Locus 4087

Sequence ID	3L_DroMel_CAF1
Location	11,902,526 – 11,902,618
Length	92
Max. P	0.964370

overview

Window 9

Location	11,902,526 – 11,902,618
Length	92
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	78.52
Mean single sequence MFE	-22.15
Consensus MFE	-17.31
Energy contribution	-17.23
Covariance contribution	-0.08
Combinations/Pair	1.19
Mean z-score	-2.03
Structure conservation index	0.78
SVM decision value	1.57
SVM RNA-class probability	0.964370
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11902526 92 + 23771897
A---AACAGACAUAUUUUGACACUUGGCCAAAAAAAGAAGAAAAAAGUCAAGACGAAGUGUUGG-CGGCU--CGCCCGAAAUCCAACGGGCAAGUGAC
.---..((((.....)))).(((((((((.................(((((.((...)).))))-)))))--.(((((........)))))))))).. ( -21.92)
>DroSim_CAF1 78675 90 + 1
A---AACAGACACAUUUUGACACUUGGCC-AAAAAAGAUGAAA-AAAACAAGACGAAGUGUUGG-CGGCU--CGCCCGAAAUCCAACGGGCAAGUGAC
.---......(((...(..((((((.(.(-.............-.......).).))))))..)-.....--.(((((........)))))..))).. ( -20.55)
>DroEre_CAF1 79952 75 + 1
A---AACAGACACAUUUUGACACUUGGCC-AAAA----------------AGACGAAGUGUUGG-CGGCU--CGCCCGAAAUCCAACGGGCAAGUGAC
.---......(((...(..((((((.(.(-....----------------.).).))))))..)-.....--.(((((........)))))..))).. ( -22.20)
>DroYak_CAF1 81819 78 + 1
A---AACAGACACAUUUUGACACUUGGCC-AAAA----------------AGACGAAGUGUUGGGCCGCCAACACCCGAAAUCCAACGGGCAAGUGAC
.---..((((.....)))).((((((.((-....----------------.......(((((((....)))))))..(.....)...)).)))))).. ( -21.50)
>DroAna_CAF1 73001 93 + 1
AGGCACCAGACACUUUUUGACACUUGGCC-AAAAAUACAGAAA-UACAGAAAACUGUGUGUUGA-CGAGC--CGCCCGAAAUCCAGCGGGCAAGUGAC
.(((.(..(((((((((((.(....)..)-)))))........-.((((....)))))))))..-.).))--)(((((........)))))....... ( -24.60)
>consensus
A___AACAGACACAUUUUGACACUUGGCC_AAAAA____GAAA__A___AAGACGAAGUGUUGG_CGGCU__CGCCCGAAAUCCAACGGGCAAGUGAC
..........(((...(..((((((.(..........................).))))))..).........(((((........)))))..))).. (-17.31 = -17.23 +  -0.08)

alignment

secondary structure

dotplot

Window 0

Location	11,902,526 – 11,902,618
Length	92
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	78.52
Mean single sequence MFE	-23.92
Consensus MFE	-16.23
Energy contribution	-16.51
Covariance contribution	0.28
Combinations/Pair	1.11
Mean z-score	-1.61
Structure conservation index	0.68
SVM decision value	0.31
SVM RNA-class probability	0.682885
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11902526 92 - 23771897
GUCACUUGCCCGUUGGAUUUCGGGCG--AGCCG-CCAACACUUCGUCUUGACUUUUUUCUUCUUUUUUUGGCCAAGUGUCAAAAUAUGUCUGUU---U
((..((((((((........))))))--))..)-)..((((((.(((......................))).))))))...............---. ( -21.45)
>DroSim_CAF1 78675 90 - 1
GUCACUUGCCCGUUGGAUUUCGGGCG--AGCCG-CCAACACUUCGUCUUGUUUU-UUUCAUCUUUUUU-GGCCAAGUGUCAAAAUGUGUCUGUU---U
((..((((((((........))))))--))..)-)..((((((.(((.......-.............-))).))))))...............---. ( -21.55)
>DroEre_CAF1 79952 75 - 1
GUCACUUGCCCGUUGGAUUUCGGGCG--AGCCG-CCAACACUUCGUCU----------------UUUU-GGCCAAGUGUCAAAAUGUGUCUGUU---U
((..((((((((........))))))--))..)-)..((((((.(((.----------------....-))).))))))...............---. ( -23.20)
>DroYak_CAF1 81819 78 - 1
GUCACUUGCCCGUUGGAUUUCGGGUGUUGGCGGCCCAACACUUCGUCU----------------UUUU-GGCCAAGUGUCAAAAUGUGUCUGUU---U
(.((((((.(((..((((...(((((((((....))))))))).))))----------------...)-)).)))))).)..............---. ( -26.10)
>DroAna_CAF1 73001 93 - 1
GUCACUUGCCCGCUGGAUUUCGGGCG--GCUCG-UCAACACACAGUUUUCUGUA-UUUCUGUAUUUUU-GGCCAAGUGUCAAAAAGUGUCUGGUGCCU
.......(((((........)))))(--((...-(((((((((((....)))).-........(((((-(((.....)))))))))))).))).))). ( -27.30)
>consensus
GUCACUUGCCCGUUGGAUUUCGGGCG__AGCCG_CCAACACUUCGUCUU___U__UUUC____UUUUU_GGCCAAGUGUCAAAAUGUGUCUGUU___U
(.(((..(((((........)))))............((((((.(((......................))).))))))......))).)........ (-16.23 = -16.51 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:09 2006