Locus 1754

Sequence ID	2L_DroMel_CAF1
Location	4,794,248 – 4,794,392
Length	144
Max. P	0.986874

overview

Window 6

Location	4,794,248 – 4,794,364
Length	116
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	79.17
Mean single sequence MFE	-26.05
Consensus MFE	-15.71
Energy contribution	-16.21
Covariance contribution	0.50
Combinations/Pair	1.20
Mean z-score	-2.69
Structure conservation index	0.60
SVM decision value	2.06
SVM RNA-class probability	0.986874
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4794248 116 + 22407834
GCUCUUCGACACAGUGCUAUAAAAAUCACAUAACAUAAUUUAUAGCAGUGUAAGUUGAACUGAGGCUUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUUACAUUUUAUAGCAAGAA
.((((((((((((.(((((((((...............))))))))).)))..))))))..)))((.....))....(((((((....(((((......))))).))))))).... ( -28.86)
>DroSec_CAF1 242335 116 + 1
GCUGUUCGACACAGUGCCAUAAAUAUUCCAUAACAUAAUUUAUAGCAGUUUAAGUUCAACUGAGGCUUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUAACAUUUUAUCGCAAGAA
(((((....(((((((((((((((.............))))))..(((((.......)))))........)))))))))....)))))((((((....))))))...((....)). ( -30.42)
>DroSim_CAF1 219570 105 + 1
GCUAUUCGACACAGUGCCAUAAAUAUUGUAUAACAUAAUUUAUAGCAGUUUAAGU-----------UUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUAACAUUUUAUCGCAAGAA
(((......((((((((((.(((((((((((((......)))).)))))....))-----------)).))))))))))......)))((((((....))))))...((....)). ( -26.70)
>DroYak_CAF1 230573 109 + 1
GCUUUUUAACACG--GCUAUAAAUCUCCUAUAAUAUAAUUUAAAGCA----AAGUUCAACUGAGCCUUAUAGCUAUGUGCUGCAAAGCAAU-UUAUUGUACAUUUUAUAGAAAAAU
(((((...(((..--(((((((.....((.(((......))).))..----..((((....)))).)))))))..))).....)))))...-........................ ( -18.20)
>consensus
GCUAUUCGACACAGUGCCAUAAAUAUCCCAUAACAUAAUUUAUAGCAGUUUAAGUUCAACUGAGGCUUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUAACAUUUUAUAGCAAGAA
(((((....((((((((((..................................................))))))))))....)))))(((((......)))))............ (-15.71 = -16.21 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	4,794,284 – 4,794,392
Length	108
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	83.02
Mean single sequence MFE	-23.15
Consensus MFE	-13.77
Energy contribution	-16.40
Covariance contribution	2.63
Combinations/Pair	1.10
Mean z-score	-1.91
Structure conservation index	0.60
SVM decision value	0.04
SVM RNA-class probability	0.552173
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4794284 108 + 22407834
AAUUUAUAGCAGUGUAAGUUGAACUGAGGCUUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUUACAUUUUAUAGCAAGAACGAAACUUGGUGUUAUAUUAGACUGUUA
......(((((((.(((.....((..((...((((......(((((((....(((((......))))).)))))))....)))).))..))......))).))))))) ( -26.30)
>DroSec_CAF1 242371 108 + 1
AAUUUAUAGCAGUUUAAGUUCAACUGAGGCUUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUAACAUUUUAUCGCAAGAACGAAACUUGGUGUUAUAUUAGACUGUUA
......(((((((((((.....((..(((((..((((.....))))...)))((((((....))))))...((....))......))..))......))))))))))) ( -28.50)
>DroSim_CAF1 219606 97 + 1
AAUUUAUAGCAGUUUAAGU-----------UUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUAACAUUUUAUCGCAAGAACGAAACUUGGUGUUAUAUUAGACUGUUA
......(((((((((((..-----------...(((((((((........)))))))))..(((((((...(((......))).....)))))))..))))))))))) ( -24.10)
>DroYak_CAF1 230607 103 + 1
AAUUUAAAGCA----AAGUUCAACUGAGCCUUAUAGCUAUGUGCUGCAAAGCAAU-UUAUUGUACAUUUUAUAGAAAAAUUUAAACUUGGUGUUAUAUUAUUCUGUUA
.......((((----(.((((....)))).))...)))((((((...(((....)-))...))))))...((((((.(((...(((.....)))..))).)))))).. ( -13.70)
>consensus
AAUUUAUAGCAGUUUAAGUUCAACUGAGGCUUUUGGCAUUGUGCUAUACAGCAAUGUUAUUUAACAUUUUAUAGCAAGAACGAAACUUGGUGUUAUAUUAGACUGUUA
......(((((((((((................(((((((((........)))))))))..(((((((...(((......))).....)))))))..))))))))))) (-13.77 = -16.40 +   2.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:19 2006