Locus 3991

Sequence ID	2R_DroMel_CAF1
Location	13,196,861 – 13,196,952
Length	91
Max. P	0.938369

overview

Window 3

Location	13,196,861 – 13,196,952
Length	91
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	81.68
Mean single sequence MFE	-26.22
Consensus MFE	-17.45
Energy contribution	-17.90
Covariance contribution	0.45
Combinations/Pair	1.08
Mean z-score	-2.34
Structure conservation index	0.67
SVM decision value	1.27
SVM RNA-class probability	0.938369
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13196861 91 + 20766785
UUGUUU-UAUGAG--------GAGGAUUCUAAUUUGUUUUUCUUACUCGAAGAAUGCCCACUGUACAACCCGUUUGGGUCCGUGGGCGUUUUUAUUAAGC
......-..((((--------((((((........))))))))))....((((((((((((.(....((((....))))).))))))))))))....... ( -27.70)
>DroSec_CAF1 7491 100 + 1
UUGUUUGUAUGAAACCCACUUGAGGAUUCUAAUUUGUUUUUCUUACUCGAAGAAUGCCCACUGUACAACCCGUUUGGGUCCGUGGGCGUUUUCAUUAAGC
..(((((.((((.......(((((.....................))))).((((((((((.(....((((....))))).))))))))))))))))))) ( -25.70)
>DroSim_CAF1 7433 100 + 1
UUGUUUGUAUGAAACCCACUUGAGGAUUCUAAUUUGUUUUUCUUACUCGAAGAAUGCCCACUGUACAACCCGUUUGUGUCCGUGGGCGUUUUCAUUAAGC
..(((((.((((.......(((((.....................))))).((((((((((.((((((.....))))).).))))))))))))))))))) ( -25.00)
>DroEre_CAF1 7659 100 + 1
UUGUCUUCAUGAAGUCCACUUGAGGUUUCUAAUAGGGGUUUCUUACUUGAAGAAUGCUCACUGUACAACAACUUUGUGUCCGUGGGCGUUUUCAUUAAGC
...((((((.(((..((.((..((....))...))))..))).....))))))((((((((.((((((.....))))).).))))))))........... ( -26.30)
>DroYak_CAF1 7821 86 + 1
UUGUUU---UGAAAAUCUCUUGAGGUCU-----------AUCUUACUUUAAGAAUGCCCACUGUACAACAAGUUUGUGUCCGUGGGCGUUUUCAUUAAGC
......---(((((((.(((((((((..-----------.....)))))))))..((((((.((((((.....))))).).)))))))))))))...... ( -26.40)
>consensus
UUGUUU_UAUGAAACCCACUUGAGGAUUCUAAUUUGUUUUUCUUACUCGAAGAAUGCCCACUGUACAACCCGUUUGUGUCCGUGGGCGUUUUCAUUAAGC
....................((((((..(......)...)))))).....(((((((((((.((((((.....))))).).)))))))))))........ (-17.45 = -17.90 +   0.45)

alignment

secondary structure

dotplot

Window 4

Location	13,196,861 – 13,196,952
Length	91
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	81.68
Mean single sequence MFE	-20.72
Consensus MFE	-14.56
Energy contribution	-15.84
Covariance contribution	1.28
Combinations/Pair	1.05
Mean z-score	-1.68
Structure conservation index	0.70
SVM decision value	0.23
SVM RNA-class probability	0.645572
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13196861 91 - 20766785
GCUUAAUAAAAACGCCCACGGACCCAAACGGGUUGUACAGUGGGCAUUCUUCGAGUAAGAAAAACAAAUUAGAAUCCUC--------CUCAUA-AAACAA
..(((((......((((((.(((((....))))).....)))))).(((((.....)))))......))))).......--------......-...... ( -20.20)
>DroSec_CAF1 7491 100 - 1
GCUUAAUGAAAACGCCCACGGACCCAAACGGGUUGUACAGUGGGCAUUCUUCGAGUAAGAAAAACAAAUUAGAAUCCUCAAGUGGGUUUCAUACAAACAA
......((((((.((((((.(((((....))))).....)))))).)).)))).(((.((((..((....((....))....))..)))).)))...... ( -26.00)
>DroSim_CAF1 7433 100 - 1
GCUUAAUGAAAACGCCCACGGACACAAACGGGUUGUACAGUGGGCAUUCUUCGAGUAAGAAAAACAAAUUAGAAUCCUCAAGUGGGUUUCAUACAAACAA
......((((((.((((((..((((......).)))...)))))).)).)))).(((.((((..((....((....))....))..)))).)))...... ( -21.50)
>DroEre_CAF1 7659 100 - 1
GCUUAAUGAAAACGCCCACGGACACAAAGUUGUUGUACAGUGAGCAUUCUUCAAGUAAGAAACCCCUAUUAGAAACCUCAAGUGGACUUCAUGAAGACAA
.(((.(((((...((.(((..(((((....)).)))...))).)).(((((.....)))))....(((((.((....)).)))))..))))).))).... ( -16.60)
>DroYak_CAF1 7821 86 - 1
GCUUAAUGAAAACGCCCACGGACACAAACUUGUUGUACAGUGGGCAUUCUUAAAGUAAGAU-----------AGACCUCAAGAGAUUUUCA---AAACAA
......(((((((((((((..(((((....)).)))...))))))..(((((...))))).-----------...........).))))))---...... ( -19.30)
>consensus
GCUUAAUGAAAACGCCCACGGACACAAACGGGUUGUACAGUGGGCAUUCUUCGAGUAAGAAAAACAAAUUAGAAUCCUCAAGUGGGUUUCAUA_AAACAA
.....(((((...((((((.(((((....))))).....)))))).(((((.....)))))..........................)))))........ (-14.56 = -15.84 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:09 2006