Locus 5126

Sequence ID	X_DroMel_CAF1
Location	13,391,437 – 13,391,556
Length	119
Max. P	0.932526

overview

Window 0

Location	13,391,437 – 13,391,556
Length	119
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.59
Mean single sequence MFE	-36.83
Consensus MFE	-25.62
Energy contribution	-26.23
Covariance contribution	0.61
Combinations/Pair	1.19
Mean z-score	-1.25
Structure conservation index	0.70
SVM decision value	0.16
SVM RNA-class probability	0.612444
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13391437 119 + 22224390
AGUGUCAACGAGAAGGAGUACACGGUGCGGGCGGAUGUCAAGGACACGCCACCCACCUCCGAUUUUGACGACGAGCUGAGUGGUCAGUUCUAAAAAUUGGUCAAAGGGAUUUCCCUUUA
.(((((..(.....)..).))))((((.(((((..((((...)))))))).).)))).((((((((......(((((((....)))))))..))))))))..((((((....)))))). ( -39.60)
>DroSec_CAF1 4030 119 + 1
AGUGUCAACGAGAAGGAGUACACUGUGCGGGCGGAUGUCAAGGACACGCCACCCUCCUCCGAUUUCGACGACGAGCUGAGUGGUCAACUUUAAAAAUUACUUAAAGGGAAAUGCCUUUA
..((((..(((((.(((((((...))))(((.((.((((...))))..)).)))...)))..)))))..))))...((((((((...........))))))))(((((.....))))). ( -31.20)
>DroSim_CAF1 7454 119 + 1
AGUGUCAACGAGAAGGAGUACACGGUGCGGGCGGAUGUCAAGGACACGCCACCCACCUCCGAUUUCGACGACGAGCUGAGUGGUCAGCUCUAAAAAUGAGUCAAAGGUAAAUGCCUUUA
...(((..(((((.((((....)((((.(((((..((((...)))))))).).)))))))..)))))..)))(((((((....)))))))............((((((....)))))). ( -40.90)
>DroEre_CAF1 6867 112 + 1
AGUGUCAACGAGAAGGAGUACACGGUGCGGGCGGAUGUCAAGGACACGCCACCCACCUCCGAUUUCGAUGACGAGCUGAAUGGUCAGCUCUAGGAAUUGGGCAA-------UCCCUGCC
...((((.(((((.((((....)((((.(((((..((((...)))))))).).)))))))..))))).))))(((((((....)))))))..((....(((...-------.)))..)) ( -41.30)
>DroYak_CAF1 4423 107 + 1
AGUGUCAACGAGAAGGAGUACACGGUGCGUGCGGAUGUUAAGGACACGCCACCCAGCUCCGAUUUCGAGGACGAGCUUAAUGGUCAGCUCUAGAAGUUGGCCAA-------GAA-----
..((((..(((((.(((((....(((((((((..........).)))).))))..)))))..)))))..)))).......(((((((((.....))))))))).-------...----- ( -38.50)
>DroAna_CAF1 4394 100 + 1
AAUGUCAACGACAAGGACUACACGGUGCGGGCCGAUGUGAAGGACACAGCGCCCACCUCUGACUUCGAUGAUGAGCUGAGUGGUCAGCUUUGAA--UCAGGU-----------------
...((((.......(.(((....))).)((((...((((.....))))..)))).....))))...(((...(((((((....)))))))...)--))....----------------- ( -29.50)
>consensus
AGUGUCAACGAGAAGGAGUACACGGUGCGGGCGGAUGUCAAGGACACGCCACCCACCUCCGAUUUCGACGACGAGCUGAGUGGUCAGCUCUAAAAAUUAGUCAA_______UCCCUUUA
...(((..(((((.(((((((...))))(((.((.((((...))))..)).)))...)))..)))))..)))(((((((....)))))))............................. (-25.62 = -26.23 +   0.61)

alignment

secondary structure

dotplot

Window 1

Location	13,391,437 – 13,391,556
Length	119
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.59
Mean single sequence MFE	-38.03
Consensus MFE	-27.71
Energy contribution	-29.93
Covariance contribution	2.22
Combinations/Pair	1.10
Mean z-score	-2.13
Structure conservation index	0.73
SVM decision value	1.22
SVM RNA-class probability	0.932526
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13391437 119 - 22224390
UAAAGGGAAAUCCCUUUGACCAAUUUUUAGAACUGACCACUCAGCUCGUCGUCAAAAUCGGAGGUGGGUGGCGUGUCCUUGACAUCCGCCCGCACCGUGUACUCCUUCUCGUUGACACU
(((((((....)))))))...........((.((((....)))).))...(((((....((((((((((((.(((((...)))))))))))))((...)).))))......)))))... ( -40.70)
>DroSec_CAF1 4030 119 - 1
UAAAGGCAUUUCCCUUUAAGUAAUUUUUAAAGUUGACCACUCAGCUCGUCGUCGAAAUCGGAGGAGGGUGGCGUGUCCUUGACAUCCGCCCGCACAGUGUACUCCUUCUCGUUGACACU
((((((......))))))............((((((....)))))).((((.(((....((((((((((((.(((((...)))))))))))((.....))..))))))))).))))... ( -37.30)
>DroSim_CAF1 7454 119 - 1
UAAAGGCAUUUACCUUUGACUCAUUUUUAGAGCUGACCACUCAGCUCGUCGUCGAAAUCGGAGGUGGGUGGCGUGUCCUUGACAUCCGCCCGCACCGUGUACUCCUUCUCGUUGACACU
((((((......))))))...........(((((((....)))))))((((.(((....((((((((((((.(((((...)))))))))))))((...)).))))...))).))))... ( -45.00)
>DroEre_CAF1 6867 112 - 1
GGCAGGGA-------UUGCCCAAUUCCUAGAGCUGACCAUUCAGCUCGUCAUCGAAAUCGGAGGUGGGUGGCGUGUCCUUGACAUCCGCCCGCACCGUGUACUCCUUCUCGUUGACACU
...(((((-------((....))))))).(((((((....)))))))((((.(((....((((((((((((.(((((...)))))))))))))((...)).))))...))).))))... ( -47.90)
>DroYak_CAF1 4423 107 - 1
-----UUC-------UUGGCCAACUUCUAGAGCUGACCAUUAAGCUCGUCCUCGAAAUCGGAGCUGGGUGGCGUGUCCUUAACAUCCGCACGCACCGUGUACUCCUUCUCGUUGACACU
-----...-------..............(((((........)))))(((..(((....((((...((((.(((((...........))))))))).....))))...)))..)))... ( -29.90)
>DroAna_CAF1 4394 100 - 1
-----------------ACCUGA--UUCAAAGCUGACCACUCAGCUCAUCAUCGAAGUCAGAGGUGGGCGCUGUGUCCUUCACAUCGGCCCGCACCGUGUAGUCCUUGUCGUUGACAUU
-----------------..((((--((....(((((....)))))((......)))))))).((((((.(((((((.....))).)))))).))))..........((((...)))).. ( -27.40)
>consensus
UAAAGGCA_______UUGACCAAUUUUUAGAGCUGACCACUCAGCUCGUCGUCGAAAUCGGAGGUGGGUGGCGUGUCCUUGACAUCCGCCCGCACCGUGUACUCCUUCUCGUUGACACU
.............................(((((((....)))))))((((.(((....((((((((((((.(((((...)))))))))))))........))))...))).))))... (-27.71 = -29.93 +   2.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:39 2006