Locus 1910

Sequence ID	3L_DroMel_CAF1
Location	5,348,555 – 5,348,694
Length	139
Max. P	0.837984

overview

Window 1

Location	5,348,555 – 5,348,656
Length	101
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	90.31
Mean single sequence MFE	-14.59
Consensus MFE	-11.57
Energy contribution	-11.45
Covariance contribution	-0.12
Combinations/Pair	1.14
Mean z-score	-1.99
Structure conservation index	0.79
SVM decision value	0.74
SVM RNA-class probability	0.837984
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5348555 101 + 23771897
ACAACUCAACGACGCAGUCAUCAACAUCCUGACAAUAUAAUUUAU-UUAAAUUCUUCUCCUUCUCGCCAAAUAAAAAGAGGAAGCCAACUUCCCUUUCAGAA
..........(((...))).........((((........(((((-((....................)))))))(((.(((((....)))))))))))).. ( -10.75)
>DroSec_CAF1 96377 102 + 1
ACAACUCAACGACGCAGUCUUCUACAUCCUGACAAUAUAUUUUUUUUUUCAAUCUUCCCCUGCUCACCAAAUAAAAAGGGGAAGCCAACUUCCUCUUCAGAA
.....((.........(((...........)))....................((((((((...............))))))))...............)). ( -14.36)
>DroSim_CAF1 98164 101 + 1
ACAACUCAACGACGCAGUCUUCUACAUCCUGACAAUAUAAUUUAU-UUAAAUUCUUCCCCUGCUCGCCAAAUAAAAAGGGGAAGCCAACUUCCUCUUCAGAA
.....((..(((.((((((...........)))((((.....)))-).............)))))).........(((((((((....)))))))))..)). ( -16.70)
>DroYak_CAF1 105084 101 + 1
ACAACUCAACAACGUAGUCUUCUACUUCCUGACAAUAUAAUUUAU-UUAAAUUCUACCCCUGCUCGCAAAAUAAAAAGGGGAAGCCAACUUCCCUUUCAGAA
.............((((....))))...((((........(((((-((....................))))))).((((((((....)))))))))))).. ( -16.55)
>consensus
ACAACUCAACGACGCAGUCUUCUACAUCCUGACAAUAUAAUUUAU_UUAAAUUCUUCCCCUGCUCGCCAAAUAAAAAGGGGAAGCCAACUUCCCCUUCAGAA
.....((.........(((...........)))..........................................(((((((((....)))))))))..)). (-11.57 = -11.45 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	5,348,594 – 5,348,694
Length	100
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	81.49
Mean single sequence MFE	-30.00
Consensus MFE	-22.22
Energy contribution	-22.14
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-1.57
Structure conservation index	0.74
SVM decision value	0.15
SVM RNA-class probability	0.606910
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5348594 100 - 23771897
CCUAC--ACCUGUGGCUGUCGUCGCUGGAAGUCAUCAAUCUUCUGA-AAGGGAAGUUGGCUUCCUCUUUUUA------------UUUGGCGAGAAGGAG--AAG-AAUUUAA-AUAAAU
.....--....(((((....))))).((((((((.....(((((..-...))))).))))))))(((((((.------------(((.....))).)))--)))-)......-...... ( -24.50)
>DroSec_CAF1 96416 103 - 1
CCUACACACCUGUGGCUGUCGUCGCUGGAAGUCAUCAAUCUUCUGA-AGAGGAAGUUGGCUUCCCCUUUUUA------------UUUGGUGAGCAGGGG--AAG-AUUGAAAAAAAAAA
........((.(((((....))))).))......((((((((((..-...(((((....)))))(((.((((------------(...))))).)))))--)))-)))))......... ( -30.90)
>DroSim_CAF1 98203 102 - 1
CCUACACACCUGUGGCUGUCGUCGCUGGAAGUCAUCAAUCUUCUGA-AGAGGAAGUUGGCUUCCCCUUUUUA------------UUUGGCGAGCAGGGG--AAG-AAUUUAA-AUAAAU
(((.(((....))).((((..(((((((((((((....(((((...-.)))))...))))))))........------------...))))))))))))--...-.......-...... ( -29.00)
>DroYak_CAF1 105123 99 - 1
-CUAC--ACCUGUGGCUGUCGUCGCUGGAAGUCAUCAAUCUUCUGA-AAGGGAAGUUGGCUUCCCCUUUUUA------------UUUUGCGAGCAGGGG--UAG-AAUUUAA-AUAAAU
-((((--.((((((((....)))((.(((((........)))))((-((((((((....))).)))))))..------------....))..))))).)--)))-.......-...... ( -29.30)
>DroAna_CAF1 98402 118 - 1
CCCACGCACCUGUGGCUGUCGUCGCUGGAAGUCAUCAAUCUUCCCAAAAGGGAACUUGACUUCCCCUUUCUCCCCGGAGGUCCUUUUCUCAAGCGCGGGAGUUGAAAAUAAA-AUAAAU
(((.(((....(((((....))))).((((((((......(((((....)))))..))))))))....((((....))))............))).))).............-...... ( -36.30)
>consensus
CCUAC_CACCUGUGGCUGUCGUCGCUGGAAGUCAUCAAUCUUCUGA_AAGGGAAGUUGGCUUCCCCUUUUUA____________UUUGGCGAGCAGGGG__AAG_AAUUUAA_AUAAAU
........((((((((....))))).((((((((.....(((((......))))).))))))))..............................)))...................... (-22.22 = -22.14 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:47 2006