Locus 9327

Sequence ID	3R_DroMel_CAF1
Location	24,789,304 – 24,789,448
Length	144
Max. P	0.998898

overview

Window 2

Location	24,789,304 – 24,789,419
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	81.09
Mean single sequence MFE	-24.98
Consensus MFE	-16.08
Energy contribution	-16.68
Covariance contribution	0.60
Combinations/Pair	1.25
Mean z-score	-2.29
Structure conservation index	0.64
SVM decision value	1.19
SVM RNA-class probability	0.928942
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24789304 115 + 27905053
AAUGGAGUUGACUGACAGUAUGUGGGAUUUCUUAAAAGCAAAAACAAAAAAAAAAAAAAGAAGUAUAAGCCGAAGGGCAAAUCCAAUGCACAAAUUGUCUGAGGGGCGGUUGACC
......((..(((((((((.((((.((((((((........................)))))))....(((....)))........).)))).))))))........)))..)). ( -24.66)
>DroSec_CAF1 5714 98 + 1
AAUGGAGUUGACUGACAGUAUGUGGGAUUUCUUGGAAGCAAAA---------AAAAAAAGAAGGAUAAGCCGAAGGGCAAGUCCAAUGCACAAAUUGUCUGAGG--------ACC
......(((..(.((((((.((((.(..(((((..........---------.....)))))((((..(((....)))..))))..).)))).)))))).)..)--------)). ( -26.46)
>DroSim_CAF1 5688 95 + 1
AAUGGAGUUGACUGACAGUAUGUGGGAUUUCUUGGAAGCAAAA------------AAAAGAAGGAUAAGCCGAAGGGCAAGUCCAAUGGACAAAUUGUCUGAGG--------ACC
......(((..(.((((((.(((.....(((((..........------------..)))))((((..(((....)))..)))).....))).)))))).)..)--------)). ( -23.60)
>DroEre_CAF1 432 102 + 1
AAUGGAGUUGACUGACAGUAUGUGGGAUUUCCUGUCAGC-AAA------------AAAAGCAGGAUAACCCGAAAGGCAAAUCCAAUACACAAAAUGUUUGAGGGGCGGUUAACC
......((((((((.(.((((...(((((((((((....-...------------....))))))....((....))..))))).)))).(((.....))).)...)))))))). ( -26.40)
>DroYak_CAF1 413 103 + 1
AAUGGAGUUGACUGACAGCAUGUGGGAUUUCUUGGCAGCCGAA------------AAAAAAAGGAUAAGCCAAAAGAAAAAUCCAAUAUACAAACUGUCUGAGGGGCGGUUGACC
......((..((((((((..((((((((((((((((..((...------------.......))....))))..)))..)))))....))))..)))))........)))..)). ( -23.80)
>consensus
AAUGGAGUUGACUGACAGUAUGUGGGAUUUCUUGGAAGCAAAA____________AAAAGAAGGAUAAGCCGAAGGGCAAAUCCAAUGCACAAAUUGUCUGAGGGGCGGUU_ACC
...........(.((((((.((((((....))..............................((((..(((....)))..))))....)))).)))))).).............. (-16.08 = -16.68 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	24,789,339 – 24,789,448
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	76.74
Mean single sequence MFE	-23.35
Consensus MFE	-11.24
Energy contribution	-11.96
Covariance contribution	0.72
Combinations/Pair	1.24
Mean z-score	-3.03
Structure conservation index	0.48
SVM decision value	3.27
SVM RNA-class probability	0.998898
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24789339 109 + 27905053
AAGCAAAAACAAAAAAAAAAAAAAGAAGUAUAAGCCGAAGGGCAAAUCCAAUGCACAAAUUGUCUGAGGGGCGGUUGACCUUUAUUGUGUUUUGGGAAAUGCUUUAAAU
........................(((((((..(((....)))...(((((.((((((......((((((........)))))))))))).)))))..))))))).... ( -28.60)
>DroSec_CAF1 5749 92 + 1
AAGCAAAA---------AAAAAAAGAAGGAUAAGCCGAAGGGCAAGUCCAAUGCACAAAUUGUCUGAGG--------ACCUUUAUUGUGUUUUGGGAAAUGCUUUAAAU
(((((...---------................(((....)))...(((((.((((((...(((....)--------)).....)))))).)))))...)))))..... ( -24.40)
>DroSim_CAF1 5723 89 + 1
AAGCAAAA------------AAAAGAAGGAUAAGCCGAAGGGCAAGUCCAAUGGACAAAUUGUCUGAGG--------ACCUUUAUUGUGUUUUGUGAAAUGCUUUAAAU
(((((...------------....((((.(((((((....)))..((((...((((.....))))..))--------)).....)))).))))......)))))..... ( -22.92)
>DroEre_CAF1 467 96 + 1
CAGC-AAA------------AAAAGCAGGAUAACCCGAAAGGCAAAUCCAAUACACAAAAUGUUUGAGGGGCGGUUAACCUUCAUUGGGCUUUGGAAAAUACUUCAAAU
....-...------------.(((((.((((...((....))...))))...............((((((........))))))....)))))................ ( -21.40)
>DroYak_CAF1 448 96 + 1
CAGCCGAA------------AAAAAAAGGAUAAGCCAAAAGAAAAAUCCAAUAUACAAACUGUCUGAGGGGCGGUUGACCUUUAU-GGUCUUUUCGAAAUACUUAAAAU
....((((------------((.....((((..............))))........(((((((.....)))))))((((.....-))))))))))............. ( -19.44)
>consensus
AAGCAAAA____________AAAAGAAGGAUAAGCCGAAGGGCAAAUCCAAUGCACAAAUUGUCUGAGGGGCGGUU_ACCUUUAUUGUGUUUUGGGAAAUGCUUUAAAU
.((((......................((((..(((....)))..))))...............((((((........))))))...)))).................. (-11.24 = -11.96 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:50 2006