Locus 5820

Sequence ID 2R_DroMel_CAF1
Location 18,433,525 – 18,433,615
Length 90
Max. P 0.921333
window9321 window9322

overview

Window 1

Location 18,433,525 – 18,433,615
Length 90
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 80.52
Mean single sequence MFE -29.58
Consensus MFE -19.76
Energy contribution -19.57
Covariance contribution -0.19
Combinations/Pair 1.10
Mean z-score -2.48
Structure conservation index 0.67
SVM decision value 1.14
SVM RNA-class probability 0.921333
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18433525 90 + 20766785
GUG--UGUGUAACCCUCGAUUGAACUCCUAAUUUGGAGUUGCAACUU-----UCCAAGCUUCUGCGUCUCUGUGUUCCCGAGGCCGACGCACUCGCC
(.(--(((((...(((((.(((((((((......)))))).)))...-----.....((....)).............)))))...)))))).)... ( -28.90)
>DroSec_CAF1 7639 81 + 1
AUG--UGUGUAACCCUCAAUUGAACUCCUAAUUUGGAGUUGCAACUU-----UCCGAGC---------UCUGGGCUUCCGAGGCUGACGCACUAGCC
..(--(((((...((((..(((((((((......)))))).)))...-----...((((---------.....))))..))))...))))))..... ( -27.50)
>DroSim_CAF1 6984 81 + 1
AUG--UGUGUAACCCUCAAUUGAACUCCUAAUUUGGAGUUGCAACUU-----UCCGAGC---------UCUGGGUUUCCGAGGCUGACGCACUAGCC
..(--(((((...((((..(((((((((......)))))).)))...-----((((...---------..)))).....))))...))))))..... ( -26.00)
>DroEre_CAF1 6735 90 + 1
GUG--UGUGUAACCCUCAAUUGAACUCCUAAUUUGGAGUUGCAACUU-----UCCGAGCUUCUGAGUCUCUAAGUUGCCGAGGCCGACGCACUCUCC
(.(--(((((...((((.....((((((......))))))(((((((-----...(((((....)).))).))))))).))))...)))))).)... ( -34.40)
>DroYak_CAF1 6796 92 + 1
GUGUGUGUGUAACCCUCAAUUGAACUCCUAAUUUGGAGUUGCAACUU-----UCCGAGAUUCAGAGUCUCUGGGUUUCCGAGGCCGACGCACUCGUG
..(.((((((...((((..(((((((((......)))))).)))...-----...(((((((((.....))))))))).))))...)))))).)... ( -34.90)
>DroAna_CAF1 7243 94 + 1
GUG--UGCGUAGCCCCCCAUUGAACUCCUAAUUUGGAGUUGCAACUUGUAAUUGAAAGCCUUCCCGACGCCGAG-ACCCGAGGCCGACGCACUCGUC
(.(--(((((.(((.....(((((((((......)))))).)))((((...(((..........)))...))))-......)))..)))))).)... ( -25.80)
>consensus
GUG__UGUGUAACCCUCAAUUGAACUCCUAAUUUGGAGUUGCAACUU_____UCCGAGCUUC_G_GUCUCUGGGUUUCCGAGGCCGACGCACUCGCC
.....(((((...((((..(((((((((......)))))).)))(((........))).....................))))...)))))...... (-19.76 = -19.57 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,433,525 – 18,433,615
Length 90
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 80.52
Mean single sequence MFE -28.92
Consensus MFE -19.11
Energy contribution -18.95
Covariance contribution -0.16
Combinations/Pair 1.14
Mean z-score -1.95
Structure conservation index 0.66
SVM decision value 0.68
SVM RNA-class probability 0.821886
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18433525 90 - 20766785
GGCGAGUGCGUCGGCCUCGGGAACACAGAGACGCAGAAGCUUGGA-----AAGUUGCAACUCCAAAUUAGGAGUUCAAUCGAGGGUUACACA--CAC
.....(((.((.(.(((((.............((....)).....-----..((((.((((((......))))))))))))))).).)).))--).. ( -25.80)
>DroSec_CAF1 7639 81 - 1
GGCUAGUGCGUCAGCCUCGGAAGCCCAGA---------GCUCGGA-----AAGUUGCAACUCCAAAUUAGGAGUUCAAUUGAGGGUUACACA--CAU
.....(((.((.(.((((((....))...---------.......-----.(((((.((((((......))))))))))))))).).)).))--).. ( -25.30)
>DroSim_CAF1 6984 81 - 1
GGCUAGUGCGUCAGCCUCGGAAACCCAGA---------GCUCGGA-----AAGUUGCAACUCCAAAUUAGGAGUUCAAUUGAGGGUUACACA--CAU
.....(((.((.(.((((((....))...---------.......-----.(((((.((((((......))))))))))))))).).)).))--).. ( -25.30)
>DroEre_CAF1 6735 90 - 1
GGAGAGUGCGUCGGCCUCGGCAACUUAGAGACUCAGAAGCUCGGA-----AAGUUGCAACUCCAAAUUAGGAGUUCAAUUGAGGGUUACACA--CAC
.....(((.((.(.((((((((((((.(((.((....)))))...-----)))))))((((((......))))))....))))).).)).))--).. ( -31.90)
>DroYak_CAF1 6796 92 - 1
CACGAGUGCGUCGGCCUCGGAAACCCAGAGACUCUGAAUCUCGGA-----AAGUUGCAACUCCAAAUUAGGAGUUCAAUUGAGGGUUACACACACAC
..((((.((....))))))(.(((((.((((.......))))...-----.(((((.((((((......)))))))))))..))))).)........ ( -29.30)
>DroAna_CAF1 7243 94 - 1
GACGAGUGCGUCGGCCUCGGGU-CUCGGCGUCGGGAAGGCUUUCAAUUACAAGUUGCAACUCCAAAUUAGGAGUUCAAUGGGGGGCUACGCA--CAC
.....((((((.((((((...(-((((....)))))................((((.((((((......))))))))))..)))))))))))--).. ( -35.90)
>consensus
GGCGAGUGCGUCGGCCUCGGAAACCCAGAGAC_C_GAAGCUCGGA_____AAGUUGCAACUCCAAAUUAGGAGUUCAAUUGAGGGUUACACA__CAC
......((.((.(.(((((....)...........................(((((.((((((......))))))))))))))).).)).))..... (-19.11 = -18.95 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:15 2006