Locus 1822

Sequence ID	3L_DroMel_CAF1
Location	5,104,324 – 5,104,482
Length	158
Max. P	0.682272

overview

Window 4

Location	5,104,324 – 5,104,444
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.42
Mean single sequence MFE	-31.27
Consensus MFE	-27.21
Energy contribution	-27.90
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-1.75
Structure conservation index	0.87
SVM decision value	0.31
SVM RNA-class probability	0.682272
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5104324 120 - 23771897
UUUGAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACAUUUAUGGGCGUGGCUGUAACAUGUGCGAUAUGUCUCAAUCCCGGCGAAUUUUUAGUGGGAGAUAAUAAAUUUUAUUACGC
...((((((((..((((((((.(((((.((......)).))))).))))))))..(((.....)))))))))))....(((((.(.........))))))(((((......))))).... ( -28.10)
>DroSec_CAF1 297269 120 - 1
UUUAAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGCGAGAUGUCUCAAUCCCGGCGAAUUUAUAGUGGGAGAUAAUAAAUUUUGUUACGC
.............((((((((..(((((........)))))....))))))))..((((((.....(((....))).(((((.((.........)).)).))).........)))))).. ( -32.00)
>DroSim_CAF1 318922 120 - 1
UUUGAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGCGAGAUGUCUCAAUCCCGGCGAAUUUAUAGUGGGAGAUAAUAAAUUUUAUUACGC
.......((((((((((((((..(((((........)))))....)))))).(((((((....((((.(((......))).).)))...)))))))))))))))................ ( -31.60)
>DroYak_CAF1 309600 120 - 1
UUUGAUAUAUUUCCCAUGCCCCUGGGACUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGUGAGAUGUCUCAAUCUCGGCGAAUUUAUAGUGGGAGAUAAUAAAUUUUAUUGCAC
.......((((((((((((((.(((((.((......)).))))).)))))).(((((((....((((((((......))))).)))...)))))))))))))))................ ( -33.40)
>consensus
UUUGAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGCGAGAUGUCUCAAUCCCGGCGAAUUUAUAGUGGGAGAUAAUAAAUUUUAUUACGC
.......((((((((((((((.(((((.((......)).))))).)))))).(((((((....((((.(((......))).).)))...)))))))))))))))................ (-27.21 = -27.90 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	5,104,364 – 5,104,482
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.15
Mean single sequence MFE	-30.20
Consensus MFE	-19.64
Energy contribution	-20.33
Covariance contribution	0.69
Combinations/Pair	1.07
Mean z-score	-1.87
Structure conservation index	0.65
SVM decision value	0.27
SVM RNA-class probability	0.660310
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5104364 118 - 23771897
CUUUGUCGUCGGCUUGUCUCGCGCGGUUU--AAAUUCAUGUUUGAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACAUUUAUGGGCGUGGCUGUAACAUGUGCGAUAUGUCUCAAUC
..........(((.....(((((((..((--((((....))))))..(((...((((((((.(((((.((......)).))))).))))))))..)))...)))))))...)))...... ( -28.80)
>DroSec_CAF1 297309 93 - 1
CUU-------------------------U--AAAGUCAUGUUUAAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGCGAGAUGUCUCAAUC
...-------------------------.--...(((((((....((((....((((((((..(((((........)))))....)))))))).))))))))).))(((....))).... ( -23.80)
>DroSim_CAF1 318962 118 - 1
CUUUGUCGUCGGCUUGUCUCGCGCGGUUU--AAAGUCAUGUUUGAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGCGAGAUGUCUCAAUC
..........(((..(((((((((((((.--...((((....)))).......((((((((..(((((........)))))....))))))))....))).)))))))))))))...... ( -36.90)
>DroYak_CAF1 309640 120 - 1
CUUUGUCGUCGGCUUGUCUCGCGUGGUUUUAAAACUCAUGUUUGAUAUAUUUCCCAUGCCCCUGGGACUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGUGAGAUGUCUCAAUC
...(((...((((.((((..((((((((....))).)))))..)))).......(((((((.(((((.((......)).))))).)))))))))))..)))....((((....))))... ( -31.30)
>consensus
CUUUGUCGUCGGCUUGUCUCGCGCGGUUU__AAAGUCAUGUUUGAUAUAUUUCCCAUGCCCCUGGGUUUUUUAAUUAACUUUUAUGGGCGUGGCUGUAACAUGUGCGAGAUGUCUCAAUC
.........................................((((.(((((((((((((((.(((((.((......)).))))).))))))))..(((.....)))))))))).)))).. (-19.64 = -20.33 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:38 2006