Locus 5549

Sequence ID	X_DroMel_CAF1
Location	14,355,335 – 14,355,469
Length	134
Max. P	0.728585

overview

Window 6

Location	14,355,335 – 14,355,432
Length	97
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	87.54
Mean single sequence MFE	-22.05
Consensus MFE	-13.99
Energy contribution	-14.42
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-2.15
Structure conservation index	0.63
SVM decision value	0.13
SVM RNA-class probability	0.598410
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14355335 97 - 22224390
-AAAAUGGCAUAUUUGCCA-----------AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUAUUGAGUUAGUUUACCAUGUAAUUAGGCAACCUGUUGUACA
-....(((((....)))))-----------...((((((((.((((((((....))))))))((((.....))))..))))))))((((..((((...))))...)))) ( -22.60)
>DroSec_CAF1 69837 97 - 1
-AAAAUGACAUAUUUGCCA-----------AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUAUUUAGUUAGUUUACCAUGUAAUUAGGCAACCUCUUGUACA
-......(((...(((((.-----------.((((((((((.((((((((....)))))))).....((......)))))))))).)).....))))).....)))... ( -17.50)
>DroSim_CAF1 65117 97 - 1
-AAAAUGACAUAUUUGCCA-----------AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUAUUGAGUUAGUUUACCAUGUAAUUAGGCAACCUGUUGUGCA
-...(..(((...(((((.-----------.((((((((((.((((((((....))))))))((((.....))))..)))))))).)).....)))))..)))..)... ( -20.90)
>DroYak_CAF1 72017 109 - 1
AAAAAUGGCACAUUCGCCAUCGUUUUGCCAAGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGCAUUCAGUUUGUUUACCUUGUAAUUAGGCAACCCAGUGUAAA
....(((((......))))).(..((((((((((((((((((.(((((((....))))))))))))))...))))))..((((...))))...)))))..)........ ( -27.20)
>consensus
_AAAAUGACAUAUUUGCCA___________AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUAUUGAGUUAGUUUACCAUGUAAUUAGGCAACCUGUUGUACA
.......(((...(((((............((((((((((((.(((((((....)))))))))))))...))))))...((((...))))...))))).....)))... (-13.99 = -14.42 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	14,355,375 – 14,355,469
Length	94
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	86.70
Mean single sequence MFE	-20.85
Consensus MFE	-13.93
Energy contribution	-13.99
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-2.04
Structure conservation index	0.67
SVM decision value	0.42
SVM RNA-class probability	0.728585
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14355375 94 - 22224390
GUGCUUAACCGACCCUAAUGUUUAUGCAGUAUUUACA----AAAAUGGCAUAUUUGCCA-----------AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUA
..........(((.....(((((((.((((((((((.----....(((((....)))))-----------.....)))))).)))))))))))...))).......... ( -20.10)
>DroSec_CAF1 69877 94 - 1
GUGCUUAACUGUCCCUAAUGUUUAUGCAGUAUUUACA----AAAAUGACAUAUUUGCCA-----------AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUA
.(((..(((..........)))...))).....((((----((.......((((((((.-----------....))))))))((((((((....)))))))).)))))) ( -18.90)
>DroSim_CAF1 65157 94 - 1
GUGCUUAACCGUCCCUAAUGUUUAUGCAGUAUUUACA----AAAAUGACAUAUUUGCCA-----------AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUA
.(((.(((.(((.....))).))).))).....((((----((.......((((((((.-----------....))))))))((((((((....)))))))).)))))) ( -19.30)
>DroYak_CAF1 72057 109 - 1
GUGCUCAACCGCCCCGGAUGUUUAUGCAAUAAUUACACAAAAAAAUGGCACAUUCGCCAUCGUUUUGCCAAGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGCA
.(((.((.(((...))).)).....))).........(((((..(((((......)))))..)))))........(((((((.(((((((....)))))))))))))). ( -25.10)
>consensus
GUGCUUAACCGUCCCUAAUGUUUAUGCAGUAUUUACA____AAAAUGACAUAUUUGCCA___________AGCUGGUAAAUAAUUGAUAAAUAAUUGUCAAUAUUUGUA
.(((..(((..........)))...)))...................((((((((((((..............)))))))))((((((((....))))))))...))). (-13.93 = -13.99 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:41 2006