Locus 1819

Sequence ID 3R_DroMel_CAF1
Location 5,199,485 – 5,199,613
Length 128
Max. P 0.774636
window2993 window2994

overview

Window 3

Location 5,199,485 – 5,199,591
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.04
Mean single sequence MFE -29.55
Consensus MFE -22.05
Energy contribution -21.72
Covariance contribution -0.33
Combinations/Pair 1.32
Mean z-score -1.14
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.592318
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5199485 106 - 27905053
GACGAGGUGGUGCGCAAGAAAUCUGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGCUGCGCACGCGCUUCGAGGAGAACUACAUAAAGGGUGA-----------GUGAGA---AAUGA
..(((((((((((((..............(((((....)))))((.(((....))).)))))))).)))))))......(((.(((.....))))-----------))....---..... ( -33.30)
>DroPse_CAF1 5720 117 - 1
GACGAGGUGCUGCGCAAGAAGACCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGCUGCGCACGCGUUUCGAGGAGCACUACAUUAAAGGUAACCCGAUCCCGACUGAGA---AAUGG
..(((..((((((((..............(((((....)))))((.(((....))).))))))).)))..))).(((....(((.......)))......))).........---..... ( -29.20)
>DroGri_CAF1 7217 108 - 1
GACGAAGUUGUGCGUAAGAAGGGCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGUUGCGCACGCGCUUCGAAGAGCACUACAUAAAAGGUGA-----------GUGCCCC-CAUUGG
..(((((((((((((((............(((((....)))))...(((....))).))))))))).))))))....(((((.(((.....))))-----------))))...-...... ( -33.90)
>DroWil_CAF1 6103 106 - 1
GACGAAGUGGUGCGUAAGAAGAGCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGUUGCGUACACGUUUCGAGGAGCACUAUAUAAAGGGUAA-----------GCCUCC---AUUCC
..(((((((((((((((............(((((....)))))...(((....))).)))))))).))))))).((((((((........)))..-----------).))))---..... ( -26.80)
>DroMoj_CAF1 8163 109 - 1
GACGAAGUUGUGCGCAAGAAGAGCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGUUACGCACGCGCUUUGAAGAGCACUACAUAAAAGGUGA-----------GUAACACCCAAUGA
......((.((((.(......(((...(.(((((....))))))..))).((((((((.......))))))))..).)))).))......((((.-----------....))))...... ( -26.70)
>DroAna_CAF1 5520 106 - 1
GACGAGGUGGUUCGCAAGAAAUCCGAAUAUCAGAAACAUUUGGAAGGCUACAAGGCUCUGCGCACGCGCUUCGAGGAGCACUAUAUUAAAGGUAA-----------UUUAAU---AUUUA
..(((((((((.((((.....(((((((.........))))))).((((....)))).)))).)).))))))).........((((((((.....-----------))))))---))... ( -27.40)
>consensus
GACGAAGUGGUGCGCAAGAAGACCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGCUGCGCACGCGCUUCGAGGAGCACUACAUAAAAGGUAA___________GUGACA___AAUGA
..((((((((((((((.............(((((....)))))...(((....)))..))))))).)))))))............................................... (-22.05 = -21.72 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,199,511 – 5,199,613
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.33
Mean single sequence MFE -32.17
Consensus MFE -23.76
Energy contribution -23.48
Covariance contribution -0.27
Combinations/Pair 1.41
Mean z-score -1.28
Structure conservation index 0.74
SVM decision value 0.54
SVM RNA-class probability 0.774636
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5199511 102 - 27905053
CC-----UC----UUG---------UCAUUCCAGCUCACCGACGAGGUGGUGCGCAAGAAAUCUGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGCUGCGCACGCGCUUCGAGGAGAA
((-----((----..(---------((.............)))((((((((((((..............(((((....)))))((.(((....))).)))))))).)))))))))).... ( -36.22)
>DroVir_CAF1 6085 105 - 1
CU-----UU----UUG------UAUGCAUUGCAGCUUACAGACGAAGUUGUGCGAAAGAAAAGCGAAUACCAAAAACAUUUGGAGGGUUACAAGGCGCUGCGCACGCGCUUUGAAGAGCA
..-----.(----(((------((.((......)).))))))((((((((((((.......((((....(((((....))))).(.....)....)))).)))))).))))))....... ( -27.10)
>DroGri_CAF1 7245 105 - 1
CU-----UU----UCU------UAUGCAUUGCAGUUGACAGACGAAGUUGUGCGUAAGAAGGGCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGUUGCGCACGCGCUUCGAAGAGCA
((-----((----(((------(((((((.((.(((....)))...)).))))))))((((.(((....(((((....))))).(.((.((.....)).)).).))).)))))))))).. ( -34.10)
>DroWil_CAF1 6129 106 - 1
CU-----UUUUUUUUG---------CUUUUGCAGUUGACUGACGAAGUGGUGCGUAAGAAGAGCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGUUGCGUACACGUUUCGAGGAGCA
..-----.......((---------(((((.(((....))).(((((((((((((((............(((((....)))))...(((....))).)))))))).)))))))))))))) ( -29.00)
>DroAna_CAF1 5546 112 - 1
CUUCUCUUU----UUGUAUUU----UUUUUCCAGCUCACCGACGAGGUGGUUCGCAAGAAAUCCGAAUAUCAGAAACAUUUGGAAGGCUACAAGGCUCUGCGCACGCGCUUCGAGGAGCA
.........----........----........((((.....(((((((((.((((.....(((((((.........))))))).((((....)))).)))).)).)))))))..)))). ( -30.20)
>DroPer_CAF1 5726 111 - 1
CU-----UU----GUGAUCUCUCACUCAUUUCAGCUCACUGACGAGGUGCUGCGCAAGAAGACCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGCUGCGCACGCGUUUCGAGGAGCA
..-----..----((((....))))........((((.((..(((..((((((((..............(((((....)))))((.(((....))).))))))).)))..))))))))). ( -36.40)
>consensus
CU_____UU____UUG_________UCAUUGCAGCUCACAGACGAAGUGGUGCGCAAGAAAACCGAAUACCAAAAACAUUUGGAGGGCUACAAGGCGCUGCGCACGCGCUUCGAGGAGCA
.................................((((.....(((((((((((((..............(((((....)))))((.(((....))).)))))))).)))))))..)))). (-23.76 = -23.48 +  -0.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:17 2006