Locus 8691

Sequence ID	3L_DroMel_CAF1
Location	22,534,685 – 22,534,816
Length	131
Max. P	0.827041

overview

Window 4

Location	22,534,685 – 22,534,794
Length	109
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	92.47
Mean single sequence MFE	-34.32
Consensus MFE	-27.61
Energy contribution	-28.05
Covariance contribution	0.44
Combinations/Pair	1.12
Mean z-score	-2.09
Structure conservation index	0.80
SVM decision value	0.70
SVM RNA-class probability	0.827041
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22534685 109 - 23771897
GGUAGAAAAUAGUGAAGGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGU--GGGCCCGUAUGUGAGUGUGGCAAUUUCACAAAUUAUAAA
...........((((((..(((((((.....)))).)))..((((((((..((((((.(((.((....))--.)))..)))))).)))).)))).)))))).......... ( -34.50)
>DroSec_CAF1 18186 111 - 1
GGUAGAAAGUGGUGGCAGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGUAUGUGCCCGUGUGUGAGUGUGGCAAUUUCACAAAUUAUAAA
(((((....((((((((..(((((((.....)))).)))..)).))))))......))))).(((.(((....))).))).((((((.........))))))......... ( -32.60)
>DroSim_CAF1 19303 111 - 1
GGUAGAAAGUGGUGGCAGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGUAUGUGCCCGUGUGUGAGUGUGGCAAUUUCACAAAUUAUAAA
(((((....((((((((..(((((((.....)))).)))..)).))))))......))))).(((.(((....))).))).((((((.........))))))......... ( -32.60)
>DroEre_CAF1 17605 108 - 1
GGUAGAAAGAGCUGGAAGUCGGGGUGGAA-ACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGU--GGGCCCGUAUGUGAGUGUGGCAAUUUCGCAAAUUAUAAA
..........((.((((.((((((((...-.)))).)))).((((((((..((((((.(((.((....))--.)))..)))))).)))).)))).)))))).......... ( -37.60)
>consensus
GGUAGAAAGUGGUGGAAGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGU__GGGCCCGUAUGUGAGUGUGGCAAUUUCACAAAUUAUAAA
...........((((((..(((((((.....)))).)))..((((((((..((((((.(((.((....))...)))..)))))).)))).)))).)))))).......... (-27.61 = -28.05 +   0.44)

alignment

secondary structure

dotplot

Window 5

Location	22,534,724 – 22,534,816
Length	92
Sequences	4
Columns	93
Reading direction	reverse
Mean pairwise identity	87.79
Mean single sequence MFE	-28.43
Consensus MFE	-20.70
Energy contribution	-23.07
Covariance contribution	2.37
Combinations/Pair	1.07
Mean z-score	-1.54
Structure conservation index	0.73
SVM decision value	0.11
SVM RNA-class probability	0.588318
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22534724 92 - 23771897
GACCUGUUUCCGGGUGGCAAGAGGUAGAAAAUAGUGAAGGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGU-
.(((((....))))).(((...(((((....(((((..((.(((((((.....)))).)))....)))))))......)))))....)))..- ( -25.50)
>DroSec_CAF1 18226 93 - 1
GACCUGUUUCCGGGUGGCAAGAGGUAGAAAGUGGUGGCAGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGUA
.(((((....))))).(((...(((((....((((((((..(((((((.....)))).)))..)).))))))......)))))....)))... ( -32.00)
>DroSim_CAF1 19343 93 - 1
GACCUGUUUCCGGGUGGCAAGAGGUAGAAAGUGGUGGCAGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGUA
.(((((....))))).(((...(((((....((((((((..(((((((.....)))).)))..)).))))))......)))))....)))... ( -32.00)
>DroEre_CAF1 17644 81 - 1
GACCUG----------CCAAGAGGUAGAAAGAGCUGGAAGUCGGGGUGGAA-ACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGU-
...(((----------((....)))))........((...((((((((...-.)))).))))...))........((((.........))))- ( -24.20)
>consensus
GACCUGUUUCCGGGUGGCAAGAGGUAGAAAGUGGUGGAAGACGGGGUGAAAGACACCACUGAAUGCCCAUUAAACAUGCUGCCAACGUGCGU_
.(((((....))))).(((...(((((....((((((((..(((((((.....)))).)))..)).))))))......)))))....)))... (-20.70 = -23.07 +   2.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:26 2006