Locus 1170

Sequence ID 3L_DroMel_CAF1
Location 3,363,593 – 3,363,705
Length 112
Max. P 0.776175
window1825 window1826

overview

Window 5

Location 3,363,593 – 3,363,705
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.01
Mean single sequence MFE -34.42
Consensus MFE -25.98
Energy contribution -26.02
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.93
Structure conservation index 0.75
SVM decision value 0.33
SVM RNA-class probability 0.693199
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3363593 112 + 23771897
AAUAAAGGCAGCGCGACAAACGAUCUCGAGACG-GCGAAAUAUCUUGUCGCCAUAAUUGGAAUUUAAUACUUCCGGUUGGGCAACAACGUUUGCAAGC-------CGCGAGACGCCCAGA
......(((....((.....)).(((((...((-((.....((.((((.(((.(((((((((........)))))))))))).)))).))......))-------))))))).))).... ( -33.10)
>DroSec_CAF1 30771 119 + 1
AAUAAAGGCAGCGCGACAAACGAUCUCGAGACG-GCGAAAUAUCUUGUCGCCAUAAUUGGAAUUUAAUACUUCCGGUUGGGCAACAACGUUUGCGAGCCGCGAGCCGCGAGACGCCCAGA
......(((.((.((.((((((..........(-((((......)))))(((.(((((((((........)))))))))))).....)))))))).))((((...))))....))).... ( -38.30)
>DroSim_CAF1 28469 112 + 1
AAUAAAGGCAGCGCGACAAACGAUCUCGAGACG-GCGAAAUAUCUUGUCGCCAUAAUUGGAAUUUAAUACUUCCGGUUGGGCAACAACGUUUGCGAGC-------CGCGAGACGCCCAGA
......(((.((.((.((((((..........(-((((......)))))(((.(((((((((........)))))))))))).....)))))))).))-------(....)..))).... ( -34.90)
>DroEre_CAF1 29551 106 + 1
AAUAAAGGCAGCGCGACAAACGAUCUCGAGACGGGCAAAAUAUCUUGUCGCCAUAAUUGGAAUUUAAUACUUCCGGUUGGGCAACAACGUUUGC--------------GAGACGCCCAGA
......(((..(.((.((((((.......((((((........))))))(((.(((((((((........)))))))))))).....)))))))--------------).)..))).... ( -33.70)
>DroYak_CAF1 29362 105 + 1
AAUAAAGGCAGCGCGACAAACGAUCUCGAGACG-GCGAAAUAUCUUGUCGCCAUAAUUGGAAUUUAAUACUUCCGGUUGGGCAACAACGUUUGC--------------GAGACGCCCAGA
......(((..(.((.((((((..........(-((((......)))))(((.(((((((((........)))))))))))).....)))))))--------------).)..))).... ( -32.10)
>consensus
AAUAAAGGCAGCGCGACAAACGAUCUCGAGACG_GCGAAAUAUCUUGUCGCCAUAAUUGGAAUUUAAUACUUCCGGUUGGGCAACAACGUUUGC_AGC_______CGCGAGACGCCCAGA
......(((....((.....)).((((.......(((((.....((((.(((.(((((((((........)))))))))))).))))..)))))..((........)))))).))).... (-25.98 = -26.02 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,363,593 – 3,363,705
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.01
Mean single sequence MFE -34.68
Consensus MFE -27.76
Energy contribution -28.80
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.66
Structure conservation index 0.80
SVM decision value 0.54
SVM RNA-class probability 0.776175
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3363593 112 - 23771897
UCUGGGCGUCUCGCG-------GCUUGCAAACGUUGUUGCCCAACCGGAAGUAUUAAAUUCCAAUUAUGGCGACAAGAUAUUUCGC-CGUCUCGAGAUCGUUUGUCGCGCUGCCUUUAUU
...(((((...((((-------((..((.....((((((((.....((((........))))......))))))))...((((((.-.....)))))).))..)))))).)))))..... ( -35.20)
>DroSec_CAF1 30771 119 - 1
UCUGGGCGUCUCGCGGCUCGCGGCUCGCAAACGUUGUUGCCCAACCGGAAGUAUUAAAUUCCAAUUAUGGCGACAAGAUAUUUCGC-CGUCUCGAGAUCGUUUGUCGCGCUGCCUUUAUU
...(((((...((((((..((((((((...(((((((((((.....((((........))))......))))))))((....))..-)))..)))).))))..)))))).)))))..... ( -41.40)
>DroSim_CAF1 28469 112 - 1
UCUGGGCGUCUCGCG-------GCUCGCAAACGUUGUUGCCCAACCGGAAGUAUUAAAUUCCAAUUAUGGCGACAAGAUAUUUCGC-CGUCUCGAGAUCGUUUGUCGCGCUGCCUUUAUU
............(((-------((.((((((((((((((((.....((((........))))......))))))))...((((((.-.....)))))))))))).)).)))))....... ( -34.80)
>DroEre_CAF1 29551 106 - 1
UCUGGGCGUCUC--------------GCAAACGUUGUUGCCCAACCGGAAGUAUUAAAUUCCAAUUAUGGCGACAAGAUAUUUUGCCCGUCUCGAGAUCGUUUGUCGCGCUGCCUUUAUU
...(((((.(.(--------------(((((((((((((((.....((((........))))......))))))))...((((((.......)))))))))))).)).).)))))..... ( -29.70)
>DroYak_CAF1 29362 105 - 1
UCUGGGCGUCUC--------------GCAAACGUUGUUGCCCAACCGGAAGUAUUAAAUUCCAAUUAUGGCGACAAGAUAUUUCGC-CGUCUCGAGAUCGUUUGUCGCGCUGCCUUUAUU
...(((((.(.(--------------(((((((((((((((.....((((........))))......))))))))...((((((.-.....)))))))))))).)).).)))))..... ( -32.30)
>consensus
UCUGGGCGUCUCGCG_______GCU_GCAAACGUUGUUGCCCAACCGGAAGUAUUAAAUUCCAAUUAUGGCGACAAGAUAUUUCGC_CGUCUCGAGAUCGUUUGUCGCGCUGCCUUUAUU
...(((((...((((...........(((((((((((((((.....((((........))))......))))))))...((((((.......))))))))))))))))).)))))..... (-27.76 = -28.80 +   1.04)

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 10:01:01 2006