Locus 2608

Sequence ID	X_DroMel_CAF1
Location	6,995,590 – 6,995,750
Length	160
Max. P	0.947757

overview

Window 9

Location	6,995,590 – 6,995,710
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-29.30
Consensus MFE	-27.42
Energy contribution	-27.53
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.62
Structure conservation index	0.94
SVM decision value	1.38
SVM RNA-class probability	0.947757
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6995590 120 + 22224390
UUCGCUGUUAUCCUUUUGCAACAUUGCACACAAUACAAUAUAUGCGAUUUUGGGAUCGGUGAAAGCCCACCCUUUCCUUUCUCCCAUUUCUAUUGCGUGUGCAGAUGCAUUGCUUGCAUU
...((............)).....(((((((.(((.....)))(((((..(((((..((.(((((......)))))))...))))).....))))))))))))((((((.....)))))) ( -31.20)
>DroSec_CAF1 17946 120 + 1
UUCGCUGUUAUCCUUUUGCAACAUUGCACACAAUACAAUAUAUGCGAUUUUGGGAUCGCUGAAAGCCCACCCUUUCCCUUCACCCAUUUCUAUUGCGUGUGCAGAUGCAUUGCUUGCAUU
...((............)).....(((((((.(((.....)))(((((..((((......(((((......)))))......)))).....))))))))))))((((((.....)))))) ( -28.20)
>DroSim_CAF1 3096 120 + 1
UUCGCUGUUAUCCUUUUGCAACAUUGCACACAAUACAAUAUAUGCGAUUUUGGGAUCGCUGAAAGCCCACCCUUUCCCUUCUCCCAUUUCUAUUGCGUGUACAGAUGCAUUGCUUGCAUU
....(((.........((((....))))..........((((((((((..(((((.....(((((......))))).....))))).....)))))))))))))(((((.....))))). ( -28.50)
>consensus
UUCGCUGUUAUCCUUUUGCAACAUUGCACACAAUACAAUAUAUGCGAUUUUGGGAUCGCUGAAAGCCCACCCUUUCCCUUCUCCCAUUUCUAUUGCGUGUGCAGAUGCAUUGCUUGCAUU
....((((........((((....))))...........(((((((((..(((((.....(((((......))))).....))))).....)))))))))))))(((((.....))))). (-27.42 = -27.53 +   0.11)

alignment

secondary structure

dotplot

Window 0

Location	6,995,590 – 6,995,710
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-32.47
Consensus MFE	-31.05
Energy contribution	-31.17
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.22
Structure conservation index	0.96
SVM decision value	1.09
SVM RNA-class probability	0.913300
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6995590 120 - 22224390
AAUGCAAGCAAUGCAUCUGCACACGCAAUAGAAAUGGGAGAAAGGAAAGGGUGGGCUUUCACCGAUCCCAAAAUCGCAUAUAUUGUAUUGUGUGCAAUGUUGCAAAAGGAUAACAGCGAA
..(((..(((..((((.(((((((((((((...(((.((....(((...(((((....)))))..))).....)).))).))))))...))))))))))))))....(.....).))).. ( -34.10)
>DroSec_CAF1 17946 120 - 1
AAUGCAAGCAAUGCAUCUGCACACGCAAUAGAAAUGGGUGAAGGGAAAGGGUGGGCUUUCAGCGAUCCCAAAAUCGCAUAUAUUGUAUUGUGUGCAAUGUUGCAAAAGGAUAACAGCGAA
..(((..(((..((((.(((((((((((((...((((((...((((...(.(((....))).)..))))...))).))).))))))...))))))))))))))....(.....).))).. ( -32.10)
>DroSim_CAF1 3096 120 - 1
AAUGCAAGCAAUGCAUCUGUACACGCAAUAGAAAUGGGAGAAGGGAAAGGGUGGGCUUUCAGCGAUCCCAAAAUCGCAUAUAUUGUAUUGUGUGCAAUGUUGCAAAAGGAUAACAGCGAA
..((((.(((((((((((((.......)))))..(((((.....(((((......))))).....))))).............)))))))).)))).(((((...........))))).. ( -31.20)
>consensus
AAUGCAAGCAAUGCAUCUGCACACGCAAUAGAAAUGGGAGAAGGGAAAGGGUGGGCUUUCAGCGAUCCCAAAAUCGCAUAUAUUGUAUUGUGUGCAAUGUUGCAAAAGGAUAACAGCGAA
..(((..(((..((((.(((((((((((((((..(((((.....(((((......))))).....)))))...)).....))))))...))))))))))))))....(.....).))).. (-31.05 = -31.17 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	6,995,630 – 6,995,750
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-26.63
Consensus MFE	-25.70
Energy contribution	-26.03
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.96
SVM decision value	0.36
SVM RNA-class probability	0.703996
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6995630 120 + 22224390
UAUGCGAUUUUGGGAUCGGUGAAAGCCCACCCUUUCCUUUCUCCCAUUUCUAUUGCGUGUGCAGAUGCAUUGCUUGCAUUCUAAUUUCCAUCAUUUUCGCAAAUAAUUGAUUUGUGUUCG
((((((((..(((((..((.(((((......)))))))...))))).....))))))))....((((((.....)))))).................(((((((.....))))))).... ( -28.00)
>DroSec_CAF1 17986 120 + 1
UAUGCGAUUUUGGGAUCGCUGAAAGCCCACCCUUUCCCUUCACCCAUUUCUAUUGCGUGUGCAGAUGCAUUGCUUGCAUUCUAAUUUCCAUCAUUUUCGCAAAUAAUUGAUUUGUGUUCG
((((((((..((((......(((((......)))))......)))).....))))))))....((((((.....)))))).................(((((((.....))))))).... ( -25.00)
>DroSim_CAF1 3136 120 + 1
UAUGCGAUUUUGGGAUCGCUGAAAGCCCACCCUUUCCCUUCUCCCAUUUCUAUUGCGUGUACAGAUGCAUUGCUUGCAUUCUAAUUUCCAUCAUUUUCGCAAAUAAUUGAUUUGUGUUCG
((((((((..(((((.....(((((......))))).....))))).....))))))))....((((((.....)))))).................(((((((.....))))))).... ( -26.90)
>consensus
UAUGCGAUUUUGGGAUCGCUGAAAGCCCACCCUUUCCCUUCUCCCAUUUCUAUUGCGUGUGCAGAUGCAUUGCUUGCAUUCUAAUUUCCAUCAUUUUCGCAAAUAAUUGAUUUGUGUUCG
((((((((..(((((.....(((((......))))).....))))).....))))))))....((((((.....)))))).................(((((((.....))))))).... (-25.70 = -26.03 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:03 2006