Locus 5346

Sequence ID	X_DroMel_CAF1
Location	13,932,095 – 13,932,197
Length	102
Max. P	0.718025

overview

Window 1

Location	13,932,095 – 13,932,197
Length	102
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	84.94
Mean single sequence MFE	-32.48
Consensus MFE	-25.56
Energy contribution	-25.62
Covariance contribution	0.06
Combinations/Pair	1.05
Mean z-score	-1.67
Structure conservation index	0.79
SVM decision value	0.39
SVM RNA-class probability	0.718025
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13932095 102 + 22224390
GCUUGGAUUUGG------AUUCCGAUUUCAGAGCCAGCUUGGGGAUCCACAUCCACAUUCACAUCCAUUCGGACGGACGUUCAUCCAUCGUGGCUGUGCCACUUCAAC
...(((((.(((------((((((....).(((....))).)))))))).)))))........(((....))).(((......)))...(((((...)))))...... ( -29.80)
>DroSec_CAF1 12071 96 + 1
GCUUGGAUUUGG------AUUCGGAUUUCGGAGCCAGCUUGGGGAUCCACAUC------CACAUCCAUUCGGACGGACGUUCAUCCAUCGUGGCUGUGCCACUUUAAC
(..(((((.(((------((..((((..(.(((....))).)..))))..)))------)).)))))..)((((....)))).......(((((...)))))...... ( -36.30)
>DroSim_CAF1 15648 102 + 1
GCUUGGAUUUGG------AUUCGGAUUUCGGAGCCAGCUUGGGGAUCCACAUCCACAUCCACAUCCAUUCGGACGGACGUUCAUCCAUCGUGGCUGUGCCACUUCAAC
...(((((.(((------((..((((..(.(((....))).)..))))..))))).)))))..(((....))).(((......)))...(((((...)))))...... ( -36.50)
>DroYak_CAF1 14238 89 + 1
GCUUGGAUUUGGAUUCGGAUUCGGAUUUCGGAGCCAGUUUGGGGAUCCA-------------------UCGGACGGACGUUCAUCCAUCGUGGCUGUGCCACUUCAAC
..(((((..(((((........((((..(.(((....))).)..)))).-------------------..((((....)))))))))..(((((...)))))))))). ( -27.30)
>consensus
GCUUGGAUUUGG______AUUCGGAUUUCGGAGCCAGCUUGGGGAUCCACAUC______CACAUCCAUUCGGACGGACGUUCAUCCAUCGUGGCUGUGCCACUUCAAC
...(((((..............((((..(.(((....))).)..))))......................((((....)))))))))..(((((...)))))...... (-25.56 = -25.62 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	13,932,095 – 13,932,197
Length	102
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	84.94
Mean single sequence MFE	-32.16
Consensus MFE	-20.31
Energy contribution	-20.12
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-1.72
Structure conservation index	0.63
SVM decision value	0.01
SVM RNA-class probability	0.538908
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13932095 102 - 22224390
GUUGAAGUGGCACAGCCACGAUGGAUGAACGUCCGUCCGAAUGGAUGUGAAUGUGGAUGUGGAUCCCCAAGCUGGCUCUGAAAUCGGAAU------CCAAAUCCAAGC
......(((((...))))).....((..((((((((....))))))))..)).(((((.(((((..((.....)).((((....))))))------))).)))))... ( -31.20)
>DroSec_CAF1 12071 96 - 1
GUUAAAGUGGCACAGCCACGAUGGAUGAACGUCCGUCCGAAUGGAUGUG------GAUGUGGAUCCCCAAGCUGGCUCCGAAAUCCGAAU------CCAAAUCCAAGC
......(((((...)))))(((((((....)))))))....(((((.((------(((.(((((..(..((....))..)..))))).))------))).)))))... ( -35.10)
>DroSim_CAF1 15648 102 - 1
GUUGAAGUGGCACAGCCACGAUGGAUGAACGUCCGUCCGAAUGGAUGUGGAUGUGGAUGUGGAUCCCCAAGCUGGCUCCGAAAUCCGAAU------CCAAAUCCAAGC
......(((((...)))))(((((((....)))))))....(((((.(((((.(((((.((((.((.......)).))))..))))).))------))).)))))... ( -40.40)
>DroYak_CAF1 14238 89 - 1
GUUGAAGUGGCACAGCCACGAUGGAUGAACGUCCGUCCGA-------------------UGGAUCCCCAAACUGGCUCCGAAAUCCGAAUCCGAAUCCAAAUCCAAGC
((((..(((((...)))))(((((((....))))))))))-------------------)((((........(((...((.....))...))).......)))).... ( -21.96)
>consensus
GUUGAAGUGGCACAGCCACGAUGGAUGAACGUCCGUCCGAAUGGAUGUG______GAUGUGGAUCCCCAAGCUGGCUCCGAAAUCCGAAU______CCAAAUCCAAGC
......(((((...)))))(((((((....)))))))......................((((.((.......)).))))............................ (-20.31 = -20.12 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:42 2006