Locus 2959

Sequence ID	X_DroMel_CAF1
Location	7,900,814 – 7,900,971
Length	157
Max. P	0.969745

overview

Window 4

Location	7,900,814 – 7,900,931
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.51
Mean single sequence MFE	-53.60
Consensus MFE	-42.88
Energy contribution	-44.62
Covariance contribution	1.75
Combinations/Pair	1.02
Mean z-score	-4.28
Structure conservation index	0.80
SVM decision value	0.73
SVM RNA-class probability	0.835086
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7900814 117 + 22224390
UCUCCUCCUUUUCCACUGAUUUGAUCCUCCUUGCGAUUCCUUCGUUAGAGGGUAUGUAGGG-G--GGGUGAAAGUGGGUUUAGGGGGGGGAACUGGUCUUAUGUGGCCGGUGACCACCUC
...((((((..((((((...((.((((((((((((...(((((....)))))..)))))))-)--)))).))))))))...))))))((..(((((((......)))))))..))..... ( -58.60)
>DroSec_CAF1 1438 117 + 1
UCUCCUCCCUGUCCUCGGAUUUGAUCCUCCUUGCGAUUCCUUCGUUUGAGGGUAUGUUGGGGG--GGGUG-AAGUGGGUUUAGGGGGGGGAACUGGUCUUAUGUGGCCGGUGACCACCUC
(((((((((((..(((..((((.((((((((..((((.(((((....)))))...))))))))--)))).-)))))))..)))))))))))(((((((......)))))))......... ( -54.70)
>DroSim_CAF1 4553 115 + 1
UCUCCUCCCUGUCCUCUGAUUUGAUCCUCCUUGCGAUUCCUUCGUUUGAGGGUAUGUUGGG-G--GGGUG-AAGUGGGUUUAGGGG-GGGAACUGGUCUUAUGUGGCCGGUGACCACCUC
(((((.(((((..(((..((((.((((((((.(((...(((((....)))))..))).)))-)--)))).-)))))))..))))))-))))(((((((......)))))))......... ( -51.70)
>DroYak_CAF1 4575 118 + 1
UCUCCUCCUUGUCCUCUAAUUUGAUCCUCCUUGCGAUUCCUUCGUAUGAGGGUAUGUAGGG-GGAGGGUGAAAAUGGGUUUAGGGG-GGGAACUGGUCUUAUGUGGCCGGUGACCACCUC
(((((((((...(((....(((.((((((((((((...(((((....)))))..))))..)-))))))).)))..)))...)))))-))))(((((((......)))))))......... ( -49.40)
>consensus
UCUCCUCCCUGUCCUCUGAUUUGAUCCUCCUUGCGAUUCCUUCGUUUGAGGGUAUGUAGGG_G__GGGUG_AAGUGGGUUUAGGGG_GGGAACUGGUCUUAUGUGGCCGGUGACCACCUC
(((((((((((..(((...(((.((((.(((((((...(((((....)))))..)))))))....)))).)))..)))..)))))))))))(((((((......)))))))......... (-42.88 = -44.62 +   1.75)

alignment

secondary structure

dotplot

Window 5

Location	7,900,854 – 7,900,971
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.08
Mean single sequence MFE	-52.63
Consensus MFE	-45.05
Energy contribution	-45.98
Covariance contribution	0.94
Combinations/Pair	1.05
Mean z-score	-3.16
Structure conservation index	0.86
SVM decision value	1.65
SVM RNA-class probability	0.969745
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7900854 117 + 22224390
UUCGUUAGAGGGUAUGUAGGG-G--GGGUGAAAGUGGGUUUAGGGGGGGGAACUGGUCUUAUGUGGCCGGUGACCACCUCCUCCUCCUGCGACUGAUUACGCCUUCUCCUGCUGUUCUUG
.......(((..((.((((((-(--(((((..(((.((((((((((((((((((((((......))))))).......))))))))))).)))).))).))))))).)))))))..))). ( -54.11)
>DroSec_CAF1 1478 117 + 1
UUCGUUUGAGGGUAUGUUGGGGG--GGGUG-AAGUGGGUUUAGGGGGGGGAACUGGUCUUAUGUGGCCGGUGACCACCUCCUCCUCCUGCGACUGACUACGCCUUCUCCUGCUGUUCCUG
........((((...((.(((((--(((((-.(((.((((((((((((((((((((((......))))))).......))))))))))).)))).))).)))))))))).))...)))). ( -58.31)
>DroSim_CAF1 4593 115 + 1
UUCGUUUGAGGGUAUGUUGGG-G--GGGUG-AAGUGGGUUUAGGGG-GGGAACUGGUCUUAUGUGGCCGGUGACCACCUCCUCCUCCUGCGACUGACUACGCCUUCUCCUGCUGUUCCUG
........((((...((.(((-(--(((((-.(((.((((((((((-(((((((((((......))))))).......))).))))))).)))).))).))))))).)).))...)))). ( -50.11)
>DroYak_CAF1 4615 118 + 1
UUCGUAUGAGGGUAUGUAGGG-GGAGGGUGAAAAUGGGUUUAGGGG-GGGAACUGGUCUUAUGUGGCCGGUGACCACCUCCUCCUCCUGCGACUGACAACGCCUACUCCUGCUGUUCCUG
........((((...((((((-(..(((((....(.((((((((((-(((((((((((......))))))).......))).))))))).)))).)...))))).)))))))...)))). ( -48.01)
>consensus
UUCGUUUGAGGGUAUGUAGGG_G__GGGUG_AAGUGGGUUUAGGGG_GGGAACUGGUCUUAUGUGGCCGGUGACCACCUCCUCCUCCUGCGACUGACUACGCCUUCUCCUGCUGUUCCUG
........((((...((((((....(((((...((.((((((((((((((((((((((......))))))).......))))))))))).)))).))..)))))..))))))...)))). (-45.05 = -45.98 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:44 2006