Locus 6103

Sequence ID	3L_DroMel_CAF1
Location	16,200,523 – 16,200,643
Length	120
Max. P	0.956973

overview

Window 3

Location	16,200,523 – 16,200,643
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.50
Mean single sequence MFE	-35.44
Consensus MFE	-31.94
Energy contribution	-31.90
Covariance contribution	-0.04
Combinations/Pair	1.21
Mean z-score	-1.55
Structure conservation index	0.90
SVM decision value	1.47
SVM RNA-class probability	0.956973
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16200523 120 + 23771897
AAGUAUAAAUAUACUUUCUAGGAAGUUCCCGCAUCUAAAUUUAUUGCUACUUCAAUAGAGUCUUGUUGCCCGGUGGAGCCACUUGGUUUAAUCAGAGUAAUGGGUAUGCGGAUGCGGGCG
............(((((....))))).(((((((((...(((((((......)))))))..((..(((((.(((.(((((....))))).))).).))))..)).....))))))))).. ( -35.80)
>DroSec_CAF1 19471 120 + 1
AAGUAUAAAUAUACUUUCUAGGAAGUUCCCGCAUCUAAAUUUAUUGCUCCUUCGACAGAGUCUUGUUGCCCGGUGGAGCCACUUGGUUUAAUCAGAGCAAUGGGUAUGCGGAUGCGGGCG
............(((((....))))).(((((((((..(((((((((((...((((((....))))))...(((.(((((....))))).))).)))))))))))....))))))))).. ( -40.50)
>DroSim_CAF1 21317 120 + 1
AAGUAUAAAUAUACUUUCUAGGAAGUUCCCGCAUCUAAAUUUAUUGCUCCUUCGACAGAGUCUUGUUGCCCGGUGGAGCCACUUGGUUUAAUCAGAGCAAUGGGUAUGCGGAUGCGGGCG
............(((((....))))).(((((((((..(((((((((((...((((((....))))))...(((.(((((....))))).))).)))))))))))....))))))))).. ( -40.50)
>DroEre_CAF1 18913 120 + 1
GAGUAUAAAUAUACUUUCUAGGAAGUUUCCAUAUUUAAAUUUAUUAUUCUUUUGAUAGAGUCUUGUUGCCCGGCGGAGCCACUUGGUUUAAUCAGAGCAAUGGGUAUGCCGAUGCGGGUG
.....((((((((((((....)))))....)))))))..(((((((......)))))))........((((((..(((((....)))))..))...(((.(((.....))).))))))). ( -27.10)
>DroYak_CAF1 55787 120 + 1
AAGUAUAAAUAUACUUUCUAGGAAGUUCCCGCAUCUAAAUUUAUUAUUCCCUUGACAGAGUCUUGUUGCCCGGUGGAGCCACUUGGUUUAAUCAGAGCAAUGGGUAUGCCGAUGCGGGCG
............(((((....))))).((((((((..........((((........))))((..(((((.(((.(((((....))))).))).).))))..))......)))))))).. ( -33.30)
>consensus
AAGUAUAAAUAUACUUUCUAGGAAGUUCCCGCAUCUAAAUUUAUUGCUCCUUCGACAGAGUCUUGUUGCCCGGUGGAGCCACUUGGUUUAAUCAGAGCAAUGGGUAUGCGGAUGCGGGCG
............(((((....))))).(((((((((..(((((((((((...((((((....))))))...(((.(((((....))))).))).)))))))))))....))))))))).. (-31.94 = -31.90 +  -0.04)

alignment

secondary structure

dotplot

Window 4

Location	16,200,523 – 16,200,643
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.50
Mean single sequence MFE	-28.27
Consensus MFE	-23.35
Energy contribution	-24.15
Covariance contribution	0.80
Combinations/Pair	1.17
Mean z-score	-1.42
Structure conservation index	0.83
SVM decision value	0.27
SVM RNA-class probability	0.661681
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16200523 120 - 23771897
CGCCCGCAUCCGCAUACCCAUUACUCUGAUUAAACCAAGUGGCUCCACCGGGCAACAAGACUCUAUUGAAGUAGCAAUAAAUUUAGAUGCGGGAACUUCCUAGAAAGUAUAUUUAUACUU
..((((((((..............(((.......((..(((....)))..)).....)))...(((((......)))))......))))))))...........((((((....)))))) ( -25.70)
>DroSec_CAF1 19471 120 - 1
CGCCCGCAUCCGCAUACCCAUUGCUCUGAUUAAACCAAGUGGCUCCACCGGGCAACAAGACUCUGUCGAAGGAGCAAUAAAUUUAGAUGCGGGAACUUCCUAGAAAGUAUAUUUAUACUU
..((((((((.........((((((((.......((..(((....)))..))......(((...)))...)))))))).......))))))))...........((((((....)))))) ( -33.29)
>DroSim_CAF1 21317 120 - 1
CGCCCGCAUCCGCAUACCCAUUGCUCUGAUUAAACCAAGUGGCUCCACCGGGCAACAAGACUCUGUCGAAGGAGCAAUAAAUUUAGAUGCGGGAACUUCCUAGAAAGUAUAUUUAUACUU
..((((((((.........((((((((.......((..(((....)))..))......(((...)))...)))))))).......))))))))...........((((((....)))))) ( -33.29)
>DroEre_CAF1 18913 120 - 1
CACCCGCAUCGGCAUACCCAUUGCUCUGAUUAAACCAAGUGGCUCCGCCGGGCAACAAGACUCUAUCAAAAGAAUAAUAAAUUUAAAUAUGGAAACUUCCUAGAAAGUAUAUUUAUACUC
.....((.(((((....(((((...............)))))....)))))))........((((((....)).................(((....))))))).(((((....))))). ( -17.66)
>DroYak_CAF1 55787 120 - 1
CGCCCGCAUCGGCAUACCCAUUGCUCUGAUUAAACCAAGUGGCUCCACCGGGCAACAAGACUCUGUCAAGGGAAUAAUAAAUUUAGAUGCGGGAACUUCCUAGAAAGUAUAUUUAUACUU
..((((((((......(((.((((((((.......)).(((....))).))))))...(((...)))..)))..(((.....)))))))))))...........((((((....)))))) ( -31.40)
>consensus
CGCCCGCAUCCGCAUACCCAUUGCUCUGAUUAAACCAAGUGGCUCCACCGGGCAACAAGACUCUGUCGAAGGAGCAAUAAAUUUAGAUGCGGGAACUUCCUAGAAAGUAUAUUUAUACUU
..((((((((.........((((((((.......((..(((....)))..))......((.....))...)))))))).......))))))))...........((((((....)))))) (-23.35 = -24.15 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:06 2006