Locus 3999

Sequence ID	X_DroMel_CAF1
Location	10,593,593 – 10,593,734
Length	141
Max. P	0.987340

overview

Window 5

Location	10,593,593 – 10,593,699
Length	106
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-28.56
Consensus MFE	-23.10
Energy contribution	-24.22
Covariance contribution	1.12
Combinations/Pair	1.16
Mean z-score	-2.41
Structure conservation index	0.81
SVM decision value	2.08
SVM RNA-class probability	0.987340
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10593593 106 - 22224390
AAUCUACAUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCGAUUAAACUUAACCUAACAUUGGAAAAAAUCCAGGGGAAAAGGAUGCGCUAUUCGAGCGCUCGAUU
((((...(((((((((((...(......)...)))))))))))....(((..(((....(((((.....))))))))..)))((.(((((.....))))))))))) ( -28.40)
>DroSec_CAF1 2509 106 - 1
AAUAUAUGUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCAAUGAAACUUAACCUAACACUGGAAAAAUUCCAGGGAAAAAGGAUGCGCUAUUCGAGCGCCCGAUU
.......(((((((((((...(......)...))))))))))).........(((....(((((.....)))))......)))..(((((.....)))))...... ( -29.40)
>DroSim_CAF1 2528 106 - 1
AAUCUACGUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCAAUGAAACUUAACCUAACACUGGUAAAAUUCCAGGGAAAAAGGAUGCGCUAUUCGAGCGCUCGAUU
((((..((((((((((((...(......)...))))))))))))........(((....((((.......))))......)))..(((((.....)))))..)))) ( -31.30)
>DroEre_CAF1 2570 102 - 1
AAUCUAUAUUGGAAUCGUAAGCUUUAACGUCGGCGAUUCCUACGAGACUUAACCUAACACUGGUAAAACUCCAGGGGAAAAGGACGCGCUAUUCGAGC----GAUU
..(((.....((((((((..((......))..))))))))....)))(((..(((....((((.......)))))))..)))....((((.....)))----)... ( -26.50)
>DroYak_CAF1 2574 106 - 1
AAUCUAUAUUGGAAUCGUUAUCUUUAACGUCGGCGAUUCCAACGAGACUUAACCUAACACUGGUAAAACUCCAGGGGAAAAGGAUGCGCUAUUCGAGCAAUCGAUU
..(((...(((((((((((..(......)..)))))))))))..)))(((..(((....((((.......)))))))..)))..........((((....)))).. ( -27.20)
>consensus
AAUCUAUAUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCAAUGAAACUUAACCUAACACUGGUAAAACUCCAGGGGAAAAGGAUGCGCUAUUCGAGCGCUCGAUU
......((((((((((((...(......)...))))))))))))........(((....((((.......))))......)))..(((((.....)))))...... (-23.10 = -24.22 +   1.12)

alignment

secondary structure

dotplot

Window 6

Location	10,593,619 – 10,593,734
Length	115
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	89.90
Mean single sequence MFE	-29.46
Consensus MFE	-24.19
Energy contribution	-23.99
Covariance contribution	-0.20
Combinations/Pair	1.29
Mean z-score	-2.30
Structure conservation index	0.82
SVM decision value	2.07
SVM RNA-class probability	0.987172
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10593619 115 - 22224390
GAUUCGAGGUAACCUCCACCGCCAUCAAA--AAGGGGAAUCUACAUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCGAUUAAACUUAACCUAACAUUGGAAAAAAUCCAGGGGAAA
.....((((...))))..((.((......--.(((..((.....(((((((((((...(......)...))))))))))).....))..))).....((((.....))))))))... ( -27.80)
>DroSec_CAF1 2535 115 - 1
GAUUCGAGGUAACCCUCACCGCCAUCAAA--AAGGGGAAUAUAUGUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCAAUGAAACUUAACCUAACACUGGAAAAAUUCCAGGGAAAA
.....((((....)))).((.........--.(((..((.....(((((((((((...(......)...))))))))))).....))..)))....(((((.....))))))).... ( -30.80)
>DroSim_CAF1 2554 115 - 1
GAUUCGAGGUAACCUCCACCGCCAUCAAA--AAGGGGAAUCUACGUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCAAUGAAACUUAACCUAACACUGGUAAAAUUCCAGGGAAAA
..(((.((((....(((.((.........--..))))).....((((((((((((...(......)...)))))))))))).......))))....((((.......)))).))).. ( -30.90)
>DroEre_CAF1 2592 115 - 1
GAUUCGAGGUAACCUGCAAGGCCACCAAA--AAUGGGAAUCUAUAUUGGAAUCGUAAGCUUUAACGUCGGCGAUUCCUACGAGACUUAACCUAACACUGGUAAAACUCCAGGGGAAA
(((((..(((..........))).(((..--..))))))))......((((((((..((......))..))))))))............(((....((((.......)))))))... ( -28.20)
>DroYak_CAF1 2600 117 - 1
GAUUCGAGGUAACCUCCACCGCCACCAAAAAAAAGGGAAUCUAUAUUGGAAUCGUUAUCUUUAACGUCGGCGAUUCCAACGAGACUUAACCUAACACUGGUAAAACUCCAGGGGAAA
..(((((((...))))........((.......(((...(((...(((((((((((..(......)..)))))))))))..))).....)))....((((.......))))))))). ( -29.60)
>consensus
GAUUCGAGGUAACCUCCACCGCCAUCAAA__AAGGGGAAUCUAUAUUGGAAUCGUAAUCUUUAACGUCAGCGAUUCCAAUGAAACUUAACCUAACACUGGUAAAACUCCAGGGGAAA
..(((.((((..((((.................))))......((((((((((((...(......)...)))))))))))).......))))....((((.......)))).))).. (-24.19 = -23.99 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:56 2006