Locus 2641

Sequence ID	3L_DroMel_CAF1
Location	7,291,159 – 7,291,253
Length	94
Max. P	0.934588

overview

Window 3

Location	7,291,159 – 7,291,253
Length	94
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	57.05
Mean single sequence MFE	-25.62
Consensus MFE	-9.38
Energy contribution	-10.74
Covariance contribution	1.36
Combinations/Pair	1.35
Mean z-score	-2.27
Structure conservation index	0.37
SVM decision value	1.18
SVM RNA-class probability	0.926841
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7291159 94 + 23771897
CAUUUUGGCCAAGAGAAUAGCCACCUACUGUGCUCCA-UCGAUUUGCAGUUUUGGCCACUUACAAGCCGCCCUCUGUGCACACACAUUUUGGCCA
.....(((((((((.....((((...(((((..((..-..))...)))))..))))..................((((....))))))))))))) ( -24.50)
>DroSim_CAF1 52750 77 + 1
UAUAUUGGCCAAGAGGAUAG--ACCCAC------CCA-ACGCUUUGCAGUUUUGGCCGCUUACAA---------UGUGCACACACAUUUUGGCCA
......((((((((((....--..))..------...-..((...))..))))))))(((...((---------((((....))))))..))).. ( -21.00)
>DroEre_CAF1 49497 79 + 1
CAUUUUGGCCAAGGGGACAGCCACCC--------------AAUGUGCAGUUUUGGCCGCUUACAAGCCGCCCUCUGUGC--ACACAAUGUGGCCA
.....((((((.(((........)))--------------..((..(((....(((.(((....))).)))..)))..)--).......)))))) ( -30.80)
>DroYak_CAF1 50354 93 + 1
CAAUUUGGCCAAGAACAUAGCCACCCACUGUGGGCCAUUCAAUGUGCAGUUUUGGCCGCUUACAAGCCGCCCUCUGUGC--ACACAAUUUGGCCA
.....((((((((.......((((.....)))).........((..(((....(((.(((....))).)))..)))..)--).....)))))))) ( -31.40)
>DroMoj_CAF1 94825 77 + 1
UUUGCAGCUAAUCAAAUUGCAUGUGU--------------AUUCGGUCUUUCGUCCAGGUAUUCAGCUGGG--CUGACUAGGCAU--GUUUGCAA
.((((((...........((((((.(--------------(.((((....))((((((........)))))--).)).)).))))--)))))))) ( -20.40)
>consensus
CAUUUUGGCCAAGAGAAUAGCCACCCAC______CCA__CAAUGUGCAGUUUUGGCCGCUUACAAGCCGCCCUCUGUGCA_ACACAAUUUGGCCA
......(((((((........................................(((.(((....))).)))...((((....)))).))))))). ( -9.38 = -10.74 +   1.36)

alignment

secondary structure

dotplot

Window 4

Location	7,291,159 – 7,291,253
Length	94
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	57.05
Mean single sequence MFE	-28.88
Consensus MFE	-10.32
Energy contribution	-12.64
Covariance contribution	2.32
Combinations/Pair	1.19
Mean z-score	-2.41
Structure conservation index	0.36
SVM decision value	1.24
SVM RNA-class probability	0.934588
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7291159 94 - 23771897
UGGCCAAAAUGUGUGUGCACAGAGGGCGGCUUGUAAGUGGCCAAAACUGCAAAUCGA-UGGAGCACAGUAGGUGGCUAUUCUCUUGGCCAAAAUG
..(((....((((....))))...)))((((.(..((((((((..((((....((..-..))...))))...))))))))..)..))))...... ( -32.10)
>DroSim_CAF1 52750 77 - 1
UGGCCAAAAUGUGUGUGCACA---------UUGUAAGCGGCCAAAACUGCAAAGCGU-UGG------GUGGGU--CUAUCCUCUUGGCCAAUAUA
(((((((((((((....))))---------))....((((......)))).......-.((------(((...--.)))))..)))))))..... ( -24.70)
>DroEre_CAF1 49497 79 - 1
UGGCCACAUUGUGU--GCACAGAGGGCGGCUUGUAAGCGGCCAAAACUGCACAUU--------------GGGUGGCUGUCCCCUUGGCCAAAAUG
((((((....((((--(((.....(((.(((....))).))).....))))))).--------------(((........))).))))))..... ( -32.60)
>DroYak_CAF1 50354 93 - 1
UGGCCAAAUUGUGU--GCACAGAGGGCGGCUUGUAAGCGGCCAAAACUGCACAUUGAAUGGCCCACAGUGGGUGGCUAUGUUCUUGGCCAAAUUG
.(((((....((((--(((.....(((.(((....))).))).....)))))))....)))))..((((...((((((......)))))).)))) ( -39.70)
>DroMoj_CAF1 94825 77 - 1
UUGCAAAC--AUGCCUAGUCAG--CCCAGCUGAAUACCUGGACGAAAGACCGAAU--------------ACACAUGCAAUUUGAUUAGCUGCAAA
(((((...--..((.(((((((--....((((..((..(((.(....).)))..)--------------)..)).))...)))))))))))))). ( -15.30)
>consensus
UGGCCAAAAUGUGU_UGCACAGAGGGCGGCUUGUAAGCGGCCAAAACUGCAAAUUG__UGG______GUGGGUGGCUAUCCUCUUGGCCAAAAUG
((((((...((((....))))...(((.(((....))).)))..........................................))))))..... (-10.32 = -12.64 +   2.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:19 2006