Locus 5553

Sequence ID	X_DroMel_CAF1
Location	14,362,054 – 14,362,168
Length	114
Max. P	0.984837

overview

Window 2

Location	14,362,054 – 14,362,168
Length	114
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	96.97
Mean single sequence MFE	-34.11
Consensus MFE	-32.38
Energy contribution	-32.69
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-2.57
Structure conservation index	0.95
SVM decision value	1.63
SVM RNA-class probability	0.968593
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14362054 114 + 22224390
GGGAUUACAGGGGACAAACUUUAUCUACAAAUCGUUUGCAUCGCAGAUCAGGUUUGUCCACACUUAGCCAAACUUUGGCCGCCUCAUCCGGAGUCCUU---UCUCCGGCAUUAUCCU
(((((...(((((((((((((.((((.(..............).)))).)))))))))).......((((.....))))..)))...((((((.....---.))))))....))))) ( -36.24)
>DroSec_CAF1 76479 114 + 1
GGGAUUACAGGGGACAAACUUUAUCUACAAAUCGUUUGCAUCGCAGAUCAGGUUUGUCCACACUUAGCCAAACUUUGGCCGCCUCAUCCGGAGUCCUU---UCUCCGGCAUUAUCCU
(((((...(((((((((((((.((((.(..............).)))).)))))))))).......((((.....))))..)))...((((((.....---.))))))....))))) ( -36.24)
>DroSim_CAF1 70698 114 + 1
GGGAUUACAGGGGACAAACUUUAUCUACAAAUCGUUUGCAUCGCAGAUCAGGUUUGUCCACACUUAGCCAAACUUUGGUCGCCUCAUCCGGAGUCCUU---UCUCCGGCAUUAUCCU
(((((...(((((((((((((.((((.(..............).)))).)))))))))).......((((.....))))..)))...((((((.....---.))))))....))))) ( -34.24)
>DroYak_CAF1 78762 117 + 1
GGGAUUACAGGGGACAAACUUUACCUACAAAUCGUUUGCAUCGCAGAUCAGGUUUGUCCACACUUAGCCAAACUUUAGCCGCCUCAUCCGGAGUCCUUCUUGCUCCGGCAUUAUCCU
(((((...(((((((((((((............((((((...)))))).)))))))))).......((.........))..)))...(((((((.......)))))))....))))) ( -29.72)
>consensus
GGGAUUACAGGGGACAAACUUUAUCUACAAAUCGUUUGCAUCGCAGAUCAGGUUUGUCCACACUUAGCCAAACUUUGGCCGCCUCAUCCGGAGUCCUU___UCUCCGGCAUUAUCCU
(((((...(((((((((((((.((((.(..............).)))).)))))))))).......((((.....))))..)))...((((((.........))))))....))))) (-32.38 = -32.69 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	14,362,054 – 14,362,168
Length	114
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	96.97
Mean single sequence MFE	-40.02
Consensus MFE	-39.03
Energy contribution	-38.90
Covariance contribution	-0.13
Combinations/Pair	1.06
Mean z-score	-2.84
Structure conservation index	0.98
SVM decision value	1.99
SVM RNA-class probability	0.984837
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14362054 114 - 22224390
AGGAUAAUGCCGGAGA---AAGGACUCCGGAUGAGGCGGCCAAAGUUUGGCUAAGUGUGGACAAACCUGAUCUGCGAUGCAAACGAUUUGUAGAUAAAGUUUGUCCCCUGUAAUCCC
.((((....((((((.---.....))))))...(((.(((((.....)))))......((((((((...((((((((..........))))))))...)))))))))))...)))). ( -42.00)
>DroSec_CAF1 76479 114 - 1
AGGAUAAUGCCGGAGA---AAGGACUCCGGAUGAGGCGGCCAAAGUUUGGCUAAGUGUGGACAAACCUGAUCUGCGAUGCAAACGAUUUGUAGAUAAAGUUUGUCCCCUGUAAUCCC
.((((....((((((.---.....))))))...(((.(((((.....)))))......((((((((...((((((((..........))))))))...)))))))))))...)))). ( -42.00)
>DroSim_CAF1 70698 114 - 1
AGGAUAAUGCCGGAGA---AAGGACUCCGGAUGAGGCGACCAAAGUUUGGCUAAGUGUGGACAAACCUGAUCUGCGAUGCAAACGAUUUGUAGAUAAAGUUUGUCCCCUGUAAUCCC
.((((....((((((.---.....))))))...(((.(.(((.....)))).......((((((((...((((((((..........))))))))...)))))))))))...)))). ( -37.10)
>DroYak_CAF1 78762 117 - 1
AGGAUAAUGCCGGAGCAAGAAGGACUCCGGAUGAGGCGGCUAAAGUUUGGCUAAGUGUGGACAAACCUGAUCUGCGAUGCAAACGAUUUGUAGGUAAAGUUUGUCCCCUGUAAUCCC
.((((....(((((((......).))))))...(((.(((((.....)))))......((((((((...((((((((..........))))))))...)))))))))))...)))). ( -39.00)
>consensus
AGGAUAAUGCCGGAGA___AAGGACUCCGGAUGAGGCGGCCAAAGUUUGGCUAAGUGUGGACAAACCUGAUCUGCGAUGCAAACGAUUUGUAGAUAAAGUUUGUCCCCUGUAAUCCC
.((((....((((((.........))))))...(((.(((((.....)))))......((((((((...((((((((..........))))))))...)))))))))))...)))). (-39.03 = -38.90 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:46 2006