Locus 2962

Sequence ID 2L_DroMel_CAF1
Location 8,500,763 – 8,500,942
Length 179
Max. P 0.953521
window4704 window4705

overview

Window 4

Location 8,500,763 – 8,500,869
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.58
Mean single sequence MFE -27.88
Consensus MFE -19.68
Energy contribution -19.96
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -2.16
Structure conservation index 0.71
SVM decision value 1.43
SVM RNA-class probability 0.953521
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8500763 106 - 22407834
AACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCAAUGCUUUUAGCCUCCGCAAGUUAAAUGCUCCAACCU--------------CCAACCCCCUUUUGGAUAUCCUCCUCACCU
.......(((((((((((.....(..((((((((.(((((..((((...((....))))))....)))))))))..--------------..))))..).....)))))))))))..... ( -31.50)
>DroSec_CAF1 10206 119 - 1
AACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUCGUGGGCAAUGCUUUUAGC-UCCGCAAGUUAAAUGCUCCAAACCCCUUUCCCCCAACCCCAAUCCCCUUUUGGAUUUCCUCCUCACCU
.......(((((((............(((((..(.(((....((.((((((-(.....))))))).)).......)))....)..)))))..(((((......))))))))))))..... ( -29.30)
>DroSim_CAF1 9415 119 - 1
AACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCAAUGCUUUUAGCCUCCGCAAGUUAAAUGCUCCAACCCCCUUUCCCCC-UCCCCAAUCCCCUUUUGGAUUUCCUCCUCACCU
.......(((((((....((((....((..((((.(((....((.((((((........)))))).))..................-.)))))))..))....)))).)))))))..... ( -28.80)
>DroEre_CAF1 9833 86 - 1
AACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCAAUGCUUUUAGCCUCCGCAAGUUAAAUGCUCCGACAA----GC------------------------------CCUCACCU
......(((((........)))))..((((((((.(((((..((((...((....))))))....))))))))).)----))------------------------------)....... ( -22.40)
>DroYak_CAF1 10404 99 - 1
AACUCCCAGGAGGACGUUAUCCUGUCGGUUGUUGUGGGCAAUGCUUUUAGCCUCCGCAAGUUAAAUGCUCCAACCU----UCCCCC-----------------GGAUUUGCUCCUCACCU
.........(((((.((.((((.(..((..((((.(((((..((((...((....))))))....)))))))))..----.))..)-----------------))))..))))))).... ( -27.40)
>consensus
AACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCAAUGCUUUUAGCCUCCGCAAGUUAAAUGCUCCAACCC____UCCCCC____CCAA_CCCCUUUUGGAUUUCCUCCUCACCU
((((..(((((........)))))..))))((((.(((((..((.....))...(....).....))))))))).............................................. (-19.68 = -19.96 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,500,829 – 8,500,942
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.20
Mean single sequence MFE -36.44
Consensus MFE -30.72
Energy contribution -31.36
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -0.97
Structure conservation index 0.84
SVM decision value 0.33
SVM RNA-class probability 0.690593
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8500829 113 - 22407834
UCCAAA------UCCACGUUCUCAUCCACGUCCUGAAAGUCUCGGUCUCGAAAGAAACCCAAGGCGGCGCUCGCGUG-GCAACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCA
......------((((((.......((((((..((...((((.(((.((....)).)))..))))..))...)))))-)(((((..(((((........)))))..))))).)))))).. ( -38.60)
>DroSec_CAF1 10285 107 - 1
------------UCCACGUCCUCAUCCACGUCCUGAAAGUCUCGUUCUCGAAAGAAACCCAAGGCGCCGCUCGCGUG-GCAACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUCGUGGGCA
------------((((((.(..(((((...(((((...((((.(((.((....)))))...))))(((((....)))-))......))))))))))....((....))..).)))))).. ( -36.00)
>DroSim_CAF1 9494 108 - 1
------------NNNNNNNNNNNNNNNNNNNNCUGAAAGUCUCGGUCUCGAAAGAAACCCAAGGCGGCGCUCGCGUGGGCAACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCA
------------..........................((((.(((.((....)).)))..))))...(((((((...((((((..(((((........)))))..))))))))))))). ( -35.20)
>DroEre_CAF1 9879 95 - 1
UCCACGUC------------------------CUGAAAGGCUCGGUCUCGCAAGAAACCCAAGGCGGCGCUCGCGUG-GCAACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCA
....((((------------------------((....))...(((.((....)).)))...))))..(((((((..-((((((..(((((........)))))..))))))))))))). ( -36.30)
>DroYak_CAF1 10463 119 - 1
UCCACGUCCUCAUCCUCAUCCUCUUCCAUGACCUGAAAGUCUCUGUGCCGACAGAAACCCAAGGCGGCGCUCGCGUG-GCAACUCCCAGGAGGACGUUAUCCUGUCGGUUGUUGUGGGCA
....((((.(((...((((........))))..)))..((.(((((....))))).))....))))..(((((((..-((((((..(((((........)))))..))))))))))))). ( -36.10)
>consensus
UCCA________UCC_C_U_CUC_UCCA_G_CCUGAAAGUCUCGGUCUCGAAAGAAACCCAAGGCGGCGCUCGCGUG_GCAACUCCCAGGAGGAUGUUAUCCUGUCGGUUGUUGUGGGCA
......................................((((.(((.((....)).)))..))))...(((((((...((((((..(((((........)))))..))))))))))))). (-30.72 = -31.36 +   0.64)

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 10:40:42 2006