Locus 945

Sequence ID	3L_DroMel_CAF1
Location	2,833,593 – 2,833,725
Length	132
Max. P	0.909303

overview

Window 4

Location	2,833,593 – 2,833,688
Length	95
Sequences	3
Columns	95
Reading direction	reverse
Mean pairwise identity	93.59
Mean single sequence MFE	-29.14
Consensus MFE	-23.69
Energy contribution	-24.13
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-2.46
Structure conservation index	0.81
SVM decision value	0.36
SVM RNA-class probability	0.705456
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2833593 95 - 23771897
AAAUCCACUUCCAACCACCCCUGUUACCCCUGUGGAAGCAGCUCUCCUCUUUGUGGCUCAUCACUCACGUCACUUUAUGCGGCGUGGAGAGUGGA
...(((.((((((...................))))))..(((((((.....((((....))))..(((((.(.....).))))))))))))))) ( -26.71)
>DroSec_CAF1 78627 91 - 1
AAAUCCACUUCCAACCACC-GAGUUACCCCUGUGGAAGCAGC-CUCCUCUUUGUGGCUCAUCACUCACGUCACUUUAUGUGGCGUGGA--GUGGA
...(((((((.........-(((((((....(.(((......-.))).)...)))))))......((((((((.....))))))))))--))))) ( -32.70)
>DroSim_CAF1 69211 91 - 1
AAAUCCACAUCCAACCACC-GAGUUACCCCUGUGGAAGCAGC-CUCCUCUUUGUGGCUCAUCACUUACGUCACUUUAUGCGGCGUGGA--GUGGA
...(((((.(((.......-(((((((....(.(((......-.))).)...))))))).......(((((.(.....).))))))))--))))) ( -28.00)
>consensus
AAAUCCACUUCCAACCACC_GAGUUACCCCUGUGGAAGCAGC_CUCCUCUUUGUGGCUCAUCACUCACGUCACUUUAUGCGGCGUGGA__GUGGA
...(((((............(((((((....(.(((........))).)...))))))).....(((((((.(.....).)))))))...))))) (-23.69 = -24.13 +   0.45)

alignment

secondary structure

dotplot

Window 5

Location	2,833,614 – 2,833,725
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	91.57
Mean single sequence MFE	-30.88
Consensus MFE	-24.64
Energy contribution	-24.48
Covariance contribution	-0.16
Combinations/Pair	1.14
Mean z-score	-1.91
Structure conservation index	0.80
SVM decision value	1.06
SVM RNA-class probability	0.909303
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2833614 111 + 23771897
AGUGACGUGAGUGAUGAGCCACAAAGAGGAGAGCUGCUUCCACAGGGGUAACAGGGGUGGUUGGAAGUGGAUUUAAUCAUGAAUGAAACUCAUUAUAGAGUCACAAGCUUA
.(((((....((((((((((((...(((.(....).)))((((...(....)....))))......))))......(((....)))..))))))))...)))))....... ( -26.70)
>DroSec_CAF1 78646 109 + 1
AGUGACGUGAGUGAUGAGCCACAAAGAGGAG-GCUGCUUCCACAGGGGUAACUC-GGUGGUUGGAAGUGGAUUUAAUCAUGAAUGAAACUCAUUACAGAGUCACAAGCUUA
.(((((....((((((((((.......))..-.(..(((((((.(((....)))-....).))))))..)..................))))))))...)))))....... ( -32.10)
>DroSim_CAF1 69230 109 + 1
AGUGACGUAAGUGAUGAGCCACAAAGAGGAG-GCUGCUUCCACAGGGGUAACUC-GGUGGUUGGAUGUGGAUUUAAUCAUGAAUGAAACUCAUUAUAGAGUCACAAGCUUA
.(((((....((((((((..........(((-..((((((....)))))).)))-.((((((((((....))))))))))........))))))))...)))))....... ( -30.90)
>DroEre_CAF1 81383 110 + 1
AGUGACGUGAGUGAUGAGCCAGAAGGAGGAGAGCUGCUGCCACACGGGUAACUC-GGUGGUUGGAAGAAGAUGUAAUCAUGAAUGAAACUCAUUACGGAGUCACAAGCUUA
.(((((....(((((((((((..((.((.....)).))(((((.((((...)))-)))))))))............(((....)))..))))))))...)))))....... ( -32.40)
>DroYak_CAF1 81855 110 + 1
AGUGACGUGAGUGAUGAGCCAGAAAGAGCAGAGCUGCUGCCACACGGGUAACUC-GGUGGUUGAAAGGAGAUUUAACAAUGAAUGAAACUCAUUAUGGAGUCACAAGCUUA
.(((((....((((((((((......((((....))))(((((.((((...)))-)))))).....))..(((((....)))))....))))))))...)))))....... ( -32.30)
>consensus
AGUGACGUGAGUGAUGAGCCACAAAGAGGAGAGCUGCUUCCACAGGGGUAACUC_GGUGGUUGGAAGUGGAUUUAAUCAUGAAUGAAACUCAUUAUAGAGUCACAAGCUUA
.(((((....((((((((((.....(.((((.....))))).....))........(((((((((......)))))))))........))))))))...)))))....... (-24.64 = -24.48 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:05 2006