Locus 477

Sequence ID 2R_DroMel_CAF1
Location 2,683,293 – 2,683,460
Length 167
Max. P 0.998862
window902 window903 window904

overview

Window 2

Location 2,683,293 – 2,683,394
Length 101
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 74.91
Mean single sequence MFE -14.83
Consensus MFE -9.99
Energy contribution -9.67
Covariance contribution -0.33
Combinations/Pair 1.20
Mean z-score -1.32
Structure conservation index 0.67
SVM decision value 0.08
SVM RNA-class probability 0.571743
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2683293 101 + 20766785
UAUCAAAGAGAAUAUUUCCGUUUGAGGGAUUAAUUAACAACCUGUUAGAACAAGGCAUAAUCUAAUGUGCAUAGUUUACAUCUCAUCUAUCACUAUAAUAU
.......((((.((.((((......)))).))..((((.....))))((((...(((((......)))))...))))...))))................. ( -15.90)
>DroSec_CAF1 115896 77 + 1
UAUCAAAGAGAUUAUUUCCAUUGGAGGGAUUAAUCAAGAAUCUGUUAGAACAACGCAUAAUCUAAUGUGGAU------------------------AAUAA
((((.....(((((.((((......)))).)))))..................(((((......))))))))------------------------).... ( -14.80)
>DroSim_CAF1 114176 77 + 1
UAUCAAAGAGAUUAUUUCCGUUGGAGGGAUUAAUCAACAAUCUAUUAGAACAAGGCAUAAUCUAGUGUGCAU------------------------AAUAA
.........(((((.((((......)))).)))))...................(((((......)))))..------------------------..... ( -13.80)
>consensus
UAUCAAAGAGAUUAUUUCCGUUGGAGGGAUUAAUCAACAAUCUGUUAGAACAAGGCAUAAUCUAAUGUGCAU________________________AAUAA
.........(((((.((((......)))).)))))........((((((...........))))))................................... ( -9.99 =  -9.67 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,683,333 – 2,683,429
Length 96
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 73.48
Mean single sequence MFE -16.20
Consensus MFE -10.75
Energy contribution -11.87
Covariance contribution 1.11
Combinations/Pair 1.05
Mean z-score -1.63
Structure conservation index 0.66
SVM decision value 1.23
SVM RNA-class probability 0.933851
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2683333 96 + 20766785
CCUGUUAGAACAAGGCAUAAUCUAAUGUGCAUAGUUUACAUCUCAUCUAUCACUAUAAUAUUCCAUCGGUGUAUUGUUUGUUCUCCUUACUUGCAA
......(((((((.(((((......)))))........................(((((((.((...)).))))))))))))))............ ( -14.20)
>DroSec_CAF1 115936 72 + 1
UCUGUUAGAACAACGCAUAAUCUAAUGUGGAU------------------------AAUAAUCCAUCGGUGGAUUAUUUGUUCUCCUCACUUGCGA
..((..(((((((...((((((((..((((((------------------------....))))))...)))))))))))))))...))....... ( -18.80)
>DroSim_CAF1 114216 72 + 1
UCUAUUAGAACAAGGCAUAAUCUAGUGUGCAU------------------------AAUAAUCCAUCGGUGGAUUAUUUGUUAUCCUCACUUGCGA
..........(((((((((......)))))..------------------------(((((((((....)))))))))...........))))... ( -15.60)
>consensus
UCUGUUAGAACAAGGCAUAAUCUAAUGUGCAU________________________AAUAAUCCAUCGGUGGAUUAUUUGUUCUCCUCACUUGCGA
......(((((((.(((((......)))))...........................((((((((....)))))))))))))))............ (-10.75 = -11.87 +   1.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,683,359 – 2,683,460
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 76.34
Mean single sequence MFE -20.67
Consensus MFE -17.94
Energy contribution -18.83
Covariance contribution 0.89
Combinations/Pair 1.08
Mean z-score -2.22
Structure conservation index 0.87
SVM decision value 3.26
SVM RNA-class probability 0.998862
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2683359 101 - 20766785
GAAAAACGUUUUCGAACUGUGGUGCAAGGCAUUGCAAGUAAGGAGAACAAACAAUACACCGAUGGAAUAUUAUAGUGAUAGAUGAGAUGUAAACUAUGCAC
.......((((((..((((..((((...))))..).)))...))))))......................((((((.(((.......)))..))))))... ( -16.40)
>DroSec_CAF1 115962 77 - 1
GAAAAACGUUUUCGAACUGUGGUGCAAGGCAUCGCAAGUGAGGAGAACAAAUAAUCCACCGAUGGAUUAUU------------------------AUCCAC
.......((((((..((((((((((...))))))).)))...)))))).(((((((((....)))))))))------------------------...... ( -24.80)
>DroSim_CAF1 114242 77 - 1
GAAAAACGUUUUUAAACUGUGGUGCAAGGCAUCGCAAGUGAGGAUAACAAAUAAUCCACCGAUGGAUUAUU------------------------AUGCAC
.......(((((((...((((((((...))))))))..)))))))....(((((((((....)))))))))------------------------...... ( -20.80)
>consensus
GAAAAACGUUUUCGAACUGUGGUGCAAGGCAUCGCAAGUGAGGAGAACAAAUAAUCCACCGAUGGAUUAUU________________________AUGCAC
.......((((((..((((((((((...))))))).)))...)))))).(((((((((....))))))))).............................. (-17.94 = -18.83 +   0.89)

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 09:39:33 2006