Locus 196

Sequence ID 2R_DroMel_CAF1
Location 1,453,810 – 1,453,913
Length 103
Max. P 0.999475
window452 window453

overview

Window 2

Location 1,453,810 – 1,453,913
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.28
Mean single sequence MFE -34.23
Consensus MFE -30.50
Energy contribution -30.58
Covariance contribution 0.08
Combinations/Pair 1.13
Mean z-score -2.88
Structure conservation index 0.89
SVM decision value 3.64
SVM RNA-class probability 0.999475
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1453810 103 + 20766785
GUUUCGUUUUCUGAAGGUUUUUU-CGCUUCAAUCCUGUAGUUGCGGCCAGGCCAAGUCUGGCUGCAAUUAUGACUGCUCGCACUCGCUGAAGUCCUUCGUCCUU----------------
............(((((...(((-(((.........((((((((((((((((...))))))))))))))))((.((....)).)))).)))).)))))......---------------- ( -36.70)
>DroSec_CAF1 72232 103 + 1
GUUUCGUUUUCUGAAGGUUUUUU-CGCUUCAAUCCUGUAGUUGCGGCCAGGCCAAGUCUGGCUGCAAUUAUGACUGCUCGCACUCGCUGAAGUCCUUCGUCCUU----------------
............(((((...(((-(((.........((((((((((((((((...))))))))))))))))((.((....)).)))).)))).)))))......---------------- ( -36.70)
>DroSim_CAF1 70942 103 + 1
GUUUCGUUUUCUGAAGGUUUUUU-CGCUUCAAUCCUGUAGUUGCGGCCAGGCCAAGUCUGGCUGCAAUUAUGACUGCUCGCACUCGCUGAAGUCCUUCGUCCUU----------------
............(((((...(((-(((.........((((((((((((((((...))))))))))))))))((.((....)).)))).)))).)))))......---------------- ( -36.70)
>DroEre_CAF1 82259 120 + 1
GUCUCGUUUUCCGAAGGCUUUUUUCGCUUCAAUCCUGUAGUUGCGGCCAAGCCAAGUCUGGCUGCAAUUAUGACUGCUCGCACUGCCUGAAGUCCUUCGUCCUUCGCCUCUCGUCCUUCC
....((.....((((((........((((((.....(((((((((((((..(...)..)))))))))))))....((.......)).)))))).......)))))).....))....... ( -33.66)
>DroYak_CAF1 76442 103 + 1
GUUUCGUUUUCCGAAGGCUUUUUUCA-UUCAAUUCUGUAGUUGCGGGCGAGCUAAGUCUGGCUGCAAUUAUGACUGCUCGUACAGCAUGAAGUCCUUCGUCCUU----------------
...........((((((((((.....-.........((((((((((.((..(...)..)).))))))))))...((((.....)))).)))).)))))).....---------------- ( -27.40)
>consensus
GUUUCGUUUUCUGAAGGUUUUUU_CGCUUCAAUCCUGUAGUUGCGGCCAGGCCAAGUCUGGCUGCAAUUAUGACUGCUCGCACUCGCUGAAGUCCUUCGUCCUU________________
...........((((((........((((((.....((((((((((((((((...))))))))))))))))...((....)).....))))))))))))..................... (-30.50 = -30.58 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,453,810 – 1,453,913
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.28
Mean single sequence MFE -29.32
Consensus MFE -22.96
Energy contribution -23.40
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -1.74
Structure conservation index 0.78
SVM decision value 0.49
SVM RNA-class probability 0.758393
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1453810 103 - 20766785
----------------AAGGACGAAGGACUUCAGCGAGUGCGAGCAGUCAUAAUUGCAGCCAGACUUGGCCUGGCCGCAACUACAGGAUUGAAGCG-AAAAAACCUUCAGAAAACGAAAC
----------------......(((((((((....))))((...(((((.((.((((.(((((.......))))).)))).))...)))))..)).-......)))))............ ( -29.70)
>DroSec_CAF1 72232 103 - 1
----------------AAGGACGAAGGACUUCAGCGAGUGCGAGCAGUCAUAAUUGCAGCCAGACUUGGCCUGGCCGCAACUACAGGAUUGAAGCG-AAAAAACCUUCAGAAAACGAAAC
----------------......(((((((((....))))((...(((((.((.((((.(((((.......))))).)))).))...)))))..)).-......)))))............ ( -29.70)
>DroSim_CAF1 70942 103 - 1
----------------AAGGACGAAGGACUUCAGCGAGUGCGAGCAGUCAUAAUUGCAGCCAGACUUGGCCUGGCCGCAACUACAGGAUUGAAGCG-AAAAAACCUUCAGAAAACGAAAC
----------------......(((((((((....))))((...(((((.((.((((.(((((.......))))).)))).))...)))))..)).-......)))))............ ( -29.70)
>DroEre_CAF1 82259 120 - 1
GGAAGGACGAGAGGCGAAGGACGAAGGACUUCAGGCAGUGCGAGCAGUCAUAAUUGCAGCCAGACUUGGCUUGGCCGCAACUACAGGAUUGAAGCGAAAAAAGCCUUCGGAAAACGAGAC
.......(((.((((((((..(....).))))......(((...(((((.((.((((.(((((.......))))).)))).))...)))))..)))......)))))))........... ( -33.70)
>DroYak_CAF1 76442 103 - 1
----------------AAGGACGAAGGACUUCAUGCUGUACGAGCAGUCAUAAUUGCAGCCAGACUUAGCUCGCCCGCAACUACAGAAUUGAA-UGAAAAAAGCCUUCGGAAAACGAAAC
----------------.....((((((..(((((.((((((((((((((.............))))..)))))........)))))......)-)))).....))))))........... ( -23.82)
>consensus
________________AAGGACGAAGGACUUCAGCGAGUGCGAGCAGUCAUAAUUGCAGCCAGACUUGGCCUGGCCGCAACUACAGGAUUGAAGCG_AAAAAACCUUCAGAAAACGAAAC
......................((((((((......)))((...(((((.((.((((.(((((.......))))).)))).))...)))))..))........)))))............ (-22.96 = -23.40 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:09 2006