUACGAUACUUGAUCCG---CUU
......................(((((.(((((.....))))).)))-))((((((.(((...((((((((.((..(((....)))..))...)))))).)).))).)))))).---... ( -22.40)
>DroYak_CAF1 2533 100 + 1
--------------------AAAAGGCUUUGAUUUCUAAUCAAUGCUGUUGGAUCUUGUAGAACGAAGAUUAGUAGGAGUUUCUUUUGACACGGGUCUUACGAUACUUGAUCCGAUACUU
--------------------....(((.(((((.....))))).)))((((((((..(((...((((((((..((((((...)))))).....)))))).)).)))..)))))))).... ( -26.60)
>consensus
____________________AAAAGGCUUUGAUUUCUAAUCAAUGUUGUUGGAUCUUGUAGAACGAAGAUUAGUAGGAGUUUCUUUUGACACGGGUCUUACGAUACUUGAUCCG___CUU
........................(((.(((((.....))))).)))...(((((..(((...(((((((..((....(((......)))))..))))).)).)))..)))))....... (-21.22 = -21.00 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	14,469,339 – 14,469,454
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.16
Mean single sequence MFE	-35.97
Consensus MFE	-23.40
Energy contribution	-23.02
Covariance contribution	-0.37
Combinations/Pair	1.18
Mean z-score	-2.81
Structure conservation index	0.65
SVM decision value	1.02
SVM RNA-class probability	0.901187
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14469339 115 - 22224390
CAUUGACAACUUCAUUGGUGAAGUGAGGGGAAA-UGUCUUUCCGA-AAAGAACACAACUUUUGGGAAGGAGGCUCCAGAGAAG---CGGAUCAAGUAUCGUAAGACCCGUGUCAAAAGAA
..((((((((((((....))))))..(((....-..(((((((.(-((((.......))))).)))))))((.(((.......---.))))).....((....))))).))))))..... ( -33.80)
>DroSec_CAF1 12 113 - 1
CAUUGACAACUUCAUCGGGGA--UUGGGGGAAA-UGUCUUCCCGA-AAAGAACACAACUUUUUGGGAGGAGGGUCUGGAGAAG---CGGAUCAAGUAUCGUAAGACCCGUGUCAAAAGAA
..((((((.(((((.......--.)))))....-..(((((((((-((((.......)))))))))))))((((((...((.(---(.......)).))...)))))).))))))..... ( -40.80)
>DroSim_CAF1 6512 113 - 1
CAUUGACAACUUCAUCGGGGA--UUGGGGGAAA-UGUCUUCUCCA-AAAGAACACAACUUUUUGGGAGGAGGGUCUAGAGAAG---CGGAUCAAGUAUCGUAAGACCCGUGUCAAAAAAA
..((((((.(((((.......--.)))))....-..(((((.(((-((((........))))))))))))((((((...((.(---(.......)).))...)))))).))))))..... ( -33.50)
>DroYak_CAF1 2593 119 - 1
CAUUGACAACUUCAUCAGGGGA-GUGGAGGGAGUUCGUUUCCCGAAAAACAAGACAACUUUUUGGGAGGAGGGUCCCGAGAAGUAUCGGAUCAAGUAUCGUAAGACCCGUGUCAAAAGAA
..((((((((((.(((.(((((-(((((.....)))))))))).........((..(((((((((((......))))))))))).)).))).)))).((....))....))))))..... ( -35.80)
>consensus
CAUUGACAACUUCAUCGGGGA__UUGGGGGAAA_UGUCUUCCCGA_AAAGAACACAACUUUUUGGGAGGAGGGUCCAGAGAAG___CGGAUCAAGUAUCGUAAGACCCGUGUCAAAAGAA
..((((((((((.(((.(..........(((...(.(((((((((.((((.......))))))))))))).).)))..........).))).)))).((....))....))))))..... (-23.40 = -23.02 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:12 2006