Locus 5222

Sequence ID 3R_DroMel_CAF1
Location 13,671,368 – 13,671,497
Length 129
Max. P 0.951952
window8520 window8521 window8522

overview

Window 0

Location 13,671,368 – 13,671,458
Length 90
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 80.78
Mean single sequence MFE -24.15
Consensus MFE -13.52
Energy contribution -15.15
Covariance contribution 1.63
Combinations/Pair 1.10
Mean z-score -2.80
Structure conservation index 0.56
SVM decision value 1.42
SVM RNA-class probability 0.951952
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13671368 90 + 27905053
AAUCCUGGCCAAGUCACAUCAUUCUGUUUUCCAUAUACUCGUAUGUACAUAUACGAAUAUACGAGUAUA------------------UAUGAUUAUUUGUAUAGGCUU
...((((..(((((...(((((..........((((((((((((((.(......).)))))))))))))------------------)))))).)))))..))))... ( -23.80)
>DroSim_CAF1 36533 108 + 1
AAUCCCGGCCAAGUCACAUCACUCUGUUUUCCAUAUACUCGUAUGUGCAUAAACGAAUAUACGAGUAUACACAUACAUAUAUUUGUCUAUGAUUGUUUGUAUAGGCUU
......((((.......................(((((((((((((.(......).)))))))))))))...(((((.(((.((......)).))).))))).)))). ( -24.60)
>DroEre_CAF1 40229 100 + 1
AAUCCUGGCCAAGUCACAUCAUGCUGUUUUCAAUACUCGUAUAUGUACAUAUACGAAUAAACGAGUAUACUCGU--------AUGUCUAUGACUGUUUGUAUAGGCCU
......((((..((.((((.((((.((.......))..)))))))))).((((((((((.(((((....)))))--------..(((...))))))))))))))))). ( -27.30)
>DroYak_CAF1 37540 94 + 1
AAUCCUGGCCAAGUCACAUCAUGCUGUUUUCCAUAUACGAGUAUGUACAUAUAGGAAUAUACGAGUAU--------------AUGUCUAUGAUUGUUUGUAUAGGCCU
...((((..((((.((.((((((........(((((((..((((((.(......).))))))..))))--------------)))..))))))))))))..))))... ( -20.90)
>consensus
AAUCCUGGCCAAGUCACAUCAUGCUGUUUUCCAUAUACGCGUAUGUACAUAUACGAAUAUACGAGUAUA_____________AUGUCUAUGAUUGUUUGUAUAGGCCU
......((((.......................(((((((((((((.(......).)))))))))))))..................((..(....)..))..)))). (-13.52 = -15.15 +   1.63)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,671,368 – 13,671,458
Length 90
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -24.91
Consensus MFE -12.99
Energy contribution -15.05
Covariance contribution 2.06
Combinations/Pair 1.16
Mean z-score -2.79
Structure conservation index 0.52
SVM decision value 0.91
SVM RNA-class probability 0.880349
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13671368 90 - 27905053
AAGCCUAUACAAAUAAUCAUA------------------UAUACUCGUAUAUUCGUAUAUGUACAUACGAGUAUAUGGAAAACAGAAUGAUGUGACUUGGCCAGGAUU
..(((....((....(((((.------------------.....((((((((((((((......))))))))))))))........))))).))....)))....... ( -21.44)
>DroSim_CAF1 36533 108 - 1
AAGCCUAUACAAACAAUCAUAGACAAAUAUAUGUAUGUGUAUACUCGUAUAUUCGUUUAUGCACAUACGAGUAUAUGGAAAACAGAGUGAUGUGACUUGGCCGGGAUU
..(((....((....(((((......((((.((((((((((((..((......))..)))))))))))).)))).((.....))..))))).))....)))....... ( -26.70)
>DroEre_CAF1 40229 100 - 1
AGGCCUAUACAAACAGUCAUAGACAU--------ACGAGUAUACUCGUUUAUUCGUAUAUGUACAUAUACGAGUAUUGAAAACAGCAUGAUGUGACUUGGCCAGGAUU
.((((.........(((((((..(((--------(((((....))))).(((((((((((....)))))))))))...........))).))))))).))))...... ( -31.10)
>DroYak_CAF1 37540 94 - 1
AGGCCUAUACAAACAAUCAUAGACAU--------------AUACUCGUAUAUUCCUAUAUGUACAUACUCGUAUAUGGAAAACAGCAUGAUGUGACUUGGCCAGGAUU
.((((....((....(((((.....(--------------(((....))))((((((((((........)))))).))))......))))).))....))))...... ( -20.40)
>consensus
AAGCCUAUACAAACAAUCAUAGACAU_____________UAUACUCGUAUAUUCGUAUAUGUACAUACGAGUAUAUGGAAAACAGAAUGAUGUGACUUGGCCAGGAUU
.((((....((....(((((.........................(((((((((((((......)))))))))))))(....)...))))).))....))))...... (-12.99 = -15.05 +   2.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,671,396 – 13,671,497
Length 101
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 82.99
Mean single sequence MFE -26.17
Consensus MFE -15.45
Energy contribution -17.32
Covariance contribution 1.88
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.59
SVM decision value 0.45
SVM RNA-class probability 0.740385
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13671396 101 + 27905053
UUCCAUAUACUCGUAUGUACAUAUACGAAUAUACGAGUAUA------------------UAUGAUUAUUUGUAUAGGCUUAACGUGCCGAAAAUGUGUUUAUGAAUCAAUAUUGCGCAU
(((.((((((((((((((.(......).)))))))))))))------------------)...............(((.......)))))).((((((.(((......)))..)))))) ( -26.30)
>DroSim_CAF1 36561 118 + 1
UUCCAUAUACUCGUAUGUGCAUAAACGAAUAUACGAGUAUACACAUACAUAUAUUUGUCUAUGAUUGUUUGUAUAGGCUUAACGUGCCGA-AAUGUGUUUAUGAAUCAAUAUUGCGCAU
.....(((((((((((((.(......).)))))))))))))...(((((.(((.((......)).))).))))).(((.......)))..-.((((((.(((......)))..)))))) ( -28.40)
>DroEre_CAF1 40257 110 + 1
UUCAAUACUCGUAUAUGUACAUAUACGAAUAAACGAGUAUACUCGU--------AUGUCUAUGACUGUUUGUAUAGGCCUAACGUGCCGA-AAUGUGUUUAUGAAUCAAUAUUGCGCAC
(((.((((((((((((....))))))))(((.(((((....)))))--------.)))............)))).((((....).)))))-).(((((.(((......)))..))))). ( -26.90)
>DroYak_CAF1 37568 104 + 1
UUCCAUAUACGAGUAUGUACAUAUAGGAAUAUACGAGUAU--------------AUGUCUAUGAUUGUUUGUAUAGGCCUAACGUGCCGA-AAUGUGUUUAUGAAUCAAUAUUGCGCAC
((((((((((..((((((.(......).))))))..))))--------------)))..................((((....).)))))-).(((((.(((......)))..))))). ( -23.10)
>consensus
UUCCAUAUACGCGUAUGUACAUAUACGAAUAUACGAGUAUA_____________AUGUCUAUGAUUGUUUGUAUAGGCCUAACGUGCCGA_AAUGUGUUUAUGAAUCAAUAUUGCGCAC
.....(((((((((((((.(......).)))))))))))))..................................(((.......))).....(((((.(((......)))..))))). (-15.45 = -17.32 +   1.88)

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 11:49:28 2006