Locus 1244

Sequence ID	X_DroMel_CAF1
Location	3,706,836 – 3,706,970
Length	134
Max. P	0.999986

overview

Window 9

Location	3,706,836 – 3,706,932
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	95.62
Mean single sequence MFE	-40.52
Consensus MFE	-39.22
Energy contribution	-39.38
Covariance contribution	0.16
Combinations/Pair	1.09
Mean z-score	-3.14
Structure conservation index	0.97
SVM decision value	5.40
SVM RNA-class probability	0.999986
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3706836 96 - 22224390
GUCUUCGAGGCAUCGAAGACGCGGCUAUCCGAAGUAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGACACUGCCAGCGGAGUGGAUGAGCCCCAUA
((((((((....))))))))(.(((((((((.....((...((((..((((((......))))))..))))....))....))))).)))).)... ( -40.30)
>DroSec_CAF1 46506 96 - 1
GUCUUCGAGGCAUCGAAGACGCGGCUAUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGCCACUGCCAGCGGAGUGGAUGAGCCCCAUA
((((((((....))))))))(.(((((((((.....((...(((((..(((((......)))))..)))))....))....))))).)))).)... ( -43.50)
>DroSim_CAF1 43760 96 - 1
GUCUUCGAGGCAUCGAAGACGCGGCUAUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGCCACUGCCAGCGGAGUGGAUGAGCCCCAUA
((((((((....))))))))(.(((((((((.....((...(((((..(((((......)))))..)))))....))....))))).)))).)... ( -43.50)
>DroEre_CAF1 46048 96 - 1
GUCUUCGAGGCAUCGAAGACGCGGCUGUCUGAAAUAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGCCACUGCCAGCGGAGUGGAUGAGUCCCAUA
((((((((....))))))))(.(((((((((.....((...(((((..(((((......)))))..)))))....))....))))).)))).)... ( -40.80)
>DroYak_CAF1 43443 96 - 1
GUCUUCGAGGCAUCGAAGAAGCGGCUGUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGAGCCACUGCCAGCGGAGUGGAUGAUUCCCAUA
.(((((((....))))))).(((((((..(....)..))..((((((.(((((......))))).))))))))).))(((((.....))))).... ( -34.50)
>consensus
GUCUUCGAGGCAUCGAAGACGCGGCUAUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGCCACUGCCAGCGGAGUGGAUGAGCCCCAUA
((((((((....))))))))(.(((((((((.....((...((((((((((((......))))))))))))....))....))))).)))).)... (-39.22 = -39.38 +   0.16)

alignment

secondary structure

dotplot

Window 0

Location	3,706,865 – 3,706,970
Length	105
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	92.25
Mean single sequence MFE	-29.86
Consensus MFE	-25.22
Energy contribution	-25.46
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-1.54
Structure conservation index	0.84
SVM decision value	0.80
SVM RNA-class probability	0.852892
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3706865 105 + 22224390
UCACAAGUUGCACCACUCGCACCACUUUCGCUACUUCGGAUAGCCGCGUCUUCGAUGCCUCGAAGACGCCACCCU--UAAGAAUUGCAGCUCAGGCGAAGAAUCUCU
((.(.(((((((.................(((((....).)))).((((((((((....))))))))))......--.......)))))))...).))......... ( -31.10)
>DroSec_CAF1 46535 107 + 1
GCACAAGUUGCACCACUCGCACCACUUUCGCUCUUUCAGAUAGCCGCGUCUUCGAUGCCUCGAAGACGCCAGAAUUGCAAGAAUUGCAGCUCAGGCGAAGAAUCUCU
((..(((((((.......)))..))))..))(((((......(((((((((((((....))))))))))..((.(((((.....))))).)).))))))))...... ( -32.80)
>DroSim_CAF1 43789 105 + 1
GCACAAGUUGCACCACUCGCACCACUUUCGCUCUUUCAGAUAGCCGCGUCUUCGAUGCCUCGAAGACGCCACCCC--UAAGAAUUGCAGCUCAGGCGAAGAAUCUCU
((...(((((((.................(((.........))).((((((((((....))))))))))......--.......)))))))...))........... ( -28.50)
>DroEre_CAF1 46077 105 + 1
GCACAAGUUGCACCACUCGCACCACUUUCGCUAUUUCAGACAGCCGCGUCUUCGAUGCCUCGAAGACGCCACCCG--GAAGAAUUGCAGCUCAGGUGAAGAAUCUCU
.(((.(((((((....((...((......(((.........))).((((((((((....)))))))))).....)--)..))..)))))))...))).......... ( -30.50)
>DroYak_CAF1 43472 105 + 1
GCUCAAGUUGCACCACUCGCACCACUUUCGCUCUUUCAGACAGCCGCUUCUUCGAUGCCUCGAAGACGCCACCCG--GAAGAAUUGCAGCUCAGGUGGAGGAUCUCU
(((..(((((((......((.........))((((((.(.....)((.(((((((....))))))).)).....)--)))))..)))))))..)))((((...)))) ( -26.40)
>consensus
GCACAAGUUGCACCACUCGCACCACUUUCGCUCUUUCAGAUAGCCGCGUCUUCGAUGCCUCGAAGACGCCACCCG__GAAGAAUUGCAGCUCAGGCGAAGAAUCUCU
((...(((((((.................(((.........))).((((((((((....))))))))))...............)))))))...))........... (-25.22 = -25.46 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	3,706,865 – 3,706,970
Length	105
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	92.25
Mean single sequence MFE	-38.19
Consensus MFE	-31.26
Energy contribution	-31.82
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.82
SVM decision value	0.63
SVM RNA-class probability	0.803725
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3706865 105 - 22224390
AGAGAUUCUUCGCCUGAGCUGCAAUUCUUA--AGGGUGGCGUCUUCGAGGCAUCGAAGACGCGGCUAUCCGAAGUAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGA
.........((((.(..(((((..(((...--..(((.((((((((((....)))))))))).)))....))))))))..).)))).((((((......)))))).. ( -38.70)
>DroSec_CAF1 46535 107 - 1
AGAGAUUCUUCGCCUGAGCUGCAAUUCUUGCAAUUCUGGCGUCUUCGAGGCAUCGAAGACGCGGCUAUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGC
..((((.....(((.(((.((((.....)))).)))..((((((((((....))))))))))))).))))......((....)).(..(((((......)))))..) ( -38.90)
>DroSim_CAF1 43789 105 - 1
AGAGAUUCUUCGCCUGAGCUGCAAUUCUUA--GGGGUGGCGUCUUCGAGGCAUCGAAGACGCGGCUAUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGC
......(((((.((((((........))))--))(((.((((((((((....)))))))))).)))....).))))((....)).(..(((((......)))))..) ( -40.60)
>DroEre_CAF1 46077 105 - 1
AGAGAUUCUUCACCUGAGCUGCAAUUCUUC--CGGGUGGCGUCUUCGAGGCAUCGAAGACGCGGCUGUCUGAAAUAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGC
.....(((..((((((..............--))))))((((((((((....)))))))))).(((((.....))))))))....(..(((((......)))))..) ( -37.44)
>DroYak_CAF1 43472 105 - 1
AGAGAUCCUCCACCUGAGCUGCAAUUCUUC--CGGGUGGCGUCUUCGAGGCAUCGAAGAAGCGGCUGUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGAGC
....((((((((((...........((((.--((((..((.(((((((....)))))))....))..)))).))))((....)))))).))).)))........... ( -35.30)
>consensus
AGAGAUUCUUCGCCUGAGCUGCAAUUCUUA__AGGGUGGCGUCUUCGAGGCAUCGAAGACGCGGCUAUCUGAAAGAGCGAAAGUGGUGCGAGUGGUGCAACUUGUGC
..........((((..((((((.((((......))))...((((((((....))))))))))))))..........((....))))))(((((......)))))... (-31.26 = -31.82 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:51 2006