Locus 4052

Sequence ID 3R_DroMel_CAF1
Location 11,045,293 – 11,045,453
Length 160
Max. P 0.950278
window6491 window6492 window6493

overview

Window 1

Location 11,045,293 – 11,045,413
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -49.30
Consensus MFE -47.92
Energy contribution -48.03
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.97
SVM decision value 0.78
SVM RNA-class probability 0.849048
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11045293 120 + 27905053
AGACGAUCUGGGAGAGCUGCCGCCUAUGAUGGAGGAACUAAGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCCAUGUGGCCACAGGAAAUCCU
.........((((...(((..(((....(((((((...((((.((((..(((((((..(............)..)))))))..)))).))))...)))))))..)))..)))....)))) ( -48.20)
>DroSec_CAF1 8062 120 + 1
AGACGAUCUGGGUGAGCUGCCGCCCAUGAUGGAGGAACUAAGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCUAUGUGGCCCCAGGAAAUCCU
......((((((......(((((.....(((((((...((((.((((..(((((((..(............)..)))))))..)))).))))...))))))))))))))))))....... ( -48.70)
>DroSim_CAF1 8080 120 + 1
AGACGAUCUGGGUGAGCUGCCGCCCAUGAUGGAGGAACUAAGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCCAUGUGGCCCCAGGAAAUCCU
......((((((......(((((.....(((((((...((((.((((..(((((((..(............)..)))))))..)))).))))...))))))))))))))))))....... ( -51.00)
>consensus
AGACGAUCUGGGUGAGCUGCCGCCCAUGAUGGAGGAACUAAGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCCAUGUGGCCCCAGGAAAUCCU
......((((((......(((((.....(((((((...((((.((((..(((((((..(............)..)))))))..)))).))))...))))))))))))))))))....... (-47.92 = -48.03 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,045,333 – 11,045,453
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -55.10
Consensus MFE -55.10
Energy contribution -55.10
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 1.00
SVM decision value 1.40
SVM RNA-class probability 0.950278
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11045333 120 + 27905053
AGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCCAUGUGGCCACAGGAAAUCCUAGCCAAGCUGGGCGGUGGCGCGGAAUUGGCUUCCGGCCCA
..((.(((((((((((..(............)..))))))..(((((.((.(((((((.....((((...(((....))).))))....))))))))).))))).........))))))) ( -55.00)
>DroSec_CAF1 8102 120 + 1
AGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCUAUGUGGCCCCAGGAAAUCCUAGCCAAGCUGGGCGGUGGCGCGGAAUUGGCUUCCGGCCCA
..((.(((((((((((..(............)..))))))..(((((.((.(((((((.....((((...(((....))).))))....))))))))).))))).........))))))) ( -55.00)
>DroSim_CAF1 8120 120 + 1
AGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCCAUGUGGCCCCAGGAAAUCCUAGCCAAGCUGGGCGGUGGUGCGGAAUUGGCUUCCGGCCCA
..((.(((((((((((..(............)..))))))..(((((.((.(((((((.....((((...(((....))).))))....))))))))).))))).........))))))) ( -55.30)
>consensus
AGUGUGGCCGAUGGCCUGCGACCAAAUCCCGGUGGGCCAUUCUCCGCUCUUACCGCCUCCAUGUGGCCCCAGGAAAUCCUAGCCAAGCUGGGCGGUGGCGCGGAAUUGGCUUCCGGCCCA
..((.(((((((((((..(............)..))))))..(((((.((.(((((((.....((((...(((....))).))))....))))))))).))))).........))))))) (-55.10 = -55.10 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,045,333 – 11,045,453
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -52.27
Consensus MFE -52.27
Energy contribution -52.27
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 1.00
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11045333 120 - 27905053
UGGGCCGGAAGCCAAUUCCGCGCCACCGCCCAGCUUGGCUAGGAUUUCCUGUGGCCACAUGGAGGCGGUAAGAGCGGAGAAUGGCCCACCGGGAUUUGGUCGCAGGCCAUCGGCCACACU
..((((((.......((((((...(((((((....((((((((....)))..)))))....).))))))....))))))..(((((.((((.....))))....)))))))))))..... ( -53.00)
>DroSec_CAF1 8102 120 - 1
UGGGCCGGAAGCCAAUUCCGCGCCACCGCCCAGCUUGGCUAGGAUUUCCUGGGGCCACAUAGAGGCGGUAAGAGCGGAGAAUGGCCCACCGGGAUUUGGUCGCAGGCCAUCGGCCACACU
..((((((.......((((((...(((((((....((((((((....)))..)))))....).))))))....))))))..(((((.((((.....))))....)))))))))))..... ( -51.90)
>DroSim_CAF1 8120 120 - 1
UGGGCCGGAAGCCAAUUCCGCACCACCGCCCAGCUUGGCUAGGAUUUCCUGGGGCCACAUGGAGGCGGUAAGAGCGGAGAAUGGCCCACCGGGAUUUGGUCGCAGGCCAUCGGCCACACU
..((((((.......((((((...(((((((....((((((((....)))..)))))....).))))))....))))))..(((((.((((.....))))....)))))))))))..... ( -51.90)
>consensus
UGGGCCGGAAGCCAAUUCCGCGCCACCGCCCAGCUUGGCUAGGAUUUCCUGGGGCCACAUGGAGGCGGUAAGAGCGGAGAAUGGCCCACCGGGAUUUGGUCGCAGGCCAUCGGCCACACU
..((((((.......((((((...(((((((....((((((((....)))..)))))....).))))))....))))))..(((((.((((.....))))....)))))))))))..... (-52.27 = -52.27 +   0.00)

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 11:16:53 2006