Locus 2883

Sequence ID	X_DroMel_CAF1
Location	7,707,652 – 7,707,810
Length	158
Max. P	0.937078

overview

Window 4

Location	7,707,652 – 7,707,770
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	75.28
Mean single sequence MFE	-37.45
Consensus MFE	-24.19
Energy contribution	-25.82
Covariance contribution	1.63
Combinations/Pair	1.04
Mean z-score	-1.52
Structure conservation index	0.65
SVM decision value	-0.03
SVM RNA-class probability	0.518800
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7707652 118 - 22224390
AUCCGGCCACGCCCCGUCCUGCCCACCUA--AACGCAAAGCCCACAAAGGCAGCGGGAACAACCGCUGCACAAUGUGGCAAAUGUUGGCCACUCAUUACGGAUUGCCGAGGUGCCAACUG
.....((((((....((..(((.......--...)))..))........(((((((......)))))))....))))))....((((((.(((.....(((....))).))))))))).. ( -38.90)
>DroSec_CAF1 6263 90 - 1
--------------------------CUA--AACGCAACGCCCAC--UGGCAGCGGGAACAACCGCCGCACAAUGUGGCAAAUGUUGGCCACUCAUUACGGAUUGCCGAGGUGCCAACUG
--------------------------...--........(((((.--((((.((((......)))).)).)).)).)))....((((((.(((.....(((....))).))))))))).. ( -31.70)
>DroSim_CAF1 15545 116 - 1
AUCCGGCCACGCCACGUCCUGCCCACCUA--AACGCAACGCCCAC--UGGCAGCGGGAACAACCGCCGCACAAUGUGGCAAAUGUUGGCCACUCAUUACGGAUUGCCGAGGUGCCAACUG
..........(((((((..(((.......--........(((...--.))).((((......)))).)))..)))))))....((((((.(((.....(((....))).))))))))).. ( -39.20)
>DroEre_CAF1 5302 101 - 1
AUCCGGCCACGCCCCUUCCUGC----CCACUGGGGCA---------------GCGGUAGCAAGCGCCGCACAAUGUGGCAAAUGUUGGCCACUCAUUACGGAUUGUCGAGGUGCCAGCCG
.....((((((((((.......----.....))))).---------------(((((.......))))).....)))))....((((((..(((((........)).)))..)))))).. ( -40.00)
>consensus
AUCCGGCCACGCCCCGUCCUGC____CUA__AACGCAACGCCCAC__UGGCAGCGGGAACAACCGCCGCACAAUGUGGCAAAUGUUGGCCACUCAUUACGGAUUGCCGAGGUGCCAACUG
.....(((((((........))............((...(((......))).((((......)))).)).....)))))....((((((..(((.............)))..)))))).. (-24.19 = -25.82 +   1.63)

alignment

secondary structure

dotplot

Window 5

Location	7,707,692 – 7,707,810
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	80.90
Mean single sequence MFE	-44.90
Consensus MFE	-32.98
Energy contribution	-33.90
Covariance contribution	0.92
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.73
SVM decision value	1.26
SVM RNA-class probability	0.937078
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7707692 118 - 22224390
AGGAGGCGGCUUAGGACCAAGUUCGCUGCACAGCCGCCACAUCCGGCCACGCCCCGUCCUGCCCACCUA--AACGCAAAGCCCACAAAGGCAGCGGGAACAACCGCUGCACAAUGUGGCA
((((((((((((((((......)).)))...)))))))......(((...)))...)))).........--........(((.(((...(((((((......)))))))....)))))). ( -44.00)
>DroSim_CAF1 15585 116 - 1
AGGAGGCGGCUUAGGACCAAGUUCGCUGCACAGCCGCCACAUCCGGCCACGCCACGUCCUGCCCACCUA--AACGCAACGCCCAC--UGGCAGCGGGAACAACCGCCGCACAAUGUGGCA
.(((((((((((((((......)).)))...)))))))...)))......(((((((..(((.......--........(((...--.))).((((......)))).)))..))))))). ( -44.20)
>DroEre_CAF1 5342 101 - 1
AGGACGCGGCUUAGGAGCAAGUUCGCUGCACAGCCGCCACAUCCGGCCACGCCCCUUCCUGC----CCACUGGGGCA---------------GCGGUAGCAAGCGCCGCACAAUGUGGCA
.(((.((((((..(.(((......))).)..))))))....))).((((((((((.......----.....))))).---------------(((((.......))))).....))))). ( -46.50)
>consensus
AGGAGGCGGCUUAGGACCAAGUUCGCUGCACAGCCGCCACAUCCGGCCACGCCCCGUCCUGCCCACCUA__AACGCAA_GCCCAC___GGCAGCGGGAACAACCGCCGCACAAUGUGGCA
.(((((((((((((((......)).)))...)))))))...))).(((((((........))............((...(((......))).((((......)))).)).....))))). (-32.98 = -33.90 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:46 2006