Locus 1417

Sequence ID 3R_DroMel_CAF1
Location 4,099,776 – 4,099,936
Length 160
Max. P 0.941614
window2355 window2356 window2357

overview

Window 5

Location 4,099,776 – 4,099,896
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.07
Mean single sequence MFE -40.45
Consensus MFE -37.37
Energy contribution -37.61
Covariance contribution 0.24
Combinations/Pair 1.11
Mean z-score -1.31
Structure conservation index 0.92
SVM decision value 0.86
SVM RNA-class probability 0.867471
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4099776 120 + 27905053
UUUUUCAUCCCGGCCACUUCCUUCCGCAAAAUGUUCUCACACUUGACCCGCUGUUGGGAGACGCCCAAAGGAUCGGAUCUCGGGAACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAG
.......((((((((((((((..........(((....)))(((((((((.(.((((((..((((....))..))..)))))).).)))))))))...))))))))))).......))). ( -45.01)
>DroSec_CAF1 11653 114 + 1
UUUUUCAUCCCGGCCACUUCCUUCCGCAAAAUGUUCUCACACUUGACCCGCUGAUGGGAGACGCCCAAAGGAUCGG------GAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAG
.......((((((((((((((..........(((....)))(((((((((((((((((.....)))).....))))------....)))))))))...))))))))))).......))). ( -40.11)
>DroSim_CAF1 11693 114 + 1
UUUUUCAUCCCGGCCACUUCCUUCCGCAAAAUGUUCUCACACUUGACCCGCUGCUGGGAGACGCCCAAAGGAUCGG------GAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAG
.......((((((((((((((..........(((....)))(((((((((......(....).(((........))------)...)))))))))...))))))))))).......))). ( -40.01)
>DroEre_CAF1 11763 114 + 1
UUUUUCAUCCUAGCCACUUCCUUCCGCAAAAUGUUCUCACACUUGACCUGCUGCUGGGAGACGCCCAAAGGAUCGG------AAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAG
.......((((((((((((((..........(((....)))(((((((((...((((....).((....))..)))------....)))))))))...)))))))))).......)))). ( -36.21)
>DroYak_CAF1 11735 114 + 1
UUUUUCAUCCCCGCCACUUCCUUCCGCAAAAUGUUCUCACACUUGACCCGCUGCUGGGCGACGCCCAAAGGAUCGG------GCUACGGGUCGAGAUCGGAAGUGGUUGUGCAACAGGAG
.......(((..(((((((((..........(((....)))(((((((((((....)))...((((........))------))...))))))))...)))))))))((.....))))). ( -40.90)
>consensus
UUUUUCAUCCCGGCCACUUCCUUCCGCAAAAUGUUCUCACACUUGACCCGCUGCUGGGAGACGCCCAAAGGAUCGG______GAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAG
.......((((((((((((((..........(((....)))(((((((((((..((((.....))))..))(((........))).)))))))))...))))))))))).......))). (-37.37 = -37.61 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,099,776 – 4,099,896
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.07
Mean single sequence MFE -40.40
Consensus MFE -35.44
Energy contribution -35.96
Covariance contribution 0.52
Combinations/Pair 1.06
Mean z-score -1.38
Structure conservation index 0.88
SVM decision value 0.66
SVM RNA-class probability 0.815891
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4099776 120 - 27905053
CUCCUGUUGCUCAACCACUUCCGAUCUCGACCCGUUCCCGAGAUCCGAUCCUUUGGGCGUCUCCCAACAGCGGGUCAAGUGUGAGAACAUUUUGCGGAAGGAAGUGGCCGGGAUGAAAAA
.(((((..((.((....((((((.....((((((((...(((((((((....))))..))))).....))))))))((((((....))))))..))))))....)))))))))....... ( -42.70)
>DroSec_CAF1 11653 114 - 1
CUCCUGUUGCUCAACCACUUCCGAUCUCGACCCGUAUC------CCGAUCCUUUGGGCGUCUCCCAUCAGCGGGUCAAGUGUGAGAACAUUUUGCGGAAGGAAGUGGCCGGGAUGAAAAA
.(((((..((.((....((((((.....(((((((..(------((((....))))).(........).)))))))((((((....))))))..))))))....)))))))))....... ( -38.70)
>DroSim_CAF1 11693 114 - 1
CUCCUGUUGCUCAACCACUUCCGAUCUCGACCCGUAUC------CCGAUCCUUUGGGCGUCUCCCAGCAGCGGGUCAAGUGUGAGAACAUUUUGCGGAAGGAAGUGGCCGGGAUGAAAAA
.(((((..((.((....((((((.....(((((((...------((((....))))((........)).)))))))((((((....))))))..))))))....)))))))))....... ( -40.30)
>DroEre_CAF1 11763 114 - 1
CUCCUGUUGCUCAACCACUUCCGAUCUCGACCCGUAUU------CCGAUCCUUUGGGCGUCUCCCAGCAGCAGGUCAAGUGUGAGAACAUUUUGCGGAAGGAAGUGGCUAGGAUGAAAAA
.((((((..((......((((((.....((((.((...------((((....))))((........)).)).))))((((((....))))))..))))))..))..)).))))....... ( -34.10)
>DroYak_CAF1 11735 114 - 1
CUCCUGUUGCACAACCACUUCCGAUCUCGACCCGUAGC------CCGAUCCUUUGGGCGUCGCCCAGCAGCGGGUCAAGUGUGAGAACAUUUUGCGGAAGGAAGUGGCGGGGAUGAAAAA
.((((((..(.......((((((.....(((((((.((------((((....))))))...((...)).)))))))((((((....))))))..))))))...)..))))))........ ( -46.20)
>consensus
CUCCUGUUGCUCAACCACUUCCGAUCUCGACCCGUAUC______CCGAUCCUUUGGGCGUCUCCCAGCAGCGGGUCAAGUGUGAGAACAUUUUGCGGAAGGAAGUGGCCGGGAUGAAAAA
.(((((..((.((....((((((.....(((((((.........((((....))))((........)).)))))))((((((....))))))..))))))....)))))))))....... (-35.44 = -35.96 +   0.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,099,816 – 4,099,936
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.16
Mean single sequence MFE -42.60
Consensus MFE -38.16
Energy contribution -38.28
Covariance contribution 0.12
Combinations/Pair 1.11
Mean z-score -1.53
Structure conservation index 0.90
SVM decision value 1.32
SVM RNA-class probability 0.941614
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4099816 120 + 27905053
ACUUGACCCGCUGUUGGGAGACGCCCAAAGGAUCGGAUCUCGGGAACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAGGGGACAGCAUCUCUCCUAGGCAUCGCCAAUGUUGCUUCAA
.(((((((((.(.((((((..((((....))..))..)))))).).)))))))))..(....)...(((((((((((((((((......)))))))).(((...)))...))))).)))) ( -48.80)
>DroSec_CAF1 11693 114 + 1
ACUUGACCCGCUGAUGGGAGACGCCCAAAGGAUCGG------GAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAGGGGACAGCAUCUCUCCUAGGCAUCGCCAAUGUUGUUUCAA
.(((((((((((((((((.....)))).....))))------....)))))))))..(....)...(((((((((((((((((......)))))))).(((...)))...)))).))))) ( -41.50)
>DroSim_CAF1 11733 114 + 1
ACUUGACCCGCUGCUGGGAGACGCCCAAAGGAUCGG------GAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAGGGGACAGCAUCUCUCCUAGGCAUCGCCAAUGUUGUUUCAA
.(((((((((......(....).(((........))------)...)))))))))..(....)...(((((((((((((((((......)))))))).(((...)))...)))).))))) ( -41.40)
>DroEre_CAF1 11803 114 + 1
ACUUGACCUGCUGCUGGGAGACGCCCAAAGGAUCGG------AAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAGGGGACAGCAUCUCUUCUAGGCAUCGCCAAUGUUGUUUCAA
.(((((((((...((((....).((....))..)))------....)))))))))..(....)...((((((((((((((((((.....)))))))).(((...)))..))))).))))) ( -37.10)
>DroYak_CAF1 11775 114 + 1
ACUUGACCCGCUGCUGGGCGACGCCCAAAGGAUCGG------GCUACGGGUCGAGAUCGGAAGUGGUUGUGCAACAGGAGGGGACAGCAUCUCUUCUAGGCAUCGCCAAUGUUGUUUCAA
.(((((((((((....)))...((((........))------))...))))))))..(((...((((.((((....((((((((.....))))))))..)))).))))...)))...... ( -44.20)
>consensus
ACUUGACCCGCUGCUGGGAGACGCCCAAAGGAUCGG______GAUACGGGUCGAGAUCGGAAGUGGUUGAGCAACAGGAGGGGACAGCAUCUCUCCUAGGCAUCGCCAAUGUUGUUUCAA
.(((((((((((..((((.....))))..))(((........))).)))))))))..(....).....(((((((((((((((......)))))))).(((...)))...)))))))... (-38.16 = -38.28 +   0.12)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:57 2006