Locus 3944

Sequence ID	3L_DroMel_CAF1
Location	11,437,841 – 11,437,980
Length	139
Max. P	0.997679

overview

Window 9

Location	11,437,841 – 11,437,961
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-39.22
Consensus MFE	-35.80
Energy contribution	-36.40
Covariance contribution	0.60
Combinations/Pair	1.06
Mean z-score	-2.08
Structure conservation index	0.91
SVM decision value	2.91
SVM RNA-class probability	0.997679
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11437841 120 - 23771897
CAGCUUCAACUGCAACUGCGUCAAGGGCAUUAAGCCCAACAAGGAGAAGCUGGCAAAGAUCGUGAAUGAGUCGCUAAUGCUGGUGACAGCCCUCAAUCCGCACAUUGGCUAUGACAAGUC
(((((((..((((....)).....((((.....))))....))..)))))))((.......((((.....))))....((((....)))).........)).....((((......)))) ( -36.10)
>DroSec_CAF1 157303 120 - 1
CAGCUUCAACUGCAACUGCGUCAAAGGCAUUAAGCCUAACAAGGAGAAGCUGGCCAAGAUCGUGAAUGAGUCGCUAAUGCUGGUGACAGCCCUCAAUCCGCACAUUGGCUAUGACAAGUC
(((((((..((((....)).....((((.....))))....))..)))))))(((((...((.((.((((........((((....)))).)))).))))....)))))........... ( -38.90)
>DroSim_CAF1 168931 120 - 1
CAGCUUCAAUUGCAACUGCGUCAAAGGCAUUAAACCCAACAAGGAGAAGCUGGCCAAGAUCGUGAAUGAGUCGCUAAUGCUGGUGACAGCACUCAAUCCGCACAUUGGCUAUGACAAGUC
(((((((....((....))((.....)).......((.....)).)))))))(((((...((.((.(((((.......((((....))))))))).))))....)))))........... ( -36.01)
>DroEre_CAF1 168527 120 - 1
CAGCUUCAACUGCAACUGCGUCAAGGGCAUUCGGCCCAACAAGGAGAAGCUGGCCAAGAUCGUGAACGAGUCGCUAAUGCUGGUGACAGCCCUCAAUCCGCACAUUGGCUAUGACAAGUC
(((((((..((((....)).....((((.....))))....))..)))))))((((((((((....))).))......((((....))))..............)))))........... ( -40.90)
>DroYak_CAF1 155692 120 - 1
CAGCUUCAACUGCAACUGCGUCAAGGGCAUCAAGCCCAACAAGGAGAAGCUGGCCAAGAUCGUGAACGAGUCGCUGAUGCUGGUGACAGCCCUCAAUCCGCACAUUGGCUAUGACAAGUC
(((((((..((((....)).....((((.....))))....))..)))))))((((((((((....))).))((.(((((((....)))).....))).))...)))))........... ( -44.20)
>consensus
CAGCUUCAACUGCAACUGCGUCAAGGGCAUUAAGCCCAACAAGGAGAAGCUGGCCAAGAUCGUGAAUGAGUCGCUAAUGCUGGUGACAGCCCUCAAUCCGCACAUUGGCUAUGACAAGUC
(((((((..((((....)).....((((.....))))....))..)))))))(((((...((.((.((((........((((....)))).)))).))))....)))))........... (-35.80 = -36.40 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	11,437,881 – 11,437,980
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	92.93
Mean single sequence MFE	-29.52
Consensus MFE	-27.10
Energy contribution	-26.58
Covariance contribution	-0.52
Combinations/Pair	1.14
Mean z-score	-1.24
Structure conservation index	0.92
SVM decision value	0.55
SVM RNA-class probability	0.777010
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11437881 99 + 23771897
GCAUUAGCGACUCAUUCACGAUCUUUGCCAGCUUCUCCUUGUUGGGCUUAAUGCCCUUGACGCAGUUGCAGUUGAAGCUGAUGCACCCAUCAGCUAGGA
((((((((((.((......))))....(((((........))))))).))))))(((..((((....)).))..)((((((((....)))))))).)). ( -30.60)
>DroSec_CAF1 157343 99 + 1
GCAUUAGCGACUCAUUCACGAUCUUGGCCAGCUUCUCCUUGUUAGGCUUAAUGCCUUUGACGCAGUUGCAGUUGAAGCUGAUGCACCCAUCAGCUAGAA
...(((((((.....))..(((....(((((((((..((.(((((((.....))))..)))((....))))..)))))))..))....))).))))).. ( -27.00)
>DroSim_CAF1 168971 99 + 1
GCAUUAGCGACUCAUUCACGAUCUUGGCCAGCUUCUCCUUGUUGGGUUUAAUGCCUUUGACGCAGUUGCAAUUGAAGCUGAUGCACCCAUCAGCUAGAA
......(((((................(((((........)))))......(((.......))))))))......((((((((....)))))))).... ( -25.40)
>DroEre_CAF1 168567 99 + 1
GCAUUAGCGACUCGUUCACGAUCUUGGCCAGCUUCUCCUUGUUGGGCCGAAUGCCCUUGACGCAGUUGCAGUUGAAGCUGAUGCAGCCAUCCGCUACGA
....(((((..(((....)))...(((((((((((..((.(((((((.....))))..)))((....))))..))))))).....))))..)))))... ( -31.60)
>DroYak_CAF1 155732 99 + 1
GCAUCAGCGACUCGUUCACGAUCUUGGCCAGCUUCUCCUUGUUGGGCUUGAUGCCCUUGACGCAGUUGCAGUUGAAGCUGAUGCAACCAUCCGCUAUAA
((((((((((.(((....))))).....(((((.(..((((((((((.....))))..)))).))..).)))))..))))))))............... ( -33.00)
>consensus
GCAUUAGCGACUCAUUCACGAUCUUGGCCAGCUUCUCCUUGUUGGGCUUAAUGCCCUUGACGCAGUUGCAGUUGAAGCUGAUGCACCCAUCAGCUAGAA
((((((((((.((......)))).....(((((.(..((((((((((.....))))..)))).))..).)))))..))))))))............... (-27.10 = -26.58 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:36 2006