Locus 9955

Sequence ID	3R_DroMel_CAF1
Location	26,680,808 – 26,680,959
Length	151
Max. P	0.997661

overview

Window 3

Location	26,680,808 – 26,680,928
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-34.28
Consensus MFE	-31.26
Energy contribution	-31.54
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-2.32
Structure conservation index	0.91
SVM decision value	2.90
SVM RNA-class probability	0.997661
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26680808 120 - 27905053
GAAUACACUCAUCUCUGUUUAUUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUUGCCAGCGAAAACUCAUUUACCUCCGGCUGCACGUUGCUUGGCCAUUGUGA
..................((((..(((((((.(((((..((((((...(....)...))))))((((...(....)((....))..........))))....))))))))))))..)))) ( -31.60)
>DroSec_CAF1 271408 120 - 1
GAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAAACUCAUUUACCUCCGGCUGCACGUUGGUUGGCCAUUGUGA
..................((((..((((((((.((((..((((((...(....)...))))))((((((((....))))...............))))....))))))))))))..)))) ( -35.06)
>DroSim_CAF1 268174 120 - 1
GAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAAACUCAUUUACCUCCGGCUGCACGUUGGUUGGCCAUUGUGA
..................((((..((((((((.((((..((((((...(....)...))))))((((((((....))))...............))))....))))))))))))..)))) ( -35.06)
>DroEre_CAF1 287310 120 - 1
GAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCGGCGAAAACUCAUUUACCUCCGGCUGCACGUUGGUUGGCCAUUGUGA
..................((((..((((((((.((((..((((((...(....)...)))))).((....(((((.(.............).))))).))..))))))))))))..)))) ( -38.22)
>DroYak_CAF1 276390 120 - 1
GAAUACACUCAUAUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAAACUCAUUUACCUCCGGCUGCACGUUGCUCGGCCAUUGUGA
..................((((..(((((...(((((..((((((...(....)...))))))((((((((....))))...............))))....)))))..)))))..)))) ( -31.46)
>consensus
GAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAAACUCAUUUACCUCCGGCUGCACGUUGGUUGGCCAUUGUGA
..................((((..((((((((.((((..((((((...(....)...))))))((((((((....))))...............))))....))))))))))))..)))) (-31.26 = -31.54 +   0.28)

alignment

secondary structure

dotplot

Window 4

Location	26,680,848 – 26,680,959
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.59
Mean single sequence MFE	-30.24
Consensus MFE	-25.99
Energy contribution	-26.27
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	0.86
SVM decision value	0.23
SVM RNA-class probability	0.642909
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26680848 111 - 27905053
UCAUCGCUACUGCCAUG---------GAUGUGUGUCAGUGGAAUACACUCAUCUCUGUUUAUUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUUGCCAGCGAAA
...(((((.....((.(---------((((.((((.........)))).))))).))........(((.((.((.....((((((...(....)...)))))).)).)).)))))))).. ( -29.20)
>DroSec_CAF1 271448 111 - 1
UCAUCGCUACUGCCAUG---------GAUGUGUGUCAGUGGAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAA
...(((((.....((.(---------((((.((((.........)))).))))).))........(((.((.((.....((((((...(....)...)))))).)).)).)))))))).. ( -29.20)
>DroSim_CAF1 268214 111 - 1
UCAUCGCCACUGCCAUG---------GAUGUGUGUCAGUGGAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAA
...((((......((.(---------((((.((((.........)))).))))).)).......((((.((.((.....((((((...(....)...)))))).)).)).)))))))).. ( -28.50)
>DroEre_CAF1 287350 111 - 1
UCAUCGCUAUUGCCAUG---------GAUGUGUGUCAGUGGAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCGGCGAAA
...(((((.....((.(---------((((.((((.........)))).))))).))........(((.((.((.....((((((...(....)...)))))).)).)).)))))))).. ( -29.20)
>DroYak_CAF1 276430 120 - 1
UCAUCGCUAUUGCCAUGGAAUGGAUGGAUGUGUGUCAGUGGAAUACACUCAUAUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAA
...(((((...((((.((..((((((((((((....((((.....)))))))))))))))))).))))...........((((((...(....)...))))))..........))))).. ( -35.10)
>consensus
UCAUCGCUACUGCCAUG_________GAUGUGUGUCAGUGGAAUACACUCAUCUCUGUUUACUUUGGCCAACGCAAUUCGAACAAUUUGGCAACUGUUUGUUCAGCCUUCGCCAGCGAAA
...(((((...((((...........((((.((((.........)))).))))...........))))...........((((((...(....)...))))))..........))))).. (-25.99 = -26.27 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:45:37 2006