Locus 3328

Sequence ID	2L_DroMel_CAF1
Location	9,634,955 – 9,635,073
Length	118
Max. P	0.986525

overview

Window 0

Location	9,634,955 – 9,635,073
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.38
Mean single sequence MFE	-27.14
Consensus MFE	-16.56
Energy contribution	-16.96
Covariance contribution	0.40
Combinations/Pair	1.20
Mean z-score	-3.41
Structure conservation index	0.61
SVM decision value	2.04
SVM RNA-class probability	0.986525
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9634955 118 + 22407834
-AUUGAUUUUCAAAAUAUCAAAUGAAUGCUUGCACCGUUACUGGAGUACAUUUAAUCAUUCAUUGUGUUUCAUCUAUAAAUGAAAUACAACAUUA-UAUGAGUGAAUAAUCUGAUCAAUA
-(((((((..............((((((..(((.(((....))).))))))))).((((((((((((((((((......))))))))))......-.)))))))).......))))))). ( -26.51)
>DroSec_CAF1 35557 118 + 1
-AUUGAUUUUAAUAAUAUCAGAUGAAUGCUUGCACCGUUAGUGGAGUACUUUUAAUCAUUCAUUGUGUUUCAUUUAAAAAUGAAACACAACAUUA-UAUGAGUGAAUAAUCUGAUCAAUA
-...............(((((((...(((((.(((.....)))))))).......(((((((((((((((((((....)))))))))))......-.))))))))...)))))))..... ( -30.21)
>DroSim_CAF1 34846 108 + 1
-AUUGAUUUUAAUAAUAUCAGAUGAAUGCUUGCACCGUUACUGGAGUACUUUUAAUCAUUCAUUGUGUUUCAUUUAAAAAUGAC----------A-UAUGAGUGAAUAAUCUGAUCAAUA
-...............(((((((.......(((.(((....))).))).......((((((((.(((..(((((....))))))----------)-)))))))))...)))))))..... ( -20.90)
>DroEre_CAF1 37721 116 + 1
AAUUGAUUUCACCAAUAUCAGAUGAAUGCUUGCAUCCUUGCUGGUUUGC----AAUCAUUCAUUGUAUUUCGUCUAUAAAUGAAAUACAACAUCUUUAUGAGAGAUUAAUAUGAUCAAUA
.(((((((((..........((((((((.(((((.((.....))..)))----)).))))))))(((((((((......))))))))).............))))))))).......... ( -32.20)
>DroYak_CAF1 37350 119 + 1
AAUUGAUUUCAAUAAUAUCAGAUGAGUGCUUUCAUCGUUAUUGGUGUACUUUAAAUCAUUCAUUGUAUUUCAUCUAUAAAUGAAAUACAACAUCU-UAUAAGCGAAUAAUCUGAUCAAUA
.((((....))))...(((((((...(((((.(((((....)))))................(((((((((((......))))))))))).....-...)))))....)))))))..... ( -25.90)
>consensus
_AUUGAUUUUAAUAAUAUCAGAUGAAUGCUUGCACCGUUACUGGAGUACUUUUAAUCAUUCAUUGUGUUUCAUCUAUAAAUGAAAUACAACAUCA_UAUGAGUGAAUAAUCUGAUCAAUA
.(((((((.........(((((((((((.(((....................))).))))))))(((((((((......)))))))))..........)))...........))))))). (-16.56 = -16.96 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	9,634,955 – 9,635,073
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.38
Mean single sequence MFE	-25.34
Consensus MFE	-17.36
Energy contribution	-20.08
Covariance contribution	2.72
Combinations/Pair	1.13
Mean z-score	-2.99
Structure conservation index	0.69
SVM decision value	2.03
SVM RNA-class probability	0.986197
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9634955 118 - 22407834
UAUUGAUCAGAUUAUUCACUCAUA-UAAUGUUGUAUUUCAUUUAUAGAUGAAACACAAUGAAUGAUUAAAUGUACUCCAGUAACGGUGCAAGCAUUCAUUUGAUAUUUUGAAAAUCAAU-
.((((((((((.((((........-....(((((.(((((((....))))))).)))))((((((.....((((((........)))))).....)))))))))).)))))...)))))- ( -24.50)
>DroSec_CAF1 35557 118 - 1
UAUUGAUCAGAUUAUUCACUCAUA-UAAUGUUGUGUUUCAUUUUUAAAUGAAACACAAUGAAUGAUUAAAAGUACUCCACUAACGGUGCAAGCAUUCAUCUGAUAUUAUUAAAAUCAAU-
.....(((((((............-....(((((((((((((....)))))))))))))(((((.......(((((........)))))...))))))))))))...............- ( -28.50)
>DroSim_CAF1 34846 108 - 1
UAUUGAUCAGAUUAUUCACUCAUA-U----------GUCAUUUUUAAAUGAAACACAAUGAAUGAUUAAAAGUACUCCAGUAACGGUGCAAGCAUUCAUCUGAUAUUAUUAAAAUCAAU-
.....(((((((((.(((.((((.-.----------.(((((....)))))......)))).))).)))..(((((........))))).........))))))...............- ( -17.70)
>DroEre_CAF1 37721 116 - 1
UAUUGAUCAUAUUAAUCUCUCAUAAAGAUGUUGUAUUUCAUUUAUAGACGAAAUACAAUGAAUGAUU----GCAAACCAGCAAGGAUGCAAGCAUUCAUCUGAUAUUGGUGAAAUCAAUU
.((((((..(((((((.((......((((((((((((((.((....)).))))))))))(((((.((----(((..((.....)).))))).))))))))))).)))))))..)))))). ( -28.70)
>DroYak_CAF1 37350 119 - 1
UAUUGAUCAGAUUAUUCGCUUAUA-AGAUGUUGUAUUUCAUUUAUAGAUGAAAUACAAUGAAUGAUUUAAAGUACACCAAUAACGAUGAAAGCACUCAUCUGAUAUUAUUGAAAUCAAUU
.((((((.(((((((((.((....-))..(((((((((((((....)))))))))))))))))))))).........((((((.(((((......))))).....))))))..)))))). ( -27.30)
>consensus
UAUUGAUCAGAUUAUUCACUCAUA_UAAUGUUGUAUUUCAUUUAUAGAUGAAACACAAUGAAUGAUUAAAAGUACUCCAGUAACGGUGCAAGCAUUCAUCUGAUAUUAUUAAAAUCAAU_
.....(((((((.................(((((((((((((....)))))))))))))(((((.......(((((........)))))...))))))))))))................ (-17.36 = -20.08 +   2.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:53 2006