Locus 2344

Sequence ID	3R_DroMel_CAF1
Location	6,675,924 – 6,676,019
Length	95
Max. P	0.850102

overview

Window 4

Location	6,675,924 – 6,676,019
Length	95
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	82.07
Mean single sequence MFE	-19.86
Consensus MFE	-10.14
Energy contribution	-10.52
Covariance contribution	0.38
Combinations/Pair	1.17
Mean z-score	-2.24
Structure conservation index	0.51
SVM decision value	0.26
SVM RNA-class probability	0.655903
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6675924 95 + 27905053
UAGCUGAGUUUCCAUUAUUUACAUACUU----AAAU----GUAUGACUCCAAUGAAAACAUUUAUGCUCGCAGAAAGCUCAAACAAGGGAGCUGUUUUAACUA
..((.((((............(((((..----....----))))).....((((....))))...))))))....(((((........))))).......... ( -16.80)
>DroSec_CAF1 60537 85 + 1
UAGCUCAGUUCCCAUUAUUUACAU------------------AUGAUUCCCAUGAAAACAUUUAUACUCACAGAAAGCUCUCACAAGGGAGCUGUUUUAACUA
(((..((((((((..........(------------------(((.....))))..................((......))....))))))))..))).... ( -15.10)
>DroSim_CAF1 61523 95 + 1
UAGCUACGUUUUCAUUAUUUACAUACUU----AAAU----GUAUGAUUCCCAUGAAAACAUUUAUACUCCCAGAAAGCUCUCACAAGGGAGCUGUUUUAACUA
.......((((((((......(((((..----....----)))))......))))))))................(((((((....))))))).......... ( -22.40)
>DroEre_CAF1 61682 103 + 1
UAGCUCGGUUCCCAUUACUUACAUACAUACUUAAAUGUGCGUAUAACUCCCAUGAAAACAUUUGUUCUCGCAGAAAGCUCUCCCAAGGGAGCUGUUUUAGCUA
(((((((((((((......(((.(((((......))))).)))..........((.(((....))).))((.....))........))))))))....))))) ( -23.50)
>DroYak_CAF1 62212 94 + 1
UAGCUCAGUUCCCAUUAUUUACAUACUUAUU---------GUAUGACUCCUAGGAAAACAUUUAUACUCGCAGAAAGCUCUCACAAGGGAGCUGGUUUAACUA
.(((.((((((((........(((((.....---------)))))........................((.....))........)))))))))))...... ( -21.50)
>consensus
UAGCUCAGUUCCCAUUAUUUACAUACUU____AAAU____GUAUGACUCCCAUGAAAACAUUUAUACUCGCAGAAAGCUCUCACAAGGGAGCUGUUUUAACUA
(((..((((((((........(((((..............)))))...........................((....))......))))))))..))).... (-10.14 = -10.52 +   0.38)

alignment

secondary structure

dotplot

Window 5

Location	6,675,924 – 6,676,019
Length	95
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	82.07
Mean single sequence MFE	-23.82
Consensus MFE	-15.50
Energy contribution	-15.08
Covariance contribution	-0.42
Combinations/Pair	1.17
Mean z-score	-2.13
Structure conservation index	0.65
SVM decision value	0.78
SVM RNA-class probability	0.850102
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6675924 95 - 27905053
UAGUUAAAACAGCUCCCUUGUUUGAGCUUUCUGCGAGCAUAAAUGUUUUCAUUGGAGUCAUAC----AUUU----AAGUAUGUAAAUAAUGGAAACUCAGCUA
..........((((.....(((((.((((.....)))).)))))((((((((((....(((((----....----..)))))....))))))))))..)))). ( -22.90)
>DroSec_CAF1 60537 85 - 1
UAGUUAAAACAGCUCCCUUGUGAGAGCUUUCUGUGAGUAUAAAUGUUUUCAUGGGAAUCAU------------------AUGUAAAUAAUGGGAACUGAGCUA
(((((....(((.((((..((....))((((((((((..........))))))))))....------------------...........)))).)))))))) ( -18.80)
>DroSim_CAF1 61523 95 - 1
UAGUUAAAACAGCUCCCUUGUGAGAGCUUUCUGGGAGUAUAAAUGUUUUCAUGGGAAUCAUAC----AUUU----AAGUAUGUAAAUAAUGAAAACGUAGCUA
(((((......((((((..((....)).....))))))....((((((((((......(((((----....----..)))))......))))))))))))))) ( -28.80)
>DroEre_CAF1 61682 103 - 1
UAGCUAAAACAGCUCCCUUGGGAGAGCUUUCUGCGAGAACAAAUGUUUUCAUGGGAGUUAUACGCACAUUUAAGUAUGUAUGUAAGUAAUGGGAACCGAGCUA
(((((.....(((((((........((.....))((((((....))))))..))))))).((((.((((......)))).))))..............))))) ( -27.60)
>DroYak_CAF1 62212 94 - 1
UAGUUAAACCAGCUCCCUUGUGAGAGCUUUCUGCGAGUAUAAAUGUUUUCCUAGGAGUCAUAC---------AAUAAGUAUGUAAAUAAUGGGAACUGAGCUA
..........(((((.(((((.((......)))))))..........((((((..(..(((((---------.....)))))....)..))))))..))))). ( -21.00)
>consensus
UAGUUAAAACAGCUCCCUUGUGAGAGCUUUCUGCGAGUAUAAAUGUUUUCAUGGGAGUCAUAC____AUUU____AAGUAUGUAAAUAAUGGGAACUGAGCUA
(((((.....(((((........)))))................((((((((......(((((..............)))))......))))))))..))))) (-15.50 = -15.08 +  -0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:02 2006