Locus 7519

Sequence ID	3R_DroMel_CAF1
Location	20,122,508 – 20,122,628
Length	120
Max. P	0.793047

overview

Window 3

Location	20,122,508 – 20,122,628
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-20.92
Consensus MFE	-19.84
Energy contribution	-20.04
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.13
Structure conservation index	0.95
SVM decision value	0.03
SVM RNA-class probability	0.548603
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20122508 120 + 27905053
UUGUCUGCAUUUUCAAAGCGCUUUUAGCGAUAUCACAACAGUGAAAUCUGUGAAACUUAUCGCAUAACGAUCAUAAUAAUUGAUUCACAACUCUUGCUGACUCAUUAUGUGUAAUUUUCU
..(((.(((.................((((((.....((((......))))......)))))).....(((((.......))))).........))).)))................... ( -20.90)
>DroSec_CAF1 6520 120 + 1
UUGUCUGCAUUUUCAAAUCGCUUUUAGCGAUAUCACAACAGUGAAAUCUCUGAAACUUAUCGCAUAACGAUCAUAAUAAUUGAUUCACAACUCUUGCUGACUCAUUAUGUGUAAUUUUCU
................(((((.....))))).((((....)))).......((((.(((.(((((((.((((((((.(.(((.....))).).))).))).)).)))))))))).)))). ( -20.40)
>DroSim_CAF1 6605 120 + 1
UUGUCUGCAUUUUCAAAUCGCCUUUAGCGAUAUCACAACAGUGAAAUCUGUGAAACUUAUCGCAUAACGAUCAUAAUAAUUGAUUCACAACUCUUGCUGACUCAUUAUGUGUAAUUUUCU
..(((.(((.......(((((.....))))).((((....))))....((((((.....(((.....)))(((.......))))))))).....))).)))................... ( -21.50)
>DroEre_CAF1 6740 120 + 1
UUGUCUGCAUUUUCAAAGCGCUUUUAGCGAUAUCACAACAGUGAAAUCUGUGAAACUUAUCGCAUAACGAUCAUAAUAAUUGAUUCACAACACUUGCUGACUCAUUAUGUGUAAUUUUCU
..(((.(((.................((((((.....((((......))))......)))))).....(((((.......))))).........))).)))................... ( -20.90)
>DroYak_CAF1 6789 120 + 1
UUGUCUGCAUUUUCAAAGCGCCUUUAGCGAUAUCACAACAGUGAAAUCUGUGAUACUUAUCGCAUAACGAUCAUAAUAAUUGAUUCACAACUCUUGCUGACUCAUUAUGUGUAAUUUUAC
..(((.(((.................((((((.....((((......))))......)))))).....(((((.......))))).........))).)))................... ( -20.90)
>consensus
UUGUCUGCAUUUUCAAAGCGCUUUUAGCGAUAUCACAACAGUGAAAUCUGUGAAACUUAUCGCAUAACGAUCAUAAUAAUUGAUUCACAACUCUUGCUGACUCAUUAUGUGUAAUUUUCU
..(((.(((.................((((((.....((((......))))......)))))).....(((((.......))))).........))).)))................... (-19.84 = -20.04 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	20,122,508 – 20,122,628
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-25.70
Consensus MFE	-23.14
Energy contribution	-23.74
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.90
SVM decision value	0.59
SVM RNA-class probability	0.793047
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20122508 120 - 27905053
AGAAAAUUACACAUAAUGAGUCAGCAAGAGUUGUGAAUCAAUUAUUAUGAUCGUUAUGCGAUAAGUUUCACAGAUUUCACUGUUGUGAUAUCGCUAAAAGCGCUUUGAAAAUGCAGACAA
.((((.((((.((((((((.(((.....(((((.....)))))....))))))))))).).))).))))...(((.((((....)))).)))((.....))((.........))...... ( -26.10)
>DroSec_CAF1 6520 120 - 1
AGAAAAUUACACAUAAUGAGUCAGCAAGAGUUGUGAAUCAAUUAUUAUGAUCGUUAUGCGAUAAGUUUCAGAGAUUUCACUGUUGUGAUAUCGCUAAAAGCGAUUUGAAAAUGCAGACAA
.((((.((((.((((((((.(((.....(((((.....)))))....))))))))))).).))).))))..........((((..(.(.(((((.....))))).).)....)))).... ( -26.60)
>DroSim_CAF1 6605 120 - 1
AGAAAAUUACACAUAAUGAGUCAGCAAGAGUUGUGAAUCAAUUAUUAUGAUCGUUAUGCGAUAAGUUUCACAGAUUUCACUGUUGUGAUAUCGCUAAAGGCGAUUUGAAAAUGCAGACAA
.((((.((((.((((((((.(((.....(((((.....)))))....))))))))))).).))).))))..........((((..(.(.(((((.....))))).).)....)))).... ( -26.70)
>DroEre_CAF1 6740 120 - 1
AGAAAAUUACACAUAAUGAGUCAGCAAGUGUUGUGAAUCAAUUAUUAUGAUCGUUAUGCGAUAAGUUUCACAGAUUUCACUGUUGUGAUAUCGCUAAAAGCGCUUUGAAAAUGCAGACAA
.((((.((((.((((((((.(((......((((.....)))).....))))))))))).).))).))))...(((.((((....)))).)))((.....))((.........))...... ( -24.90)
>DroYak_CAF1 6789 120 - 1
GUAAAAUUACACAUAAUGAGUCAGCAAGAGUUGUGAAUCAAUUAUUAUGAUCGUUAUGCGAUAAGUAUCACAGAUUUCACUGUUGUGAUAUCGCUAAAGGCGCUUUGAAAAUGCAGACAA
(((......(.((((((((.(((.....(((((.....)))))....))))))))))).)..((((......(((.((((....)))).)))((.....))))))......)))...... ( -24.20)
>consensus
AGAAAAUUACACAUAAUGAGUCAGCAAGAGUUGUGAAUCAAUUAUUAUGAUCGUUAUGCGAUAAGUUUCACAGAUUUCACUGUUGUGAUAUCGCUAAAAGCGCUUUGAAAAUGCAGACAA
.((((.((((.((((((((.(((.....(((((.....)))))....))))))))))).).))).))))...(((.((((....)))).)))((.....))(.((((......))))).. (-23.14 = -23.74 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:47:56 2006