Locus 2156

Sequence ID	3R_DroMel_CAF1
Location	6,177,826 – 6,178,037
Length	211
Max. P	0.946222

overview

Window 9

Location	6,177,826 – 6,177,945
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.49
Mean single sequence MFE	-25.30
Consensus MFE	-21.82
Energy contribution	-21.98
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.59
Structure conservation index	0.86
SVM decision value	0.80
SVM RNA-class probability	0.853215
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6177826 119 + 27905053
CAAAAGCUUUUCUCCCACCUUCUC-CAUCUCUUUCGCACUGUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGGCAGCAAAGAAAGAAAUUAGUGAAACAAAAAU
........................-...........(((((...((((((((..(((......)))..)).((((((((.........))))))))))))))...))))).......... ( -24.10)
>DroSec_CAF1 30047 119 + 1
CAAAAGCUUUUCUCCCACCUUCUC-CAUCUCUUUCGCACGGUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGACAGCAAAGAAAGAAAUUAGUGAAACAAAAAU
........................-......((((((..((((.((((((((..(((......)))..)).(((((((((......)).))))))))))))))))).))))))....... ( -22.20)
>DroSim_CAF1 33611 119 + 1
CAAAAGCUUUUCUCCCACCUUCUC-CAUCUCUUUCGCACGGUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGGCAGCAAAGAAAGAAAUUAGUGAAACAAAAAU
........................-......((((((..((((.((((((((..(((......)))..)).((((((((.........)))))))))))))))))).))))))....... ( -23.20)
>DroEre_CAF1 29312 120 + 1
CAAAAGCUUUUCUCCCACCUUCGCCCAUCUCUUUCGCACCGUUCUCUUUCCUCUCCGAGGUUUCGGCAACCUUUGUUGCUGCAACAUGGCAGCAAAGAAAGAAAUUAGCGAAACAAAAAU
...................(((((..((.((((((...(((.((((..........))))...))).........(((((((......))))))).)))))).))..)))))........ ( -29.00)
>DroYak_CAF1 30254 120 + 1
CAAAAGCUUUUCUCCCACCUUCUCCCAUCUCUUUCGCACUGUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCUGCAACAUAGCAGCAAAGAAAGAAAUUAGCGAAACAAAAAU
...............................((((((...(((.((((((((..(((......)))..)).....(((((((......))))))).)))))))))..))))))....... ( -28.00)
>consensus
CAAAAGCUUUUCUCCCACCUUCUC_CAUCUCUUUCGCACGGUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGGCAGCAAAGAAAGAAAUUAGUGAAACAAAAAU
...............................((((((...(((.((((((((..(((......)))..)).((((((((.........)))))))))))))))))..))))))....... (-21.82 = -21.98 +   0.16)

alignment

secondary structure

dotplot

Window 0

Location	6,177,826 – 6,177,945
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.49
Mean single sequence MFE	-35.92
Consensus MFE	-30.00
Energy contribution	-29.80
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-2.03
Structure conservation index	0.84
SVM decision value	1.36
SVM RNA-class probability	0.946222
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6177826 119 - 27905053
AUUUUUGUUUCACUAAUUUCUUUCUUUGCUGCCAUGUUGCUGCAACAAAGGUUGCCGAAACCUCGGAGACGAAAGAGAACAGUGCGAAAGAGAUG-GAGAAGGUGGGAGAAAAGCUUUUG
.(((((.(..((((..(((((.(((((..(((..((((.(((((((....))))).......(((....)))...))))))..)))..))))).)-)))).))))..).)))))...... ( -34.60)
>DroSec_CAF1 30047 119 - 1
AUUUUUGUUUCACUAAUUUCUUUCUUUGCUGUCAUGUUGCUGCAACAAAGGUUGCCGAAACCUCGGAGACGAAAGAGAACCGUGCGAAAGAGAUG-GAGAAGGUGGGAGAAAAGCUUUUG
.(((((.(..((((..((((((((.((((.((......)).)))).....((..((((....))))..)))))))))).((((.(....)..)))-)....))))..).)))))...... ( -34.10)
>DroSim_CAF1 33611 119 - 1
AUUUUUGUUUCACUAAUUUCUUUCUUUGCUGCCAUGUUGCUGCAACAAAGGUUGCCGAAACCUCGGAGACGAAAGAGAACCGUGCGAAAGAGAUG-GAGAAGGUGGGAGAAAAGCUUUUG
.(((((.(..((((..((((((((.((((.((......)).)))).....((..((((....))))..)))))))))).((((.(....)..)))-)....))))..).)))))...... ( -35.80)
>DroEre_CAF1 29312 120 - 1
AUUUUUGUUUCGCUAAUUUCUUUCUUUGCUGCCAUGUUGCAGCAACAAAGGUUGCCGAAACCUCGGAGAGGAAAGAGAACGGUGCGAAAGAGAUGGGCGAAGGUGGGAGAAAAGCUUUUG
...(((.((((((...((((((((((((((((......)))))..(..(((((.....)))))..).))))))))))).....)))))).)))....(((((((.........))))))) ( -36.60)
>DroYak_CAF1 30254 120 - 1
AUUUUUGUUUCGCUAAUUUCUUUCUUUGCUGCUAUGUUGCAGCAACAAAGGUUGCCGAAACCUCGGAGACGAAAGAGAACAGUGCGAAAGAGAUGGGAGAAGGUGGGAGAAAAGCUUUUG
.(((((.(..((((..((((((((.(((((((......))))))).....((..((((....))))..)))))))))).((...(....)...))......))))..).)))))...... ( -38.50)
>consensus
AUUUUUGUUUCACUAAUUUCUUUCUUUGCUGCCAUGUUGCUGCAACAAAGGUUGCCGAAACCUCGGAGACGAAAGAGAACAGUGCGAAAGAGAUG_GAGAAGGUGGGAGAAAAGCUUUUG
.(((((.(..((((..((((((((.((((.((......)).)))).....((..((((....))))..))))))))))......(....)...........))))..).)))))...... (-30.00 = -29.80 +  -0.20)

alignment

secondary structure

dotplot

Window 1

Location	6,177,865 – 6,177,969
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.31
Mean single sequence MFE	-25.11
Consensus MFE	-19.26
Energy contribution	-19.42
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	0.77
SVM decision value	0.66
SVM RNA-class probability	0.814150
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6177865 104 + 27905053
GUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGGCAGCAAAGAAAGAAAUUAGUGAAACAAAAAUCAAAGCAAAAAGCCA----------------ACAAAGAAC
(((((...(((....)))(((((..((...(((((((((.........)))))))))...........(((........)))..))...))))).----------------....))))) ( -22.30)
>DroSec_CAF1 30086 104 + 1
GUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGACAGCAAAGAAAGAAAUUAGUGAAACAAAAAUCAAAGCAAAAAGCCA----------------ACAAAGAGC
...((((((((....)))(((((..((...((((((((((......)).))))))))...........(((........)))..))...))))).----------------...))))). ( -21.70)
>DroSim_CAF1 33650 104 + 1
GUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGGCAGCAAAGAAAGAAAUUAGUGAAACAAAAAUCAAAGCAAAAAGCCA----------------ACAAAGAGC
...((((((((....)))(((((..((...(((((((((.........)))))))))...........(((........)))..))...))))).----------------...))))). ( -22.70)
>DroEre_CAF1 29352 118 + 1
GUUCUCUUUCCUCUCCGAGGUUUCGGCAACCUUUGUUGCUGCAACAUGGCAGCAAAGAAAGAAAUUAGCGAAACAAAAAUCAAAUCAAAAAGCCA--GCCAGCAGAGCCCGGCAAAGAAC
((((((((((......((((((.....))))))..(((((((......))))))).)))))).............................(((.--(((....).))..)))...)))) ( -28.20)
>DroYak_CAF1 30294 120 + 1
GUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCUGCAACAUAGCAGCAAAGAAAGAAAUUAGCGAAACAAAAAUCAAAGCAAAAAGCCAAAGCCAACAGAGCCCAGCAAAGAAC
(((((...(((....)))(((((.(((...(((((((((((.....)))))))))))..........((...............)).....))).)))))...)))))............ ( -30.66)
>consensus
GUUCUCUUUCGUCUCCGAGGUUUCGGCAACCUUUGUUGCAGCAACAUGGCAGCAAAGAAAGAAAUUAGUGAAACAAAAAUCAAAGCAAAAAGCCA________________ACAAAGAAC
(((((..((((....))))((((((....)(((((((((.........)))))))))............))))).........................................))))) (-19.26 = -19.42 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	6,177,945 – 6,178,037
Length	92
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	86.16
Mean single sequence MFE	-29.98
Consensus MFE	-25.50
Energy contribution	-25.90
Covariance contribution	0.40
Combinations/Pair	1.08
Mean z-score	-1.68
Structure conservation index	0.85
SVM decision value	0.62
SVM RNA-class probability	0.801849
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6177945 92 + 27905053
CAAAGCAAAAAGCCA----------------ACAAAGAACAACUUCAAAGUUCAACGCGCUUUCCACUGGGGCCUUUCAAAUGGGGCGAUUUCAGUGGGUGGCGGCAC
...........(((.----------------.....((((.........)))).....(((.((((((((((((((......)))))...))))))))).)))))).. ( -30.60)
>DroSec_CAF1 30166 92 + 1
CAAAGCAAAAAGCCA----------------ACAAAGAGCAACUUCAAAGUUCAACGCGCUUUCCACUGGGGCCUUUCAAAAGGGGCGAUUUCAGUGGGUGGCGACAC
....((.....))..----------------.....((((.........))))...(((((.((((((((((((((......)))))...))))))))).)))).).. ( -26.70)
>DroSim_CAF1 33730 92 + 1
CAAAGCAAAAAGCCA----------------ACAAAGAGCAACUUCAAAGUUCAACGCGCUUUCCACUGGGGCCUUUCAAAUGGGGCGAUUUCAGUGGGUGGCGACAC
....((.....))..----------------.....((((.........))))...(((((.((((((((((((((......)))))...))))))))).)))).).. ( -26.90)
>DroEre_CAF1 29432 106 + 1
CAAAUCAAAAAGCCA--GCCAGCAGAGCCCGGCAAAGAACAACUUCAAAGUUCAACGCGCUUUCCACUGGGCUCUUUCAAGUGGGGCGAUUUCAGUGGGUGGCGGCGC
...........(((.--((((..(((((.((.....((((.........))))..)).)))))((((((((((((.......)))))....))))))).))))))).. ( -33.70)
>DroYak_CAF1 30374 108 + 1
CAAAGCAAAAAGCCAAAGCCAACAGAGCCCAGCAAAGAACAACUUCAAAGUUCAACGCGCUUUCCACUGGGGCCUUUCAAGUGGGGCGAUUUCUGUGGGUGGCGGCAC
...........(((...(((.(((((((((((....(((....)))(((((.......)))))...)))))(((((......)))))...)))))).)))...))).. ( -32.00)
>consensus
CAAAGCAAAAAGCCA________________ACAAAGAACAACUUCAAAGUUCAACGCGCUUUCCACUGGGGCCUUUCAAAUGGGGCGAUUUCAGUGGGUGGCGGCAC
...........(((......................((((.........)))).....(((.((((((((((((((......)))))...))))))))).)))))).. (-25.50 = -25.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:42 2006