Locus 1928

Sequence ID	X_DroMel_CAF1
Location	5,303,268 – 5,303,417
Length	149
Max. P	0.986785

overview

Window 2

Location	5,303,268 – 5,303,377
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.23
Mean single sequence MFE	-30.06
Consensus MFE	-24.80
Energy contribution	-25.08
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-1.81
Structure conservation index	0.83
SVM decision value	1.18
SVM RNA-class probability	0.926316
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5303268 109 + 22224390
AGACACGCGCCCAUUGUUAUUAUAUUGGCAUUAUUGCGAAACAAGCGGGCC--------A---CCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCAC
.....((((((...(((....)))..)))....(((.....))))))((((--------(---(.(((..((((((((.((((.....)))).))))))))....)))....)))))).. ( -30.20)
>DroSec_CAF1 39986 112 + 1
AGACACGCGCCCAUUGUUAUUAUAUUGGCAUUAUUGCGAAACAAGCGGGCC--------ACCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCAC
.....((((((...(((....)))..)))....(((.....))))))((((--------((....(((..((((((((.((((.....)))).))))))))....)))....)))))).. ( -31.20)
>DroSim_CAF1 30788 112 + 1
AGACACGCGCCCAUUGUUAUUAUAUUGGCAUUAUUGCGAAACAAGCGGGCC--------ACCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCAC
.....((((((...(((....)))..)))....(((.....))))))((((--------((....(((..((((((((.((((.....)))).))))))))....)))....)))))).. ( -31.20)
>DroEre_CAF1 41332 107 + 1
AGACACGCGCCCAUUGUUAUUAUAUUGGCAUUAUUGCGAAACAAGCG------------GCCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGU-GCCAC
.((((...((((.............((((....(((.....)))...------------)))).......((((((((.((((.....)))).)))))))))))))))).....-..... ( -28.60)
>DroYak_CAF1 41912 120 + 1
AAACACGCGCCCAUUGUUAUUAUAUUGGCAUUAUUGCGAAACAAGCGAGCCAGCGAGGGACCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUUGCCAC
....(((.((((..(((.......(((((....((((.......)))))))))...((.....)))))..((((((((.((((.....)))).)))))))))))))))............ ( -29.10)
>consensus
AGACACGCGCCCAUUGUUAUUAUAUUGGCAUUAUUGCGAAACAAGCGGGCC________ACCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCAC
.((((...((((..(((((......)))))...((((.......))))......................((((((((.((((.....)))).))))))))))))))))........... (-24.80 = -25.08 +   0.28)

alignment

secondary structure

dotplot

Window 3

Location	5,303,308 – 5,303,417
Length	109
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	85.41
Mean single sequence MFE	-31.85
Consensus MFE	-22.38
Energy contribution	-23.25
Covariance contribution	0.88
Combinations/Pair	1.04
Mean z-score	-3.44
Structure conservation index	0.70
SVM decision value	2.05
SVM RNA-class probability	0.986785
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5303308 109 + 22224390
ACAAGCGGGCCA---CCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCACGCCCCCUUCUCACCACACCCCCCCCCCCCGCCACCAUUGU
....(((((...---.......((((((((.((((.....)))).))))))))((((.(((.....)))...))))......................)))))......... ( -28.10)
>DroSec_CAF1 40026 104 + 1
ACAAGCGGGCCACCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCACGCCUCCACC---CGAGGCAGCCCC-----CCCUCUAUUGU
...((.(((.............((((((((.((((.....)))).))))))))((((((((.(.((((........)))).---.).)))))))).-----))).))..... ( -35.00)
>DroSim_CAF1 30828 109 + 1
ACAAGCGGGCCACCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCACGCCCCCACC---CGAGGCAGCCCCCCCCCCCCUCUAUUGU
...((.(((.............((((((((.((((.....)))).))))))))((((((((.(.((((........)))).---.).))))))))......))).))..... ( -35.20)
>DroEre_CAF1 41372 99 + 1
ACAAGCG----GCCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGU-GCCACGCCCACUCC---CGAGGCAGCCCC-----CCCCCCAUUGU
((((..(----(..........((((((((.((((.....)))).))))))))((((((((.((((-(.......))))..---.).)))))))).-----....)).)))) ( -29.10)
>consensus
ACAAGCGGGCCACCACCACAUACAAAUUGCUCAAUUCAAAAUUGUGUAAUUUGGGGCUGUCACAGUGGCCACGCCCCCACC___CGAGGCAGCCCC_____CCCUCCAUUGU
....(((((((((....(((..((((((((.((((.....)))).))))))))....)))....)))))).)))...................................... (-22.38 = -23.25 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:03 2006