Locus 8372

Sequence ID	3L_DroMel_CAF1
Location	21,995,182 – 21,995,299
Length	117
Max. P	0.756736

overview

Window 2

Location	21,995,182 – 21,995,299
Length	117
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	89.32
Mean single sequence MFE	-37.90
Consensus MFE	-30.10
Energy contribution	-30.48
Covariance contribution	0.37
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.79
SVM decision value	0.22
SVM RNA-class probability	0.641146
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21995182 117 + 23771897
GGAGCUGUGGAGGAGCUGCAUGCCAGCAUCCUGGGCCUCCAGCUGGCUGUGCCGGAGUGGGAGGUAAUAAGCACAAUGAUAGUAUUUCAUUUCAUUACUAAUAAUAACGGAUAGCUU
.((((((((.((((((((.....)))).))))..((((((..(((((...)))))....))))))......))).....(((((...........)))))............))))) ( -36.80)
>DroSec_CAF1 125130 117 + 1
GGAGCUGUGGAGGAGCUGCAUGCCAGCGUCCUGGGCCUCCAGCUGGCUGUGCCGGAGUGGGAGGUAAUAAGCACAAUGAUAGUGUUUCAUUUCAUUAUUAAUAGUAAUGGAUAGCUU
.(((((((..((((((((.....)))).))))..((((((..(((((...)))))....))))))...((((((.......))))))....(((((((.....)))))))))))))) ( -41.20)
>DroSim_CAF1 122302 117 + 1
GGAGCUGUGGAGGAGCUGCAUGCCAGCGUCCUGGGCCUCCAGCUGGCUGUGCCGGAGUGGGAGGUAAUAAGCACAAUGAUAGUGUUUCAUUUCAUUAUUAAUAGUAAUGGAUAGCUU
.(((((((..((((((((.....)))).))))..((((((..(((((...)))))....))))))...((((((.......))))))....(((((((.....)))))))))))))) ( -41.20)
>DroEre_CAF1 117812 107 + 1
GGAGCUGUGGAUGAGCUGCAUGCCAGCGUCCUGGGCCUCCAGCUGGCUGUGCCGGAGUGGGAGGUAAUGAACAUAACGAUAAUAUUCCACUUCAAUAUUAAUGGUAA----------
(((((((.(.(((.....))).))))).)))...((((((..(((((...)))))....))))))...........((.(((((((.......))))))).))....---------- ( -32.40)
>consensus
GGAGCUGUGGAGGAGCUGCAUGCCAGCGUCCUGGGCCUCCAGCUGGCUGUGCCGGAGUGGGAGGUAAUAAGCACAAUGAUAGUAUUUCAUUUCAUUAUUAAUAGUAAUGGAUAGCUU
(((((((((.((((((((.....)))).))))..((((((..(((((...)))))....))))))......))))........)))))............................. (-30.10 = -30.48 +   0.37)

alignment

secondary structure

dotplot

Window 3

Location	21,995,182 – 21,995,299
Length	117
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	89.32
Mean single sequence MFE	-29.25
Consensus MFE	-23.77
Energy contribution	-23.28
Covariance contribution	-0.50
Combinations/Pair	1.17
Mean z-score	-1.71
Structure conservation index	0.81
SVM decision value	0.49
SVM RNA-class probability	0.756736
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21995182 117 - 23771897
AAGCUAUCCGUUAUUAUUAGUAAUGAAAUGAAAUACUAUCAUUGUGCUUAUUACCUCCCACUCCGGCACAGCCAGCUGGAGGCCCAGGAUGCUGGCAUGCAGCUCCUCCACAGCUCC
.((((...((((((.....)))))).(((((.......)))))(((..............(((((((.......)))))))....((((.((((.....)))))))).))))))).. ( -30.80)
>DroSec_CAF1 125130 117 - 1
AAGCUAUCCAUUACUAUUAAUAAUGAAAUGAAACACUAUCAUUGUGCUUAUUACCUCCCACUCCGGCACAGCCAGCUGGAGGCCCAGGACGCUGGCAUGCAGCUCCUCCACAGCUCC
.((((...(((((.......))))).(((((.......)))))(((..............(((((((.......)))))))....((((.((((.....)))))))).))))))).. ( -29.00)
>DroSim_CAF1 122302 117 - 1
AAGCUAUCCAUUACUAUUAAUAAUGAAAUGAAACACUAUCAUUGUGCUUAUUACCUCCCACUCCGGCACAGCCAGCUGGAGGCCCAGGACGCUGGCAUGCAGCUCCUCCACAGCUCC
.((((...(((((.......))))).(((((.......)))))(((..............(((((((.......)))))))....((((.((((.....)))))))).))))))).. ( -29.00)
>DroEre_CAF1 117812 107 - 1
----------UUACCAUUAAUAUUGAAGUGGAAUAUUAUCGUUAUGUUCAUUACCUCCCACUCCGGCACAGCCAGCUGGAGGCCCAGGACGCUGGCAUGCAGCUCAUCCACAGCUCC
----------.................(((((.....................(((....(((((((.......)))))))....)))..((((.....))))...)))))...... ( -28.20)
>consensus
AAGCUAUCCAUUACUAUUAAUAAUGAAAUGAAACACUAUCAUUGUGCUUAUUACCUCCCACUCCGGCACAGCCAGCUGGAGGCCCAGGACGCUGGCAUGCAGCUCCUCCACAGCUCC
...................(((((((............)))))))(((.....(((....(((((((.......)))))))....)))..((((.....))))........)))... (-23.77 = -23.28 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:43 2006