Locus 7738

Sequence ID	X_DroMel_CAF1
Location	19,249,755 – 19,249,904
Length	149
Max. P	0.842285

overview

Window 1

Location	19,249,755 – 19,249,864
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	97.42
Mean single sequence MFE	-32.46
Consensus MFE	-26.60
Energy contribution	-26.84
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.00
Structure conservation index	0.82
SVM decision value	0.76
SVM RNA-class probability	0.842285
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19249755 109 + 22224390
AUGUAUGGCAAAGAUGCGGUAUCCUGAUGUAAUUCCCGCCUCCUCGCCGUCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUU
((((..(((...((.((((................)))).))...)))((((....((((......))))((((......))))....)))).......))))...... ( -26.99)
>DroSec_CAF1 36593 108 + 1
AUGUAUGGCAAAGAUGCGGUGUCCUGAUGUAAUUC-CGCCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUU
...........((((((((((((.(((((((.(((-.(((........))).))).))))))).......((((......)))).....)))))....))))))).... ( -33.60)
>DroSim_CAF1 37991 108 + 1
AUGUAUGGCAAAGAUGCGGUGUCCUGAUGUAAUUC-CGCCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUU
...........((((((((((((.(((((((.(((-.(((........))).))).))))))).......((((......)))).....)))))....))))))).... ( -33.60)
>DroEre_CAF1 33970 108 + 1
AUGUAUGGUAAAGAUGCGGUGUCCUGAUGUAAUUC-CGCCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUGAAGGCAUUAAGCGCAUUUAAUU
...........((((((((((((.(((((((.(((-.(((........))).))).))))))).......((((......)))).....)))))....))))))).... ( -33.00)
>DroYak_CAF1 35813 108 + 1
AUGUAUGGCAAAGAUGCGGUGUCCUGAUGUAAUUC-CGCCUCCUCGGCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUU
...........((((((((((((.(((((((.(((-.(((.(....).))).))).))))))).......((((......)))).....)))))....))))))).... ( -35.10)
>consensus
AUGUAUGGCAAAGAUGCGGUGUCCUGAUGUAAUUC_CGCCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUU
...........((((((((((((.(((((((.(((..(((........))).))).))))))).......((((......)))).....)))))....))))))).... (-26.60 = -26.84 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	19,249,793 – 19,249,904
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	96.21
Mean single sequence MFE	-30.54
Consensus MFE	-25.92
Energy contribution	-26.12
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.85
SVM decision value	0.02
SVM RNA-class probability	0.545422
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19249793 111 + 22224390
CCUCCUCGCCGUCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUUUGAAGUGGCAGGAUGAAUGGAAAUUUGCAACGAGGCAAAA
...(((((((((((....((((......))))((((......))))....)))).....((.(((((......))))))).))..((((....))))....)))))..... ( -29.90)
>DroSec_CAF1 36630 111 + 1
CCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUUUGAAGUGGCAGGAUGAAUGGAAAUUUGCAACGAGGCAAAC
...(((((...((((..(((((......))))))))).......(((......((((..((.(((((......)))))))..))))(((....))))))..)))))..... ( -28.90)
>DroSim_CAF1 38028 111 + 1
CCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUUUGAAGUGGCAGGAUGAAUGGAAAUUUGCAACGAGGCAAAC
...(((((...((((..(((((......))))))))).......(((......((((..((.(((((......)))))))..))))(((....))))))..)))))..... ( -28.90)
>DroEre_CAF1 34007 108 + 1
CCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUGAAGGCAUUAAGCGCAUUUAAUUUGAAGUGGCAGGAUGAAUGGAAAUUUGC--CGAGGCAAC-
...(((((((........((((......))))((((......)))).....))).....((.(((((......))))))).((.(((((....))))))--)))))....- ( -30.90)
>DroYak_CAF1 35850 108 + 1
CCUCCUCGGCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUUUGAAGUGGCAGGAUGAAUGGAAAUUUGC--CGAGGCAAC-
...((((((((((((..(((((......)))))))))................((((..((.(((((......)))))))..))))..........)))--)))))....- ( -34.10)
>consensus
CCUCCUCGCCGGCUGAACUGCAUCAUAUUGCAGCGGCAACAACCGCAUAAAGACAUUAAGCGCAUUUAAUUUGAAGUGGCAGGAUGAAUGGAAAUUUGCAACGAGGCAAA_
...(((((...((.....((((......))))((((......)))).......((((..((.(((((......)))))))..))))...........))..)))))..... (-25.92 = -26.12 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:26 2006