Locus 2065

Sequence ID	2L_DroMel_CAF1
Location	5,574,703 – 5,574,900
Length	197
Max. P	0.927119

overview

Window 9

Location	5,574,703 – 5,574,820
Length	117
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	98.86
Mean single sequence MFE	-31.11
Consensus MFE	-31.26
Energy contribution	-31.04
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	1.00
SVM decision value	0.37
SVM RNA-class probability	0.706867
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5574703 117 + 22407834
GUGGCAGUUGCUGCAGCUGUGUGCGUGUGCUGGGGAUUUGGCAAAUUGAUUUGAGAUUUACUAUUAAGAUGAUUUCCAUGCAUUUUGCAUGCUGUUGCCCAAAUUAUUUUCAUAUUA
..(((....)))(((((.(((((((.(((((((..((((((.(((((.......))))).))).......)))..))).))))..))))))).)))))................... ( -30.91)
>DroSec_CAF1 18781 117 + 1
GCGGCAGUUGCUGCAGCUGUGUGCGUGUGCUGGGGAUUUAGCAAAUUGAUUUGAGAUUUACUAUUAAGAUGAUUUCCAUGCAUUUUGCAUGCUGUUGCCCAAAUUAUUUUCAUAUUA
(((((....)))))(((.(((((((.(((((((..((((((.(((((.......))))).))).......)))..))).))))..))))))).)))..................... ( -31.51)
>DroSim_CAF1 20424 117 + 1
GUGGCAGUUGCUGCAGCUGUGUGCGUGUGCUGGGGAUUUGGCAAAUUGAUUUGAGAUUUACUAUUAAGAUGAUUUCCAUGCAUUUUGCAUGCUGUUGCCCAAAUUAUUUUCAUAUUA
..(((....)))(((((.(((((((.(((((((..((((((.(((((.......))))).))).......)))..))).))))..))))))).)))))................... ( -30.91)
>consensus
GUGGCAGUUGCUGCAGCUGUGUGCGUGUGCUGGGGAUUUGGCAAAUUGAUUUGAGAUUUACUAUUAAGAUGAUUUCCAUGCAUUUUGCAUGCUGUUGCCCAAAUUAUUUUCAUAUUA
..(((....)))(((((.(((((((.(((((((..((((((.(((((.......))))).))).......)))..))).))))..))))))).)))))................... (-31.26 = -31.04 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	5,574,740 – 5,574,860
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.50
Mean single sequence MFE	-20.46
Consensus MFE	-18.56
Energy contribution	-18.60
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.63
Structure conservation index	0.91
SVM decision value	0.98
SVM RNA-class probability	0.894296
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5574740 120 - 22407834
GGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAUGGAAAUCAUCUUAAUAGUAAAUCUCAAAUCAAUUUGCCAA
.((((........(((((((((.((((.........)))).)))))))))...(((((((......(((((.....)))))((.....))............))))))).....)))).. ( -21.40)
>DroSec_CAF1 18818 120 - 1
GGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAUGGAAAUCAUCUUAAUAGUAAAUCUCAAAUCAAUUUGCUAA
..((...(((((.(((((((((.((((.........)))).))))))))).)))))...)).....(((((.....))))).............((((((((.........)))))))). ( -22.90)
>DroSim_CAF1 20461 120 - 1
GGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAUGGAAAUCAUCUUAAUAGUAAAUCUCAAAUCAAUUUGCCAA
.((((........(((((((((.((((.........)))).)))))))))...(((((((......(((((.....)))))((.....))............))))))).....)))).. ( -21.40)
>DroEre_CAF1 18730 119 - 1
-GUCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAUGGAAAUCAUCUUAAUAGUAAAUCUCAAAUCAAUUUGCCAA
-(((...(((((.(((((((((.((((.........)))).))))))))).)))))..))).....(((((.....)))))...............((((((.........))))))... ( -20.20)
>DroYak_CAF1 18585 119 - 1
-GGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUUCAUGGAAAUCAUCUUAAUAGUAAAUCUCAAAUCAAUUUGCCAA
-((((........(((((((((.((((.........)))).)))))))))...(((((((......((((.......))))((.....))............))))))).....)))).. ( -16.40)
>consensus
GGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAUGGAAAUCAUCUUAAUAGUAAAUCUCAAAUCAAUUUGCCAA
.......(((((.(((((((((.((((.........)))).))))))))).)))))..(((((...(((((.....)))))((.((...((....))...)).))........))))).. (-18.56 = -18.60 +   0.04)

alignment

secondary structure

dotplot

Window 1

Location	5,574,780 – 5,574,900
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.66
Mean single sequence MFE	-27.10
Consensus MFE	-21.40
Energy contribution	-22.44
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-2.25
Structure conservation index	0.79
SVM decision value	1.18
SVM RNA-class probability	0.927119
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5574780 120 - 22407834
GCUUUCGCAAAAUGCCAUGCCUUCUUGUCAUUGAAUUUAGGGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAU
((....))....(((((((((((...((......))...))))))).(((((.(((((((((.((((.........)))).))))))))).)))))..))))...((((.....)))).. ( -25.50)
>DroSec_CAF1 18858 120 - 1
GCUUGAGCCAAAUGCCAUGCCUUCUUGUCAUUGAAUUCGGGGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAU
(((...(((.((((((.((..(((........)))..))..))))))(((((.(((((((((.((((.........)))).))))))))).)))))..)))...)))((((.....)))) ( -28.40)
>DroSim_CAF1 20501 120 - 1
GCUUGCGCCAAAUGCCAUGCCUUCUUGUCAUUGAAUUCGGGGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAU
((((((.((((((...((((((((..((......))..)))))))).......(((((((((.((((.........)))).)))))))))...)))))))))..)))((((.....)))) ( -30.20)
>DroEre_CAF1 18770 119 - 1
GCAUGCGCCAAAUGCCAUGCCUUCUUGUCAUUGAAUUUGG-GUCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAU
((((((.((((((.(.(((.(.....).))).).))))))-(((...(((((.(((((((((.((((.........)))).))))))))).)))))..)))....))))))......... ( -30.50)
>DroYak_CAF1 18625 119 - 1
CCAAUCGCAAUAUGUCAUGCCUUCUUGUCAUUGAAUUUAG-GGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUUCAU
......(((...(((..(((((...((((...........-))))..(((((.(((((((((.((((.........)))).))))))))).))))).))))))))...)))......... ( -20.90)
>consensus
GCUUGCGCCAAAUGCCAUGCCUUCUUGUCAUUGAAUUUGGGGGCAUUAAUUAGUUUCGUAUUCAUUACAAAAUCUAUAAUUAAUAUGAAAAUAAUUUGGGCAACAGCAUGCAAAAUGCAU
............((((((((((((...((...))....)))))))).(((((.(((((((((.((((.........)))).))))))))).)))))..))))...((((.....)))).. (-21.40 = -22.44 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:34 2006