Locus 3834

Sequence ID	2R_DroMel_CAF1
Location	12,654,794 – 12,654,974
Length	180
Max. P	0.996195

overview

Window 7

Location	12,654,794 – 12,654,900
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	92.73
Mean single sequence MFE	-33.52
Consensus MFE	-29.48
Energy contribution	-29.60
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-2.03
Structure conservation index	0.88
SVM decision value	2.52
SVM RNA-class probability	0.994876
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12654794 106 + 20766785
GAAUCUAGCUUGGCUUAUAUGUUGCUGAUUUCUCAGUCUAAAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAAAGCCAAAGCCACUCUCUCUG
......((..((((((.............(((.(((...((((((.....))))))...))))))((((((((.((...)).)))))))).))))))..))..... ( -31.60)
>DroSec_CAF1 12945 106 + 1
GAAUCUAGCUUGGCUUAUAAGUUGCUGAUUUCUCAGUCUAAAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUG
....(((((((((((....))))(((((....)))))...))))))).(((((((((.....)))))))))((((((((((((..........)))).)))))))) ( -32.90)
>DroSim_CAF1 14625 106 + 1
GAAUCUAGCUUGGCUUAUAAGUUGCCGAUUUCUCAGUCUAAAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUG
....((((((((((.........)))(((......)))..))))))).(((((((((.....)))))))))((((((((((((..........)))).)))))))) ( -33.60)
>DroEre_CAF1 11949 104 + 1
GAAUCGAGCUGGGCUUAUA-GUUGCUAAUUUCUCAGUCAAAAGCUGGCAAAGCUUCCAUC-GGAGGGCUUUCGGAGAGAUUGCGAGAAGCAAAGCAACUCUCUCUG
.......(((..((((...-.((((.((((((((.((((.....))))(((((((((...-))).))))))..)))))))))))).))))..)))........... ( -31.50)
>DroYak_CAF1 13872 105 + 1
GAAUCGAGCUAGGCUUAUA-GUUGCCAAUUUCUCAGCCAAAAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUGGCGAGAACCAAAGCCACUCUCUCUG
.....(((((.(((.....-...)))...(((.(((..(((((((.....)))))))..))))))))))).((((((((((((..........)))).)))))))) ( -38.00)
>consensus
GAAUCUAGCUUGGCUUAUA_GUUGCUGAUUUCUCAGUCUAAAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUG
......((((.(((.........)))...(((.(((...((((((.....))))))...))))))))))..((((((((((((..........)))).)))))))) (-29.48 = -29.60 +   0.12)

alignment

secondary structure

dotplot

Window 8

Location	12,654,834 – 12,654,934
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	89.80
Mean single sequence MFE	-27.40
Consensus MFE	-24.72
Energy contribution	-24.88
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-2.10
Structure conservation index	0.90
SVM decision value	2.67
SVM RNA-class probability	0.996195
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12654834 100 + 20766785
AAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAAAGCCAAAGCCACUCUCUCUGAUCGUUUUUAAAAGACAAUACUUAAAAUUUACCA
(((((.....)))))...(((.((((((..(((((((((((((....).)))......)))))))))..))))))...)))................... ( -25.30)
>DroSec_CAF1 12985 100 + 1
AAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUGAUCGUUUUUAAAAGACAAUACCGAAAAUUGACCA
(((((.....)))))...(((.((((((..(((((((((((((..........)))).)))))))))..))))))...)))((((.......)))).... ( -28.20)
>DroSim_CAF1 14665 100 + 1
AAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUGAUCGUUUUUAAAAGACAAUACCGAAAAUUGACCA
(((((.....)))))...(((.((((((..(((((((((((((..........)))).)))))))))..))))))...)))((((.......)))).... ( -28.20)
>DroEre_CAF1 11988 99 + 1
AAGCUGGCAAAGCUUCCAUC-GGAGGGCUUUCGGAGAGAUUGCGAGAAGCAAAGCAACUCUCUCUGAUCGUUUUUUAACUACAAUUUCAAAAGUUGACCA
(((((.....))))).....-(((((((..(((((((((((((..........)))).)))))))))..)))))((((((...........)))))))). ( -27.60)
>DroYak_CAF1 13911 100 + 1
AAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUGGCGAGAACCAAAGCCACUCUCUCUGAUCGUUUUGAAACUACAAUUUUAACAAUGUACCU
(((((.....)))))......(((((((..(((((((((((((..........)))).)))))))))..))))).....((((..........)))))). ( -27.70)
>consensus
AAGCUGGCAAAGCUUUUAUCUGGAGGGCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUGAUCGUUUUUAAAAGACAAUACCAAAAAUUGACCA
(((((.....))))).......((((((..(((((((((((((..........)))).)))))))))..))))))......................... (-24.72 = -24.88 +   0.16)

alignment

secondary structure

dotplot

Window 9

Location	12,654,860 – 12,654,974
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	88.77
Mean single sequence MFE	-26.58
Consensus MFE	-21.74
Energy contribution	-22.50
Covariance contribution	0.76
Combinations/Pair	1.04
Mean z-score	-1.88
Structure conservation index	0.82
SVM decision value	1.11
SVM RNA-class probability	0.916586
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12654860 114 + 20766785
GCUUUCGGAGAGAUUGCGAAAGCCAAAGCCACUCUCUCUGAUCGUUUUUAAAAGACAAUACUUAAAAUUUACCAAAUGUAUUAACUUGACCAGUAAAUAUUGGUUAGCCAUCAG
((..(((((((((((((....).)))......)))))))))..))...........(((((................)))))...(((((((((....)))))))))....... ( -23.69)
>DroSec_CAF1 13011 114 + 1
GCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUGAUCGUUUUUAAAAGACAAUACCGAAAAUUGACCAAAUGUAUUAACUUGACCAGUAAAUAUUGGUUAGCCAUCAG
((..(((((((((((((..........)))).)))))))))..)).................((...(((((((...(((((.(((.....))).))))))))))))...)).. ( -26.90)
>DroSim_CAF1 14691 114 + 1
GCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUGAUCGUUUUUAAAAGACAAUACCGAAAAUUGACCAAAUGUAUUAACUUGACCAGUAAAUAUUGGUUAGCCAUCAG
((..(((((((((((((..........)))).)))))))))..)).................((...(((((((...(((((.(((.....))).))))))))))))...)).. ( -26.90)
>DroEre_CAF1 12013 114 + 1
GCUUUCGGAGAGAUUGCGAGAAGCAAAGCAACUCUCUCUGAUCGUUUUUUAACUACAAUUUCAAAAGUUGACCAUAUGCAUUAGCAUGUCCAGUAAACAUUAGUUAGCCAUCAG
((..(((((((((((((..........)))).)))))))))..))...((((((((((((.....)))))...((((((....))))))...........)))))))....... ( -28.10)
>DroYak_CAF1 13937 114 + 1
GCUUUCGGAGAGAUGGCGAGAACCAAAGCCACUCUCUCUGAUCGUUUUGAAACUACAAUUUUAACAAUGUACCUUAUGUAUUAACAUGUCCAGUAAAUAUUGGUAAGCCAUCAG
(((.(((((((((((((..........)))).))))))))).((((((((((......)))))).))))((((....(((((.((.......)).))))).)))))))...... ( -27.30)
>consensus
GCUUUCGGAGAGAUUGCGAGAACCAAAGCAACUCUCUCUGAUCGUUUUUAAAAGACAAUACCAAAAAUUGACCAAAUGUAUUAACUUGACCAGUAAAUAUUGGUUAGCCAUCAG
((..(((((((((((((..........)))).))))))))).............................................((((((((....))))))))))...... (-21.74 = -22.50 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:05 2006