Locus 2771

Sequence ID	2L_DroMel_CAF1
Location	7,839,555 – 7,839,645
Length	90
Max. P	0.938214

overview

Window 3

Location	7,839,555 – 7,839,645
Length	90
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	73.79
Mean single sequence MFE	-16.68
Consensus MFE	-4.20
Energy contribution	-5.24
Covariance contribution	1.04
Combinations/Pair	1.15
Mean z-score	-1.98
Structure conservation index	0.25
SVM decision value	1.12
SVM RNA-class probability	0.918511
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7839555 90 + 22407834
CUAAUUUCAUACACGUAAAUAUUUACACUUGCAUGUUUACAAUGUGCAU-----------------------AUAAAAUAUAAAAAUGAGAAGUACACCCAAUGAAAGCAGUC
((..((((((....((((((((.((....)).))))))))..(((((..-----------------------....................)))))....))))))..)).. ( -11.45)
>DroSec_CAF1 11600 113 + 1
CUAAUUUCAUACACGUAAAUAUUUACACGUGCACGUUUACAAUGUACAUAUGUACAUUGUACAUAUGUACAUAUAAAAUAUAAAAAAGAGAAGUACACCAAAUGAAAGGAAUC
....((((((....((((....))))..((((..(....).((((((((((((((...))))))))))))))....................)))).....))))))...... ( -25.40)
>DroSim_CAF1 12745 94 + 1
AUAAUUUCAUACACGUAAAUAUUUACACGUGCAUGUUCACAAUGUACAUAUGU-------------------AUAAAAUAUAAAAAUGAGAAGUACACCAAAUAAAAGGACUC
...((((.(((((.((((....))))..((((((.......))))))...)))-------------------)).))))..................((........)).... ( -12.40)
>DroEre_CAF1 11969 91 + 1
CAAAUUUGAUGCAUGUAAAUAUUUACCCUUACAUGUGUGCGAUGUGCAUAUG----------------------AAACAGAAAAAAUGGAACGUACUCCUAAUAAAAGGACUU
..........((((((((..........))))))))(((((...(.(((...----------------------...........))).).)))))((((......))))... ( -14.44)
>DroYak_CAF1 12160 94 + 1
CAAAUUUCAUACAUGUAAAUAUUUACACUCGCAUGUGUACAAUUUACAUAUAU-------------------UUAAAGGAGAAACAUGGAAAGUACUCCUAAUGAAAGGACUC
....((((((..((((((((...(((((......)))))..))))))))....-------------------....(((((..((.......)).))))).))))))...... ( -19.70)
>consensus
CUAAUUUCAUACACGUAAAUAUUUACACUUGCAUGUUUACAAUGUACAUAUGU___________________AUAAAAUAUAAAAAUGAGAAGUACACCAAAUGAAAGGACUC
....((((((....((((((((.((....)).))))))))...((((.............................................)))).....))))))...... ( -4.20 =  -5.24 +   1.04)

alignment

secondary structure

dotplot

Window 4

Location	7,839,555 – 7,839,645
Length	90
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	73.79
Mean single sequence MFE	-20.51
Consensus MFE	-6.82
Energy contribution	-7.42
Covariance contribution	0.60
Combinations/Pair	1.31
Mean z-score	-2.07
Structure conservation index	0.33
SVM decision value	1.27
SVM RNA-class probability	0.938214
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7839555 90 - 22407834
GACUGCUUUCAUUGGGUGUACUUCUCAUUUUUAUAUUUUAU-----------------------AUGCACAUUGUAAACAUGCAAGUGUAAAUAUUUACGUGUAUGAAAUUAG
..(((.(((((.((((.......))))....(((((..(((-----------------------.(((((.(((((....)))))))))).))).....)))))))))).))) ( -14.60)
>DroSec_CAF1 11600 113 - 1
GAUUCCUUUCAUUUGGUGUACUUCUCUUUUUUAUAUUUUAUAUGUACAUAUGUACAAUGUACAUAUGUACAUUGUAAACGUGCACGUGUAAAUAUUUACGUGUAUGAAAUUAG
.((.((........)).)).................(((((((((((((((((((...))))))))))))).))))))((((((((((........))))))))))....... ( -32.40)
>DroSim_CAF1 12745 94 - 1
GAGUCCUUUUAUUUGGUGUACUUCUCAUUUUUAUAUUUUAU-------------------ACAUAUGUACAUUGUGAACAUGCACGUGUAAAUAUUUACGUGUAUGAAAUUAU
.......(((((..(((((((....................-------------------......))))))))))))((((((((((........))))))))))....... ( -18.87)
>DroEre_CAF1 11969 91 - 1
AAGUCCUUUUAUUAGGAGUACGUUCCAUUUUUUCUGUUU----------------------CAUAUGCACAUCGCACACAUGUAAGGGUAAAUAUUUACAUGCAUCAAAUUUG
.(.((((......)))).)....................----------------------....(((.....)))..((((((((........))))))))........... ( -12.30)
>DroYak_CAF1 12160 94 - 1
GAGUCCUUUCAUUAGGAGUACUUUCCAUGUUUCUCCUUUAA-------------------AUAUAUGUAAAUUGUACACAUGCGAGUGUAAAUAUUUACAUGUAUGAAAUUUG
......((((...(((((.((.......))..)))))....-------------------((((((((((((..(((((......)))))...)))))))))))))))).... ( -24.40)
>consensus
GAGUCCUUUCAUUAGGUGUACUUCUCAUUUUUAUAUUUUAU___________________ACAUAUGUACAUUGUAAACAUGCAAGUGUAAAUAUUUACGUGUAUGAAAUUAG
..............(((((((.............................................))))))).....((((((.(((........))).))))))....... ( -6.82 =  -7.42 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:49 2006