Locus 4610

Sequence ID	2L_DroMel_CAF1
Location	13,190,667 – 13,190,769
Length	102
Max. P	0.775946

overview

Window 8

Location	13,190,667 – 13,190,769
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.99
Mean single sequence MFE	-28.50
Consensus MFE	-18.88
Energy contribution	-19.88
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.28
Structure conservation index	0.66
SVM decision value	0.21
SVM RNA-class probability	0.633791
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13190667 102 + 22407834
AUAGAAUAUGGAAGGCGUAAAGCUUUUCUAUUUGUUGAU--AUUGACAACGGUUGGU---GGCCA---GCU---------GUUGGGCCAAAGCUGAUAAGAGCA-AUGAGCCCAUAAAAC
...(((((.(((((((.....))))))))))))(((...--...)))(((((((((.---..)))---)))---------)))((((((..(((......))).-.)).))))....... ( -32.30)
>DroSec_CAF1 11063 120 + 1
AUAGAAUAUGGAAGGCGUAAAGCUUUUCUAUUUGUUGAUAAAUUGACAACGGUUGGUGGUGGCCAAAAGCUUGGGGAAAGGUUGGGGAAAAGCUGAUAAGAGCAAAUGAGCCCAUAAAAC
......(((((.........(((((((((..((((..(....)..))))...(((((....))))).(((((......)))))..))))))))).......((......))))))).... ( -25.90)
>DroSim_CAF1 11024 108 + 1
AUAGAAUAUGGAAGGCGUAAAGCUUUUCUAUUUGUUGAUAAAUUGACAACGGUUGGUGGUGGCCA---GCU---------GUUGGGGAAAAGCUGAUAAGAACAAAUGAGCCCAUAAAAC
......((((((((((.....)))))..((((((((......((..(((((((((((....))))---)))---------))))..))....((....))))))))))...))))).... ( -30.30)
>DroYak_CAF1 11200 104 + 1
AUGGAAUAUGGAAGGCGUAAAGCUUUUCUAUUUGUUGAUAAAUUGACAACGGUUAGU---GGCCA---GCU---------GUUGG-GAAAAGCUGAUAAGAGCAAAUGAGCCCAUAAAAC
((((.....(((((((.....)))))))((((((((.....((((((....))))))---...((---(((---------.....-....))))).....))))))))...))))..... ( -25.50)
>consensus
AUAGAAUAUGGAAGGCGUAAAGCUUUUCUAUUUGUUGAUAAAUUGACAACGGUUGGU___GGCCA___GCU_________GUUGGGGAAAAGCUGAUAAGAGCAAAUGAGCCCAUAAAAC
......(((((.........(((((((((..((((..(....)..)))).((((......)))).....................))))))))).......((......))))))).... (-18.88 = -19.88 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	13,190,667 – 13,190,769
Length	102
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.99
Mean single sequence MFE	-18.95
Consensus MFE	-16.23
Energy contribution	-16.35
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-1.65
Structure conservation index	0.86
SVM decision value	0.54
SVM RNA-class probability	0.775946
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13190667 102 - 22407834
GUUUUAUGGGCUCAU-UGCUCUUAUCAGCUUUGGCCCAAC---------AGC---UGGCC---ACCAACCGUUGUCAAU--AUCAACAAAUAGAAAAGCUUUACGCCUUCCAUAUUCUAU
(((((.(((((.((.-.(((......)))..)))))))((---------(((---.((..---.....)))))))....--.............)))))..................... ( -20.80)
>DroSec_CAF1 11063 120 - 1
GUUUUAUGGGCUCAUUUGCUCUUAUCAGCUUUUCCCCAACCUUUCCCCAAGCUUUUGGCCACCACCAACCGUUGUCAAUUUAUCAACAAAUAGAAAAGCUUUACGCCUUCCAUAUUCUAU
....(((((((......)).......((((((((....................((((......))))..((((.........)))).....)))))))).........)))))...... ( -19.60)
>DroSim_CAF1 11024 108 - 1
GUUUUAUGGGCUCAUUUGUUCUUAUCAGCUUUUCCCCAAC---------AGC---UGGCCACCACCAACCGUUGUCAAUUUAUCAACAAAUAGAAAAGCUUUACGCCUUCCAUAUUCUAU
....(((((((......)).......((((((((..((((---------.(.---(((......))).).))))...((((......)))).)))))))).........)))))...... ( -17.00)
>DroYak_CAF1 11200 104 - 1
GUUUUAUGGGCUCAUUUGCUCUUAUCAGCUUUUC-CCAAC---------AGC---UGGCC---ACUAACCGUUGUCAAUUUAUCAACAAAUAGAAAAGCUUUACGCCUUCCAUAUUCCAU
....(((((((......)).......((((((((-(((..---------...---)))..---.......((((.........)))).....)))))))).........)))))...... ( -18.40)
>consensus
GUUUUAUGGGCUCAUUUGCUCUUAUCAGCUUUUCCCCAAC_________AGC___UGGCC___ACCAACCGUUGUCAAUUUAUCAACAAAUAGAAAAGCUUUACGCCUUCCAUAUUCUAU
....(((((((......)).......((((((((.....................(((......)))...((((.........)))).....)))))))).........)))))...... (-16.23 = -16.35 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:31 2006