Locus 3116

Sequence ID 2L_DroMel_CAF1
Location 8,864,126 – 8,864,301
Length 175
Max. P 0.755266
window4953 window4954 window4955

overview

Window 3

Location 8,864,126 – 8,864,221
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 70.60
Mean single sequence MFE -28.78
Consensus MFE -14.57
Energy contribution -14.05
Covariance contribution -0.52
Combinations/Pair 1.52
Mean z-score -1.61
Structure conservation index 0.51
SVM decision value 0.41
SVM RNA-class probability 0.723949
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8864126 95 - 22407834
GGGCCACGCCGAUCAUCACGAAACUGAUAAUGAGCGGGCUCAAGUCGUGGAUGAAAUGGCAGCCAAACAAGGUGGUACACACAACCACCAGACCU
(((((.(((..((.((((......)))).))..))))))))..(((.(((.((......)).))).....((((((.......)))))).))).. ( -31.10)
>DroSec_CAF1 74363 95 - 1
GGGCCACGCCGAUCAUCACGAAACUAAUAGUGAGCGGGCUCAAAUCGUCAAUGAGAUGGCAGCCAAACAAGGUGGUACACACAACCACCAGACCC
(((((.(((......((((..........)))))))))))).....(((.......(((...))).....((((((.......)))))).))).. ( -27.70)
>DroSim_CAF1 72867 95 - 1
AGGCCACGCCGAUCAUCACGAAACUGAUAGUGAGCGGGCUCAAAUCGUCAAUGAGAUGGCAGCCAAACAAGGUGGUACACACAACCACCAGACCC
.(((...((((.((((.((((.((.....))(((....)))...))))..))))..)))).)))......((((((.......))))))...... ( -27.80)
>DroEre_CAF1 78630 95 - 1
GGGCCACGCCGAUCAUCACGAAGCUGACGACGAGUGUGCUCAACUUGUCGAUAAGAUAGCAACCGAACAAAGUGGUGCAGACAACCACUACAGCC
.(((...)))............((((.((((((((.......))))))))....................((((((.......)))))).)))). ( -27.30)
>DroYak_CAF1 76576 95 - 1
GCGCCACGCCGAUCAUCACGCCAAUGAUGACGAACGUGGUCAAGUCGUCAAUCAGAUAGGUGCCGAACAAGGUGGUGCACACAACCACCACGCUA
((((((((.((.((((((......))))))))..))))))....(((...(((.....)))..)))....((((((.......))))))..)).. ( -30.00)
>DroAna_CAF1 76046 95 - 1
GAGUCACGCCGAAGACGGCCAGAACCAAGGGCAGCGUCCCUAGGCCAGUAGCGGAUUGGGCACCACCCAACGUAGUCAUGGCCACCACGAAGCAU
(..((..((((....))))........((((......)))).(((((...(((...((((.....)))).))).....))))).....))..).. ( -28.80)
>consensus
GGGCCACGCCGAUCAUCACGAAACUGAUAAUGAGCGGGCUCAAGUCGUCAAUGAGAUGGCAGCCAAACAAGGUGGUACACACAACCACCAGACCC
.(((..(((.....((((......)))).....)))........(((((.....)))))..)))......((((((.......))))))...... (-14.57 = -14.05 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,864,151 – 8,864,261
Length 110
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 74.67
Mean single sequence MFE -34.15
Consensus MFE -22.47
Energy contribution -21.09
Covariance contribution -1.38
Combinations/Pair 1.63
Mean z-score -1.28
Structure conservation index 0.66
SVM decision value 0.49
SVM RNA-class probability 0.755266
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8864151 110 + 22407834
UUGUUUGGCUGCCAUUUCAUCCACGACUUGAGCCCGCUCAUUAUCAGUUUCGUGAUGAUCGGCGUGGCCCUGAUCAUUAUGUUACUCAACUUCUCUGGGGCCAUGUGCCC
......(((.(((...(((((.((((((((((....)))).....))..)))))))))..)))((((((((........((.....))........))))))))..))). ( -33.69)
>DroSec_CAF1 74388 110 + 1
UUGUUUGGCUGCCAUCUCAUUGACGAUUUGAGCCCGCUCACUAUUAGUUUCGUGAUGAUCGGCGUGGCCCUGAUCAUUCUGUUUCUCAACUUCUCAGGGGCCAUGUGCCC
......(((.((((((((((.((((((.((((....))))..))).)))..)))).))).)))((((((((........((.....))........))))))))..))). ( -33.49)
>DroSim_CAF1 72892 110 + 1
UUGUUUGGCUGCCAUCUCAUUGACGAUUUGAGCCCGCUCACUAUCAGUUUCGUGAUGAUCGGCGUGGCCUUGAUCAUUCUGUUUCUCAACUUCUCAGGGGCCAUGUGCCC
......(((.((((((((((.((((((.((((....))))..))).)))..)))).))).)))((((((((........((.....))........))))))))..))). ( -32.79)
>DroEre_CAF1 78655 110 + 1
UUGUUCGGUUGCUAUCUUAUCGACAAGUUGAGCACACUCGUCGUCAGCUUCGUGAUGAUCGGCGUGGCCCUGAUCAUCGUGAUUCUUAACUUUUCGGGGGCUAUGUGCCC
...................((((.((((((((..(((.((..(....)..)).(((((((((.(....)))))))))))))...)))))))).))))((((.....)))) ( -31.90)
>DroYak_CAF1 76601 110 + 1
UUGUUCGGCACCUAUCUGAUUGACGACUUGACCACGUUCGUCAUCAUUGGCGUGAUGAUCGGCGUGGCGCUGAUCAUACUGAUUCUCAACUUCGCGGGUGCCAUGUGUCC
......(((((((...((((.((((((........).)))))))))...(((..((((((((((...))))))))))..((.....))....))))))))))........ ( -37.90)
>DroAna_CAF1 76071 110 + 1
UUGGGUGGUGCCCAAUCCGCUACUGGCCUAGGGACGCUGCCCUUGGUUCUGGCCGUCUUCGGCGUGACUCUCAUCGUCCUCAUUCUUAACUUUUCUGGAGCGAUGUGCCC
..(((..((((((...(((....)))....))).)))..)))..(((....((((....))))........((((((((.................))).))))).))). ( -35.13)
>consensus
UUGUUUGGCUGCCAUCUCAUUGACGACUUGAGCACGCUCACCAUCAGUUUCGUGAUGAUCGGCGUGGCCCUGAUCAUUCUGAUUCUCAACUUCUCAGGGGCCAUGUGCCC
......(((..............(((..((((....)))).(((((......))))).)))((((((((((........((.....))........))))))))))))). (-22.47 = -21.09 +  -1.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,864,191 – 8,864,301
Length 110
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.38
Mean single sequence MFE -40.63
Consensus MFE -26.60
Energy contribution -26.55
Covariance contribution -0.05
Combinations/Pair 1.42
Mean z-score -1.34
Structure conservation index 0.65
SVM decision value 0.22
SVM RNA-class probability 0.639526
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8864191 110 + 22407834
UUAUC-AGUUUCGUGAUGAUCGGCGUGGCCC---UGAUCAUUAUGUUACUCAACUUCUCUGGGGCCAUGUGCCCGCAGGAGUUCCUGCCCGGCGGUGUUUGCUCCACGCUGCUG
.....-(((..((((((((((((.(....))---)))))))))))..)))...........((((.....))))(((((....))))).(((((((((.......))))))))) ( -42.90)
>DroSec_CAF1 74428 110 + 1
CUAUU-AGUUUCGUGAUGAUCGGCGUGGCCC---UGAUCAUUCUGUUUCUCAACUUCUCAGGGGCCAUGUGCCCGCAGGAGUUCCUGCCCGGCGGUGUUUGCUCCACGCUGCUG
....(-(((..((((.......(((((((((---(........((.....))........))))))))))(((.(((((....)))))..)))...........))))..)))) ( -39.09)
>DroSim_CAF1 72932 110 + 1
CUAUC-AGUUUCGUGAUGAUCGGCGUGGCCU---UGAUCAUUCUGUUUCUCAACUUCUCAGGGGCCAUGUGCCCGCAGGAGUUCCUGCCCGGCGGUGUUUGCUCCACGCUGCUG
....(-(((..((((.......(((((((((---(........((.....))........))))))))))(((.(((((....)))))..)))...........))))..)))) ( -37.79)
>DroEre_CAF1 78695 110 + 1
UCGUC-AGCUUCGUGAUGAUCGGCGUGGCCC---UGAUCAUCGUGAUUCUUAACUUUUCGGGGGCUAUGUGCCCACAGGAGUUCCUGCCCGGCGGUGUCUGUUCCACGCUGCUA
(((((-(......)))))).((((((((..(---.((.((((((..............(((((((.....)))).((((....)))).))))))))))).)..))))))))... ( -42.23)
>DroWil_CAF1 124285 110 + 1
CUGUGGUGCUGA----UGGUGGUGCUGGCUACAGUCGUGGUGUUGAUAUUGAAUUUCUCCGGGGCCAAGUGCCCGCAGCAGCUUCUGCCGGGCGGAAUCUGCUCCACUUCUCUG
..((((.((.((----(..((((.((((((((....)))))...((.........))..))).))))..((((((..((((...))))))))))..))).)).))))....... ( -37.40)
>DroYak_CAF1 76641 110 + 1
UCAUC-AUUGGCGUGAUGAUCGGCGUGGCGC---UGAUCAUACUGAUUCUCAACUUCGCGGGUGCCAUGUGUCCGCAGGAGUUCCUGCCCGGUGGUGUCUGUUCCACGCUGCUA
(((((-((....))))))).((((((((.((---.(((..(((((......(((((((((((..(...)..))))).))))))......)))))..))).)).))))))))... ( -44.40)
>consensus
CUAUC_AGUUUCGUGAUGAUCGGCGUGGCCC___UGAUCAUUCUGAUUCUCAACUUCUCAGGGGCCAUGUGCCCGCAGGAGUUCCUGCCCGGCGGUGUCUGCUCCACGCUGCUG
......................(((((((((....((..................))....)))))))))....(((((....)))))..((((((((.......)))))))). (-26.60 = -26.55 +  -0.05)

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 10:44:42 2006