Locus 6708

Sequence ID	X_DroMel_CAF1
Location	16,733,068 – 16,733,201
Length	133
Max. P	0.999473

overview

Window 1

Location	16,733,068 – 16,733,181
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.11
Mean single sequence MFE	-48.98
Consensus MFE	-37.38
Energy contribution	-38.08
Covariance contribution	0.70
Combinations/Pair	1.00
Mean z-score	-4.35
Structure conservation index	0.76
SVM decision value	3.02
SVM RNA-class probability	0.998170
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16733068 113 + 22224390
ACUGGCCGCUGCAGAAACGUGCG---GCUGACCCAAGGCCAAUUGGCAAAUUGAAAGCGGAGUGGAGUCGUCGUUCUAAUUGGAAUCCACUUACA-GCGCCGCUCCACCUGCACA---GA
.((((((((.((......)))))---)).....(((.(((....)))...)))...((((.((((((.((.((((.(((.(((...))).))).)-))).)))))))))))).))---). ( -44.60)
>DroSec_CAF1 20840 88 + 1
----------------------------UGACCCAAGGCCAAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACA-GCGCCGCUCCACCUGCACA---GA
----------------------------.....(((.(((....)))...)))...((((.((((((.(((((((.(((.(((...))).))).)-))))))))))))))))...---.. ( -39.20)
>DroSim_CAF1 18198 113 + 1
ACUGGCCGCUGCAGAAACGUGCG---GCUGACCCAAGGCCAAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACA-GCGCCGCUCCACCUGCACA---GA
.((((((((.((......)))))---)).....(((.(((....)))...)))...((((.((((((.(((((((.(((.(((...))).))).)-)))))))))))))))).))---). ( -51.70)
>DroEre_CAF1 12166 117 + 1
ACUGGCCGCUGCAGAAACGUGCGGCGGCUGACCCAAGGCCAAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACAAGCGCCGCUCCACCUGCACA---GA
.((((((((((((......))))))))).....(((.(((....)))...)))...((((.((((((.(((((((.(((.(((...))).)))..))))))))))))))))).))---). ( -57.30)
>DroYak_CAF1 11812 117 + 1
ACUGGCCGCUGCAGAAACGUGCG---GCUGAGCCAAGGCCAAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACAAGCGCCGCUCCACCUGCACACCAGA
.((((..((((((......))))---))...(((((......))))).........((((.((((((.(((((((.(((.(((...))).)))..)))))))))))))))))...)))). ( -52.10)
>consensus
ACUGGCCGCUGCAGAAACGUGCG___GCUGACCCAAGGCCAAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACA_GCGCCGCUCCACCUGCACA___GA
...(((...((((......))))...)))....(((.(((....)))...)))...((((.((((((.((((((..(((.(((...))).)))...))))))))))))))))........ (-37.38 = -38.08 +   0.70)

alignment

secondary structure

dotplot

Window 2

Location	16,733,105 – 16,733,201
Length	96
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.39
Mean single sequence MFE	-35.72
Consensus MFE	-30.94
Energy contribution	-30.98
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.97
Structure conservation index	0.87
SVM decision value	3.63
SVM RNA-class probability	0.999473
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16733105 96 + 22224390
AAUUGGCAAAUUGAAAGCGGAGUGGAGUCGUCGUUCUAAUUGGAAUCCACUUACA-GCGCCGCUCCACCUGCACA---GAAUC--------------------AUUUGGAUGGAUGGCAA
.....((.........((((.((((((.((.((((.(((.(((...))).))).)-))).)))))))))))).((---..(((--------------------.....)))...)))).. ( -29.90)
>DroSec_CAF1 20852 96 + 1
AAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACA-GCGCCGCUCCACCUGCACA---GAAUC--------------------ACUUGGAUGUGUGGCAA
..(((.((........((((.((((((.(((((((.(((.(((...))).))).)-))))))))))))))))...---....(--------------------((......))))).))) ( -37.60)
>DroSim_CAF1 18235 96 + 1
AAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACA-GCGCCGCUCCACCUGCACA---GAAUC--------------------ACUUGGAUGUGUGGCAA
..(((.((........((((.((((((.(((((((.(((.(((...))).))).)-))))))))))))))))...---....(--------------------((......))))).))) ( -37.60)
>DroEre_CAF1 12206 97 + 1
AAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACAAGCGCCGCUCCACCUGCACA---GAAUC--------------------AGUUGGAUGUGUGGCAA
.....((.........((((.((((((.(((((((.(((.(((...))).)))..)))))))))))))))))(((---..(((--------------------.....))).))).)).. ( -35.10)
>DroYak_CAF1 11849 120 + 1
AAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACAAGCGCCGCUCCACCUGCACACCAGAAUCACAGAAUCACAGAAUCGCAGAAUUGAAUGUGUGGCAA
.....((.........((((.((((((.(((((((.(((.(((...))).)))..)))))))))))))))))..................((((.(.(((......))).).)))))).. ( -38.40)
>consensus
AAUUGGCAAAUUGAAAGCGGAGUGGAGUCGGCGUUCUAAUUGGAAUCCACUUACA_GCGCCGCUCCACCUGCACA___GAAUC____________________ACUUGGAUGUGUGGCAA
..(((.((.(((.((.((((.((((((.((((((..(((.(((...))).)))...)))))))))))))))).(....)..........................)).)))...)).))) (-30.94 = -30.98 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:24 2006