Locus 2500

Sequence ID	X_DroMel_CAF1
Location	6,640,343 – 6,640,447
Length	104
Max. P	0.826374

overview

Window 8

Location	6,640,343 – 6,640,447
Length	104
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	81.54
Mean single sequence MFE	-28.16
Consensus MFE	-17.94
Energy contribution	-18.02
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-2.07
Structure conservation index	0.64
SVM decision value	0.70
SVM RNA-class probability	0.826374
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6640343 104 + 22224390
CCCUGCCAAUGAUGACGUCACUCGCAGGUGCUGUCAUCACAAAAGUAUGUGCAUUUAUUUUCGU----UGUGUACGAUUUGUGCGAUUUGUACGAUUUGUACGAUUUU
...(((((..(((((((.((((....)))).)))))))((....)).)).)))...........----..(((((((.((((((.....)))))).)))))))..... ( -28.10)
>DroSec_CAF1 34173 107 + 1
CCCUGACAAUGAUGACGUCACUCGCAGGUGCUGUCAUCACAAAAGUAUGUGCAUUUGUUUUCGUACGAUUUGUACGAUUUGUACGAUUUGUACGAUUUGUACGAUU-U
.........((((((((.((((....)))).))))))))........((((((.......((((((((.((((((.....)))))).))))))))..))))))...-. ( -34.70)
>DroSim_CAF1 31949 89 + 1
CCCUGACAAUGAUGACGUCACUCGCAGGUGCUGUCAUCACAAAAGUAUGUGCAUUUGUUUUCGUACGAUUUGUACG------------------AUUUGUACGAUU-U
.........((((((((.((((....)))).))))))))........((((((.......((((((.....)))))------------------)..))))))...-. ( -24.80)
>DroEre_CAF1 27858 85 + 1
CCCUGCCAAUGAUGACGUCACUCGCAGGUGCUGUCAUCAGAAAAGUAUGUGCAUUUGUUUUCGC----UGUGUACG------------------AUUUGUGGGAUU-U
.((..(...((((((((.((((....)))).))))))))...((((.(((((((..((....))----.)))))))------------------)))))..))...-. ( -26.00)
>DroYak_CAF1 30182 93 + 1
CCCAGGCAACGAUGACGUCACUCGCAGGUGCUGUCAUCGCAAAAGUAUGUGCAUUUGUUUUCGC----UGUGUACGAU----------UGUGCGAUUUGUGCGAUU-U
....(....)(((((((.((((....)))).)))))))(((.((((.((..((.((((......----.....)))).----------))..)))))).)))....-. ( -27.20)
>consensus
CCCUGACAAUGAUGACGUCACUCGCAGGUGCUGUCAUCACAAAAGUAUGUGCAUUUGUUUUCGU____UGUGUACGAU__________UGU_CGAUUUGUACGAUU_U
.........((((((((.((((....)))).)))))))).........((((((...............))))))................................. (-17.94 = -18.02 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	6,640,343 – 6,640,447
Length	104
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	81.54
Mean single sequence MFE	-22.78
Consensus MFE	-13.62
Energy contribution	-13.70
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.80
Structure conservation index	0.60
SVM decision value	0.02
SVM RNA-class probability	0.541806
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6640343 104 - 22224390
AAAAUCGUACAAAUCGUACAAAUCGCACAAAUCGUACACA----ACGAAAAUAAAUGCACAUACUUUUGUGAUGACAGCACCUGCGAGUGACGUCAUCAUUGGCAGGG
......((((.....)))).....((.....((((.....----)))).........((((......))))......)).(((((.(((((.....))))).))))). ( -26.90)
>DroSec_CAF1 34173 107 - 1
A-AAUCGUACAAAUCGUACAAAUCGUACAAAUCGUACAAAUCGUACGAAAACAAAUGCACAUACUUUUGUGAUGACAGCACCUGCGAGUGACGUCAUCAUUGUCAGGG
.-....(((......((((.....))))...((((((.....)))))).......))).....(((..((((((((..(((......)))..))))))))....))). ( -25.70)
>DroSim_CAF1 31949 89 - 1
A-AAUCGUACAAAU------------------CGUACAAAUCGUACGAAAACAAAUGCACAUACUUUUGUGAUGACAGCACCUGCGAGUGACGUCAUCAUUGUCAGGG
.-....(.((((.(------------------(((((.....))))))..(((((..........)))))((((((..(((......)))..)))))).))))).... ( -20.90)
>DroEre_CAF1 27858 85 - 1
A-AAUCCCACAAAU------------------CGUACACA----GCGAAAACAAAUGCACAUACUUUUCUGAUGACAGCACCUGCGAGUGACGUCAUCAUUGGCAGGG
.-...(((.....(------------------(((.....----)))).......(((.((........(((((((..(((......)))..))))))).)))))))) ( -20.10)
>DroYak_CAF1 30182 93 - 1
A-AAUCGCACAAAUCGCACA----------AUCGUACACA----GCGAAAACAAAUGCACAUACUUUUGCGAUGACAGCACCUGCGAGUGACGUCAUCGUUGCCUGGG
.-....(((......(((..----------.((((.....----)))).......)))..........((((((((..(((......)))..)))))))))))..... ( -20.30)
>consensus
A_AAUCGUACAAAUCG_ACA__________AUCGUACACA____ACGAAAACAAAUGCACAUACUUUUGUGAUGACAGCACCUGCGAGUGACGUCAUCAUUGGCAGGG
...............................................................(((..((((((((..(((......)))..))))))))....))). (-13.62 = -13.70 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:21 2006