Locus 2124

Sequence ID	3L_DroMel_CAF1
Location	5,809,532 – 5,809,663
Length	131
Max. P	0.878542

overview

Window 4

Location	5,809,532 – 5,809,642
Length	110
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	91.21
Mean single sequence MFE	-34.43
Consensus MFE	-28.82
Energy contribution	-29.93
Covariance contribution	1.11
Combinations/Pair	1.03
Mean z-score	-2.40
Structure conservation index	0.84
SVM decision value	0.62
SVM RNA-class probability	0.803577
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5809532 110 + 23771897
AGCACACAUGCAUAUACGCGGACAGAGUAGAGUGUCUGUCUGUGUGGGCCAAACAAAGCUUGGGAACCAAAAAGGCCAACACGCGCUGAAACGUGGUUAAAGUGGCCAUU
.(((....)))...((((((((((((........))))))))))))(((((......((((.(....)....)))).(((.((((......)))))))....)))))... ( -36.30)
>DroSec_CAF1 17459 110 + 1
AGCACACAUACCAAUACGCGAACAGAGUAGAGUGUCUGUCUGUGUGGGCCAAACAAAGCUUGGGAACCAAAAAGGCCAACACGCGCUGAAACGUGGUUAAAGUGGCCAUU
..((((((.((..((((.(..........).))))..)).))))))(((((......((((.(....)....)))).(((.((((......)))))))....)))))... ( -28.90)
>DroEre_CAF1 17638 102 + 1
AGCACACAG----AUACACGGCCAGAGUUGAG----UGUCUGUGUGGGCCAAACAAAGCUUGGGAACCAAAAAGGCCAACACGCGCUGAAACGUGGUUAAAGUGGCCAUU
..(((((((----((((.((((....)))).)----))))))))))(((((......((((.(....)....)))).(((.((((......)))))))....)))))... ( -38.10)
>consensus
AGCACACAU_C__AUACGCGGACAGAGUAGAGUGUCUGUCUGUGUGGGCCAAACAAAGCUUGGGAACCAAAAAGGCCAACACGCGCUGAAACGUGGUUAAAGUGGCCAUU
..............((((((((((((........))))))))))))(((((......((((.(....)....)))).(((.((((......)))))))....)))))... (-28.82 = -29.93 +   1.11)

alignment

secondary structure

dotplot

Window 5

Location	5,809,568 – 5,809,663
Length	95
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	83.09
Mean single sequence MFE	-32.48
Consensus MFE	-26.05
Energy contribution	-26.86
Covariance contribution	0.81
Combinations/Pair	1.07
Mean z-score	-2.36
Structure conservation index	0.80
SVM decision value	0.90
SVM RNA-class probability	0.878542
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5809568 95 - 23771897
GGUCAACGCGCGCGCCUGCCCAAUGGCCACUUUAACCACGUUUCAGCGCGUGUUGGCCUUUUUGGUUCCCAAGCUUUGUUUGGCCCAC--ACAGACA
((((((((((((((((........)))......(((...)))...)))))))))))))....(((...((((((...)))))).))).--....... ( -34.50)
>DroPse_CAF1 18934 87 - 1
GGUCAACGCGCGCGCCUGCCCAAUGGCCACGUUA----------AGCGCGUGUUGGCCUUUUUGGUUCCCAAGCUUUGUUUGCCACAAGCACAGAUA
(((((((((((((((..(((....)))...))..----------.)))))))))))))..(((((...)))))((.((((((...)))))).))... ( -33.20)
>DroEre_CAF1 17666 95 - 1
GGUCAACGCGCGCGCCUGCCCAAUGGCCACUUUAACCACGUUUCAGCGCGUGUUGGCCUUUUUGGUUCCCAAGCUUUGUUUGGCCCAC--ACAGACA
((((((((((((((((........)))......(((...)))...)))))))))))))....(((...((((((...)))))).))).--....... ( -34.50)
>DroYak_CAF1 18322 95 - 1
GGUCAACGCGCGCGCCUGGCCAAUGGCCACUUUAACCACGUUUCAGCGCGUGUUGGCCUUUUUGGUUCCCAAGCUUUGUUUGGCCCAC--ACACACA
(((((((((((((...(((((...)))))....(((...)))...)))))))))))))....(((...((((((...)))))).))).--....... ( -36.80)
>DroAna_CAF1 17727 75 - 1
GGUGAAGGCGCGCGCCUGCUCACUGGA-------------------CGCGUGUUG-CUUUUUUGGUUCCCAAGCUUUGUUUGCCCCAA--ACACACA
.(((..((((((((((........)).-------------------)))))))).-....(((((....(((((...)))))..))))--))))... ( -22.70)
>DroPer_CAF1 18990 87 - 1
GGUCAACGCGCGCGCCUGCCCAAUGGCCACGUUA----------AGCGCGUGUUGGCCUUUUUGGUUCCCAAGCUUUGUUUGCCACAAGCACAGAUA
(((((((((((((((..(((....)))...))..----------.)))))))))))))..(((((...)))))((.((((((...)))))).))... ( -33.20)
>consensus
GGUCAACGCGCGCGCCUGCCCAAUGGCCACUUUA__________AGCGCGUGUUGGCCUUUUUGGUUCCCAAGCUUUGUUUGCCCCAA__ACAGACA
((((((((((((((((........)))..................)))))))))))))..(((((...)))))...((((((.........)))))) (-26.05 = -26.86 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:56 2006