Locus 5219

Sequence ID	3R_DroMel_CAF1
Location	13,664,083 – 13,664,173
Length	90
Max. P	0.993900

overview

Window 5

Location	13,664,083 – 13,664,173
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	91.24
Mean single sequence MFE	-22.47
Consensus MFE	-20.78
Energy contribution	-21.00
Covariance contribution	0.22
Combinations/Pair	1.09
Mean z-score	-2.08
Structure conservation index	0.92
SVM decision value	2.43
SVM RNA-class probability	0.993900
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13664083 90 + 27905053
AGUCCUGAAUUGCAGUCACAUUUUUGGCAUAUGUCACCACACAACCACAUAUGCAAUUACAGGACUCGAGGCAGGCAAGCAGUUACAUUG
(((((((((((((.((((......))))((((((............)))))))))))).)))))))....((......)).......... ( -23.60)
>DroSec_CAF1 29236 90 + 1
AGUCCUGAAUUGCAGUCACAUUUUUGGCAUAUGUCACCACACAACCACAUAUGCAAUUACAGGACUCGAGGCAGGCAAGCAGUUACAUUG
(((((((((((((.((((......))))((((((............)))))))))))).)))))))....((......)).......... ( -23.60)
>DroSim_CAF1 29251 90 + 1
AGUCCUGAAUUGCAGUCACAUUUUUGGCAUAUGUCACCACACAACCACAUAUGCAAUUACAGGACUCGAGGCAGGCAAGCAGUUACAUUG
(((((((((((((.((((......))))((((((............)))))))))))).)))))))....((......)).......... ( -23.60)
>DroEre_CAF1 33098 90 + 1
AGUCCUGAAUUGCAGUCACAUUUUUGGCAUAUGUCACCACACAACCACAUAUGCAAUUACAGGACUAGAGGCAGGCAAGCAGUUACAUUG
(((((((((((((.((((......))))((((((............)))))))))))).)))))))....((......)).......... ( -24.20)
>DroYak_CAF1 29462 86 + 1
AGUCCUGAAUUGCAGUCACAUUUUUGGCAUAUGUCACCACACAACCACAUAUGCAAUUACAGGACACGAG----GCAAGCAGUUACAUAG
.((((((((((((.((((......))))((((((............)))))))))))).))))))..(..----((.....))..).... ( -22.70)
>DroAna_CAF1 24442 79 + 1
----CUGAGUUGCAGCCACAUUUUUGGCAUAUGUCACCAUG---CCACAUAUGCAAUUACAGGACUCGAGC----CAUACAGUUACAUUG
----(((((((((.((((......))))((((((.......---..)))))))))))).))).........----............... ( -17.10)
>consensus
AGUCCUGAAUUGCAGUCACAUUUUUGGCAUAUGUCACCACACAACCACAUAUGCAAUUACAGGACUCGAGGCAGGCAAGCAGUUACAUUG
.((((((((((((.((((......))))((((((............)))))))))))).))))))......................... (-20.78 = -21.00 +   0.22)

alignment

secondary structure

dotplot

Window 6

Location	13,664,083 – 13,664,173
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	91.24
Mean single sequence MFE	-27.72
Consensus MFE	-23.85
Energy contribution	-24.88
Covariance contribution	1.03
Combinations/Pair	1.04
Mean z-score	-2.52
Structure conservation index	0.86
SVM decision value	1.73
SVM RNA-class probability	0.974359
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13664083 90 - 27905053
CAAUGUAACUGCUUGCCUGCCUCGAGUCCUGUAAUUGCAUAUGUGGUUGUGUGGUGACAUAUGCCAAAAAUGUGACUGCAAUUCAGGACU
..........((......))....(((((((.((((((((((.((((.(((((....)))))))))...)))....)))))))))))))) ( -29.10)
>DroSec_CAF1 29236 90 - 1
CAAUGUAACUGCUUGCCUGCCUCGAGUCCUGUAAUUGCAUAUGUGGUUGUGUGGUGACAUAUGCCAAAAAUGUGACUGCAAUUCAGGACU
..........((......))....(((((((.((((((((((.((((.(((((....)))))))))...)))....)))))))))))))) ( -29.10)
>DroSim_CAF1 29251 90 - 1
CAAUGUAACUGCUUGCCUGCCUCGAGUCCUGUAAUUGCAUAUGUGGUUGUGUGGUGACAUAUGCCAAAAAUGUGACUGCAAUUCAGGACU
..........((......))....(((((((.((((((((((.((((.(((((....)))))))))...)))....)))))))))))))) ( -29.10)
>DroEre_CAF1 33098 90 - 1
CAAUGUAACUGCUUGCCUGCCUCUAGUCCUGUAAUUGCAUAUGUGGUUGUGUGGUGACAUAUGCCAAAAAUGUGACUGCAAUUCAGGACU
..........((......))....(((((((.((((((((((.((((.(((((....)))))))))...)))....)))))))))))))) ( -28.90)
>DroYak_CAF1 29462 86 - 1
CUAUGUAACUGCUUGC----CUCGUGUCCUGUAAUUGCAUAUGUGGUUGUGUGGUGACAUAUGCCAAAAAUGUGACUGCAAUUCAGGACU
................----.....((((((.((((((((((.((((.(((((....)))))))))...)))....))))))))))))). ( -27.50)
>DroAna_CAF1 24442 79 - 1
CAAUGUAACUGUAUG----GCUCGAGUCCUGUAAUUGCAUAUGUGG---CAUGGUGACAUAUGCCAAAAAUGUGGCUGCAACUCAG----
...............----....((((..((((.(..(((...(((---((((....))..)))))...)))..).))))))))..---- ( -22.60)
>consensus
CAAUGUAACUGCUUGCCUGCCUCGAGUCCUGUAAUUGCAUAUGUGGUUGUGUGGUGACAUAUGCCAAAAAUGUGACUGCAAUUCAGGACU
.........................((((((.((((((((((.((((.(((((....)))))))))...)))....))))))))))))). (-23.85 = -24.88 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:22 2006