Locus 8493

Sequence ID	3L_DroMel_CAF1
Location	22,285,656 – 22,285,807
Length	151
Max. P	0.982387

overview

Window 9

Location	22,285,656 – 22,285,770
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.75
Mean single sequence MFE	-32.44
Consensus MFE	-25.25
Energy contribution	-26.19
Covariance contribution	0.94
Combinations/Pair	1.09
Mean z-score	-2.43
Structure conservation index	0.78
SVM decision value	1.27
SVM RNA-class probability	0.938275
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22285656 114 + 23771897
GGCUUCAUUUGCCAUUAUCUUGUUGCAGUUGC------AGCUCCUCCGUGCUGCUGCGGUUAGUUAGUUCGCUUUAAUUUAUCGCUGCAAACAAAUUGCGGACAUCUUUCCUGCUGCAAC
(((.......)))........((((((((.((------(((........))))).(((((.((((((......)))))).))))).((((.....))))(((......))).)))))))) ( -36.20)
>DroSec_CAF1 44037 114 + 1
GGCUUCAUUUGCCAUUAUCUUGUUGCAGUUGC------AGCUCCUCCGCGCUGCUGCGGUUAGUUAGUUCGCUUUAAUUUAUCGCUGCAAACAUUUUGCGGACAUCUUCCCUGCUGCAAC
(((.......)))........((((((((.((------(((........))))).(((((.((((((......)))))).))))).((((.....))))(((.....)))..)))))))) ( -35.00)
>DroEre_CAF1 42627 114 + 1
GGCUUCAUUUGCCAUUAUCUGGUUGCAGCUCC------AGCUCCUCCGCUCUGCUGCGGCUAUUUAGUUGGCUUUAAUUUAUCGCUGCAAACAUGUUGCGGAUAUCUUCCCUGCUGCAAG
.((..((...(((((((..((((((((((...------(((......)))..))))))))))..))).)))).........((((.(((....))).))))..........))..))... ( -34.40)
>DroYak_CAF1 8499 120 + 1
GGCUUCAUUUGCCAUUAUCUUGUUGCAGUUGCAGUUAUAGCUUCUUCGCUCUGCUCCGGUUAGUUAGUUCGCUUUAAUUUAUCGAUGCAAACAUUUUGCCGACAUCUUUCCUGCUUCAAC
(((.......)))......(((..((((..((((....(((......)))))))..((((......(((.((..............)).))).....)))).........))))..))). ( -24.14)
>consensus
GGCUUCAUUUGCCAUUAUCUUGUUGCAGUUGC______AGCUCCUCCGCGCUGCUGCGGUUAGUUAGUUCGCUUUAAUUUAUCGCUGCAAACAUUUUGCGGACAUCUUCCCUGCUGCAAC
(((.......)))........((((((((.........((....(((((..(((.(((((.((((((......)))))).))))).)))........)))))...)).....)))))))) (-25.25 = -26.19 +   0.94)

alignment

secondary structure

dotplot

Window 0

Location	22,285,690 – 22,285,807
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.80
Mean single sequence MFE	-30.04
Consensus MFE	-20.25
Energy contribution	-21.12
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-2.44
Structure conservation index	0.67
SVM decision value	1.91
SVM RNA-class probability	0.982387
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22285690 117 + 23771897
CUCCUCCGUGCUGCUGCGGUUAGUUAGUUCGCUUUAAUUUAUCGCUGCAAACAAAUUGCGGACAUCUUUCCUGCUGCAACCUGCAGCUCAUUCUCCUUUAGCUGGUACC---GCAGCUAC
............((((((((((((((((((((.........................)))))).........(((((.....)))))...........))))))..)))---)))))... ( -35.31)
>DroSec_CAF1 44071 120 + 1
CUCCUCCGCGCUGCUGCGGUUAGUUAGUUCGCUUUAAUUUAUCGCUGCAAACAUUUUGCGGACAUCUUCCCUGCUGCAACCCGCAGCUCAUUCUCCUUUAGCUGGUACCGCCGCAGCUAC
.........(((((.(((((((((((((((((.........................)))))).........(((((.....)))))...........))))))..))))).)))))... ( -38.31)
>DroEre_CAF1 42661 99 + 1
CUCCUCCGCUCUGCUGCGGCUAUUUAGUUGGCUUUAAUUUAUCGCUGCAAACAUGUUGCGGAUAUCUUCCCUGCUGCAAGCCGCAGCUUAC---------------AUU------GCUAC
.......((...(((((((((...((((.((........((((((.(((....))).)).)))).....)).))))..)))))))))....---------------...------))... ( -28.82)
>DroYak_CAF1 8539 114 + 1
CUUCUUCGCUCUGCUCCGGUUAGUUAGUUCGCUUUAAUUUAUCGAUGCAAACAUUUUGCCGACAUCUUUCCUGCUUCAACCCGCAGCUUAUCCCCUUUUUGCUGGUACU------GCUAC
.......((..(((..((((.((((((......)))))).))))..))).......(((((.((......((((........)))).............)).)))))..------))... ( -17.71)
>consensus
CUCCUCCGCGCUGCUGCGGUUAGUUAGUUCGCUUUAAUUUAUCGCUGCAAACAUUUUGCGGACAUCUUCCCUGCUGCAACCCGCAGCUCAUUCUCCUUUAGCUGGUACC______GCUAC
....(((((..(((.(((((.((((((......)))))).))))).)))........)))))..........(((((.....)))))................................. (-20.25 = -21.12 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:00 2006