Locus 438

Sequence ID	2R_DroMel_CAF1
Location	2,524,347 – 2,524,497
Length	150
Max. P	0.794549

overview

Window 3

Location	2,524,347 – 2,524,457
Length	110
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	81.56
Mean single sequence MFE	-36.35
Consensus MFE	-21.40
Energy contribution	-20.90
Covariance contribution	-0.50
Combinations/Pair	1.21
Mean z-score	-2.03
Structure conservation index	0.59
SVM decision value	0.27
SVM RNA-class probability	0.660364
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2524347 110 + 20766785
GAAAACAAAAGACUGCGUAGUACGUGUGGAAAAGUGUUGUGCAAGGGA--------GUCGGGCGGCGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCA
..............(((.....)))(.((((((((.(((..(.(((((--------(..(((.((((((.....)))))).)))...))))))......)..)))...))))))))). ( -35.70)
>DroSim_CAF1 2457 118 + 1
GAAAACAAAAGACUGCGUAGUACGUGUGGAAAAGUGUUGUGCAAGGAGUGCGGGGCGGAGGGUGAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAGAGUGCAGUGAACUUUUCCCA
..............(((.....)))(.((((((((....((((....((.(((((.((((((.(((((((.....))))))))))))).)))))))....))))....))))))))). ( -43.30)
>DroEre_CAF1 4830 102 + 1
GAAAACAAAAGACUGCGCAGUAUGCGAAGAAAAGUGGG------GGCA--------AUGGG--AAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCA
.....((.....((.(((.....))).)).....))..------....--------.((((--((((.((.((((((((((..((........))..)))))))))).)))))))))) ( -30.40)
>DroYak_CAF1 2506 104 + 1
GAAAAUAAAAGACUGCGUAGUACGUGAUGAAAAGUACG------GGCA--------GUGGGGAAAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCU
...........(((((...((((..........)))).------.)))--------))(((((((((....((((((((((..((........))..))))))))))..))))))))) ( -36.00)
>consensus
GAAAACAAAAGACUGCGUAGUACGUGAGGAAAAGUGUG______GGCA________GUGGGG_AAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCA
..............(((.....)))..................................(((.((((.((.((((((((((..((........))..)))))))))).))))))))). (-21.40 = -20.90 +  -0.50)

alignment

secondary structure

dotplot

Window 4

Location	2,524,385 – 2,524,497
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.74
Mean single sequence MFE	-36.58
Consensus MFE	-24.08
Energy contribution	-24.57
Covariance contribution	0.50
Combinations/Pair	1.08
Mean z-score	-2.03
Structure conservation index	0.66
SVM decision value	0.60
SVM RNA-class probability	0.794549
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2524385 112 + 20766785
GUGCAAGGGA--------GUCGGGCGGCGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCAUUUUCCCCACUUGAAUCUUCGAGUCCCAUUGACGCGGCCU
((((((((((--------.(((((..(...((.((((((((((..((........))..)))))))))).)).)..))).............((....)))).)))).))).)))..... ( -33.60)
>DroSim_CAF1 2495 120 + 1
GUGCAAGGAGUGCGGGGCGGAGGGUGAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAGAGUGCAGUGAACUUUUCCCAUUUUCCCCACUUGAAUCUUCGAGCCCCAUUGACGCGGCCU
((((((((.(.((((((..((.((.((((.((.((((((((((..((........))..)))))))))).)).)))))).))..))))..((((....))))))))).))).)))..... ( -41.70)
>DroEre_CAF1 4868 103 + 1
------GGCA--------AUGGG--AAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCAUU-UCCCCACUUGAAUCUUCGAGCCCCCUUCACGCGUCCU
------((.(--------(((((--((((.((.((((((((((..((........))..)))))))))).))))))))))))-.))...(((((....)))))................. ( -33.60)
>DroYak_CAF1 2544 104 + 1
------GGCA--------GUGGGGAAAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCUUU-U-CCCACUUGAAUCUUCGAGUCCCAUUGACGCGGCCU
------(((.--------(((((((((((....((((((((((..((........))..))))))))))..))))))))...-.-...((((((....))))))........))).))). ( -37.40)
>consensus
______GGCA________GUGGGG_AAAGCGUAUGCUGCGCUUCCUCUUCUCCUUGACAAAGUGCAGUGAACUUUUCCCAUU_UCCCCACUUGAAUCUUCGAGCCCCAUUGACGCGGCCU
.....................((((...((((..(((((((((..((........))..))))))))).....................(((((....)))))........)))).)))) (-24.08 = -24.57 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:35 2006