Locus 56

Sequence ID	2L_DroMel_CAF1
Location	217,615 – 217,720
Length	105
Max. P	0.947164

overview

Window 2

Location	217,615 – 217,720
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	92.57
Mean single sequence MFE	-25.10
Consensus MFE	-23.54
Energy contribution	-23.10
Covariance contribution	-0.44
Combinations/Pair	1.26
Mean z-score	-1.39
Structure conservation index	0.94
SVM decision value	1.21
SVM RNA-class probability	0.930757
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 217615 105 + 22407834
AUUCCUUUUCGGGCGAUUCCGAAUCCCCAGAACAGUUUUCUUCUGUAUUAGGGGCAGCUUCAUCUGCCUCCAUUUCUGACACUUUACCAUCAGGAACUGCAGGGG
....((.((((((.(((.....)))))).))).))....((((((((...(((((((......))))).)).(((((((..........))))))).)))))))) ( -29.90)
>DroSec_CAF1 9917 105 + 1
AUCCCUUUUCGGGCGAUUCCGAUUCCCCAGAACAGUUUUCUUCUGUAUUAGAGGCAACUUCAUCUGCCUCCAUUUCUGACACUUUACCAUCAGGAACUACAGGGG
....((.((((((.((.......))))).))).))....((((((((...((((((........))))))..(((((((..........))))))).)))))))) ( -27.80)
>DroSim_CAF1 9903 105 + 1
AUUCCUUUUCGGGCGAUUCCGAUUCCCCAGAACAGUUUUCUUCUGUAUUAGAGACAACUUCAUCUGCCUCCAUUUCUGACACUUUACCAUCAGGAACUACAGGGG
........(((((....)))))..(((((((..((((.((((........)))).))))...))).......(((((((..........))))))).....)))) ( -21.20)
>DroEre_CAF1 10202 105 + 1
AUUCCUUUUCGGGCGAUUUCGAUUCCCCAGAACAGUUUUCUUCUGUAUUAGAGGCAACUUCAUCUGCCUCCAUUUCUGACACUUUAACAUCAGAAGCUCCAGGGG
....((.((((((.((.......))))).))).))....((((((.....((((((........))))))..(((((((..........)))))))...)))))) ( -25.20)
>DroYak_CAF1 11958 105 + 1
AUUCCUUUUCGGGCGGUUUCAAUUCCCCAGAACAUUUUUCUUCUGUAUUAGAGGCGACAUCAUCUGUCUCCAUUUCUGACACUUUAACAUCAGGGGCUCCAGGGG
...((((...((((((.......))(((((((........))))((.(((((((.((((.....)))).))...))))).))..........))))))).)))). ( -21.40)
>consensus
AUUCCUUUUCGGGCGAUUCCGAUUCCCCAGAACAGUUUUCUUCUGUAUUAGAGGCAACUUCAUCUGCCUCCAUUUCUGACACUUUACCAUCAGGAACUACAGGGG
....((.((((((.((.......))))).))).))....((((((((...((((((........))))))..(((((((..........))))))).)))))))) (-23.54 = -23.10 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	217,615 – 217,720
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	92.57
Mean single sequence MFE	-32.02
Consensus MFE	-24.78
Energy contribution	-25.34
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-2.41
Structure conservation index	0.77
SVM decision value	1.37
SVM RNA-class probability	0.947164
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 217615 105 - 22407834
CCCCUGCAGUUCCUGAUGGUAAAGUGUCAGAAAUGGAGGCAGAUGAAGCUGCCCCUAAUACAGAAGAAAACUGUUCUGGGGAUUCGGAAUCGCCCGAAAAGGAAU
((((.((((((.(((((........)))))....((.(((((......))))))).............))))))...)))).(((((......)))))....... ( -35.10)
>DroSec_CAF1 9917 105 - 1
CCCCUGUAGUUCCUGAUGGUAAAGUGUCAGAAAUGGAGGCAGAUGAAGUUGCCUCUAAUACAGAAGAAAACUGUUCUGGGGAAUCGGAAUCGCCCGAAAAGGGAU
.((((....((((((((........))).....(((((((((......)))))))))...(((((.(....).))))))))))((((......))))..)))).. ( -33.10)
>DroSim_CAF1 9903 105 - 1
CCCCUGUAGUUCCUGAUGGUAAAGUGUCAGAAAUGGAGGCAGAUGAAGUUGUCUCUAAUACAGAAGAAAACUGUUCUGGGGAAUCGGAAUCGCCCGAAAAGGAAU
((((((((....(((((........)))))...(((((((((......))))))))).))))..((((.....))))))))..((((......))))........ ( -29.30)
>DroEre_CAF1 10202 105 - 1
CCCCUGGAGCUUCUGAUGUUAAAGUGUCAGAAAUGGAGGCAGAUGAAGUUGCCUCUAAUACAGAAGAAAACUGUUCUGGGGAAUCGAAAUCGCCCGAAAAGGAAU
.(((..((((((((((..(....)..)))))).(((((((((......)))))))))...............))))..)))..(((........)))........ ( -35.50)
>DroYak_CAF1 11958 105 - 1
CCCCUGGAGCCCCUGAUGUUAAAGUGUCAGAAAUGGAGACAGAUGAUGUCGCCUCUAAUACAGAAGAAAAAUGUUCUGGGGAAUUGAAACCGCCCGAAAAGGAAU
.(((..((((..((((..(....)..))))....((.((((.....)))).))...................))))..)))............((.....))... ( -27.10)
>consensus
CCCCUGGAGUUCCUGAUGGUAAAGUGUCAGAAAUGGAGGCAGAUGAAGUUGCCUCUAAUACAGAAGAAAACUGUUCUGGGGAAUCGGAAUCGCCCGAAAAGGAAU
.(((........(((((........)))))...(((((((((......)))))))))...(((((.(....).))))))))..((((......))))........ (-24.78 = -25.34 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:30 2006