Locus 8446

Sequence ID	3L_DroMel_CAF1
Location	22,201,887 – 22,202,005
Length	118
Max. P	0.939117

overview

Window 8

Location	22,201,887 – 22,202,005
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.37
Mean single sequence MFE	-33.55
Consensus MFE	-23.30
Energy contribution	-24.42
Covariance contribution	1.13
Combinations/Pair	1.14
Mean z-score	-2.01
Structure conservation index	0.69
SVM decision value	0.88
SVM RNA-class probability	0.873707
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22201887 118 + 23771897
GGAGUUUGAUUUCGGACAAGCGAAUUCGUCCUGGGCAAGGCCAAGGACAAAUUUGGCCAUUUGACGGAAUUCGAUUUUUAUUUGAUUUCAAUAAUCGUUAGUUAAAAUCUUAGU--GGCA
...(((((....)))))...((((((.(((((.(((...))).))))).))))))((((((((((......(((((.....(((....))).)))))...))))).......))--))). ( -31.61)
>DroSec_CAF1 60819 120 + 1
GGAGUUUGAUUUCGGACAAGCGAAUUCGUCCUGGGCAAGGCCAAGGACAAAUUUGGCCAUCUGACGGAAGUCGAUUUCUAUCCGAUUUCAAUAAUCGUUAGUUACAAUCUUAGAUAGGCA
...(((((....)))))...((((((.(((((.(((...))).))))).))))))((((((((((....)))((((.(((..(((((.....))))).)))....))))..)))).))). ( -39.20)
>DroEre_CAF1 60620 104 + 1
GGAGUACGUUUUCGGACAAGCGAUUUCGUCCUGGGCAAGGCCAAGGACAAAGUUGGCAAUCUGACGGAAGUGGAUUUCUAUCUGAUUUUAAUAAUCGUUA----------------GUCA
((((.....)))).(((.(((((((..(((((.(((...))).)))))..((.(((.(((((.((....))))))).))).)).........))))))).----------------))). ( -31.90)
>DroYak_CAF1 72348 107 + 1
GGCGUACGAUUUCGAACAAGCGAUUUCGUCCUGGGCAAGGCCAAGGACGAAUUUGGCAAUCUGACGGAAGUCGAUUUCUAUCUGAUAUCAACAAUCUUUU-----------ACU--GGCA
.((((.((....)).))...(((.((((((((.(((...))).)))))))).))))).....(((....)))(((.((.....)).)))...........-----------...--.... ( -31.50)
>consensus
GGAGUACGAUUUCGGACAAGCGAAUUCGUCCUGGGCAAGGCCAAGGACAAAUUUGGCAAUCUGACGGAAGUCGAUUUCUAUCUGAUUUCAAUAAUCGUUA___________AGU__GGCA
...(((((....)))))...((((((.(((((.(((...))).))))).))))))(((....(((....)))((..((.....))..))...........................))). (-23.30 = -24.42 +   1.13)

alignment

secondary structure

dotplot

Window 9

Location	22,201,887 – 22,202,005
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.37
Mean single sequence MFE	-28.95
Consensus MFE	-19.41
Energy contribution	-19.48
Covariance contribution	0.06
Combinations/Pair	1.16
Mean z-score	-2.26
Structure conservation index	0.67
SVM decision value	1.28
SVM RNA-class probability	0.939117
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22201887 118 - 23771897
UGCC--ACUAAGAUUUUAACUAACGAUUAUUGAAAUCAAAUAAAAAUCGAAUUCCGUCAAAUGGCCAAAUUUGUCCUUGGCCUUGCCCAGGACGAAUUCGCUUGUCCGAAAUCAAACUCC
....--.....(((((((((....)....))))))))...........((.(((.(.((...(((..((((((((((.(((...))).)))))))))).))))).).))).))....... ( -26.30)
>DroSec_CAF1 60819 120 - 1
UGCCUAUCUAAGAUUGUAACUAACGAUUAUUGAAAUCGGAUAGAAAUCGACUUCCGUCAGAUGGCCAAAUUUGUCCUUGGCCUUGCCCAGGACGAAUUCGCUUGUCCGAAAUCAAACUCC
...........((((((.....)))))).((((..(((((((...((((((....))).)))(((..((((((((((.(((...))).)))))))))).))))))))))..))))..... ( -35.50)
>DroEre_CAF1 60620 104 - 1
UGAC----------------UAACGAUUAUUAAAAUCAGAUAGAAAUCCACUUCCGUCAGAUUGCCAACUUUGUCCUUGGCCUUGCCCAGGACGAAAUCGCUUGUCCGAAAACGUACUCC
.(((----------------...(((((.....((((.((..(((......)))..)).)))).......(((((((.(((...))).))))))))))))...))).............. ( -25.00)
>DroYak_CAF1 72348 107 - 1
UGCC--AGU-----------AAAAGAUUGUUGAUAUCAGAUAGAAAUCGACUUCCGUCAGAUUGCCAAAUUCGUCCUUGGCCUUGCCCAGGACGAAAUCGCUUGUUCGAAAUCGUACGCC
....--.((-----------(...((((((((((.((.....)).)))))).....((..((.((....((((((((.(((...))).))))))))...))..))..)))))).)))... ( -29.00)
>consensus
UGCC__ACU___________UAACGAUUAUUGAAAUCAGAUAGAAAUCGACUUCCGUCAGAUGGCCAAAUUUGUCCUUGGCCUUGCCCAGGACGAAAUCGCUUGUCCGAAAUCAAACUCC
........................((((.(((........))).))))((.(((.(.(((...((..((((((((((.(((...))).)))))))))).))))).).))).))....... (-19.41 = -19.48 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:32 2006