Locus 9973

Sequence ID	3R_DroMel_CAF1
Location	26,690,535 – 26,690,651
Length	116
Max. P	0.692885

overview

Window 5

Location	26,690,535 – 26,690,651
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.20
Mean single sequence MFE	-29.58
Consensus MFE	-15.60
Energy contribution	-16.20
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.66
Structure conservation index	0.53
SVM decision value	0.33
SVM RNA-class probability	0.692885
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26690535 116 + 27905053
AUCUCCCCA---UCUCAAACUCCUGGCCUUCUCCUUGCUCGCUCUCUUUUCCACCAGGAAUAAAUGGAUCGAAUUUCCCGACGAGUUUGGCGAGUU-UGGUUUUGACUUCUGAUGGAAAU
......(((---(((((((..((..((..((.((..(((((.((....((((....)))).....(((.......))).)))))))..)).)))).-.)).))))).....))))).... ( -29.30)
>DroSec_CAF1 281261 103 + 1
AUCUCCCCAUCAUCUCAAACUACUUGCCU----------------CCUUUCCACCAGGAAUAAAUGGAUCGUAUUUCCCGACGAGUUUGGCGAGUU-UGGUUUUGACUUCUGAUGGAAAU
......((((((..(((((((((((((((----------------((.((((....)))).....)))((((........))))....))))))).-.)).)))))....)))))).... ( -29.00)
>DroSim_CAF1 278026 103 + 1
AUCUCCCCAUCAUCUGAAACUCCUUGCCU----------------CCUUUCCACCAGGAAUAAAUGGAUCGUAUUUCCCGACGAGUUUGGCGAGCU-UGGUUUUGACUUCUGAUGGAAAU
......((((((((.((((((.(((((((----------------((.((((....)))).....)))((((........))))....))))))..-.))))))))....)))))).... ( -27.60)
>DroEre_CAF1 297279 113 + 1
AUCUCCCCAUC-UCUCAAAGUCCUUAUU------UCGCUCGCUCUCUUUUCCACCAGGAAUAAAUGGAUCGUAUUUCCCGACGAGUUUAGCGAGUUUUGGUUUUGACUUCUGAUGGAAAU
......(((((-..((((((.((....(------(((((.((((((..((((....)))).....(((.......))).)).))))..))))))....)))))))).....))))).... ( -30.20)
>DroYak_CAF1 286315 111 + 1
AUCUCCCCAUC---UCAAAGUCCUUAUU------UCGCUCGCUCUCUUUUCCACCAGGAAUAAAUGGAUCGUAUUUCCCGACGAGUUUAGCGAGUUUUGGCUUUGACUUCUGAUGGAAAU
......(((((---((((((.((....(------(((((.((((((..((((....)))).....(((.......))).)).))))..))))))....)))))))).....))))).... ( -31.80)
>consensus
AUCUCCCCAUC_UCUCAAACUCCUUGCCU_____U_GCUCGCUCUCUUUUCCACCAGGAAUAAAUGGAUCGUAUUUCCCGACGAGUUUGGCGAGUU_UGGUUUUGACUUCUGAUGGAAAU
...............................................((((((.(((((......((((((...(((((((.....)))).)))...))))))....))))).)))))). (-15.60 = -16.20 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	26,690,535 – 26,690,651
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.20
Mean single sequence MFE	-30.50
Consensus MFE	-18.02
Energy contribution	-18.90
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-1.99
Structure conservation index	0.59
SVM decision value	-0.05
SVM RNA-class probability	0.505827
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26690535 116 - 27905053
AUUUCCAUCAGAAGUCAAAACCA-AACUCGCCAAACUCGUCGGGAAAUUCGAUCCAUUUAUUCCUGGUGGAAAAGAGAGCGAGCAAGGAGAAGGCCAGGAGUUUGAGA---UGGGGAGAU
.(..(((((.(....).....((-(((((......((((((.(((.......))).(((.((((....)))).))))).))))...((......))..))))))).))---)))..)... ( -30.40)
>DroSec_CAF1 281261 103 - 1
AUUUCCAUCAGAAGUCAAAACCA-AACUCGCCAAACUCGUCGGGAAAUACGAUCCAUUUAUUCCUGGUGGAAAGG----------------AGGCAAGUAGUUUGAGAUGAUGGGGAGAU
.(..((((((....(((((....-.(((.(((.......(((.......)))((((((.......))))))....----------------.))).)))..)))))..))))))..)... ( -28.10)
>DroSim_CAF1 278026 103 - 1
AUUUCCAUCAGAAGUCAAAACCA-AGCUCGCCAAACUCGUCGGGAAAUACGAUCCAUUUAUUCCUGGUGGAAAGG----------------AGGCAAGGAGUUUCAGAUGAUGGGGAGAU
.(..(((((((....)......(-((((((((.......(((.......)))((((((.......))))))....----------------.)))...))))))....))))))..)... ( -25.50)
>DroEre_CAF1 297279 113 - 1
AUUUCCAUCAGAAGUCAAAACCAAAACUCGCUAAACUCGUCGGGAAAUACGAUCCAUUUAUUCCUGGUGGAAAAGAGAGCGAGCGA------AAUAAGGACUUUGAGA-GAUGGGGAGAU
.(..(((((.((((((..........((((((...(((.(((.......)))((((((.......))))))...)))))))))...------......))))))....-)))))..)... ( -33.71)
>DroYak_CAF1 286315 111 - 1
AUUUCCAUCAGAAGUCAAAGCCAAAACUCGCUAAACUCGUCGGGAAAUACGAUCCAUUUAUUCCUGGUGGAAAAGAGAGCGAGCGA------AAUAAGGACUUUGA---GAUGGGGAGAU
.(..(((((.((((((..........((((((...(((.(((.......)))((((((.......))))))...)))))))))...------......))))))..---)))))..)... ( -34.81)
>consensus
AUUUCCAUCAGAAGUCAAAACCA_AACUCGCCAAACUCGUCGGGAAAUACGAUCCAUUUAUUCCUGGUGGAAAAGAGAGCGAGC_A_____AGGCAAGGAGUUUGAGA_GAUGGGGAGAU
.(..(((((.((.((..........))))..(((((((.(((.......)))((((((.......))))))...........................)))))))....)))))..)... (-18.02 = -18.90 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:06 2006