Locus 3289

Sequence ID	2R_DroMel_CAF1
Location	11,229,113 – 11,229,214
Length	101
Max. P	0.940215

overview

Window 5

Location	11,229,113 – 11,229,214
Length	101
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	92.04
Mean single sequence MFE	-33.80
Consensus MFE	-28.39
Energy contribution	-28.70
Covariance contribution	0.31
Combinations/Pair	1.07
Mean z-score	-2.29
Structure conservation index	0.84
SVM decision value	1.28
SVM RNA-class probability	0.940215
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11229113 101 + 20766785
UCCAUCCGCCGAUGCUGUU------------GCUAUUGGCAUUGCCAUUGCCAUUGCUGCUGCGCUUUGUAUUGUGUGCAACUUUGUUGGCAAUAACAAUAACAAUUGCCAGA
.......((((((((....------------)).))))))((((..(((((((.....(.(((((..........))))).).....)))))))..))))............. ( -28.20)
>DroSec_CAF1 16063 113 + 1
UCCAUCCGCCGAUGCUGUUGCCAUUGCCAUUGCUAUUGGCAUUGGCAUUGCCAUUGCUGCUGCGCUUUGUAUUGUGUGCAACUUUGUUGGCAAUAACAAUAACAAUUGCCAGA
.......((.(((((...(((((.(((((.......))))).)))))..).))))))..(((.((.(((((((((.((((((...))).)))...))))).))))..))))). ( -35.50)
>DroSim_CAF1 17610 113 + 1
UCCAUCCGCCGGUGCUGUUGCCAUUGCCAUUGCUAUUGGCAUUGGCAUUGCCAUUGCUGCUGCGCUUUGUAUUGUGUGCAACUUUGUUGGCAAUAACAAUAACAAUUGCCAGA
..........(((..((((((((.(((((.......))))).))))(((((((.....(.(((((..........))))).).....)))))))......))))...)))... ( -35.90)
>DroEre_CAF1 16289 113 + 1
UCCAUCCGGCGAUGCUGUUGCCAUUGCCAUUGCCAUUGCCAUUGGCAUUGCCAUUGCUGCUGCGCUUUGUAUUGUGUGCAACUUUGUAGGCAAUAACAAUAACAAUUGCCAGA
.......((((((..(((((..((((((..(((((.......)))))....((..(.(((.((((........))))))).)..))..))))))..)))))...))))))... ( -35.60)
>consensus
UCCAUCCGCCGAUGCUGUUGCCAUUGCCAUUGCUAUUGGCAUUGGCAUUGCCAUUGCUGCUGCGCUUUGUAUUGUGUGCAACUUUGUUGGCAAUAACAAUAACAAUUGCCAGA
.......((((((((.((.((....)).)).)).))))))((((..(((((((.....(.(((((..........))))).).....)))))))..))))............. (-28.39 = -28.70 +   0.31)

alignment

secondary structure

dotplot

Window 6

Location	11,229,113 – 11,229,214
Length	101
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	92.04
Mean single sequence MFE	-38.80
Consensus MFE	-28.58
Energy contribution	-28.95
Covariance contribution	0.37
Combinations/Pair	1.00
Mean z-score	-4.05
Structure conservation index	0.74
SVM decision value	0.47
SVM RNA-class probability	0.749836
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11229113 101 - 20766785
UCUGGCAAUUGUUAUUGUUAUUGCCAACAAAGUUGCACACAAUACAAAGCGCAGCAGCAAUGGCAAUGGCAAUGCCAAUAGC------------AACAGCAUCGGCGGAUGGA
.(((((.((((.((((((((((((((.....(((((.(..........).))))).....)))))))))))))).)))).))------------..)))((((....)))).. ( -33.10)
>DroSec_CAF1 16063 113 - 1
UCUGGCAAUUGUUAUUGUUAUUGCCAACAAAGUUGCACACAAUACAAAGCGCAGCAGCAAUGGCAAUGCCAAUGCCAAUAGCAAUGGCAAUGGCAACAGCAUCGGCGGAUGGA
((((.(...((((.((((((((((((.....(((((.(..........).))))).(((.((((...)))).))).........)))))))))))).))))..).)))).... ( -39.00)
>DroSim_CAF1 17610 113 - 1
UCUGGCAAUUGUUAUUGUUAUUGCCAACAAAGUUGCACACAAUACAAAGCGCAGCAGCAAUGGCAAUGCCAAUGCCAAUAGCAAUGGCAAUGGCAACAGCACCGGCGGAUGGA
((((.(...((((.((((((((((((.....(((((.(..........).))))).(((.((((...)))).))).........)))))))))))).))))..).)))).... ( -38.30)
>DroEre_CAF1 16289 113 - 1
UCUGGCAAUUGUUAUUGUUAUUGCCUACAAAGUUGCACACAAUACAAAGCGCAGCAGCAAUGGCAAUGCCAAUGGCAAUGGCAAUGGCAAUGGCAACAGCAUCGCCGGAUGGA
((((((.((((((((((((((((((......(((((.(..........).))))).....((((...))))..))))))))))))))))))(....)......)))))).... ( -44.80)
>consensus
UCUGGCAAUUGUUAUUGUUAUUGCCAACAAAGUUGCACACAAUACAAAGCGCAGCAGCAAUGGCAAUGCCAAUGCCAAUAGCAAUGGCAAUGGCAACAGCAUCGGCGGAUGGA
((((.(.((((..((((..(((((((.....(((((.(..........).))))).....)))))))..))))..)))).((....((....))....))...).)))).... (-28.58 = -28.95 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:54 2006