Locus 3292

Sequence ID	X_DroMel_CAF1
Location	8,760,037 – 8,760,167
Length	130
Max. P	0.985107

overview

Window 0

Location	8,760,037 – 8,760,127
Length	90
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	81.11
Mean single sequence MFE	-24.78
Consensus MFE	-16.17
Energy contribution	-16.55
Covariance contribution	0.38
Combinations/Pair	1.10
Mean z-score	-2.68
Structure conservation index	0.65
SVM decision value	2.00
SVM RNA-class probability	0.985107
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8760037 90 + 22224390
UUAACCCUAA----------CAAUU----------GCAAUUAAUCAUUUGUUUGCGAAUGCAAAUGAAAUGGCGAAAGUUUUU-GCCAUUUUUGUAGCAUAUAAAUUGUGU
.........(----------(((((----------((((.(((....))).))))..((((....(((((((((((....)))-))))))))....))))...)))))).. ( -23.50)
>DroSec_CAF1 8047 99 + 1
UUAACCAUUA----------CAAUUACAAUUUGCGGCAAUUAAUCAUUUGUUUACGAAUGCAAAUGAAAUGGCGAAAGUUUUU-GCCAUUCUUGCAGCAUAUAAAUU-UGC
..........----------(((........(((.((((....((((((((........))))))))(((((((((....)))-)))))).)))).))).......)-)). ( -24.36)
>DroSim_CAF1 9010 99 + 1
UUAACCCUUA----------CAAUUACAAUUUGCGGCAAUUAAUCAUUUGUUUACGAAUGCAAAUGAAAUGGCGAAAGUUUUU-GCCAUUCUUGCAGCAUAUAAAUU-UGC
..........----------(((........(((.((((....((((((((........))))))))(((((((((....)))-)))))).)))).))).......)-)). ( -24.36)
>DroEre_CAF1 7212 108 + 1
UUAACCCGCGUUUGCCGUCUCAAUUACAAUUGGCGGCCAUUAAUCAUUUGUUUGUGAAUGCAAAUGAAAUGGUGAAAGUUUGGUGCCAUUCUUGCAGCAU--AAAUU-CGC
.......(((...((((((............))))))......((((((((........)))))))).(((.((.(((..((....))..))).)).)))--.....-))) ( -26.90)
>consensus
UUAACCCUUA__________CAAUUACAAUUUGCGGCAAUUAAUCAUUUGUUUACGAAUGCAAAUGAAAUGGCGAAAGUUUUU_GCCAUUCUUGCAGCAUAUAAAUU_UGC
................................((.((((....((((((((........))))))))((((((...........)))))).)))).))............. (-16.17 = -16.55 +   0.38)

alignment

secondary structure

dotplot

Window 1

Location	8,760,056 – 8,760,167
Length	111
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	80.44
Mean single sequence MFE	-29.90
Consensus MFE	-15.64
Energy contribution	-17.20
Covariance contribution	1.56
Combinations/Pair	1.12
Mean z-score	-2.43
Structure conservation index	0.52
SVM decision value	1.08
SVM RNA-class probability	0.912072
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8760056 111 + 22224390
UUAAUCAUUUGUUUGCGAAUGCAAAUGAAAUGGCGAAAGUUUUU-GCCAUUUUUGUAGCAUAUAAAUUGUGUUUUGUGCGAUAAAGUGCGCAGCAAGGGUGUGGGGUUGACC
((((((....((((((....))))))(((((((((((....)))-)))))))).....(((((...((((....((((((......))))))))))..))))).)))))).. ( -31.00)
>DroSec_CAF1 8076 109 + 1
UUAAUCAUUUGUUUACGAAUGCAAAUGAAAUGGCGAAAGUUUUU-GCCAUUCUUGCAGCAUAUAAAUU-UGCUUUGUGCGAUA-AGUACGCAGCAAGGGUGGGGGGUCGACC
....((((((((........))))))))...(((....)))(((-.((((((((((((((........-))))..((((....-.))))...)))))))))).)))...... ( -34.10)
>DroSim_CAF1 9039 105 + 1
UUAAUCAUUUGUUUACGAAUGCAAAUGAAAUGGCGAAAGUUUUU-GCCAUUCUUGCAGCAUAUAAAUU-UGCUUUGUGCGAUA-AGUACGCA----GGGUGAGGGGUCGACC
....((((((((........))))))))(((((((((....)))-))))))(((((((((........-))))..((((....-.)))))))----))....((......)) ( -31.30)
>DroEre_CAF1 7251 100 + 1
UUAAUCAUUUGUUUGUGAAUGCAAAUGAAAUGGUGAAAGUUUGGUGCCAUUCUUGCAGCAU--AAAUU-CGCCUUGUGCGAUA-AGUA--CAGCAA------GGGGUCGACC
....((((((((........)))))))).(((.((.(((..((....))..))).)).)))--....(-(((((..(((....-....--..))).------.))).))).. ( -26.60)
>DroYak_CAF1 6559 86 + 1
UUAAUCAUUUGUUUGUGAAUGCAAAUGAAAUGGCGAAAGUUUUG-GCCA-----------------UU-UGCCAUGUGCGAUA-AGUA--CAGCAA----AAAGGGUCGACC
....((((((((........))))))))...(((....)))(((-(((.-----------------((-(((..(((((....-.)))--))))))----)...)))))).. ( -26.50)
>consensus
UUAAUCAUUUGUUUGCGAAUGCAAAUGAAAUGGCGAAAGUUUUU_GCCAUUCUUGCAGCAUAUAAAUU_UGCUUUGUGCGAUA_AGUACGCAGCAAGGGUGAGGGGUCGACC
....((((((((........))))))))((((((...........))))))...................(((.(((((......))))).))).........((.....)) (-15.64 = -17.20 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:45 2006