Locus 5079

Sequence ID	2L_DroMel_CAF1
Location	14,508,370 – 14,508,511
Length	141
Max. P	0.987667

overview

Window 4

Location	14,508,370 – 14,508,479
Length	109
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	95.62
Mean single sequence MFE	-28.94
Consensus MFE	-26.08
Energy contribution	-26.88
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.90
SVM decision value	2.09
SVM RNA-class probability	0.987667
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14508370 109 - 22407834
-GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUGGGCGUAGCCACUUCGCCCAGCUUUUAGCUCCAGUUCCGC
-...............(((.((((..........((((((((((((........)))))).))))))((((((((.((...)).)))))))).....)))).)))..... ( -30.70)
>DroSec_CAF1 40006 109 - 1
-GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUGGGCGUAGCCACUUCGCCCAGCUUUUAGCCCCAGUUCCAC
-...(((((.......))))).((..........((((((((((((........)))))).))))))((((((((.((...)).)))))))).....))........... ( -27.10)
>DroSim_CAF1 24709 109 - 1
-GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUGGGCGUAGCCACUUCGCCCAGCUUUUAGCCCCAGUUCCAC
-...(((((.......))))).((..........((((((((((((........)))))).))))))((((((((.((...)).)))))))).....))........... ( -27.10)
>DroEre_CAF1 33479 110 - 1
CGCACGAGUAUCUGCCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUGGGCGUAGCCACUUCACCCAGCUUUCAGCUCCAGUUGCAC
............(((.(((.((((..........((((((((((((........)))))).))))))((((((.(.((...)).).)))))).....)))).))).))). ( -29.90)
>DroYak_CAF1 29422 110 - 1
CGCAAGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUGGGCGUAGCCACUUCGCCCAGCUUUCAGCUCCACUUCCAC
.((..((((.......))))..)).....(((.(((((((((((((........)))))))).....((((((((.((...)).))))))))....))))).)))..... ( -29.90)
>consensus
_GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUGGGCGUAGCCACUUCGCCCAGCUUUUAGCUCCAGUUCCAC
................(((.((((..........((((((((((((........)))))).))))))((((((((.((...)).)))))))).....)))).)))..... (-26.08 = -26.88 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	14,508,409 – 14,508,511
Length	102
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	90.41
Mean single sequence MFE	-30.14
Consensus MFE	-22.58
Energy contribution	-22.98
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.75
SVM decision value	0.37
SVM RNA-class probability	0.710649
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14508409 102 - 22407834
GGGGGC-----AUGCACAAGCGUAAGUAUCUACAUAC----GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUG
((((((-----........(((((.((....)).)))----)).(((((.......))))).)))).)).....((((((((((((........)))))).)))))).... ( -28.90)
>DroSec_CAF1 40045 98 - 1
GGGGGC-----AUGCACAAGCGUAAGUAUCUA----C----GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUG
((((((-----........(((((......))----)----)).(((((.......))))).)))).)).....((((((((((((........)))))).)))))).... ( -28.00)
>DroSim_CAF1 24748 98 - 1
GGGGGC-----AUGCACAAGCGUAAGUAUCUA----C----GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUG
((((((-----........(((((......))----)----)).(((((.......))))).)))).)).....((((((((((((........)))))).)))))).... ( -28.00)
>DroEre_CAF1 33518 111 - 1
GGGGGCAUGGCAUGCACGAGCGUAAGUAUCUGCAUACGUACGCACGAGUAUCUGCCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUG
((((((.((((((((.((.(((((.((((....)))).))))).)).)))..))))).....)))).)).....((((((((((((........)))))).)))))).... ( -38.50)
>DroYak_CAF1 29461 106 - 1
GCGGGC-----AUGCACGAGCGUAAGUAUCUACGUAUGUACGCAAGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUG
..((((-----.(((.(..(((((.((((....)))).)))))..).)))((........))))))........((((((((((((........)))))).)))))).... ( -27.30)
>consensus
GGGGGC_____AUGCACAAGCGUAAGUAUCUAC_UAC____GUACGAGUAUCUACCACUUGAGCCCACCAGUCGAGUUAACAAAGUCAAUUCAAACUUUGUUUAGCUGUUG
((((((.....((((....)))).....................(((((.......))))).)))).)).....((((((((((((........)))))).)))))).... (-22.58 = -22.98 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:26 2006