Locus 2722

Sequence ID	X_DroMel_CAF1
Location	7,301,778 – 7,301,874
Length	96
Max. P	0.936707

overview

Window 7

Location	7,301,778 – 7,301,874
Length	96
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.23
Mean single sequence MFE	-19.87
Consensus MFE	-17.82
Energy contribution	-17.85
Covariance contribution	0.03
Combinations/Pair	1.04
Mean z-score	-1.11
Structure conservation index	0.90
SVM decision value	0.05
SVM RNA-class probability	0.561247
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7301778 96 + 22224390
-------------GUUUUUUCAUUUUUUUU--UUUUUUUGUGGCGCGCCACAGGGGUUAAUAAGUAAUCUGCAUUUUUUGACAUUUAUUUAUGUCUUCAAAUAUGUGCGGA
-------------........((((...((--..(((((((((....)))))))))..)).))))..(((((((.(((.(((((......)))))...)))...))))))) ( -21.60)
>DroVir_CAF1 71868 88 + 1
-------------GAGCUGGAG---------CUGGAGCUGGGGCACGCCACAGGGGUUAAUAAGUAAUCUGCAUUUUUUGACAUUUAUUUAUGUCUUCAAAUAUGUGCC-G
-------------.((((....---------....))))..((((((.....((((...((((((((....((.....))....))))))))..)))).....))))))-. ( -21.00)
>DroGri_CAF1 67811 88 + 1
-------------GUGUUGGAG---------UUGGAGUUGUGGCACGCCACAGGGGUUAAUAAGUAAUCUGCAUUUUUUGACAUUUAUUUAUGUCUUCAAAUAUGUGCG-A
-------------(..(.....---------((((((((((((....))))))......((((((((....((.....))....))))))))..))))))....)..).-. ( -18.70)
>DroSim_CAF1 50667 97 + 1
-------------GUUUUUUCAUUUUUUUUUUUUUUUUUGUGGCGCGCCACAGGGGUUAAUAAGUAAUCUGCAUUUUUUGACAUUUAUUUAUGUCUUCAAAUAUGUGCG-A
-------------........................((((((....))))))((((((.....))))))((((.(((.(((((......)))))...)))...)))).-. ( -18.30)
>DroYak_CAF1 78365 86 + 1
-------------GUUUUUU-----------UUUUUUUUGUGGCGCGCCACAGGGGUUAAUAAGUAAUCUGCAUUUUUUGACAUUUAUUUAUGUCUUCAAAUAUGUGCG-U
-------------.......-----------......((((((....))))))((((((.....))))))((((.(((.(((((......)))))...)))...)))).-. ( -18.30)
>DroMoj_CAF1 86223 101 + 1
GGAGACGGAACAGGAACUGAAG---------CUGGAGUUGUGGCACGCCACAGGGGUUAAUAAGUAAUCUGCAUUUUUUGACAUUUAUUUAUGUCUUCAAAUAUGUGCG-G
.....((..(((.....(((((---------(.....((((((....))))))((((((.....)))))))).......(((((......)))))))))....))).))-. ( -21.30)
>consensus
_____________GUUUUGUAG_________UUGGAGUUGUGGCACGCCACAGGGGUUAAUAAGUAAUCUGCAUUUUUUGACAUUUAUUUAUGUCUUCAAAUAUGUGCG_A
.....................................((((((....))))))((((((.....))))))((((.(((.(((((......)))))...)))...))))... (-17.82 = -17.85 +   0.03)

alignment

secondary structure

dotplot

Window 8

Location	7,301,778 – 7,301,874
Length	96
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.23
Mean single sequence MFE	-14.91
Consensus MFE	-13.17
Energy contribution	-13.33
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.88
SVM decision value	1.25
SVM RNA-class probability	0.936707
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7301778 96 - 22224390
UCCGCACAUAUUUGAAGACAUAAAUAAAUGUCAAAAAAUGCAGAUUACUUAUUAACCCCUGUGGCGCGCCACAAAAAAA--AAAAAAAAUGAAAAAAC-------------
((.(((((....))..(((((......)))))......))).))...............(((((....)))))......--.................------------- ( -14.20)
>DroVir_CAF1 71868 88 - 1
C-GGCACAUAUUUGAAGACAUAAAUAAAUGUCAAAAAAUGCAGAUUACUUAUUAACCCCUGUGGCGUGCCCCAGCUCCAG---------CUCCAGCUC-------------
.-(((((.........(((((......))))).......((((...............))))...)))))..((((....---------....)))).------------- ( -17.96)
>DroGri_CAF1 67811 88 - 1
U-CGCACAUAUUUGAAGACAUAAAUAAAUGUCAAAAAAUGCAGAUUACUUAUUAACCCCUGUGGCGUGCCACAACUCCAA---------CUCCAACAC-------------
.-.(((((....))..(((((......)))))......)))..................(((((....))))).......---------.........------------- ( -14.10)
>DroSim_CAF1 50667 97 - 1
U-CGCACAUAUUUGAAGACAUAAAUAAAUGUCAAAAAAUGCAGAUUACUUAUUAACCCCUGUGGCGCGCCACAAAAAAAAAAAAAAAAAUGAAAAAAC-------------
.-.(((((....))..(((((......)))))......)))..................(((((....))))).........................------------- ( -14.10)
>DroYak_CAF1 78365 86 - 1
A-CGCACAUAUUUGAAGACAUAAAUAAAUGUCAAAAAAUGCAGAUUACUUAUUAACCCCUGUGGCGCGCCACAAAAAAAA-----------AAAAAAC-------------
.-.(((((....))..(((((......)))))......)))..................(((((....))))).......-----------.......------------- ( -14.10)
>DroMoj_CAF1 86223 101 - 1
C-CGCACAUAUUUGAAGACAUAAAUAAAUGUCAAAAAAUGCAGAUUACUUAUUAACCCCUGUGGCGUGCCACAACUCCAG---------CUUCAGUUCCUGUUCCGUCUCC
.-((.(((...((((((((((......)))))...........................(((((....))))).......---------.)))))....)))..))..... ( -15.00)
>consensus
U_CGCACAUAUUUGAAGACAUAAAUAAAUGUCAAAAAAUGCAGAUUACUUAUUAACCCCUGUGGCGCGCCACAAAAAAAA_________CUAAAAAAC_____________
...(((((....))..(((((......)))))......)))..................(((((....)))))...................................... (-13.17 = -13.33 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:48 2006