Locus 6857

Sequence ID	X_DroMel_CAF1
Location	17,101,454 – 17,101,562
Length	108
Max. P	0.787120

overview

Window 1

Location	17,101,454 – 17,101,562
Length	108
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	87.52
Mean single sequence MFE	-33.23
Consensus MFE	-24.51
Energy contribution	-25.45
Covariance contribution	0.94
Combinations/Pair	1.15
Mean z-score	-1.42
Structure conservation index	0.74
SVM decision value	-0.00
SVM RNA-class probability	0.531966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17101454 108 + 22224390
CAAGUUGGUAAACUAUUUUCCUAACUCUGCUCAGCUGCCUGUUAGGCAAUUGAGAGUUGGAAAGGCCUGACCAAAU---UCAUGGCGUUUUGCUGGUCUAUAAUUUUGGCG
..(((..(((((...((((((.(((((...((((.((((.....)))).)))))))))))))))((((((......---))).)))..)))))..).))............ ( -30.90)
>DroSec_CAF1 108267 108 + 1
CAAGUUGGCAAACGAUUUUCCUAACUCUGCUCAGCGGCCUGUUAGGCAAUUGAGAGUUGGAAAAGCCUGACCAAAU---UCAUGGCGUUUUGCUGGCCUGUAAUUUUGGCG
((.((..((((((..((((((.(((((...((((..(((.....)))..)))))))))))))))((((((......---))).)))).)))))..)).))........... ( -35.20)
>DroSim_CAF1 98995 108 + 1
CAAGUUGGCAAACGAUUUUCCUAACUCUGCUCAGCGGCCUGUUAGGCAAUUGAGAGUUGGAAAAGCCUGACCAAAU---UCAUGGCGUUUUGCUGGCCUGUAAUUUUGGCG
((.((..((((((..((((((.(((((...((((..(((.....)))..)))))))))))))))((((((......---))).)))).)))))..)).))........... ( -35.20)
>DroYak_CAF1 103749 103 + 1
UAAGUUGGCUAACGAUUUUCCUGACUCC--------GCCUGUUAGGCAAUUGGGAGUGGGAAACGGCUGACCAAGUGUGUGGUGGCGUUUUGCUGGCCUGUAAUUUUGGCG
...((..((.(((...((((((.(((((--------(((.....))).....)))))))))))..(((.((((......))))))))))..))..)).............. ( -31.60)
>consensus
CAAGUUGGCAAACGAUUUUCCUAACUCUGCUCAGCGGCCUGUUAGGCAAUUGAGAGUUGGAAAAGCCUGACCAAAU___UCAUGGCGUUUUGCUGGCCUGUAAUUUUGGCG
......(((((((..((((((.((((((...(((..(((.....)))..)))))))))))))))((((((.........))).)))).)))))).(((.........))). (-24.51 = -25.45 +   0.94)

alignment

secondary structure

dotplot

Window 2

Location	17,101,454 – 17,101,562
Length	108
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	87.52
Mean single sequence MFE	-27.82
Consensus MFE	-21.57
Energy contribution	-21.94
Covariance contribution	0.38
Combinations/Pair	1.04
Mean z-score	-1.82
Structure conservation index	0.78
SVM decision value	0.58
SVM RNA-class probability	0.787120
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17101454 108 - 22224390
CGCCAAAAUUAUAGACCAGCAAAACGCCAUGA---AUUUGGUCAGGCCUUUCCAACUCUCAAUUGCCUAACAGGCAGCUGAGCAGAGUUAGGAAAAUAGUUUACCAACUUG
.....(((((((.(((((((.....)).....---...))))).....(((((((((((((.(((((.....))))).)))...))))).))))))))))))......... ( -27.00)
>DroSec_CAF1 108267 108 - 1
CGCCAAAAUUACAGGCCAGCAAAACGCCAUGA---AUUUGGUCAGGCUUUUCCAACUCUCAAUUGCCUAACAGGCCGCUGAGCAGAGUUAGGAAAAUCGUUUGCCAACUUG
.............(((.(((.....(((.(((---......))))))((((((((((((((...(((.....)))...)))...))))).))))))..))).)))...... ( -29.30)
>DroSim_CAF1 98995 108 - 1
CGCCAAAAUUACAGGCCAGCAAAACGCCAUGA---AUUUGGUCAGGCUUUUCCAACUCUCAAUUGCCUAACAGGCCGCUGAGCAGAGUUAGGAAAAUCGUUUGCCAACUUG
.............(((.(((.....(((.(((---......))))))((((((((((((((...(((.....)))...)))...))))).))))))..))).)))...... ( -29.30)
>DroYak_CAF1 103749 103 - 1
CGCCAAAAUUACAGGCCAGCAAAACGCCACCACACACUUGGUCAGCCGUUUCCCACUCCCAAUUGCCUAACAGGC--------GGAGUCAGGAAAAUCGUUAGCCAACUUA
.............(((.(((.....((.((((......))))..))..(((((.(((((.....(((.....)))--------)))))..)))))...))).)))...... ( -25.70)
>consensus
CGCCAAAAUUACAGGCCAGCAAAACGCCAUGA___AUUUGGUCAGGCUUUUCCAACUCUCAAUUGCCUAACAGGCCGCUGAGCAGAGUUAGGAAAAUCGUUUGCCAACUUG
.............(((.(((.....((((.........))))......(((((((((((.....(((.....)))........)))))).)))))...))).)))...... (-21.57 = -21.94 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:32 2006