Locus 1795

Sequence ID	2L_DroMel_CAF1
Location	4,949,804 – 4,949,909
Length	105
Max. P	0.918015

overview

Window 1

Location	4,949,804 – 4,949,909
Length	105
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	78.12
Mean single sequence MFE	-25.38
Consensus MFE	-10.54
Energy contribution	-12.98
Covariance contribution	2.44
Combinations/Pair	1.12
Mean z-score	-2.20
Structure conservation index	0.42
SVM decision value	0.85
SVM RNA-class probability	0.865904
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4949804 105 + 22407834
UGCUAC----AAAAAUUAUUUGUGU-----AAUCUUACGCCGUGGUUUCUACACACGAGUAAAAUUUGUUUUACACUGCGUAAAACAAGUGUAGAACACAUACAUUUUGUUGGU
.(((((----((((......(((((-----..(((.((((((((((....)).))))........(((((((((.....)))))))))))))))))))))....))))).)))) ( -26.40)
>DroSec_CAF1 5357 110 + 1
UGCUGC----AUAAUUUAUUUGUGUAAAGUAAUCUUACGCCGUGGCUUCUACACACAAGUAAAAUUUGUUUUACACUGCGUAAAACCAGUGUAGAACACAUAGAUUUUGUUGGU
..(.((----(...(((((((((((...(((....)))((....))......)))))))))))...((((((((((((.(.....))))))))))))).........))).).. ( -29.20)
>DroSim_CAF1 5165 110 + 1
UGCUGC----AUAAUUUAUUUGUGUACAGUAAUCUUACGCCGUGGUUUCUACACACGAGUAAAAUUUGUUUUACACUGCGUAAAACCUGUGUAGAACACAUAGAUUUUGUUGGU
..(.((----(.(((((((.(((.(((((.....((((((((((((....)).)))).((((((....))))))...))))))...)))))....))).))))))).))).).. ( -26.70)
>DroEre_CAF1 5534 103 + 1
ACCCAC----AUAUGUUAUUUGUCUACAAUAAAUUUACGAUGUGGUUUCUACACACGAGUAAAAUGUGCCUUACACUGUGUAAAACGAGCGUAGUAAACUU-------GUUGGU
......----................((((((.(((((.((((.((((.((((((.(.((((........)))).)))))))))))..)))).))))).))-------)))).. ( -22.50)
>DroYak_CAF1 5372 113 + 1
ACCUACAUACAUAUAUUAUUUGUGUACAAUAAUUUUACGUUGUACUUUUUACACUCGAGUCAAAUUUGACUUACACUGUGUAAAGCAAGUUUAGUAAACUUACAUCU-UUUGGU
(((..............(((((((((((((........)))))))..(((((((..((((((....)))))).....)))))))))))))...(((....)))....-...))) ( -22.10)
>consensus
UGCUAC____AUAAAUUAUUUGUGUACAAUAAUCUUACGCCGUGGUUUCUACACACGAGUAAAAUUUGUUUUACACUGCGUAAAACAAGUGUAGAACACAUACAUUUUGUUGGU
...............((((((((((.....((((.........)))).....))))))))))....(((((((((((..........)))))))))))................ (-10.54 = -12.98 +   2.44)

alignment

secondary structure

dotplot

Window 2

Location	4,949,804 – 4,949,909
Length	105
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	78.12
Mean single sequence MFE	-23.72
Consensus MFE	-13.10
Energy contribution	-13.74
Covariance contribution	0.64
Combinations/Pair	1.31
Mean z-score	-2.17
Structure conservation index	0.55
SVM decision value	1.12
SVM RNA-class probability	0.918015
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4949804 105 - 22407834
ACCAACAAAAUGUAUGUGUUCUACACUUGUUUUACGCAGUGUAAAACAAAUUUUACUCGUGUGUAGAAACCACGGCGUAAGAUU-----ACACAAAUAAUUUUU----GUAGCA
....(((((((((.(((((........((((((((.....))))))))(((((((((((((.((....))))))).))))))))-----))))).)))..))))----)).... ( -26.60)
>DroSec_CAF1 5357 110 - 1
ACCAACAAAAUCUAUGUGUUCUACACUGGUUUUACGCAGUGUAAAACAAAUUUUACUUGUGUGUAGAAGCCACGGCGUAAGAUUACUUUACACAAAUAAAUUAU----GCAGCA
....((((........((((.(((((((........))))))).))))........))))(((((((.((....))(((....))))))))))...........----...... ( -23.19)
>DroSim_CAF1 5165 110 - 1
ACCAACAAAAUCUAUGUGUUCUACACAGGUUUUACGCAGUGUAAAACAAAUUUUACUCGUGUGUAGAAACCACGGCGUAAGAUUACUGUACACAAAUAAAUUAU----GCAGCA
..............(((((.....(((((((((((.....))))))).(((((((((((((.((....))))))).)))))))).)))))))))..........----...... ( -25.30)
>DroEre_CAF1 5534 103 - 1
ACCAAC-------AAGUUUACUACGCUCGUUUUACACAGUGUAAGGCACAUUUUACUCGUGUGUAGAAACCACAUCGUAAAUUUAUUGUAGACAAAUAACAUAU----GUGGGU
(((.((-------((((((((........((((((((((.((((((....)))))).).)))))))))........)))))))).(((....))).........----)).))) ( -20.49)
>DroYak_CAF1 5372 113 - 1
ACCAAA-AGAUGUAAGUUUACUAAACUUGCUUUACACAGUGUAAGUCAAAUUUGACUCGAGUGUAAAAAGUACAACGUAAAAUUAUUGUACACAAAUAAUAUAUGUAUGUAGGU
(((...-....(((((((.....)))))))(((((((..((..(((((....))))))).)))))))...(((((((((..((((((.......)))))).))))).))))))) ( -23.00)
>consensus
ACCAACAAAAUCUAUGUGUUCUACACUGGUUUUACGCAGUGUAAAACAAAUUUUACUCGUGUGUAGAAACCACGGCGUAAGAUUACUGUACACAAAUAAAUUAU____GUAGCA
...............((((.........(((((((.....))))))).(((((((((((((.((....))))))).)))))))).....))))..................... (-13.10 = -13.74 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:29 2006