Locus 8935

Sequence ID	3R_DroMel_CAF1
Location	23,972,893 – 23,972,988
Length	95
Max. P	0.703410

overview

Window 4

Location	23,972,893 – 23,972,988
Length	95
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	81.10
Mean single sequence MFE	-29.57
Consensus MFE	-20.36
Energy contribution	-20.50
Covariance contribution	0.14
Combinations/Pair	1.21
Mean z-score	-1.63
Structure conservation index	0.69
SVM decision value	0.36
SVM RNA-class probability	0.703410
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23972893 95 + 27905053
------------GAGGCUGCCGGCAAAAUAAUAAUUGCCAUUG--CAGCCAGCUACUUGAAACUUUCCCAGC---------GACUUUGAACCGGCUGAGCAGGGCUUCACUUUUUUGU
------------..((((((.(((((........)))))...)--))))).......((((.((((.(((((---------............)))).).)))).))))......... ( -26.50)
>DroSec_CAF1 174495 91 + 1
------------GAGGCUGCCGGCGAAAUAAUAAUUGCCAUUG--CAGCCAGCUGCUUGAAACUUUCCCAGC---------GACUUU-AGCC--UUUAGCC-GGCUUCACUUUUUUGU
------------..((((((.(((((........)))))...)--))))).((((...((.....)).))))---------......-((((--.......-))))............ ( -25.60)
>DroSim_CAF1 170448 95 + 1
------------GAGGCUGCCGGCGAAAUAAUAAUUGCCAUUG--CAGCCAGCUGCUUGAAACUUUCCCAGC---------GACUUUGAGCCGGCUGAGCAGGGCUUCAUUUUUUUGU
------------((((((((.(((((........)))))...)--).((((((((((..((...........---------...))..)).)))))).))..)))))).......... ( -29.84)
>DroEre_CAF1 183094 95 + 1
------------GAAGCUGCCGGCAAAAUAAUAAUUGCCAUUG--CAGCCAGCUGCUUAAAACUUUCGCUGC---------GACUUUGAGCCGUCUGAGCAGGGCUUCACUUUUCUGU
------------((((((((.(((((........)))))...)--).((((((.(((((((....(((...)---------)).))))))).).))).))..)))))).......... ( -27.60)
>DroYak_CAF1 183509 95 + 1
------------GAAGCUGCCGGCAAAAUAAUAAUUGCCAUUG--CAGCCAGCUGCUUGAAACUUUCCCUGC---------GACUUUGAGCCGUCUGAGCAGGGCUUCACUUUUCCGU
------------(((((....(((((........)))))...(--(((....))))...........(((((---------(((........)))...)))))))))).......... ( -28.40)
>DroAna_CAF1 183175 112 + 1
AGCCCAUCAGUGGAAGCUGCCGGCAAAAU---AAUUGCCAACAAACAG-CAGCUGCCUGAAACUUUAUCAGCAAAGGCAAGGACUCUGGGCCGGCUGAACAGGGCUUCACUUU--UGU
(((((.((((.(..((((((.(((((...---..)))))........)-))))).))))).......(((((...(((.((....))..))).)))))...))))).......--... ( -39.50)
>consensus
____________GAAGCUGCCGGCAAAAUAAUAAUUGCCAUUG__CAGCCAGCUGCUUGAAACUUUCCCAGC_________GACUUUGAGCCGGCUGAGCAGGGCUUCACUUUUUUGU
............((((((...(((((........)))))........((((((.(((((((.......................))))))).).))).))..)))))).......... (-20.36 = -20.50 +   0.14)

alignment

secondary structure

dotplot

Window 5

Location	23,972,893 – 23,972,988
Length	95
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	81.10
Mean single sequence MFE	-32.62
Consensus MFE	-16.30
Energy contribution	-17.30
Covariance contribution	1.00
Combinations/Pair	1.14
Mean z-score	-2.32
Structure conservation index	0.50
SVM decision value	0.02
SVM RNA-class probability	0.543682
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23972893 95 - 27905053
ACAAAAAAGUGAAGCCCUGCUCAGCCGGUUCAAAGUC---------GCUGGGAAAGUUUCAAGUAGCUGGCUG--CAAUGGCAAUUAUUAUUUUGCCGGCAGCCUC------------
.........((((((....((((((.((.......))---------))))))...)))))).......(((((--(...(((((........))))).))))))..------------ ( -32.30)
>DroSec_CAF1 174495 91 - 1
ACAAAAAAGUGAAGCC-GGCUAAA--GGCU-AAAGUC---------GCUGGGAAAGUUUCAAGCAGCUGGCUG--CAAUGGCAAUUAUUAUUUCGCCGGCAGCCUC------------
............((((-.......--))))-..(((.---------(((.(((....))).))).)))(((((--(...(((............))).))))))..------------ ( -26.90)
>DroSim_CAF1 170448 95 - 1
ACAAAAAAAUGAAGCCCUGCUCAGCCGGCUCAAAGUC---------GCUGGGAAAGUUUCAAGCAGCUGGCUG--CAAUGGCAAUUAUUAUUUCGCCGGCAGCCUC------------
.........((((((....((((((.(((.....)))---------))))))...)))))).......(((((--(...(((............))).))))))..------------ ( -32.80)
>DroEre_CAF1 183094 95 - 1
ACAGAAAAGUGAAGCCCUGCUCAGACGGCUCAAAGUC---------GCAGCGAAAGUUUUAAGCAGCUGGCUG--CAAUGGCAAUUAUUAUUUUGCCGGCAGCUUC------------
.(((.....((((((..((((..(((........)))---------..))))...)))))).....)))((((--(...(((((........))))).)))))...------------ ( -30.20)
>DroYak_CAF1 183509 95 - 1
ACGGAAAAGUGAAGCCCUGCUCAGACGGCUCAAAGUC---------GCAGGGAAAGUUUCAAGCAGCUGGCUG--CAAUGGCAAUUAUUAUUUUGCCGGCAGCUUC------------
.(((.....(((((((((((...(((........)))---------))))))....))))).....)))((((--(...(((((........))))).)))))...------------ ( -34.20)
>DroAna_CAF1 183175 112 - 1
ACA--AAAGUGAAGCCCUGUUCAGCCGGCCCAGAGUCCUUGCCUUUGCUGAUAAAGUUUCAGGCAGCUG-CUGUUUGUUGGCAAUU---AUUUUGCCGGCAGCUUCCACUGAUGGGCU
...--.......(((((...((((..(((.((((((...(((((..(((.....)))...)))))))).-)))..(((((((((..---...))))))))))))....)))).))))) ( -39.30)
>consensus
ACAAAAAAGUGAAGCCCUGCUCAGCCGGCUCAAAGUC_________GCUGGGAAAGUUUCAAGCAGCUGGCUG__CAAUGGCAAUUAUUAUUUUGCCGGCAGCCUC____________
.........((((((....(((((.......................)))))...)))))).......(((((.....((((((........)))))).))))).............. (-16.30 = -17.30 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:23:02 2006