Locus 1872

Sequence ID 2L_DroMel_CAF1
Location 5,141,303 – 5,141,420
Length 117
Max. P 0.991289
window3011 window3012

overview

Window 1

Location 5,141,303 – 5,141,420
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.75
Mean single sequence MFE -35.98
Consensus MFE -26.69
Energy contribution -26.72
Covariance contribution 0.03
Combinations/Pair 1.23
Mean z-score -2.37
Structure conservation index 0.74
SVM decision value 1.94
SVM RNA-class probability 0.983251
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5141303 117 + 22407834
CACAAAGAAACCGCCUCCAAAGACUCGGAGCUCAACCGGAGGUGUCAGCACAGAUGAUGAUAAAGACGAGGCUGAUGUUGAGAUUCAGGUUGAGCUCAGCGAUGUGAAUGAGGCGCU
...........((((((.....(((((((((((((((.(((.(.(((((((((....((.......))...))).)))))).)))).))))))))))..))).))....)))))).. ( -41.30)
>DroPse_CAF1 27427 99 + 1
GAAAAAGCAACCGCCGCAAAAGACUCGGAGCUCAACCAACGAUAUC------------------GAUGAAGAUGAUGAUGAGAUCCAAGUUGAGCUCAGCGAUGUCCAUGAGGCGCG
...........((((.((...(((((((((((((((...((.((((------------------......)))).)).((.....)).)))))))))..))).)))..)).)))).. ( -29.10)
>DroEre_CAF1 23655 117 + 1
CUAAAAGAAACCGCCUCCAAAGACUCGGAGCUCAACCGAAGGUGUCAACAGGAAUGAUGAUAAGGACGAGGAUGAUGUUGAGAUUCAGGUUGAGCUCAGCGAUGUGCAUGAGGCGCU
...........((((((.....(((((((((((((((...(((.((((((.........................)))))).)))..))))))))))..))).))....)))))).. ( -37.81)
>DroYak_CAF1 23690 117 + 1
CAUAAAGAAACCGCCUCCAAAGACUCGGAGCUCAACCAAAGGUGUCAACAGAGAUGAUGAUGAAGACGAGGAUGAUGUUGAGAUUCAGGUUGAGCUCAGCGAUGUAAAUGAGGCGCU
...........((((((.....(((((((((((((((...(((.((((((.........................)))))).)))..))))))))))..))).))....)))))).. ( -37.81)
>DroAna_CAF1 25264 111 + 1
UGUAAAGAAACCGCCGCCAAAGACUCGGGGCUCAACCGAAGAUGUCGGGCGUCAGGAGGAUG------AAAACGAUGCCGAGAUUCAGGUUGAGCUCGGCGAUGUGAAGGAGGCGCU
...........((((.((....(((((((((((((((...(((.((((.((((.........------.....)))))))).)))..))))))))))..))).))...)).)))).. ( -40.74)
>DroPer_CAF1 28371 99 + 1
GAAAAAGCAACCGCCGCAAAAGACUCGGAGCUCAACCGACGAUAUC------------------GAUGAAGAUGAUGAUGAGAUCCAAGUUGAGCUCAGCGAUGUCCAUGAGGCGCG
...........((((.((...(((((((((((((((...((.((((------------------......)))).)).((.....)).)))))))))..))).)))..)).)))).. ( -29.10)
>consensus
CAAAAAGAAACCGCCGCCAAAGACUCGGAGCUCAACCGAAGAUGUCA_CAG__AUGAUGAU___GACGAAGAUGAUGUUGAGAUUCAGGUUGAGCUCAGCGAUGUGAAUGAGGCGCU
...........((((.......(((((((((((((((...(((.((((.............................)))).)))..))))))))))..))).))......)))).. (-26.69 = -26.72 +   0.03)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 5,141,303 – 5,141,420
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 76.75
Mean single sequence MFE -34.82
Consensus MFE -23.34
Energy contribution -23.31
Covariance contribution -0.03
Combinations/Pair 1.13
Mean z-score -2.89
Structure conservation index 0.67
SVM decision value 2.26
SVM RNA-class probability 0.991289
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5141303 117 - 22407834
AGCGCCUCAUUCACAUCGCUGAGCUCAACCUGAAUCUCAACAUCAGCCUCGUCUUUAUCAUCAUCUGUGCUGACACCUCCGGUUGAGCUCCGAGUCUUUGGAGGCGGUUUCUUUGUG
..((((((.......(((..((((((((((((.....))...((((((..................).))))).......))))))))))))).......))))))........... ( -37.21)
>DroPse_CAF1 27427 99 - 1
CGCGCCUCAUGGACAUCGCUGAGCUCAACUUGGAUCUCAUCAUCAUCUUCAUC------------------GAUAUCGUUGGUUGAGCUCCGAGUCUUUUGCGGCGGUUGCUUUUUC
..((((.((.((((.(((..((((((((((..(((.((...............------------------)).)))...)))))))))))))))))..)).))))........... ( -33.16)
>DroEre_CAF1 23655 117 - 1
AGCGCCUCAUGCACAUCGCUGAGCUCAACCUGAAUCUCAACAUCAUCCUCGUCCUUAUCAUCAUUCCUGUUGACACCUUCGGUUGAGCUCCGAGUCUUUGGAGGCGGUUUCUUUUAG
..((((((.......(((..((((((((((.(((..((((((.........................))))))....)))))))))))))))).......))))))........... ( -36.65)
>DroYak_CAF1 23690 117 - 1
AGCGCCUCAUUUACAUCGCUGAGCUCAACCUGAAUCUCAACAUCAUCCUCGUCUUCAUCAUCAUCUCUGUUGACACCUUUGGUUGAGCUCCGAGUCUUUGGAGGCGGUUUCUUUAUG
..((((((.......(((..((((((((((......((((((.........................)))))).......))))))))))))).......))))))........... ( -35.87)
>DroAna_CAF1 25264 111 - 1
AGCGCCUCCUUCACAUCGCCGAGCUCAACCUGAAUCUCGGCAUCGUUUU------CAUCCUCCUGACGCCCGACAUCUUCGGUUGAGCCCCGAGUCUUUGGCGGCGGUUUCUUUACA
..((((.((......(((..(.((((((((.(((..((((...((((..------.........)))).))))....)))))))))))).)))......)).))))........... ( -33.50)
>DroPer_CAF1 28371 99 - 1
CGCGCCUCAUGGACAUCGCUGAGCUCAACUUGGAUCUCAUCAUCAUCUUCAUC------------------GAUAUCGUCGGUUGAGCUCCGAGUCUUUUGCGGCGGUUGCUUUUUC
..((((.((.((((.(((..(((((((((...(((......)))........(------------------(((...))))))))))))))))))))..)).))))........... ( -32.50)
>consensus
AGCGCCUCAUGCACAUCGCUGAGCUCAACCUGAAUCUCAACAUCAUCCUCGUC___AUCAUCAU__CUG_UGACACCUUCGGUUGAGCUCCGAGUCUUUGGAGGCGGUUUCUUUUUG
..((((.(.......(((..((((((((((((.....))...........(((..................)))......))))))))))))).......).))))........... (-23.34 = -23.31 +  -0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:27 2006