Locus 4560

Sequence ID	X_DroMel_CAF1
Location	11,986,922 – 11,987,023
Length	101
Max. P	0.898166

overview

Window 6

Location	11,986,922 – 11,987,023
Length	101
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	80.48
Mean single sequence MFE	-22.42
Consensus MFE	-17.30
Energy contribution	-17.50
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.77
SVM decision value	1.00
SVM RNA-class probability	0.898166
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11986922 101 + 22224390
CAGCCCCAUCCUUUUUUU-UUU-----------UUUUUUGGCCAAAACUUGCCAGCCAUUUUGGCCAGGACAACACCCUCGUCUUGGAAUUUUAUUUGCCACCUUUCUGGGCC
..((((............-...-----------.....((((........))))(((.....)))((((((.........))))))......................)))). ( -21.30)
>DroSec_CAF1 26308 106 + 1
GAGCCCCAUCCAUAUUUU-UUUC------GCCCUUUUUUGGCCAAAACUUGCCAGCCAUUUUGGCCAGGACAACACCCUCGUCUUGGAAUUUUAUUUGCCACCUUUCUGGGCC
..................-....------((((.....((((........(((((.....)))))((((((.........))))))...........)))).......)))). ( -23.30)
>DroSim_CAF1 26914 107 + 1
CAGCCCCAUCCAUAUUUUUUUUC------GCCCUUUUUUGGCCAAAACUUGCCAGCCAUUUUGGCCAGGACAACACCCUCGUCUUGGAAUUUUAUUUGCCACCUUUCUGGGCC
.......................------((((.....((((........(((((.....)))))((((((.........))))))...........)))).......)))). ( -23.30)
>DroEre_CAF1 25089 80 + 1
CU--------------------------------UAUUUGGCCAGGACUUGCCAGUCAUUUUGGCCAGGACGACACCCUCGUCUUGG-AUUUUAUUUGCCACCUUUCUGGGCC
..--------------------------------.....((((.(((...(((((.....)))))((((((((.....)))))))).-.................))).)))) ( -25.10)
>DroYak_CAF1 26501 113 + 1
CAGCGCCAUCCUUAUCCUUUAUCUUUUUUUUUUGUUUUUGGCCAGAACUUGCCAGCCAUUUUGGCCAGGAGAACACCCUCGUCUUGAAAUUUUAUUUGCCACCUUUCUGGGCC
....(((..............................((((((((((...(....)..))))))))))(((......))).............................))). ( -19.10)
>consensus
CAGCCCCAUCCAUAUUUU_UUUC__________UUUUUUGGCCAAAACUUGCCAGCCAUUUUGGCCAGGACAACACCCUCGUCUUGGAAUUUUAUUUGCCACCUUUCUGGGCC
.......................................((((.......(((((.....)))))((((((.........)))))).......................)))) (-17.30 = -17.50 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	11,986,922 – 11,987,023
Length	101
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	80.48
Mean single sequence MFE	-26.37
Consensus MFE	-20.50
Energy contribution	-20.70
Covariance contribution	0.20
Combinations/Pair	1.09
Mean z-score	-1.85
Structure conservation index	0.78
SVM decision value	0.90
SVM RNA-class probability	0.877142
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11986922 101 - 22224390
GGCCCAGAAAGGUGGCAAAUAAAAUUCCAAGACGAGGGUGUUGUCCUGGCCAAAAUGGCUGGCAAGUUUUGGCCAAAAAA-----------AAA-AAAAAAAGGAUGGGGCUG
(((((.....((.(((((...(..(((......)))..).)))))))(((((((((.........)))))))))......-----------...-............))))). ( -27.10)
>DroSec_CAF1 26308 106 - 1
GGCCCAGAAAGGUGGCAAAUAAAAUUCCAAGACGAGGGUGUUGUCCUGGCCAAAAUGGCUGGCAAGUUUUGGCCAAAAAAGGGC------GAAA-AAAAUAUGGAUGGGGCUC
(((((......((.....)).....((((..((....)).((((((((((((((((.........))))))))).....)))))------))..-......))))..))))). ( -28.20)
>DroSim_CAF1 26914 107 - 1
GGCCCAGAAAGGUGGCAAAUAAAAUUCCAAGACGAGGGUGUUGUCCUGGCCAAAAUGGCUGGCAAGUUUUGGCCAAAAAAGGGC------GAAAAAAAAUAUGGAUGGGGCUG
(((((......((.....)).....((((...........((((((((((((((((.........))))))))).....)))))------)).........))))..))))). ( -28.95)
>DroEre_CAF1 25089 80 - 1
GGCCCAGAAAGGUGGCAAAUAAAAU-CCAAGACGAGGGUGUCGUCCUGGCCAAAAUGACUGGCAAGUCCUGGCCAAAUA--------------------------------AG
.((((......).))).........-....(((((.....))))).((((((....((((....)))).))))))....--------------------------------.. ( -22.00)
>DroYak_CAF1 26501 113 - 1
GGCCCAGAAAGGUGGCAAAUAAAAUUUCAAGACGAGGGUGUUCUCCUGGCCAAAAUGGCUGGCAAGUUCUGGCCAAAAACAAAAAAAAAAGAUAAAGGAUAAGGAUGGCGCUG
.((((......).)))....................(((((..((((((((.....))))(((........)))...........................))))..))))). ( -25.60)
>consensus
GGCCCAGAAAGGUGGCAAAUAAAAUUCCAAGACGAGGGUGUUGUCCUGGCCAAAAUGGCUGGCAAGUUUUGGCCAAAAAA__________GAAA_AAAAUAAGGAUGGGGCUG
((((.((((...((.((..........((.(((((.....))))).))(((.....))))).))..))))))))....................................... (-20.50 = -20.70 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:08 2006