Locus 3662

Sequence ID	3R_DroMel_CAF1
Location	9,914,416 – 9,914,535
Length	119
Max. P	0.897138

overview

Window 1

Location	9,914,416 – 9,914,506
Length	90
Sequences	4
Columns	93
Reading direction	forward
Mean pairwise identity	88.89
Mean single sequence MFE	-19.95
Consensus MFE	-13.65
Energy contribution	-14.27
Covariance contribution	0.63
Combinations/Pair	1.09
Mean z-score	-1.82
Structure conservation index	0.68
SVM decision value	0.09
SVM RNA-class probability	0.579065
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9914416 90 + 27905053
CACAACCGCAAAGUAUUCAAAUCCAAUCGAAUCCACAGCCUCGACAUCAU---AUCGAAAUUGCUGUGUCAGUAUCGAUUGUGACGCAUGAUU
.......((...(....)...(((((((((...((((((.((((......---.))))....))))))......))))))).)).))...... ( -18.80)
>DroSec_CAF1 117289 90 + 1
CACAACCGCAAAGUACUCAAAUCCAAUCGAAUCCACAGCCUCGUCAUCAU---AUCGAAAUUGCUGUGUCCGUAUCGAUUGUGAUGCUUGAUU
................((((((((((((((...((((((....((.....---...))....))))))......))))))).)))..)))).. ( -19.80)
>DroSim_CAF1 121339 90 + 1
CACAACCGCAAAGUACUCAAAUCCAAUCGAAUACACAGUCUCGUCAUCAU---AUCGAAAUUGCUGUGUCCGUAUCGAUUGUGAUGCAUAAUU
.......((...(....)..((((((((((..(((((((....((.....---...))....))))))).....))))))).)))))...... ( -18.90)
>DroEre_CAF1 118375 92 + 1
CACAACUGCAGAGUACUCAUAUCCUAUUGAAUCCACAGCCUCGUCAUCAUCAAGUCGAAAUUGCUGUGUCCGUAGCGAUUGUGCUGCAUAAU-
......((((..((((....(((((((.((...((((((.(((.(........).)))....)))))))).)))).))).))))))))....- ( -22.30)
>consensus
CACAACCGCAAAGUACUCAAAUCCAAUCGAAUCCACAGCCUCGUCAUCAU___AUCGAAAUUGCUGUGUCCGUAUCGAUUGUGAUGCAUAAUU
.......((...(....)..((((((((((...((((((.(((............)))....))))))......))))))).)))))...... (-13.65 = -14.27 +   0.63)

alignment

secondary structure

dotplot

Window 2

Location	9,914,429 – 9,914,535
Length	106
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	75.71
Mean single sequence MFE	-23.25
Consensus MFE	-13.48
Energy contribution	-14.10
Covariance contribution	0.62
Combinations/Pair	1.11
Mean z-score	-2.07
Structure conservation index	0.58
SVM decision value	1.00
SVM RNA-class probability	0.897138
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9914429 106 + 27905053
UAUUCAAAUCCAAUCGAAUCCACAGCCUCGACAUCAU---AUCGAAAUUGCUGUGUCAGUAUCGAUUGUGACGCAUGAUUUAUAAUAUC----GCAGUG-UU------AUCAAAGAUAAA
.......((((((((((...((((((.((((......---.))))....))))))......)))))))((((((.((((.......)))----)..)))-))------).....)))... ( -22.90)
>DroSec_CAF1 117302 114 + 1
UACUCAAAUCCAAUCGAAUCCACAGCCUCGUCAUCAU---AUCGAAAUUGCUGUGUCCGUAUCGAUUGUGAUGCUUGAUU---AAUAUCGAGCGCAGUGAUUAUCAUUAUCAAAGAUGAA
(((((..((((((((((...((((((....((.....---...))....))))))......))))))).)))(((((((.---...)))))))).))))....(((((......))))). ( -31.30)
>DroSim_CAF1 121352 104 + 1
UACUCAAAUCCAAUCGAAUACACAGUCUCGUCAUCAU---AUCGAAAUUGCUGUGUCCGUAUCGAUUGUGAUGCAUAAUU---AAUAUC----GCAGUGAUU------AUCAAAGAUGAA
.......((((((((((..(((((((....((.....---...))....))))))).....))))))).)))........---..((((----....((...------..))..)))).. ( -20.80)
>DroEre_CAF1 118388 85 + 1
UACUCAUAUCCUAUUGAAUCCACAGCCUCGUCAUCAUCAAGUCGAAAUUGCUGUGUCCGUAGCGAUUGUGCUGCAUAAU----AAUA-------------------------------CA
...........(((((....((((((.(((.(........).)))....))))))...((((((....)))))).))))----)...-------------------------------.. ( -18.00)
>consensus
UACUCAAAUCCAAUCGAAUCCACAGCCUCGUCAUCAU___AUCGAAAUUGCUGUGUCCGUAUCGAUUGUGAUGCAUAAUU___AAUAUC____GCAGUG_UU______AUCAAAGAUGAA
.......((((((((((...((((((.(((............)))....))))))......))))))).)))................................................ (-13.48 = -14.10 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:49 2006