Locus 2966

Sequence ID	2L_DroMel_CAF1
Location	8,503,843 – 8,503,996
Length	153
Max. P	0.908374

overview

Window 2

Location	8,503,843 – 8,503,958
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.56
Mean single sequence MFE	-31.75
Consensus MFE	-23.68
Energy contribution	-24.24
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.81
Structure conservation index	0.75
SVM decision value	0.10
SVM RNA-class probability	0.582659
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8503843 115 - 22407834
AUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG-----GGGUGUUAAAAGUCAAGUGAAGUGGGCUUUAUGUAGUGCGUAGCA
((((((.....))))))(((.((((..(((...(((((((((((((....)))))))))(((..(..(..-----((.(......).))..)..)..)))))))....))).))))))). ( -30.70)
>DroSec_CAF1 13160 115 - 1
AUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG-----GGGUGUUAAAAGUCAAGUGAAGGGGGCUUUAUGUAGUGCGUAACA
......(((((..........((((((((((((..(.(((((((((....))))))))).).)))))..)-----))))))......((....))...)))))(((((.....))))).. ( -29.00)
>DroSim_CAF1 12763 115 - 1
AUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG-----GGGUGUUAAAAGUCAAGUGAAGGGGGCUUUAUGUACUGCGAACUA
((((((.....))))))((((((((((((((((..(.(((((((((....))))))))).).)))))..)-----))))))....(((...((((((....))))))..)))..)))).. ( -30.20)
>DroEre_CAF1 12757 114 - 1
AUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCGCAAAUACCAG-----GGGUGUUAAAAGUCAAGUGAAG-GGGCUUUAUGUAGUGCGUAACA
((((((.....))))))......((((((..(((((((((((((((....))))))))))).((((((..-----.)))))).....))))....))-)))).(((((.....))))).. ( -35.70)
>DroYak_CAF1 13514 119 - 1
AUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUACCCAGGCCUGGAUGUUAAAAGUCAAACGAGG-GGGCUUUAUGUAGUGCGUAACA
((((((.....))))))..((((((..(((...(((((((((((((....))))))))).......(((.......(((.......))).......)-))))))....))).)))))).. ( -33.14)
>consensus
AUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG_____GGGUGUUAAAAGUCAAGUGAAG_GGGCUUUAUGUAGUGCGUAACA
((((((.....))))))..((((((..(((....((((((((((((....)))))))))........((......)).........)))..((((((....)))))).))).)))))).. (-23.68 = -24.24 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	8,503,883 – 8,503,996
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.11
Mean single sequence MFE	-31.24
Consensus MFE	-23.62
Energy contribution	-23.66
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.30
Structure conservation index	0.76
SVM decision value	1.06
SVM RNA-class probability	0.908374
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8503883 113 - 22407834
UCCCCAAAACGAAC--CCUGCAUGAAUUUAAUUGAGCACGAUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG-----GGGUG
............((--(((((((((.......((((((...(((((.....))))))))))).((((......))))(((((((((....))))))))))))...)).))-----)))). ( -31.10)
>DroSec_CAF1 13200 113 - 1
UCCCCAAAACGAAC--CCUGCAUGAAUUUAAUUGAGCACGAUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG-----GGGUG
............((--(((((((((.......((((((...(((((.....))))))))))).((((......))))(((((((((....))))))))))))...)).))-----)))). ( -31.10)
>DroSim_CAF1 12803 113 - 1
UCCCCAAAAUGAAC--CCUGCAUGAAUUUAAUUGAGCACGAUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG-----GGGUG
............((--(((((((((.......((((((...(((((.....))))))))))).((((......))))(((((((((....))))))))))))...)).))-----)))). ( -31.10)
>DroEre_CAF1 12796 113 - 1
--CCCCAAACGACCCUGCUGCAUGUAUUUAAUUGGGCACGAUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCGCAAAUACCAG-----GGGUG
--..........(((((......((((((....((((((.((((((.....))))))))....))))........(((((((((((....))))))))))))))))))))-----))... ( -34.60)
>DroYak_CAF1 13553 117 - 1
--CCCCAAACGACU-GCCUGCAUGAAUUUAAUUGAGCACGAUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUACCCAGGCCUGGAUG
--............-(((((............((((((...(((((.....))))))))))).((((......))))(((((((((....))))))))).........)))))....... ( -28.30)
>consensus
UCCCCAAAACGAAC__CCUGCAUGAAUUUAAUUGAGCACGAUUUUCAGUCCGAAAAUGUUUACGCCUCUAAUUGGGCGAGUUUAUGAAUUCAUAAACUCUCAAAUUGCCG_____GGGUG
..(((...........................((((((...(((((.....))))))))))).((((......))))(((((((((....)))))))))................))).. (-23.62 = -23.66 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:50 2006