Locus 4431

Sequence ID	2R_DroMel_CAF1
Location	14,566,965 – 14,567,093
Length	128
Max. P	0.999631

overview

Window 1

Location	14,566,965 – 14,567,072
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	96.82
Mean single sequence MFE	-23.78
Consensus MFE	-23.36
Energy contribution	-24.04
Covariance contribution	0.68
Combinations/Pair	1.06
Mean z-score	-2.18
Structure conservation index	0.98
SVM decision value	3.81
SVM RNA-class probability	0.999631
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14566965 107 + 20766785
CAAUUUAAACAUUUAUGAGACCACCAAAUGCGAUGAGUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUUCUUGUCAGCGUUUCUUUUAAAUGUUUGC
.....((((((((((.((((......(((((((..((..((.(..(((((((........)))))))...).....)).))..)).))))))))).)))))))))). ( -24.00)
>DroSec_CAF1 199241 107 + 1
CAAUUUAAACAAUUAUGAGACCACCAAAUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUACUCGUCAGCGUUUCUUUUAAAUGUUUGC
.....((((((.(((.((((......((((((((((.........(((((((........)))))))...((......))))))).))))))))).))).)))))). ( -20.30)
>DroSim_CAF1 200683 107 + 1
CAAUUUAAACAUUUAUGAGACCACCAAAUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUACUCGUCAGCGUUUCUUUCAAAUGUUUGC
.....(((((((((..((((......((((((((((.........(((((((........)))))))...((......))))))).)))))))))..))))))))). ( -22.50)
>DroEre_CAF1 205692 107 + 1
CAGUUUAAACAUUUAUGAGACCACCAAAUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAGGUAAACAAAUGUUUCUGUAUUCGUCAGCGUUUCUUUUAAAUGUUUGC
.....((((((((((.((((......((((((((((((.((....(((((((........)))))))...))......))))))).))))))))).)))))))))). ( -26.00)
>DroYak_CAF1 212987 107 + 1
CAAUUUAAACAUUUAUGAGACCACCAAAUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUAUUCGUCAGCGUUUCUUUUAAAUGUUUGC
.....((((((((((.((((......((((((((((((.((....(((((((........)))))))...))......))))))).))))))))).)))))))))). ( -26.10)
>consensus
CAAUUUAAACAUUUAUGAGACCACCAAAUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUACUCGUCAGCGUUUCUUUUAAAUGUUUGC
.....((((((((((.((((......((((((((((((.((....(((((((........)))))))...))......))))))).))))))))).)))))))))). (-23.36 = -24.04 +   0.68)

alignment

secondary structure

dotplot

Window 2

Location	14,566,965 – 14,567,072
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	96.82
Mean single sequence MFE	-22.54
Consensus MFE	-22.46
Energy contribution	-22.50
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.56
Structure conservation index	1.00
SVM decision value	2.04
SVM RNA-class probability	0.986434
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14566965 107 - 20766785
GCAAACAUUUAAAAGAAACGCUGACAAGAACAGAAACAUUUGUUUACUUUGCAAUGUAAACAGAGAGCAACUCAUCGCAUUUGGUGGUCUCAUAAAUGUUUAAAUUG
..(((((((((..(((..(((..(...((.........(((((((((........)))))))))(((...))).))....)..))).)))..)))))))))...... ( -23.20)
>DroSec_CAF1 199241 107 - 1
GCAAACAUUUAAAAGAAACGCUGACGAGUACAGAAACAUUUGUUUACUUUGCAAUGUAAACAGAGAGCAAUUCAUCGCAUUUGGUGGUCUCAUAAUUGUUUAAAUUG
..(((((.(((..(((..(((..((((...........(((((((((........)))))))))..........)))...)..))).)))..))).)))))...... ( -20.70)
>DroSim_CAF1 200683 107 - 1
GCAAACAUUUGAAAGAAACGCUGACGAGUACAGAAACAUUUGUUUACUUUGCAAUGUAAACAGAGAGCAAUUCAUCGCAUUUGGUGGUCUCAUAAAUGUUUAAAUUG
..(((((((((..(((..(((..((((...........(((((((((........)))))))))..........)))...)..))).)))..)))))))))...... ( -23.60)
>DroEre_CAF1 205692 107 - 1
GCAAACAUUUAAAAGAAACGCUGACGAAUACAGAAACAUUUGUUUACCUUGCAAUGUAAACAGAGAGCAAUUCAUCGCAUUUGGUGGUCUCAUAAAUGUUUAAACUG
..(((((((((..(((..(((..(..............(((((((((........)))))))))..((........))..)..))).)))..)))))))))...... ( -22.00)
>DroYak_CAF1 212987 107 - 1
GCAAACAUUUAAAAGAAACGCUGACGAAUACAGAAACAUUUGUUUACUUUGCAAUGUAAACAGAGAGCAAUUCAUCGCAUUUGGUGGUCUCAUAAAUGUUUAAAUUG
..(((((((((..(((..(((..(..............(((((((((........)))))))))..((........))..)..))).)))..)))))))))...... ( -23.20)
>consensus
GCAAACAUUUAAAAGAAACGCUGACGAGUACAGAAACAUUUGUUUACUUUGCAAUGUAAACAGAGAGCAAUUCAUCGCAUUUGGUGGUCUCAUAAAUGUUUAAAUUG
..(((((((((..(((..(((..(..............(((((((((........)))))))))..((........))..)..))).)))..)))))))))...... (-22.46 = -22.50 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	14,566,992 – 14,567,093
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	96.24
Mean single sequence MFE	-22.44
Consensus MFE	-20.75
Energy contribution	-20.99
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.92
Structure conservation index	0.92
SVM decision value	2.62
SVM RNA-class probability	0.995797
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14566992 101 + 20766785
AUGCGAUGAGUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUUCUUGUCAGCGUUUCUUUUAAAUGUUUGCGAAUUUUCGAAUUUGUUUAAA
.(((((((....((.....))...)))))))...(((((((((......((((..((.(((((((.....))))))).))))))......))))))))).. ( -21.50)
>DroSec_CAF1 199268 101 + 1
AUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUACUCGUCAGCGUUUCUUUUAAAUGUUUGCGAAUUUUCGAAUUUGUUUAAA
.(((((((....((.....))...)))))))...(((((((((..........((((.(((((((.....))))))).))))........))))))))).. ( -22.27)
>DroSim_CAF1 200710 101 + 1
AUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUACUCGUCAGCGUUUCUUUCAAAUGUUUGCGAAUUUUCGAAUUUGUUUAAA
.(((((((....((.....))...)))))))...(((((((((..........((((.(((((((.....))))))).))))........))))))))).. ( -22.37)
>DroEre_CAF1 205719 101 + 1
AUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAGGUAAACAAAUGUUUCUGUAUUCGUCAGCGUUUCUUUUAAAUGUUUGCGAAUUUUCGAAUUUGUUGAAU
.(((((((....((.....))...))))))).....(((((((........((((((.(((((((.....))))))).))))))......))))))).... ( -23.04)
>DroYak_CAF1 213014 101 + 1
AUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUAUUCGUCAGCGUUUCUUUUAAAUGUUUGCGAAUUUUCGAAUUUGUUGAAU
.(((((((....((.....))...))))))).....(((((((........((((((.(((((((.....))))))).))))))......))))))).... ( -23.04)
>consensus
AUGCGAUGAAUUGCUCUCUGUUUACAUUGCAAAGUAAACAAAUGUUUCUGUACUCGUCAGCGUUUCUUUUAAAUGUUUGCGAAUUUUCGAAUUUGUUUAAA
.(((((((....((.....))...)))))))...(((((((((..........((((.(((((((.....))))))).))))........))))))))).. (-20.75 = -20.99 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:28 2006