Locus 6342

Sequence ID	X_DroMel_CAF1
Location	15,998,009 – 15,998,119
Length	110
Max. P	0.861519

overview

Window 8

Location	15,998,009 – 15,998,119
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-29.98
Consensus MFE	-25.34
Energy contribution	-26.50
Covariance contribution	1.16
Combinations/Pair	1.05
Mean z-score	-1.49
Structure conservation index	0.85
SVM decision value	0.49
SVM RNA-class probability	0.756940
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15998009 110 + 22224390
AUUCG----------CAAAUCAAUGGCAGAAUGCACUCGCUCCCAUAAACAUGGAGCGUAAAUUGAUUUUAAGAAUUUUCGCGCGUGCAUUUGUUCUGCCCUUCAUGCGUUAAGUGAACA
...((----------((.......((((((((((((..((..((((....)))).(((.(((((.........))))).)))))))))))....)))))).....))))........... ( -28.60)
>DroSec_CAF1 66063 120 + 1
AUUCGCAGACAUUAGCAAAUCAAUGGCAGAAUGCACUCGCUCCCAUAAACAUGGAGCGUAAAUUGAUUUUAAGAAUUUUCGCGCGUGCAUUUGUUCUGCCCUUCAUGCGUUAAGUGAACA
.(((((.....(((((..((.((.((((((((((((..((..((((....)))).(((.(((((.........))))).)))))))))))....)))))).)).))..)))))))))).. ( -30.60)
>DroSim_CAF1 60236 120 + 1
AUUCGCAGACAUUAGCAAAUCAAUGGCAGAAUGCACUCGCUCCCAUAAACAUGGAGCGUAAAUUGAUUUUAAGAAUUUUCGCGCGUGCAUUUGUUCUGCCCUUCAUGCGUUAAGUGAACA
.(((((.....(((((..((.((.((((((((((((..((..((((....)))).(((.(((((.........))))).)))))))))))....)))))).)).))..)))))))))).. ( -30.60)
>DroEre_CAF1 64896 120 + 1
AUUCGCAGACAUUAGCAAAUCAAUGGCAGCAUGCACUCGCUCCCAUAAACAUGGAGCGUAAAUUGAUUUUAAGAAUUUUCGCGCGUGCAUUUGUUCUGUCCUUCAUGCGUUAAGUGAACA
...((((((((..(((((((........((((((...((((((.........))))))((((.....))))...........))))))))))))).)))).....))))........... ( -26.90)
>DroYak_CAF1 49231 120 + 1
AUUCGCAGACAUUGGCAAAUCAAUGCCAGAAUGCACUCGCUCCCAUAAACAUGGAGCGUAAAUUGAUUUUAAGAAUUUUCGCGCGUGCAUUUGUUCUGCCCUUCAUGCGUUAAGUGAACA
....(((((...(((((......)))))((((((((..((..((((....)))).(((.(((((.........))))).)))))))))))))..)))))..(((((.......))))).. ( -33.20)
>consensus
AUUCGCAGACAUUAGCAAAUCAAUGGCAGAAUGCACUCGCUCCCAUAAACAUGGAGCGUAAAUUGAUUUUAAGAAUUUUCGCGCGUGCAUUUGUUCUGCCCUUCAUGCGUUAAGUGAACA
.(((((.....(((((..((.((.((((((((((((..((..((((....)))).(((.(((((.........))))).)))))))))))....)))))).)).))..)))))))))).. (-25.34 = -26.50 +   1.16)

alignment

secondary structure

dotplot

Window 9

Location	15,998,009 – 15,998,119
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.42
Mean single sequence MFE	-32.28
Consensus MFE	-26.67
Energy contribution	-27.32
Covariance contribution	0.65
Combinations/Pair	1.00
Mean z-score	-1.75
Structure conservation index	0.83
SVM decision value	0.83
SVM RNA-class probability	0.861519
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15998009 110 - 22224390
UGUUCACUUAACGCAUGAAGGGCAGAACAAAUGCACGCGCGAAAAUUCUUAAAAUCAAUUUACGCUCCAUGUUUAUGGGAGCGAGUGCAUUCUGCCAUUGAUUUG----------CGAAU
...........((((.....((((((....((((((....((....))..............((((((.........)))))).)))))))))))).......))----------))... ( -32.60)
>DroSec_CAF1 66063 120 - 1
UGUUCACUUAACGCAUGAAGGGCAGAACAAAUGCACGCGCGAAAAUUCUUAAAAUCAAUUUACGCUCCAUGUUUAUGGGAGCGAGUGCAUUCUGCCAUUGAUUUGCUAAUGUCUGCGAAU
...........((((.....((((((....((((((....((....))..............((((((.........)))))).))))))))))))...(((........)))))))... ( -32.70)
>DroSim_CAF1 60236 120 - 1
UGUUCACUUAACGCAUGAAGGGCAGAACAAAUGCACGCGCGAAAAUUCUUAAAAUCAAUUUACGCUCCAUGUUUAUGGGAGCGAGUGCAUUCUGCCAUUGAUUUGCUAAUGUCUGCGAAU
...........((((.....((((((....((((((....((....))..............((((((.........)))))).))))))))))))...(((........)))))))... ( -32.70)
>DroEre_CAF1 64896 120 - 1
UGUUCACUUAACGCAUGAAGGACAGAACAAAUGCACGCGCGAAAAUUCUUAAAAUCAAUUUACGCUCCAUGUUUAUGGGAGCGAGUGCAUGCUGCCAUUGAUUUGCUAAUGUCUGCGAAU
...........((((....((.(((.....((((((....((....))..............((((((.........)))))).)))))).)))))...(((........)))))))... ( -28.80)
>DroYak_CAF1 49231 120 - 1
UGUUCACUUAACGCAUGAAGGGCAGAACAAAUGCACGCGCGAAAAUUCUUAAAAUCAAUUUACGCUCCAUGUUUAUGGGAGCGAGUGCAUUCUGGCAUUGAUUUGCCAAUGUCUGCGAAU
.((((.(((........))).(((((.(((((((((....((....))..............((((((.........)))))).))))))).(((((......))))).))))))))))) ( -34.60)
>consensus
UGUUCACUUAACGCAUGAAGGGCAGAACAAAUGCACGCGCGAAAAUUCUUAAAAUCAAUUUACGCUCCAUGUUUAUGGGAGCGAGUGCAUUCUGCCAUUGAUUUGCUAAUGUCUGCGAAU
....................((((((....((((((....((....))..............((((((.........)))))).))))))))))))....((((((........)))))) (-26.67 = -27.32 +   0.65)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:14 2006