Locus 8191

Sequence ID	3L_DroMel_CAF1
Location	21,541,235 – 21,541,340
Length	105
Max. P	0.705616

overview

Window 4

Location	21,541,235 – 21,541,340
Length	105
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	81.41
Mean single sequence MFE	-41.57
Consensus MFE	-24.00
Energy contribution	-25.86
Covariance contribution	1.86
Combinations/Pair	1.04
Mean z-score	-2.14
Structure conservation index	0.58
SVM decision value	0.24
SVM RNA-class probability	0.648677
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21541235 105 + 23771897
AGAGCGCUUGGGC-----AGGGCCUUCCUUGUUUGGUUCACCUGGA--GGAGUUCCUUAUUUGGACCACAAUGAAGGCCGAUCCUCCGCGAUCCGUGGUCCGCCCGCCCAAC
.......((((((-----..(((((((.((((..((((((....((--((....))))...)))))))))).)))))))......(((((...))))).......)))))). ( -43.60)
>DroSec_CAF1 12785 105 + 1
AGAGCGCUUGGGC-----AGGGCCUUCCUUGUUUGGUCCACCUGGA--GGAGUUCCUUAUUUGGACCACAAUGAAGGCCGAUCCUCCGCGAGCCGUGGUCCGCCCGCCCAAC
.......((((((-----..(((((((.((((..((((((....((--((....))))...)))))))))).)))))))........(((..(....)..)))..)))))). ( -48.10)
>DroSim_CAF1 13658 105 + 1
AGAGCGCUUGGGC-----AGGGCCUUCCUUGUUUGGUCCACCUGGA--GGAGUUCCUUAUUUGGACCACAAUGAAGGCCGAUCCUCCGCGAGCCGUGGUCCGCCCGCCCAAC
.......((((((-----..(((((((.((((..((((((....((--((....))))...)))))))))).)))))))........(((..(....)..)))..)))))). ( -48.10)
>DroEre_CAF1 30483 105 + 1
AGAGCGCUUGGGC-----AGCGCCUUCCUUGUUUGGUCCACUUGGA--GGAGUUCCUUAUUUGGACCACAAUGAAGGCCGAUCCUCCGCGAGCCUCGGUCCGUCCGCCCAAC
.(.(((..(((((-----...((((((.((((..((((((....((--((....))))...)))))))))).))))))(((..(((...)))..))))))))..))).)... ( -43.50)
>DroYak_CAF1 30863 92 + 1
AGAGCGCUUGGGC-----AGGGCCUUCCAUGUUUGGUCCACUUGGA--GGAGUUCCUUAUUUGGACCACAAUGAAGGCCGAUCCUCCGCGAGCCUUGGU-------------
.(((.(((((((.-----(((((((((.((...(((((((....((--((....))))...)))))))..))))))))....))))).))))))))...------------- ( -39.30)
>DroAna_CAF1 14332 99 + 1
AGAGCGUAUGAGCGCCUCAUAGGCCGCCUUGUUUGGGCCACUUGGAAAGAGAUUCCAUAUUUGGACGACAAUGACUGCCCAGUACCCGCGAUCCG-GAUC------------
.(.((.((((((...)))))).)))((((.....))))....(((((.....))))).(((((((((......(((....))).....)).))))-))).------------ ( -26.80)
>consensus
AGAGCGCUUGGGC_____AGGGCCUUCCUUGUUUGGUCCACCUGGA__GGAGUUCCUUAUUUGGACCACAAUGAAGGCCGAUCCUCCGCGAGCCGUGGUCCGCCCGCCCAAC
...(.(((((.(........(((((((.((((..((((((...(((.......))).....)))))))))).))))))).......).)))))).................. (-24.00 = -25.86 +   1.86)

alignment

secondary structure

dotplot

Window 5

Location	21,541,235 – 21,541,340
Length	105
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	81.41
Mean single sequence MFE	-41.92
Consensus MFE	-23.90
Energy contribution	-27.52
Covariance contribution	3.61
Combinations/Pair	1.07
Mean z-score	-2.30
Structure conservation index	0.57
SVM decision value	0.36
SVM RNA-class probability	0.705616
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21541235 105 - 23771897
GUUGGGCGGGCGGACCACGGAUCGCGGAGGAUCGGCCUUCAUUGUGGUCCAAAUAAGGAACUCC--UCCAGGUGAACCAAACAAGGAAGGCCCU-----GCCCAAGCGCUCU
.(((((((((((((((((((.....(((((.....))))).)))))))))...........(((--(...((....)).....))))..)))).-----))))))....... ( -43.10)
>DroSec_CAF1 12785 105 - 1
GUUGGGCGGGCGGACCACGGCUCGCGGAGGAUCGGCCUUCAUUGUGGUCCAAAUAAGGAACUCC--UCCAGGUGGACCAAACAAGGAAGGCCCU-----GCCCAAGCGCUCU
.(((((((((((..(....)..)))........(((((((.((((((((((....(((....))--).....))))))..)))).)))))))))-----))))))....... ( -49.60)
>DroSim_CAF1 13658 105 - 1
GUUGGGCGGGCGGACCACGGCUCGCGGAGGAUCGGCCUUCAUUGUGGUCCAAAUAAGGAACUCC--UCCAGGUGGACCAAACAAGGAAGGCCCU-----GCCCAAGCGCUCU
.(((((((((((..(....)..)))........(((((((.((((((((((....(((....))--).....))))))..)))).)))))))))-----))))))....... ( -49.60)
>DroEre_CAF1 30483 105 - 1
GUUGGGCGGACGGACCGAGGCUCGCGGAGGAUCGGCCUUCAUUGUGGUCCAAAUAAGGAACUCC--UCCAAGUGGACCAAACAAGGAAGGCGCU-----GCCCAAGCGCUCU
.((((((((.((..((((..(((...)))..))))(((((.((((((((((....(((....))--).....))))))..)))).)))))))))-----))))))....... ( -45.30)
>DroYak_CAF1 30863 92 - 1
-------------ACCAAGGCUCGCGGAGGAUCGGCCUUCAUUGUGGUCCAAAUAAGGAACUCC--UCCAAGUGGACCAAACAUGGAAGGCCCU-----GCCCAAGCGCUCU
-------------.....((..(((...((...(((((((....(((((((....(((....))--).....)))))))......)))))))..-----.))...)))..)) ( -35.60)
>DroAna_CAF1 14332 99 - 1
------------GAUC-CGGAUCGCGGGUACUGGGCAGUCAUUGUCGUCCAAAUAUGGAAUCUCUUUCCAAGUGGCCCAAACAAGGCGGCCUAUGAGGCGCUCAUACGCUCU
------------...(-((.....)))(((.(((((.(((.((((.(.(((....(((((.....)))))..))).)...))))))).(((.....)))))))))))..... ( -28.30)
>consensus
GUUGGGCGGGCGGACCACGGCUCGCGGAGGAUCGGCCUUCAUUGUGGUCCAAAUAAGGAACUCC__UCCAAGUGGACCAAACAAGGAAGGCCCU_____GCCCAAGCGCUCU
.((((((.......((.(.(....).).))...(((((((.((((((((((.....(((.......)))...))))))..)))).))))))).......))))))....... (-23.90 = -27.52 +   3.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:03 2006