Locus 1494

Sequence ID	X_DroMel_CAF1
Location	4,423,988 – 4,424,113
Length	125
Max. P	0.989707

overview

Window 0

Location	4,423,988 – 4,424,103
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.98
Mean single sequence MFE	-32.06
Consensus MFE	-21.38
Energy contribution	-23.26
Covariance contribution	1.88
Combinations/Pair	1.20
Mean z-score	-1.71
Structure conservation index	0.67
SVM decision value	0.09
SVM RNA-class probability	0.577311
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423988 115 + 22224390
UGCUAGCCCCUUGA-----GAAUCAGCGUCCAUAGGGUUUCCCUAUGGAUUUUUUUUGUAUAUAUGUAUAUCGCUUUGAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAA
........((((.(-----(((((...((((((((((...))))))))))....................((.((((.(((((((....))))))).))))...))..)))))))))).. ( -38.30)
>DroSec_CAF1 26393 106 + 1
-GCUAGCCUCUUGACAUGGGAAUCAGCGUCCAUAGGGUUUCCCUAUGGAUUUUUU-UG----UUUGUAU--------GAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAA
-.......((((......((((((...((((((((((...)))))))))).((((-.(----(((...(--------.(((((((....))))))).).)))).)))))))))).)))). ( -31.50)
>DroSim_CAF1 27719 115 + 1
UGCUAGCCUCUUGACAUGGGAAUCAGCGUCCAUAGGGUUUCCCUAUGCAUUUUUU-UG----UAUGUAUAUCGCCUUAAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAA
.(((..(((........)))....))).(((.((((((((...(((((((.....-..----.)))))))((.((((.(((((((....))))))).))))...)).)))))))).))). ( -31.10)
>DroEre_CAF1 27351 108 + 1
UGCUAGCCUCUUGACAUGAGAAUCAGCGUCCAUAGGGUUUCCCUAUGGAUUUUUU-CG--------UAUACCCCCUUAAAGUGUGGGAUAA---UUGUCGGAUUGCAGGAUUCUGAGGAA
......((((..((((((((((.....((((((((((...)))))))))).))))-))--------)...(((.(.......).)))....---..)))(((((....))))).)))).. ( -32.70)
>DroYak_CAF1 26962 108 + 1
UGCUAGUCUCUCGACAUGAGAAUCAGCGUCCAUAGGGUUUCCCUAUAGAUUUUUU-CG--------UAUAUCGCCUUCAAGUGUGGGAUCA---UUGUGGGAUUAAAGGAUUCUGAGGAA
......((((.......)))).((((.((((((((((...))))))...(((..(-(.--------((((...(((........)))....---.)))).))..))))))).)))).... ( -26.70)
>consensus
UGCUAGCCUCUUGACAUGAGAAUCAGCGUCCAUAGGGUUUCCCUAUGGAUUUUUU_UG____U_UGUAUAUCGCCUUAAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAA
........((((......((((((...((((((((((...)))))))))).......................(((..(((((((....)))))))..))).......)))))))))).. (-21.38 = -23.26 +   1.88)

alignment

secondary structure

dotplot

Window 1

Location	4,423,988 – 4,424,103
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.98
Mean single sequence MFE	-28.90
Consensus MFE	-18.68
Energy contribution	-20.16
Covariance contribution	1.48
Combinations/Pair	1.08
Mean z-score	-3.22
Structure conservation index	0.65
SVM decision value	2.18
SVM RNA-class probability	0.989707
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4423988 115 - 22224390
UUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUCAAAGCGAUAUACAUAUAUACAAAAAAAAUCCAUAGGGAAACCCUAUGGACGCUGAUUC-----UCAAGGGGCUAGCA
.(((((((((((............(((((((....)))))))...((((((((....))))..........(((((((((...))))))))))))))))))-----).)))))....... ( -36.20)
>DroSec_CAF1 26393 106 - 1
UUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUC--------AUACAAA----CA-AAAAAAUCCAUAGGGAAACCCUAUGGACGCUGAUUCCCAUGUCAAGAGGCUAGC-
.......(((((............(((((((....))))))).--------.......----..-......(((((((((...)))))))))....)))))....(((....)))....- ( -26.00)
>DroSim_CAF1 27719 115 - 1
UUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUUAAGGCGAUAUACAUA----CA-AAAAAAUGCAUAGGGAAACCCUAUGGACGCUGAUUCCCAUGUCAAGAGGCUAGCA
....((((..((.......((((.(((((((....))))))).))))...........----..-........(((((((...)))))))((((.((.....))))))..))..)))).. ( -27.90)
>DroEre_CAF1 27351 108 - 1
UUCCUCAGAAUCCUGCAAUCCGACAA---UUAUCCCACACUUUAAGGGGGUAUA--------CG-AAAAAAUCCAUAGGGAAACCCUAUGGACGCUGAUUCUCAUGUCAAGAGGCUAGCA
..((((((((((..((..........---.((((((.(.......)))))))..--------..-......(((((((((...))))))))).)).))))))........))))...... ( -31.20)
>DroYak_CAF1 26962 108 - 1
UUCCUCAGAAUCCUUUAAUCCCACAA---UGAUCCCACACUUGAAGGCGAUAUA--------CG-AAAAAAUCUAUAGGGAAACCCUAUGGACGCUGAUUCUCAUGUCGAGAGACUAGCA
......((((((.....(((((.(((---((......)).)))..)).)))...--------..-......(((((((((...)))))))))....))))))...(((....)))..... ( -23.20)
>consensus
UUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUCAAGGCGAUAUACA_A____CA_AAAAAAUCCAUAGGGAAACCCUAUGGACGCUGAUUCCCAUGUCAAGAGGCUAGCA
.......(((((............(((((((....))))))).............................(((((((((...)))))))))....)))))....(((....)))..... (-18.68 = -20.16 +   1.48)

alignment

secondary structure

dotplot

Window 2

Location	4,424,023 – 4,424,113
Length	90
Sequences	3
Columns	90
Reading direction	forward
Mean pairwise identity	86.79
Mean single sequence MFE	-21.33
Consensus MFE	-14.24
Energy contribution	-15.80
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-2.16
Structure conservation index	0.67
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4424023 90 + 22224390
CCCUAUGGAUUUUUUUUGUAUAUAUGUAUAUCGCUUUGAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAAACUUUGUUUG
.(((..(((((((((.(((((....)))))...((((.(((((((....))))))).))))...)))))))))..)))............ ( -21.10)
>DroSec_CAF1 26432 77 + 1
CCCUAUGGAUUUUUU-UG----UUUGUAU--------GAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAAACUUUGAUUG
.(((..(((((((((-.(----(((...(--------.(((((((....))))))).).)))).)))))))))..)))............ ( -19.20)
>DroSim_CAF1 27759 85 + 1
CCCUAUGCAUUUUUU-UG----UAUGUAUAUCGCCUUAAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAAACUUUGAUUG
.(((((((((.....-..----.)))))).((.((((.(((((((....))))))).))))...)))))..((.(((....))).))... ( -23.70)
>consensus
CCCUAUGGAUUUUUU_UG____UAUGUAUAUCGC_UUGAAGUGUGGGAUCACACUUGAAGGAUUGAAGGAUUCUAAGGAAACUUUGAUUG
.(((..(((((((((..................((((.(((((((....))))))).))))...)))))))))..)))............ (-14.24 = -15.80 +   1.56)

alignment

secondary structure

dotplot

Window 3

Location	4,424,023 – 4,424,113
Length	90
Sequences	3
Columns	90
Reading direction	reverse
Mean pairwise identity	86.79
Mean single sequence MFE	-12.50
Consensus MFE	-9.80
Energy contribution	-9.80
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.78
SVM decision value	0.28
SVM RNA-class probability	0.665063
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4424023 90 - 22224390
CAAACAAAGUUUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUCAAAGCGAUAUACAUAUAUACAAAAAAAAUCCAUAGGG
............(((((((.....)).((((((.(((((((....)))))))..))).)))........................))))) ( -12.70)
>DroSec_CAF1 26432 77 - 1
CAAUCAAAGUUUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUC--------AUACAAA----CA-AAAAAAUCCAUAGGG
............(((((((.....))........(((((((....))))))).--------.......----..-..........))))) (  -9.80)
>DroSim_CAF1 27759 85 - 1
CAAUCAAAGUUUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUUAAGGCGAUAUACAUA----CA-AAAAAAUGCAUAGGG
............(((((((.....))...((((.(((((((....))))))).))))...........----..-..........))))) ( -15.00)
>consensus
CAAUCAAAGUUUCCUUAGAAUCCUUCAAUCCUUCAAGUGUGAUCCCACACUUCAA_GCGAUAUACAUA____CA_AAAAAAUCCAUAGGG
............(((((((.....))........(((((((....))))))).................................))))) ( -9.80 =  -9.80 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:03 2006