Locus 369

Sequence ID	X_DroMel_CAF1
Location	1,122,293 – 1,122,389
Length	96
Max. P	0.999916

overview

Window 3

Location	1,122,293 – 1,122,389
Length	96
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	88.55
Mean single sequence MFE	-26.68
Consensus MFE	-26.22
Energy contribution	-25.94
Covariance contribution	-0.28
Combinations/Pair	1.19
Mean z-score	-2.67
Structure conservation index	0.98
SVM decision value	4.53
SVM RNA-class probability	0.999916
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1122293 96 + 22224390
UGGGUGACUAAUAGAAAAUCUCGCUGCUUGCUGGCGAAUUUUUCUUAGUCGAGCUUAAACGAGAAAUAUCGACGACUCCCACCCACAAUACCCAC--A----
((((((......((((((..(((((.......)))))..))))))..(((((.(((....))).....)))))......))))))..........--.---- ( -27.30)
>DroSec_CAF1 19035 93 + 1
UGGGUGACUAACAGAAAAACUCGCUGCUUGCUAGCAAAUUUUUCUUAGUCGAGCUUAAACGAGAAAUAUCGACGACUCCCACCCACAAUACCC---------
((((((......(((((((...((((.....))))...)))))))..(((((.(((....))).....)))))......))))))........--------- ( -23.10)
>DroSim_CAF1 19972 96 + 1
UGGGUGACUAAUAGAAAAACUCGCUGCUUGCUAGCGAAUUUUUCUUAGUCGAGCUUAAACGAGAAAUAUCGACGACUCCCACCCACAAUACCCAC--A----
((((((......(((((((.((((((.....)))))).)))))))..(((((.(((....))).....)))))......))))))..........--.---- ( -28.80)
>DroEre_CAF1 20129 100 + 1
UGGGUGACUAAUAGAAAAACUUGCCGCUCGCUGGCGAAUUUUUCUUAGUCGAGCUUGAACGAGAAAUAUCGACGACUCCCACCCACAAGUCCCAAACACC--
((((((((((..(((((((.((((((.....)))))).))))))))))))(((.(((..(((......))).))))))..)))))...............-- ( -29.30)
>DroYak_CAF1 19489 102 + 1
UGGGUGACUAAUGGAAAAACUUGCUGCUUGCUGGUGAAUUUGUCUUAGUCGAGCUUAAACGAGAAAUAUCGACGAUUCCCACCCACAAGUCCCAAGCAACCA
(((....))).(((.....((((..(((((..((((.....(((...(((((.(((....))).....))))))))...))))..)))))..))))...))) ( -24.90)
>consensus
UGGGUGACUAAUAGAAAAACUCGCUGCUUGCUGGCGAAUUUUUCUUAGUCGAGCUUAAACGAGAAAUAUCGACGACUCCCACCCACAAUACCCAA__A____
((((((......(((((((.((((((.....)))))).)))))))..(((((.(((....))).....)))))......))))))................. (-26.22 = -25.94 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	1,122,293 – 1,122,389
Length	96
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	88.55
Mean single sequence MFE	-30.20
Consensus MFE	-26.88
Energy contribution	-27.92
Covariance contribution	1.04
Combinations/Pair	1.12
Mean z-score	-1.93
Structure conservation index	0.89
SVM decision value	1.86
SVM RNA-class probability	0.980394
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1122293 96 - 22224390
----U--GUGGGUAUUGUGGGUGGGAGUCGUCGAUAUUUCUCGUUUAAGCUCGACUAAGAAAAAUUCGCCAGCAAGCAGCGAGAUUUUCUAUUAGUCACCCA
----.--.(((((.....((((..(((.((..((....)).)))))..))))(((((((((((.(((((..(....).))))).))))))..)))))))))) ( -28.00)
>DroSec_CAF1 19035 93 - 1
---------GGGUAUUGUGGGUGGGAGUCGUCGAUAUUUCUCGUUUAAGCUCGACUAAGAAAAAUUUGCUAGCAAGCAGCGAGUUUUUCUGUUAGUCACCCA
---------((((.....((((..(((.((..((....)).)))))..))))((((((((((((((((((.(....))))))))))))))..))))))))). ( -32.30)
>DroSim_CAF1 19972 96 - 1
----U--GUGGGUAUUGUGGGUGGGAGUCGUCGAUAUUUCUCGUUUAAGCUCGACUAAGAAAAAUUCGCUAGCAAGCAGCGAGUUUUUCUAUUAGUCACCCA
----.--.(((((.....((((..(((.((..((....)).)))))..))))((((((((((((((((((.(....))))))))))))))..)))))))))) ( -34.50)
>DroEre_CAF1 20129 100 - 1
--GGUGUUUGGGACUUGUGGGUGGGAGUCGUCGAUAUUUCUCGUUCAAGCUCGACUAAGAAAAAUUCGCCAGCGAGCGGCAAGUUUUUCUAUUAGUCACCCA
--......((((.....((..((((((..........))))))..)).....((((((((((((((.(((.......))).)))))))))..))))).)))) ( -31.20)
>DroYak_CAF1 19489 102 - 1
UGGUUGCUUGGGACUUGUGGGUGGGAAUCGUCGAUAUUUCUCGUUUAAGCUCGACUAAGACAAAUUCACCAGCAAGCAGCAAGUUUUUCCAUUAGUCACCCA
.(((.(((((((((((((.(.(((((((.(((((....))(((........)))....)))..)))).))).).....)))))))...)))..))).))).. ( -25.00)
>consensus
____U__GUGGGUAUUGUGGGUGGGAGUCGUCGAUAUUUCUCGUUUAAGCUCGACUAAGAAAAAUUCGCCAGCAAGCAGCGAGUUUUUCUAUUAGUCACCCA
.........(((......((((..(((.((..((....)).)))))..))))((((((((((((((((((.......)))))))))))))..))))).))). (-26.88 = -27.92 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:45 2006