Locus 4366

Sequence ID	2L_DroMel_CAF1
Location	12,553,691 – 12,553,801
Length	110
Max. P	0.996438

overview

Window 7

Location	12,553,691 – 12,553,801
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.63
Mean single sequence MFE	-30.77
Consensus MFE	-10.69
Energy contribution	-11.80
Covariance contribution	1.11
Combinations/Pair	1.06
Mean z-score	-2.14
Structure conservation index	0.35
SVM decision value	0.10
SVM RNA-class probability	0.585115
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12553691 110 + 22407834
UUUGGGGUUGCAAAACUUCGGAAGCUGAAAGCAUUUUGCUGUAGCCAUCGCAU-UUUGGGGGAAGAAAUCCGA---AUUCGAGUCCAAACCGAAUUCUA--AUAG----AAGUUUUGCAG
........((((((((((((((.((((..(((.....))).))))..((.(..-.....).)).....)))((---(((((.((....)))))))))..--...)----)))))))))). ( -33.50)
>DroSec_CAF1 125847 109 + 1
UUUGGGGUUGCAAAACUUCGGAAGCUGAAAGCAUUGUGCUGUAGCCAUC--GCCUUUGGGGGAAGAAAUCCGA---GUUCGAGUCCAAACCAAAUUCUA--AUAG----AAGUUUUGCAG
........(((((((((((((..((((..(((.....))).))))....--.))(((((.(((.(((......---.)))...)))...))))).....--...)----)))))))))). ( -32.00)
>DroSim_CAF1 128622 111 + 1
UUUGGGGUUGCAAAACUUCGGAAGCUGAAAGCAUUUUGCUGUAGCCAUCUCACAUUUGGGGGAAGAAAUCCGA---GUUCGAAUACGAACCGAAUUCUA--AUAG----AAGUUUUGCAG
........((((((((((((((.((((..(((.....))).))))..(((((....))))).......)))((---(((((.........)))))))..--...)----)))))))))). ( -34.50)
>DroEre_CAF1 124780 103 + 1
UUUGGGGUUGCAAAACUUCGGAAGCUGAAAGCAUUUUGCUGUACGCAGC--GCAUUUGGGGGAAGAAAUGCGAGAAAUGCGA---------GAAUUCUA--AUAG----AAGUUUUGCAG
........(((((((((((((((.......(((((((((((....))))--((((((........))))))..)))))))..---------...)))).--...)----)))))))))). ( -34.50)
>DroYak_CAF1 129908 96 + 1
UUUGGGGUUGCAAAACUUCGCAAGCUGAAAGCAUUUCGCUGU-----------AUUUGGGGGAAGAAAUCCUA---AGUCGAGU------UGAAUUCUAGAAUAG----AAGUUUUGCAG
........(((((((((((.....(((((..((.((((....-----------((((((((.......)))))---))))))).------))..))).))....)----)))))))))). ( -28.20)
>DroAna_CAF1 125994 94 + 1
UUUAGGGUUGCAAAAGUUCCACUCCUGAAAGCAUUCUCCUGUACG---------AUGGGGGGAA---GUCCUU---AUUCC---------UUAGUCCUC--AUUGAAGCAAGUCCUGCUG
((((((((.((....))...)).))))))((((....(.(((.((---------((((((((((---......---.))))---------.....))))--))))..))).)...)))). ( -21.90)
>consensus
UUUGGGGUUGCAAAACUUCGGAAGCUGAAAGCAUUUUGCUGUAGCCAUC___CAUUUGGGGGAAGAAAUCCGA___AUUCGAGU______CGAAUUCUA__AUAG____AAGUUUUGCAG
........((((((((((...........(((.....)))...............(((((........)))))....................................)))))))))). (-10.69 = -11.80 +   1.11)

alignment

secondary structure

dotplot

Window 8

Location	12,553,691 – 12,553,801
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.63
Mean single sequence MFE	-27.33
Consensus MFE	-11.44
Energy contribution	-11.83
Covariance contribution	0.39
Combinations/Pair	1.12
Mean z-score	-3.11
Structure conservation index	0.42
SVM decision value	2.70
SVM RNA-class probability	0.996438
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12553691 110 - 22407834
CUGCAAAACUU----CUAU--UAGAAUUCGGUUUGGACUCGAAU---UCGGAUUUCUUCCCCCAAA-AUGCGAUGGCUACAGCAAAAUGCUUUCAGCUUCCGAAGUUUUGCAACCCCAAA
.((((((((((----(...--..(((((((((....)).)))))---))(((.....)))......-....(..((((..(((.....)))...))))..))))))))))))........ ( -32.30)
>DroSec_CAF1 125847 109 - 1
CUGCAAAACUU----CUAU--UAGAAUUUGGUUUGGACUCGAAC---UCGGAUUUCUUCCCCCAAAGGC--GAUGGCUACAGCACAAUGCUUUCAGCUUCCGAAGUUUUGCAACCCCAAA
.((((((((((----(...--..((((((((((((....)))))---.))))))).........(((((--(.((((....)).)).))))))........)))))))))))........ ( -30.20)
>DroSim_CAF1 128622 111 - 1
CUGCAAAACUU----CUAU--UAGAAUUCGGUUCGUAUUCGAAC---UCGGAUUUCUUCCCCCAAAUGUGAGAUGGCUACAGCAAAAUGCUUUCAGCUUCCGAAGUUUUGCAACCCCAAA
.((((((((((----(...--..((((((((((((....)))))---.)))))))................(..((((..(((.....)))...))))..))))))))))))........ ( -33.40)
>DroEre_CAF1 124780 103 - 1
CUGCAAAACUU----CUAU--UAGAAUUC---------UCGCAUUUCUCGCAUUUCUUCCCCCAAAUGC--GCUGCGUACAGCAAAAUGCUUUCAGCUUCCGAAGUUUUGCAACCCCAAA
.((((((((((----(...--..((....---------))((((((...((((((........))))))--((((....)))).))))))...........)))))))))))........ ( -29.60)
>DroYak_CAF1 129908 96 - 1
CUGCAAAACUU----CUAUUCUAGAAUUCA------ACUCGACU---UAGGAUUUCUUCCCCCAAAU-----------ACAGCGAAAUGCUUUCAGCUUGCGAAGUUUUGCAACCCCAAA
.((((((((((----(..............------........---..(((.....))).......-----------...((((...((.....)))))))))))))))))........ ( -21.20)
>DroAna_CAF1 125994 94 - 1
CAGCAGGACUUGCUUCAAU--GAGGACUAA---------GGAAU---AAGGAC---UUCCCCCCAU---------CGUACAGGAGAAUGCUUUCAGGAGUGGAACUUUUGCAACCCUAAA
..((((((.(..((((.((--((((.....---------((((.---......---))))..)).)---------)))....((((....)))).))))..)...))))))......... ( -17.30)
>consensus
CUGCAAAACUU____CUAU__UAGAAUUCG______ACUCGAAU___UCGGAUUUCUUCCCCCAAAUG___GAUGGCUACAGCAAAAUGCUUUCAGCUUCCGAAGUUUUGCAACCCCAAA
.((((((((((......................................(((.....)))....................(((.....)))...........))))))))))........ (-11.44 = -11.83 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:05 2006