Locus 7034

Sequence ID	2L_DroMel_CAF1
Location	19,634,043 – 19,634,141
Length	98
Max. P	0.780813

overview

Window 2

Location	19,634,043 – 19,634,141
Length	98
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	78.34
Mean single sequence MFE	-28.60
Consensus MFE	-16.52
Energy contribution	-17.25
Covariance contribution	0.72
Combinations/Pair	1.22
Mean z-score	-1.87
Structure conservation index	0.58
SVM decision value	0.56
SVM RNA-class probability	0.780813
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19634043 98 + 22407834
UAGCAAUCAUAAAUUGCUAAGGCCUACUCGCCGAGGAUCCUGCAGGAUUCGUUGGCAAGC-ACCAA---AAGAUGAGGGAGAGUGACAUC----UAGACCAGACCA
(((((((.....))))))).((.((....(((((((((((....)))))).)))))....-.....---.......((.(((......))----)...)))).)). ( -28.20)
>DroSec_CAF1 77385 91 + 1
UAGCAAUCAUAAAUUGCUAAGGCCUACUCGCCGAGAAUCCGGCAGGAUUCGUUGGCAAGC-ACCGA---GAGAUGAGGG--AGUGACAUC----UAGACC-----A
(((((((.....))))))).((.((.((((((((((((((....)))))).)))))....-..(..---..)..)))((--(......))----))).))-----. ( -29.10)
>DroSim_CAF1 54783 91 + 1
UAGCAAUCAUAAAUUGCUAAAGCCUACUCGCCGAGAAUCCGGCAGGAUUCGUUGGCAAGC-ACCAA---AAUAUGAGGG--AGUGACAUC----UAGACC-----A
(((((((.....))))))).....((((((((((((((((....)))))).)))))....-.((..---.......)))--)))).....----......-----. ( -27.60)
>DroEre_CAF1 53434 95 + 1
UAGCAAUCAUAAAUUGCUAAGGCCUACUCGCCGAGGAUCCUGCAGGAUUCGUUGGCAAGC-ACCCA---GAGAUGAGGG--AGUGACAUCGGACCAGACC-----A
(((((((.....))))))).((((((((((((((((((((....)))))).)))))....-.((((---....)).)))--)))).....)).)).....-----. ( -31.80)
>DroWil_CAF1 84277 84 + 1
UGGCAAUCAUAAAUUGUUAAGGCCUACUCAC--AGGAUACCGCAGGACC--UCGACAUUGUCUUUG---AAUGUGGGGG--AGGGUG-UUGGAA------------
.(((...((.....)).....))).......--..((((((.(....((--((.(((((.......---))))).))))--.)))))-))....------------ ( -19.00)
>DroYak_CAF1 53267 98 + 1
UAGCAAUCAUAAAUUGCUAAGGCCUACUCGCCGAGGAUCCUGCAGGAUUCGUUGGCAAGC-GCCAACGGAAGAUGAGGG--AGUGACAUCGGACUAGACC-----A
(((((((.....))))))).((.(((....((((...((((.((...(((((((((....-)))))))))...)).)))--)......))))..))).))-----. ( -35.90)
>consensus
UAGCAAUCAUAAAUUGCUAAGGCCUACUCGCCGAGGAUCCUGCAGGAUUCGUUGGCAAGC_ACCAA___AAGAUGAGGG__AGUGACAUC____UAGACC_____A
(((((((.....)))))))...(((.((.(((((((((((....)))))).))))).))................)))............................ (-16.52 = -17.25 +   0.72)

alignment

secondary structure

dotplot

Window 3

Location	19,634,043 – 19,634,141
Length	98
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	78.34
Mean single sequence MFE	-28.05
Consensus MFE	-15.49
Energy contribution	-17.80
Covariance contribution	2.31
Combinations/Pair	1.14
Mean z-score	-1.90
Structure conservation index	0.55
SVM decision value	0.43
SVM RNA-class probability	0.733462
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19634043 98 - 22407834
UGGUCUGGUCUA----GAUGUCACUCUCCCUCAUCUU---UUGGU-GCUUGCCAACGAAUCCUGCAGGAUCCUCGGCGAGUAGGCCUUAGCAAUUUAUGAUUGCUA
.((((((.((.(----((((...........))))).---(((((-....)))))(((((((....))))..)))..)).)))))).((((((((...)))))))) ( -28.80)
>DroSec_CAF1 77385 91 - 1
U-----GGUCUA----GAUGUCACU--CCCUCAUCUC---UCGGU-GCUUGCCAACGAAUCCUGCCGGAUUCUCGGCGAGUAGGCCUUAGCAAUUUAUGAUUGCUA
.-----((((((----((((.....--....))))).---.....-(((((((...((((((....))))))..)))))))))))).((((((((...)))))))) ( -32.70)
>DroSim_CAF1 54783 91 - 1
U-----GGUCUA----GAUGUCACU--CCCUCAUAUU---UUGGU-GCUUGCCAACGAAUCCUGCCGGAUUCUCGGCGAGUAGGCUUUAGCAAUUUAUGAUUGCUA
.-----(((((.----.........--.((.......---..)).-(((((((...((((((....))))))..)))))))))))).((((((((...)))))))) ( -27.30)
>DroEre_CAF1 53434 95 - 1
U-----GGUCUGGUCCGAUGUCACU--CCCUCAUCUC---UGGGU-GCUUGCCAACGAAUCCUGCAGGAUCCUCGGCGAGUAGGCCUUAGCAAUUUAUGAUUGCUA
.-----(((((..............--(((.......---.))).-(((((((...(.((((....)))).)..)))))))))))).((((((((...)))))))) ( -29.70)
>DroWil_CAF1 84277 84 - 1
------------UUCCAA-CACCCU--CCCCCACAUU---CAAAGACAAUGUCGA--GGUCCUGCGGUAUCCU--GUGAGUAGGCCUUAACAAUUUAUGAUUGCCA
------------......-......--......((.(---((.(((...(((..(--((.(((((........--....))))))))..))).))).))).))... ( -16.60)
>DroYak_CAF1 53267 98 - 1
U-----GGUCUAGUCCGAUGUCACU--CCCUCAUCUUCCGUUGGC-GCUUGCCAACGAAUCCUGCAGGAUCCUCGGCGAGUAGGCCUUAGCAAUUUAUGAUUGCUA
.-----((((((.((.((((.....--....))))..((((((((-....))))))((((((....))))..)))).)).)))))).((((((((...)))))))) ( -33.20)
>consensus
U_____GGUCUA____GAUGUCACU__CCCUCAUCUU___UUGGU_GCUUGCCAACGAAUCCUGCAGGAUCCUCGGCGAGUAGGCCUUAGCAAUUUAUGAUUGCUA
......(((((.....((((...........))))...........(((((((.....((((....))))....)))))))))))).((((((((...)))))))) (-15.49 = -17.80 +   2.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:47 2006