Locus 3509

Sequence ID	2R_DroMel_CAF1
Location	11,754,961 – 11,755,053
Length	92
Max. P	0.989100

overview

Window 7

Location	11,754,961 – 11,755,053
Length	92
Sequences	3
Columns	107
Reading direction	forward
Mean pairwise identity	75.08
Mean single sequence MFE	-28.00
Consensus MFE	-19.91
Energy contribution	-21.80
Covariance contribution	1.89
Combinations/Pair	1.09
Mean z-score	-1.94
Structure conservation index	0.71
SVM decision value	2.15
SVM RNA-class probability	0.989100
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11754961 92 + 20766785
UCUCCU------------CCAUGUUCUUGGAAACUGCUAAAGGCUGCGGAGUAGCGUC---UCUCUCUUCUGAGAGGUUUUCAUUGACCACUGAUAUUGCGUCGAGC
.(((((------------(((......))))....((........))))))..((.((---((((......))))))......(((((((.......)).))))))) ( -22.90)
>DroSec_CAF1 7456 107 + 1
UCUCCUUUACUUGUAGUUCCAUGUUCUUGGAACUUUCCAAAGGCUGCAGAGUAGCAGCCUUACACUCUUUUGAGAGGUUUUCAUUGACUACUGUAAUGANNNNNNNN
...(((.....((((((((((......))))))).....((((((((......)))))))))))(((....))))))...((((((.(....)))))))........ ( -29.00)
>DroSim_CAF1 6666 107 + 1
UCUCCUCUACUUGUAGUUCCAUGUUCUUGGAACUUUCCAAAGGCUGCAGAGUAGCAGCCUUACACUGUUUUGAGAGGUUUUCAUUGACCACUGUAAUCGCGUCGAGC
.((((((.((.((((((((((......))))))).....((((((((......)))))))))))..))...))).((((......))))..............))). ( -32.10)
>consensus
UCUCCU_UACUUGUAGUUCCAUGUUCUUGGAACUUUCCAAAGGCUGCAGAGUAGCAGCCUUACACUCUUUUGAGAGGUUUUCAUUGACCACUGUAAUCGCGUCGAGC
((((...........((((((......))))))......((((((((......))))))))..........))))((((......)))).................. (-19.91 = -21.80 +   1.89)

alignment

secondary structure

dotplot

Window 8

Location	11,754,961 – 11,755,053
Length	92
Sequences	3
Columns	107
Reading direction	reverse
Mean pairwise identity	75.08
Mean single sequence MFE	-28.31
Consensus MFE	-14.90
Energy contribution	-17.90
Covariance contribution	3.00
Combinations/Pair	1.00
Mean z-score	-2.39
Structure conservation index	0.53
SVM decision value	0.96
SVM RNA-class probability	0.889552
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11754961 92 - 20766785
GCUCGACGCAAUAUCAGUGGUCAAUGAAAACCUCUCAGAAGAGAGA---GACGCUACUCCGCAGCCUUUAGCAGUUUCCAAGAACAUGG------------AGGAGA
(((((((.((.......))))).........(((((....))))).---)).))..((((((........))....((((......)))------------))))). ( -22.70)
>DroSec_CAF1 7456 107 - 1
NNNNNNNNUCAUUACAGUAGUCAAUGAAAACCUCUCAAAAGAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUAAAGGAGA
........(((((((....)).))))).....((((.......(((((((((((......)))))))).....(((((((......)))))))))).......)))) ( -29.74)
>DroSim_CAF1 6666 107 - 1
GCUCGACGCGAUUACAGUGGUCAAUGAAAACCUCUCAAAACAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUAGAGGAGA
....(((((.......)).)))........((((((..........((((((((......)))))))).....(((((((......)))))))....).)))))... ( -32.50)
>consensus
GCUCGACGCAAUUACAGUGGUCAAUGAAAACCUCUCAAAAGAGUGUAAGGCUGCUACUCUGCAGCCUUUGGAAAGUUCCAAGAACAUGGAACUACAAGUA_AGGAGA
................................((((..........((((((((......)))))))).....(((((((......)))))))..........)))) (-14.90 = -17.90 +   3.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:16 2006