Locus 2469

Sequence ID 3R_DroMel_CAF1
Location 6,801,244 – 6,801,398
Length 154
Max. P 0.992005
window4044 window4045 window4046

overview

Window 4

Location 6,801,244 – 6,801,358
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.26
Mean single sequence MFE -21.58
Consensus MFE -16.00
Energy contribution -16.04
Covariance contribution 0.04
Combinations/Pair 1.18
Mean z-score -1.69
Structure conservation index 0.74
SVM decision value 0.15
SVM RNA-class probability 0.608659
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6801244 114 + 27905053
UUGAUCAAAGAA------GUACAUGCUUUAUAGCACGUAUUUCUCUUUGCCAAAUCGUCCCUUCUCUUUCAAAUGGAAGCGCUUUAAAUCACACUGGCGAAUAUCACAUUUCAAAGUAAA
((((....((((------((((.((((....)))).)))))))).(((((((...........(.(((((....))))).).............))))))).........))))...... ( -23.35)
>DroSec_CAF1 59584 114 + 1
UUGAUCACAGAA------GUACAUGCUUUAUAGCACGUAUUUCCCUUUGCCAAAUCAUUCCCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCGAAUAUCACAUUUCAAAGUAAA
((((.....(((------((((.((((....)))).)))))))..(((((((.............(((((....))))).((........))..))))))).........))))...... ( -25.50)
>DroSim_CAF1 65010 114 + 1
UUGAUCAAAGAA------GUACAUGCUUUAUAGCACGUAUUUCCCUUUGCCAAAUCAUCCCCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCGAAUAUCACAUUUCAAAGUAAA
((((.....(((------((((.((((....)))).)))))))..(((((((.............(((((....))))).((........))..))))))).........))))...... ( -25.50)
>DroEre_CAF1 45143 120 + 1
UUGAUCAAAGAAUGUUUAGUAUUUGCUGUAUAUCACGUAUUUCGCUUCGCCAAAUCGUUCCCCCUCUUACAAAUGAAAGCGCUUUAAAUCGCCCUGGCGAAUAUCACAUUUCAAAGUAAA
((((.....((.(((.((((....)))).)))))...........(((((((..(((((............)))))..(((........)))..))))))).........))))...... ( -16.60)
>DroYak_CAF1 58021 120 + 1
UUGAUCAAAGAACGUUUAGUACAUGCUUUUUAUCACGUAUUUCGCUUUGCUAAAUCGUUUUCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCAAAUAUCACAUUUCAAAGUAAA
.......................((((((.......((((((.(((.(((((((.(((((((............))))))).))))....)))..)))))))))........)))))).. ( -16.96)
>consensus
UUGAUCAAAGAA______GUACAUGCUUUAUAGCACGUAUUUCCCUUUGCCAAAUCGUUCCCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCGAAUAUCACAUUUCAAAGUAAA
((((.....((.......((((.((((....)))).)))).....(((((((.............(((((....))))).((........))..)))))))..)).....))))...... (-16.00 = -16.04 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,801,278 – 6,801,398
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.83
Mean single sequence MFE -23.36
Consensus MFE -20.58
Energy contribution -20.34
Covariance contribution -0.24
Combinations/Pair 1.17
Mean z-score -1.94
Structure conservation index 0.88
SVM decision value 2.30
SVM RNA-class probability 0.992005
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6801278 120 + 27905053
UUCUCUUUGCCAAAUCGUCCCUUCUCUUUCAAAUGGAAGCGCUUUAAAUCACACUGGCGAAUAUCACAUUUCAAAGUAAAGAAGAAUUGAAAUCAAAGCUUUUGCUGUACAAAGCCAAAU
....(((((.....(((...(((((((((.(((((((..((((............))))....)).))))).))))...)))))...)))......(((....)))...)))))...... ( -19.90)
>DroSec_CAF1 59618 120 + 1
UUCCCUUUGCCAAAUCAUUCCCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCGAAUAUCACAUUUCAAAGUAAAGAAGAAUUGAAAUCAAAGCUUUGGCUGUACAAAGCCAAAU
.....(((((((.............(((((....))))).((........))..)))))))......(((((((............)))))))......(((((((......))))))). ( -23.30)
>DroSim_CAF1 65044 120 + 1
UUCCCUUUGCCAAAUCAUCCCCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCGAAUAUCACAUUUCAAAGUAAAGAAGAAUUGAAAUCAAAGCUUUGGCUGUACAAAGCCAAAU
.....(((((((.............(((((....))))).((........))..)))))))......(((((((............)))))))......(((((((......))))))). ( -23.30)
>DroEre_CAF1 45183 120 + 1
UUCGCUUCGCCAAAUCGUUCCCCCUCUUACAAAUGAAAGCGCUUUAAAUCGCCCUGGCGAAUAUCACAUUUCAAAGUAAAGAAAAAUUGAAAUCAAAGCUUUGGCUGUACAAAGCCAAAU
...(((((((((..(((((............)))))..(((........)))..)))))).......(((((((............)))))))...)))(((((((......))))))). ( -24.80)
>DroYak_CAF1 58061 120 + 1
UUCGCUUUGCUAAAUCGUUUUCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCAAAUAUCACAUUUCAAAGUAAAGAAAAAUUGAAAUCAAAGCUUUGGCUGUACAAAGCCAAAU
...((((((........(((((...((((.(((((...(((........)))..(((......)))))))).))))....)))))........))))))(((((((......))))))). ( -25.49)
>consensus
UUCCCUUUGCCAAAUCGUUCCCCCUCUUUCAAAUGAAAGCGCUUUAAAUCGCACUGGCGAAUAUCACAUUUCAAAGUAAAGAAGAAUUGAAAUCAAAGCUUUGGCUGUACAAAGCCAAAU
.....(((((((.............(((((....))))).((........))..)))))))......(((((((..(......)..)))))))......(((((((......))))))). (-20.58 = -20.34 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,801,278 – 6,801,398
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -31.62
Consensus MFE -27.88
Energy contribution -27.72
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -1.84
Structure conservation index 0.88
SVM decision value 2.07
SVM RNA-class probability 0.987247
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6801278 120 - 27905053
AUUUGGCUUUGUACAGCAAAAGCUUUGAUUUCAAUUCUUCUUUACUUUGAAAUGUGAUAUUCGCCAGUGUGAUUUAAAGCGCUUCCAUUUGAAAGAGAAGGGACGAUUUGGCAAAGAGAA
......((((((..(((....))).......(((.((((((((.((((.(((((.((........(((((........)))))))))))).))))..)))))).)).))))))))).... ( -24.20)
>DroSec_CAF1 59618 120 - 1
AUUUGGCUUUGUACAGCCAAAGCUUUGAUUUCAAUUCUUCUUUACUUUGAAAUGUGAUAUUCGCCAGUGCGAUUUAAAGCGCUUUCAUUUGAAAGAGGGGGAAUGAUUUGGCAAAGGGAA
.(((((((......))))))).(((((...(((.(((((((((....(((((.(((....((((....)))).......))))))))....)))))))))...))).....))))).... ( -32.80)
>DroSim_CAF1 65044 120 - 1
AUUUGGCUUUGUACAGCCAAAGCUUUGAUUUCAAUUCUUCUUUACUUUGAAAUGUGAUAUUCGCCAGUGCGAUUUAAAGCGCUUUCAUUUGAAAGAGGGGGGAUGAUUUGGCAAAGGGAA
.(((((((......))))))).(((((...(((.(((((((((....(((((.(((....((((....)))).......))))))))....)))))))))...))).....))))).... ( -32.80)
>DroEre_CAF1 45183 120 - 1
AUUUGGCUUUGUACAGCCAAAGCUUUGAUUUCAAUUUUUCUUUACUUUGAAAUGUGAUAUUCGCCAGGGCGAUUUAAAGCGCUUUCAUUUGUAAGAGGGGGAACGAUUUGGCGAAGCGAA
.(((((((......)))))))((((((...((..(((..((((((..(((((.(((....((((....)))).......))))))))...)).))))..)))..)).....))))))... ( -35.20)
>DroYak_CAF1 58061 120 - 1
AUUUGGCUUUGUACAGCCAAAGCUUUGAUUUCAAUUUUUCUUUACUUUGAAAUGUGAUAUUUGCCAGUGCGAUUUAAAGCGCUUUCAUUUGAAAGAGGGAAAACGAUUUAGCAAAGCGAA
.(((((((......)))))))((((((........((((((((.((((.(((((...........(((((........)))))..))))).))))))))))))........))))))... ( -33.11)
>consensus
AUUUGGCUUUGUACAGCCAAAGCUUUGAUUUCAAUUCUUCUUUACUUUGAAAUGUGAUAUUCGCCAGUGCGAUUUAAAGCGCUUUCAUUUGAAAGAGGGGGAACGAUUUGGCAAAGCGAA
.(((((((......)))))))(((..((((....(((((((((....(((((.(((....((((....)))).......))))))))....)))))))))....)))).)))........ (-27.88 = -27.72 +  -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 10:37:09 2006