Locus 4948

Sequence ID 2L_DroMel_CAF1
Location 14,196,672 – 14,196,787
Length 115
Max. P 0.994545
window7849 window7850 window7851

overview

Window 9

Location 14,196,672 – 14,196,764
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 89.46
Mean single sequence MFE -23.64
Consensus MFE -18.86
Energy contribution -20.38
Covariance contribution 1.52
Combinations/Pair 1.19
Mean z-score -2.49
Structure conservation index 0.80
SVM decision value 2.03
SVM RNA-class probability 0.985972
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14196672 92 + 22407834
CCCUGAGCUCUGGCCCCAAAUAGACAGUCUCUCUAUCCAAAGCUUAUGGAGGGUGUUUUUAACCCACUCAGGAUUUACACUCUUCAGACUAA
...((((((.(((......(((((.......)))))))).))))))((((((((((....((.((.....)).)).))))))))))...... ( -23.50)
>DroSec_CAF1 29607 92 + 1
CCCUGAGCUCUGGCCCCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUGGAGGGUGUUUUUAACCCACUCAGGAUUAACACUCUCCAGAAUAA
......(((.(((......(((((.......)))))))).)))...(((((((((((.....((......))...)))))))))))...... ( -23.60)
>DroSim_CAF1 21795 92 + 1
CCCUGAGCUCUGGCCCCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUGGAGGGUGUUUUUAACCCACUCAGGAUUAACACUCUCCAGAAUAA
......(((.(((......(((((.......)))))))).)))...(((((((((((.....((......))...)))))))))))...... ( -23.60)
>DroEre_CAF1 29305 91 + 1
CCCUGGGCUCUGGCCCCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUAGAGGUUUAUUUUAACCCACUGAGGAUUUA-GCUCUCCAGACUAA
...((((((.(((......(((((.......)))))))).))))))(((.((((......))))..(((..((....-..))..))).))). ( -20.60)
>DroYak_CAF1 18354 91 + 1
CCCUGGGCUCUGGCCCCAAAUAGACAUCCUCUCUAUCCAAAGCCUAUGGAGGGGGAUGUUAACCCACUGAGGACUAACACCCUAUACACUA-
((.((((((.(((......(((((.......)))))))).)))))).))..((((.(((((..((.....))..)))))))))........- ( -26.90)
>consensus
CCCUGAGCUCUGGCCCCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUGGAGGGUGUUUUUAACCCACUCAGGAUUAACACUCUCCAGACUAA
...((((((.(((......(((((.......)))))))).))))))(((((((((((.....((......))...)))))))))))...... (-18.86 = -20.38 +   1.52)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,196,672 – 14,196,764
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 89.46
Mean single sequence MFE -32.22
Consensus MFE -25.90
Energy contribution -27.30
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.75
Structure conservation index 0.80
SVM decision value 2.49
SVM RNA-class probability 0.994545
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14196672 92 - 22407834
UUAGUCUGAAGAGUGUAAAUCCUGAGUGGGUUAAAAACACCCUCCAUAAGCUUUGGAUAGAGAGACUGUCUAUUUGGGGCCAGAGCUCAGGG
.((.((....)).)).....(((((((((((.......)))).......((((..((((((.......))))))..))))....))))))). ( -28.60)
>DroSec_CAF1 29607 92 - 1
UUAUUCUGGAGAGUGUUAAUCCUGAGUGGGUUAAAAACACCCUCCAUAGGCUUUGGAUAGAGAGGCUGUCUAUUUGGGGCCAGAGCUCAGGG
.(((((....))))).....(((((((((((.......))))......(((((..((((((.......))))))..)))))...))))))). ( -34.40)
>DroSim_CAF1 21795 92 - 1
UUAUUCUGGAGAGUGUUAAUCCUGAGUGGGUUAAAAACACCCUCCAUAGGCUUUGGAUAGAGAGGCUGUCUAUUUGGGGCCAGAGCUCAGGG
.(((((....))))).....(((((((((((.......))))......(((((..((((((.......))))))..)))))...))))))). ( -34.40)
>DroEre_CAF1 29305 91 - 1
UUAGUCUGGAGAGC-UAAAUCCUCAGUGGGUUAAAAUAAACCUCUAUAGGCUUUGGAUAGAGAGGCUGUCUAUUUGGGGCCAGAGCCCAGGG
....(((((.(..(-(.(((((.....)))))................(((((..((((((.......))))))..)))))))..)))))). ( -28.90)
>DroYak_CAF1 18354 91 - 1
-UAGUGUAUAGGGUGUUAGUCCUCAGUGGGUUAACAUCCCCCUCCAUAGGCUUUGGAUAGAGAGGAUGUCUAUUUGGGGCCAGAGCCCAGGG
-.........((((((((..((.....))..))))))))((((.....(((((..((((((.......))))))..))))).......)))) ( -34.80)
>consensus
UUAGUCUGGAGAGUGUUAAUCCUGAGUGGGUUAAAAACACCCUCCAUAGGCUUUGGAUAGAGAGGCUGUCUAUUUGGGGCCAGAGCUCAGGG
....................(((((((((((.......))))......(((((..((((((.......))))))..)))))...))))))). (-25.90 = -27.30 +   1.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,196,687 – 14,196,787
Length 100
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 74.57
Mean single sequence MFE -17.78
Consensus MFE -10.66
Energy contribution -11.94
Covariance contribution 1.28
Combinations/Pair 1.22
Mean z-score -1.80
Structure conservation index 0.60
SVM decision value 0.82
SVM RNA-class probability 0.858447
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14196687 100 + 22407834
CCAAAUAGACAGUCUCUCUAUCCAAAGCUUAUGGAGGGUGUUUUUAACCCACUCAGGAUUUACACUCUUCAGACUAACAAACAAAGAUCUAGUAAUAU-----------------GU
..........((((...((......))....((((((((((....((.((.....)).)).)))))))))))))).......................-----------------.. ( -15.10)
>DroSec_CAF1 29622 86 + 1
CCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUGGAGGGUGUUUUUAACCCACUCAGGAUUAACACUCUCCAGAAUAACAAA--------------UAU-----------------AU
....(((((.......)))))..........(((((((((((.....((......))...)))))))))))..........--------------...-----------------.. ( -18.20)
>DroSim_CAF1 21810 86 + 1
CCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUGGAGGGUGUUUUUAACCCACUCAGGAUUAACACUCUCCAGAAUAACAAA--------------UAU-----------------AU
....(((((.......)))))..........(((((((((((.....((......))...)))))))))))..........--------------...-----------------.. ( -18.20)
>DroEre_CAF1 29320 99 + 1
CCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUAGAGGUUUAUUUUAACCCACUGAGGAUUUA-GCUCUCCAGACUAACAAGCAAAGAUCUAUGAUUAU-----------------GU
....(((((((((((((.((.........)).)))))))............(((..((....-..))..))).............).)))))......-----------------.. ( -14.20)
>DroYak_CAF1 18369 115 + 1
CCAAAUAGACAUCCUCUCUAUCCAAAGCCUAUGGAGGGGGAUGUUAACCCACUGAGGACUAACACCCUAUACACUA--AAACAAAGAUAUAUAUAUAUGUAUAUACCAUAUAUACGU
.......((((((((((...((((.......)))))))))))))).........(((........)))........--.............((((((((.......))))))))... ( -23.20)
>consensus
CCAAAUAGACAGCCUCUCUAUCCAAAGCCUAUGGAGGGUGUUUUUAACCCACUCAGGAUUAACACUCUCCAGACUAACAAACAAAGAU_UA____UAU_________________GU
....(((((.......)))))..........(((((((((((.....((......))...))))))))))).............................................. (-10.66 = -11.94 +   1.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:46 2006