Locus 2626

Sequence ID 3R_DroMel_CAF1
Location 7,094,885 – 7,095,043
Length 158
Max. P 0.784222
window4273 window4274 window4275

overview

Window 3

Location 7,094,885 – 7,095,003
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.58
Mean single sequence MFE -30.34
Consensus MFE -22.32
Energy contribution -21.84
Covariance contribution -0.48
Combinations/Pair 1.18
Mean z-score -1.77
Structure conservation index 0.74
SVM decision value 0.25
SVM RNA-class probability 0.652722
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7094885 118 - 27905053
CUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUGAAAGCUGAACCCUCAAACCAUUUCUCCGAACUUGUUCAGGAAGCCAAACAACAGAGGGCGCUACUAUUAAAAC--
.....((((((.....))))))((..(((((((....)))))))..........(((((..........((((((....))).))).(.....)....))))).))............-- ( -28.90)
>DroSec_CAF1 27978 120 - 1
CUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUAAAAGCUGAACCCUCAAUCCAUUUAUCCGUACUUGUUCAGGAAACCAAACAACAGAGGGCGCUACUAUUAAAACGC
.....((((((.....))))))((..(((((((....)))))))...(((....(((((((.....))........(((((..(....)..)))))..))))).)))...........)) ( -29.60)
>DroSim_CAF1 30778 120 - 1
CUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUGAAAGCUGAACCCUUAAACCAUUUAUCCGAACUUGUUGAGGAAAUCAAACAACAGAGGGCGCUACUAAUAAAACGC
.....((((((.....))))))((..(((((((....)))))))...(((....(((((....(........)....(((((..(....)...)))))))))).)))...........)) ( -26.10)
>DroEre_CAF1 28763 120 - 1
CUUCUGGAUAACUUAAUUAUCCGGAGUGCCACCACCUGGUGGUUGAAAGCUGAACCCUUAAAGCAUUUAUCCGAACUUGCUUAGGAAGCCAGGCAACAGAGAGCGCCACUAUUAAGAAGC
(((((((((((.....))))))(..((((((((....))))((((...(((....(((..(((((............)))))))).)))....)))).....))))..).....))))). ( -32.70)
>DroYak_CAF1 29666 120 - 1
CUUCUGGAUAACUUAAUUAUCCGGAGUGCCACCACCUGGUGGUUGAAAGAUGAACCCUUAAACCAUUUAUCCGAACUGGCUCGGGCAGCCAAGCAACAGAGGGCGCCACUUAUAAAAAGC
..(((((((((.....)))))))))(((.(.((..(((.((((((..(((((...........))))).(((((......))))))))))).....)))..)).).)))........... ( -34.40)
>consensus
CUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUGAAAGCUGAACCCUUAAACCAUUUAUCCGAACUUGUUCAGGAAGCCAAACAACAGAGGGCGCUACUAUUAAAACGC
.....((((((.....))))))....(((((((....)))))))...((..(..(((((....(........)...(((((..(....)..)))))..)))))..)..)).......... (-22.32 = -21.84 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,094,923 – 7,095,043
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.75
Mean single sequence MFE -34.82
Consensus MFE -25.92
Energy contribution -25.96
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -2.04
Structure conservation index 0.74
SVM decision value 0.57
SVM RNA-class probability 0.784222
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7094923 120 + 27905053
ACAAGUUCGGAGAAAUGGUUUGAGGGUUCAGCUUUCAACCACCAGGUGGUGGUUCUGCGGAUAAUUAAGUUAUCCAGGAGUGAGAGAGCAGUAUUCUCUUCGCGAAAUGGAUAAAAUGAU
....(((((.((((.....(((((((.....)))))))(((((....))))))))).))))).((((..(((((((...(((((((((.....))))).))))....)))))))..)))) ( -41.20)
>DroSec_CAF1 28018 120 + 1
ACAAGUACGGAUAAAUGGAUUGAGGGUUCAGCUUUUAACCACCAGGUGGUGGUUCUGCGGAUAAUUAAGUUAUCCAGGAGUGAGAGAGCAGUAUUCUCUUUGCGAAAUGGAUAAAAUGAA
...................((((..((((.((....(((((((....)))))))..))))))..)))).(((((((...(..((((((.....))))).)..)....)))))))...... ( -31.30)
>DroSim_CAF1 30818 120 + 1
ACAAGUUCGGAUAAAUGGUUUAAGGGUUCAGCUUUCAACCACCAGGUGGUGGUUCUGCGGAUAAUUAAGUUAUCCAGGAGUGAGAGAGCAGUAUUCUCUUGGCGAUAUGGAUAAAAUGAA
....(((((.....((.(((.(((((..(.((((((.((((((....))))))(((..(((((((...))))))).)))....)))))).)....)))))))).)).)))))........ ( -32.10)
>DroEre_CAF1 28803 120 + 1
GCAAGUUCGGAUAAAUGCUUUAAGGGUUCAGCUUUCAACCACCAGGUGGUGGCACUCCGGAUAAUUAAGUUAUCCAGAAGCGAGAGCGCACUGUUCUCUUGGCGAAGAGGAUAAAAUGAA
((......((((...(......)..)))).((((((..(((((....)))))...((.(((((((...))))))).))...))))))))..(((((((((....)))))))))....... ( -35.10)
>DroYak_CAF1 29706 120 + 1
GCCAGUUCGGAUAAAUGGUUUAAGGGUUCAUCUUUCAACCACCAGGUGGUGGCACUCCGGAUAAUUAAGUUAUCCAGAAGUGAGAGAGCACUGUUCUCUUGGCGAAAUGGAUAAAAUAAA
.(((.((((..........(((((((..((.(((((..(((((....)))))(((((.(((((((...))))))).).)))).)))))...))..))))))))))).))).......... ( -34.40)
>consensus
ACAAGUUCGGAUAAAUGGUUUAAGGGUUCAGCUUUCAACCACCAGGUGGUGGUUCUGCGGAUAAUUAAGUUAUCCAGGAGUGAGAGAGCAGUAUUCUCUUGGCGAAAUGGAUAAAAUGAA
....(((((............((((......))))...(((((....))))).....)))))..(((..(((((((...(((((((((.....))))))).))....)))))))..))). (-25.92 = -25.96 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,094,923 – 7,095,043
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.75
Mean single sequence MFE -26.91
Consensus MFE -18.98
Energy contribution -19.14
Covariance contribution 0.16
Combinations/Pair 1.19
Mean z-score -2.08
Structure conservation index 0.71
SVM decision value 0.09
SVM RNA-class probability 0.578602
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7094923 120 - 27905053
AUCAUUUUAUCCAUUUCGCGAAGAGAAUACUGCUCUCUCACUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUGAAAGCUGAACCCUCAAACCAUUUCUCCGAACUUGU
..............((((.((.((((.....(((.((........((((((.....))))))....(((((((....))))))))).)))(((....))).....))))))))))..... ( -26.20)
>DroSec_CAF1 28018 120 - 1
UUCAUUUUAUCCAUUUCGCAAAGAGAAUACUGCUCUCUCACUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUAAAAGCUGAACCCUCAAUCCAUUUAUCCGUACUUGU
((((((((.........((..(((((.......))))).......((((((.....))))))))..(((((((....))))))).)))).)))).......................... ( -23.60)
>DroSim_CAF1 30818 120 - 1
UUCAUUUUAUCCAUAUCGCCAAGAGAAUACUGCUCUCUCACUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUGAAAGCUGAACCCUUAAACCAUUUAUCCGAACUUGU
(((...(((((((........(((((.......)))))......)))))))........((.((..(((((((....)))))))....)).))...................)))..... ( -22.84)
>DroEre_CAF1 28803 120 - 1
UUCAUUUUAUCCUCUUCGCCAAGAGAACAGUGCGCUCUCGCUUCUGGAUAACUUAAUUAUCCGGAGUGCCACCACCUGGUGGUUGAAAGCUGAACCCUUAAAGCAUUUAUCCGAACUUGC
(((........(((((....)))))...((((((((.(((((.((((((((.....)))))))))))((((((....)))))).)).)))(((....)))..))))).....)))..... ( -31.30)
>DroYak_CAF1 29706 120 - 1
UUUAUUUUAUCCAUUUCGCCAAGAGAACAGUGCUCUCUCACUUCUGGAUAACUUAAUUAUCCGGAGUGCCACCACCUGGUGGUUGAAAGAUGAACCCUUAAACCAUUUAUCCGAACUGGC
..........(((.((((...(((((.......)))))((((.((((((((.....))))))))))))(((((....)))))..((.(((((...........))))).)))))).))). ( -30.60)
>consensus
UUCAUUUUAUCCAUUUCGCCAAGAGAAUACUGCUCUCUCACUCCUGGAUAACUUAAUUAUCCGCAGAACCACCACCUGGUGGUUGAAAGCUGAACCCUUAAACCAUUUAUCCGAACUUGU
.................((((.((((.......))))(((((...((((((.....))))))....(((((((....)))))))...)).))).......................)))) (-18.98 = -19.14 +   0.16)

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 10:40:52 2006