Locus 1483

Sequence ID	3L_DroMel_CAF1
Location	4,324,552 – 4,324,655
Length	103
Max. P	0.788082

overview

Window 8

Location	4,324,552 – 4,324,655
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	88.88
Mean single sequence MFE	-19.21
Consensus MFE	-14.16
Energy contribution	-15.50
Covariance contribution	1.34
Combinations/Pair	1.08
Mean z-score	-3.07
Structure conservation index	0.74
SVM decision value	0.04
SVM RNA-class probability	0.552516
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4324552 103 + 23771897
GCGAAACAAUGACAAUAAAAAGCAAUAAAGAAAUUAACAAAUUGCUGGCAAAAG-----------------AAAAAAAAAAACAUUGAAAAGUGUUAGAUUCGAUUGAAGAUUGUCAUCG
........((((((((......((((...(((.........(((....)))...-----------------.........((((((....))))))...))).))))...)))))))).. ( -17.00)
>DroSec_CAF1 11217 100 + 1
GCGAAACAAUGACAAUAAAAAGCAAUAAAGAAAUUAACAAAUUGCUGGCAAGAG-----------------AAAU---AAAACAUUGAAAAGUGUUAGAUUCGAUUGAAGAUUGUCAUCG
........((((((((....((((((..............))))))..(((..(-----------------((..---..((((((....))))))...)))..)))...)))))))).. ( -19.74)
>DroSim_CAF1 9826 100 + 1
GCGAAACAAUGACAAUAAAAAGCAAUAAAGAAAUUAACAAAUUACUGGCAAGAG-----------------AAAU---AAAACAUUGAAAAGUGUUAGAUUCGAUUGAAGAUUGUCAUCG
........((((((((......((((...(((.((((((..(((.((.....(.-----------------...)---....)).)))....)))))).))).))))...)))))))).. ( -16.50)
>DroEre_CAF1 11091 100 + 1
GCGAAACAAUGACAAUAAAAAGCAAUAAAGAAAUUAACAAAUUGCUGGCGAGGG-----------------GAAU---AAAACAUUAAAAAGUGUUAAAUUCGAUUGAAGAUUGUCAUCG
........((((((((....((((((..............))))))..(((...-----------------((((---..((((((....))))))..))))..)))...)))))))).. ( -17.34)
>DroYak_CAF1 10121 100 + 1
GCGAAACAAUGACAAUGAAAAGCAAUAAAGAAAUUAACAAAUUGCUGGCCAGAG-----------------AAAU---GAAACAUUGAAAAGUGUUAAAUUCGAUUGAAGAUUGUCAUCG
........((((((((....((((((..............))))))...(((.(-----------------((..---..((((((....))))))...)))..)))...)))))))).. ( -17.54)
>DroAna_CAF1 11477 117 + 1
ACAAAACAAUGACAAUAAAAAGCAAUAAAGAAAUUAACAAAUUGCCGGCAAGAGGCCGAGGAGAGUCGAGAAAAU---AAAACACUGAAAAGUGUUAAAUUCGAUUGAAGAUUGUCAUCG
........((((((((.....(((((..............)))))((((.....)))).....(((((((.....---..((((((....))))))...)))))))....)))))))).. ( -27.14)
>consensus
GCGAAACAAUGACAAUAAAAAGCAAUAAAGAAAUUAACAAAUUGCUGGCAAGAG_________________AAAU___AAAACAUUGAAAAGUGUUAAAUUCGAUUGAAGAUUGUCAUCG
........((((((((......((((...(((.........(((....))).............................((((((....))))))...))).))))...)))))))).. (-14.16 = -15.50 +   1.34)

alignment

secondary structure

dotplot

Window 9

Location	4,324,552 – 4,324,655
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	88.88
Mean single sequence MFE	-17.43
Consensus MFE	-13.59
Energy contribution	-13.32
Covariance contribution	-0.28
Combinations/Pair	1.10
Mean z-score	-2.96
Structure conservation index	0.78
SVM decision value	0.58
SVM RNA-class probability	0.788082
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4324552 103 - 23771897
CGAUGACAAUCUUCAAUCGAAUCUAACACUUUUCAAUGUUUUUUUUUUU-----------------CUUUUGCCAGCAAUUUGUUAAUUUCUUUAUUGCUUUUUAUUGUCAUUGUUUCGC
((((((((((...(((..(((...((((........)))).......))-----------------)..)))..((((((..(.......)...))))))....))))))))))...... ( -14.90)
>DroSec_CAF1 11217 100 - 1
CGAUGACAAUCUUCAAUCGAAUCUAACACUUUUCAAUGUUUU---AUUU-----------------CUCUUGCCAGCAAUUUGUUAAUUUCUUUAUUGCUUUUUAUUGUCAUUGUUUCGC
((((((((((...(((..(((...((((........))))..---..))-----------------)..)))..((((((..(.......)...))))))....))))))))))...... ( -15.90)
>DroSim_CAF1 9826 100 - 1
CGAUGACAAUCUUCAAUCGAAUCUAACACUUUUCAAUGUUUU---AUUU-----------------CUCUUGCCAGUAAUUUGUUAAUUUCUUUAUUGCUUUUUAUUGUCAUUGUUUCGC
((((((((((...(((..(((...((((........))))..---..))-----------------)..)))..((((((..(.......)...))))))....))))))))))...... ( -13.90)
>DroEre_CAF1 11091 100 - 1
CGAUGACAAUCUUCAAUCGAAUUUAACACUUUUUAAUGUUUU---AUUC-----------------CCCUCGCCAGCAAUUUGUUAAUUUCUUUAUUGCUUUUUAUUGUCAUUGUUUCGC
((((((((((........((((..((((........))))..---))))-----------------........((((((..(.......)...))))))....))))))))))...... ( -18.00)
>DroYak_CAF1 10121 100 - 1
CGAUGACAAUCUUCAAUCGAAUUUAACACUUUUCAAUGUUUC---AUUU-----------------CUCUGGCCAGCAAUUUGUUAAUUUCUUUAUUGCUUUUCAUUGUCAUUGUUUCGC
((((((((((........(((...((((........))))..---..))-----------------)...((..((((((..(.......)...))))))..))))))))))))...... ( -16.60)
>DroAna_CAF1 11477 117 - 1
CGAUGACAAUCUUCAAUCGAAUUUAACACUUUUCAGUGUUUU---AUUUUCUCGACUCUCCUCGGCCUCUUGCCGGCAAUUUGUUAAUUUCUUUAUUGCUUUUUAUUGUCAUUGUUUUGU
((((((((((......((((((..((((((....))))))..---))....)))).......((((.....))))(((((..(.......)...))))).....))))))))))...... ( -25.30)
>consensus
CGAUGACAAUCUUCAAUCGAAUCUAACACUUUUCAAUGUUUU___AUUU_________________CUCUUGCCAGCAAUUUGUUAAUUUCUUUAUUGCUUUUUAUUGUCAUUGUUUCGC
((((((((((..............((((........))))..................................((((((..(.......)...))))))....))))))))))...... (-13.59 = -13.32 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:49 2006