Locus 3903

Sequence ID 3R_DroMel_CAF1
Location 10,634,988 – 10,635,105
Length 117
Max. P 0.672561
window6249 window6250

overview

Window 9

Location 10,634,988 – 10,635,105
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 87.23
Mean single sequence MFE -39.09
Consensus MFE -30.70
Energy contribution -31.53
Covariance contribution 0.84
Combinations/Pair 1.19
Mean z-score -2.12
Structure conservation index 0.79
SVM decision value 0.05
SVM RNA-class probability 0.560295
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10634988 117 + 27905053
CUUGCACCGUCACCCGUUCCUGCU---UUUGACGAUCUUCCCGCUCAGAUUGCUCCUCCUCGUUUUCCACGAAGGUCACAUGCAGUGGCGUGCGACGGUGCAGAAUUAAUGAAGUCCUGC
.((((((((((.(.(((..((((.---..(((((((((........)))))........((((.....))))..))))...))))..))).).))))))))))................. ( -40.00)
>DroSec_CAF1 7353 117 + 1
CUUGCACCGUCACCCGUUCCUGCU---UUUGACGAUCCUCCCGCUCAGAUUGCUCCUCCUCGUUUUCCACGAAGGUCACAUGCAGUGGCGUGCGACGGUGCAGGAUUAAUGAAGUCCUGC
...((((((((.(.(((..((((.---..((((.........((.......))......((((.....))))..))))...))))..))).).))))))))((((((.....)))))).. ( -42.90)
>DroSim_CAF1 7535 117 + 1
CUUGCACCGUCACCCGUUCCUGCU---UUUGACGAUCCUCCCGCUCAGAUUGCUCCUCCUCGUUUUCCACGAAGGUCACAUGCAGUGGCGUGCGACGGUGCAGGAUUAAUGAAGUCCUGC
...((((((((.(.(((..((((.---..((((.........((.......))......((((.....))))..))))...))))..))).).))))))))((((((.....)))))).. ( -42.90)
>DroEre_CAF1 7408 117 + 1
CUUGCACCGCCACCCGUUCCUGCU---CAUGAUGAUCCUCCCGCUCAGAUUGCACCUCCUCGCUUUCCACGAAGGUCACAUGCAGUGGCGUGCGACGGUGCAGGAUUAAUGAAGCCCUGC
(((((((((.(.(.(((..((((.---.(((.(((.(((..((....((..((........))..))..)).)))))))))))))..))).).).)))))))))................ ( -37.30)
>DroYak_CAF1 7468 117 + 1
CUUGCACCGUCACCCGUUCCUGCU---CUUGAUGAUCCUCCCGCUCAAAUUGCUCCUCCUCGUUUUCCACGAAGGUCACAUGCAGUGGCGUGCGACGGUGCAGGAUUAAUGAAGCCCUGC
(((((((((((.(.(((..((((.---..((.(((((.....((.......))......((((.....)))).))))))).))))..))).).)))))))))))................ ( -42.40)
>DroAna_CAF1 7853 108 + 1
CUUGCACCGCUGCCUGCUCCUGCCUCAUUAGCUGAUCAUCCCGCU------------CUUCACUCUCCAUAAAGGUCACAUGCAGUGGGGUGCGACGGUGCAGAAUUAACGACAUCCUGC
.(((((((((((...((....)).....))))....(((((((((------------.........((.....))........)))))))))....)))))))................. ( -29.03)
>consensus
CUUGCACCGUCACCCGUUCCUGCU___UUUGACGAUCCUCCCGCUCAGAUUGCUCCUCCUCGUUUUCCACGAAGGUCACAUGCAGUGGCGUGCGACGGUGCAGGAUUAAUGAAGUCCUGC
(((((((((((.(.(((..((((...................((.......))....((((((.....))).)))......))))..))).).)))))))))))................ (-30.70 = -31.53 +   0.84)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 0

Location 10,634,988 – 10,635,105
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 87.23
Mean single sequence MFE -42.48
Consensus MFE -36.36
Energy contribution -35.95
Covariance contribution -0.41
Combinations/Pair 1.25
Mean z-score -1.69
Structure conservation index 0.86
SVM decision value 0.30
SVM RNA-class probability 0.672561
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10634988 117 - 27905053
GCAGGACUUCAUUAAUUCUGCACCGUCGCACGCCACUGCAUGUGACCUUCGUGGAAAACGAGGAGGAGCAAUCUGAGCGGGAAGAUCGUCAAA---AGCAGGAACGGGUGACGGUGCAAG
..................(((((((((((.((...((((.(((..(((((((.....)))))).)..)))...(((.(((.....))))))..---.))))...)).))))))))))).. ( -44.00)
>DroSec_CAF1 7353 117 - 1
GCAGGACUUCAUUAAUCCUGCACCGUCGCACGCCACUGCAUGUGACCUUCGUGGAAAACGAGGAGGAGCAAUCUGAGCGGGAGGAUCGUCAAA---AGCAGGAACGGGUGACGGUGCAAG
((((((.........))))))((((((((.((...((((.(((..(((((((.....)))))).)..)))...(((.(((.....))))))..---.))))...)).))))))))..... ( -45.20)
>DroSim_CAF1 7535 117 - 1
GCAGGACUUCAUUAAUCCUGCACCGUCGCACGCCACUGCAUGUGACCUUCGUGGAAAACGAGGAGGAGCAAUCUGAGCGGGAGGAUCGUCAAA---AGCAGGAACGGGUGACGGUGCAAG
((((((.........))))))((((((((.((...((((.(((..(((((((.....)))))).)..)))...(((.(((.....))))))..---.))))...)).))))))))..... ( -45.20)
>DroEre_CAF1 7408 117 - 1
GCAGGGCUUCAUUAAUCCUGCACCGUCGCACGCCACUGCAUGUGACCUUCGUGGAAAGCGAGGAGGUGCAAUCUGAGCGGGAGGAUCAUCAUG---AGCAGGAACGGGUGGCGGUGCAAG
(((((..(.....)..)))))((((((((.((...(((((((((((((((.(....)((..(((.......)))..)).))))).))).))).---.))))...)).))))))))..... ( -42.90)
>DroYak_CAF1 7468 117 - 1
GCAGGGCUUCAUUAAUCCUGCACCGUCGCACGCCACUGCAUGUGACCUUCGUGGAAAACGAGGAGGAGCAAUUUGAGCGGGAGGAUCAUCAAG---AGCAGGAACGGGUGACGGUGCAAG
(((((..(.....)..)))))((((((((.((...((((.(((..(((((((.....)))))).)..))).(((((..((.....)).)))))---.))))...)).))))))))..... ( -44.60)
>DroAna_CAF1 7853 108 - 1
GCAGGAUGUCGUUAAUUCUGCACCGUCGCACCCCACUGCAUGUGACCUUUAUGGAGAGUGAAG------------AGCGGGAUGAUCAGCUAAUGAGGCAGGAGCAGGCAGCGGUGCAAG
(((((((.......)))))))......(((((...((((.(((..(((((((.....))))))------------.............(((.....))).)..))).)))).)))))... ( -33.00)
>consensus
GCAGGACUUCAUUAAUCCUGCACCGUCGCACGCCACUGCAUGUGACCUUCGUGGAAAACGAGGAGGAGCAAUCUGAGCGGGAGGAUCAUCAAA___AGCAGGAACGGGUGACGGUGCAAG
((((((.........))))))((((((((.((...((((.(((..(((((((.....)))))).)..)))........((.....))..........))))...)).))))))))..... (-36.36 = -35.95 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:56 2006