Locus 3369

Sequence ID 2R_DroMel_CAF1
Location 11,414,995 – 11,415,126
Length 131
Max. P 0.990052
window5504 window5505 window5506

overview

Window 4

Location 11,414,995 – 11,415,086
Length 91
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 81.51
Mean single sequence MFE -28.73
Consensus MFE -19.98
Energy contribution -21.35
Covariance contribution 1.37
Combinations/Pair 1.09
Mean z-score -2.62
Structure conservation index 0.70
SVM decision value 2.04
SVM RNA-class probability 0.986338
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11414995 91 + 20766785
AUGUCUAAAA--------AAAAAUAUAUCUGUUGGUGCUGACUGGUGACCCCAUUUGUGGGGUGACCCUGCCAUGUGGUGACACCUUAACAGUUAGCCA
..........--------................(.((((((((((.((((((....)))))).))........(((....))).....))))))))). ( -30.10)
>DroSec_CAF1 29540 88 + 1
AUGUCUAAAA--------GAA---AUAUCUGUUGGUGCUGGCUGGUGACCCCAUUUGUGGGGUGACCCCGCCAUGUGGUGACACCUUAACAGUUAGCCA
..........--------...---.((.(((((((...((((.(((.((((((....)))))).)))..)))).(((....))).))))))).)).... ( -32.10)
>DroEre_CAF1 30760 78 + 1
AUGCCUUUAA--------AAA---AUAUCUGUUG----------GUGACCCCAUUUGUGGGGUGACCCUGCCAUGUGGAGACACCUUUACUGUUAGCCA
..........--------...---.........(----------((.((((((....)))))).)))(((.((.((((((....)))))))).)))... ( -22.00)
>DroYak_CAF1 29320 92 + 1
AUGCCUUUAAAUGUCUUAAAA---AUAUUUGUUGGUGCU----GGUGACCCCAUUUAUGGGGUGACCCUGCCAUGUGGAGACACCUUUACAGUUAGCCA
..(((..(((((((.......---)))))))..)))(((----(((.((((((....)))))).)))(((....(((....))).....)))..))).. ( -30.70)
>consensus
AUGCCUAAAA________AAA___AUAUCUGUUGGUGCU____GGUGACCCCAUUUGUGGGGUGACCCUGCCAUGUGGAGACACCUUAACAGUUAGCCA
.........................((.((((.((((......(((.((((((....)))))).))).((((....)))).))))...)))).)).... (-19.98 = -21.35 +   1.37)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,414,995 – 11,415,086
Length 91
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 81.51
Mean single sequence MFE -26.78
Consensus MFE -18.35
Energy contribution -19.23
Covariance contribution 0.87
Combinations/Pair 1.05
Mean z-score -2.74
Structure conservation index 0.69
SVM decision value 2.19
SVM RNA-class probability 0.990052
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11414995 91 - 20766785
UGGCUAACUGUUAAGGUGUCACCACAUGGCAGGGUCACCCCACAAAUGGGGUCACCAGUCAGCACCAACAGAUAUAUUUUU--------UUUUAGACAU
.......(((((..(((((.......((((..(((.((((((....)))))).))).))))))))))))))..........--------.......... ( -27.11)
>DroSec_CAF1 29540 88 - 1
UGGCUAACUGUUAAGGUGUCACCACAUGGCGGGGUCACCCCACAAAUGGGGUCACCAGCCAGCACCAACAGAUAU---UUC--------UUUUAGACAU
.......(((((..(((((.......((((..(((.((((((....)))))).))).))))))))))))))....---...--------.......... ( -31.01)
>DroEre_CAF1 30760 78 - 1
UGGCUAACAGUAAAGGUGUCUCCACAUGGCAGGGUCACCCCACAAAUGGGGUCAC----------CAACAGAUAU---UUU--------UUAAAGGCAU
..(((......((((((((((((....))...(((.((((((....)))))).))----------)...))))))---)))--------)....))).. ( -23.70)
>DroYak_CAF1 29320 92 - 1
UGGCUAACUGUAAAGGUGUCUCCACAUGGCAGGGUCACCCCAUAAAUGGGGUCACC----AGCACCAACAAAUAU---UUUUAAGACAUUUAAAGGCAU
..(((.........(((((((((....)).))(((.((((((....)))))).)))----.))))).........---.((((((...))))))))).. ( -25.30)
>consensus
UGGCUAACUGUAAAGGUGUCACCACAUGGCAGGGUCACCCCACAAAUGGGGUCACC____AGCACCAACAGAUAU___UUU________UUAAAGACAU
((.((..(((((...(((....)))..)))))(((.((((((....)))))).))).....................................)).)). (-18.35 = -19.23 +   0.87)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,415,027 – 11,415,126
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 90.69
Mean single sequence MFE -30.62
Consensus MFE -27.77
Energy contribution -28.27
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -1.80
Structure conservation index 0.91
SVM decision value 1.06
SVM RNA-class probability 0.908247
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11415027 99 + 20766785
ACUGGUGACCCCAUUUGUGGGGUGACCCUGCCAUGUGGUGACACCUUAACAGUUAGCCAAGUGGCCAGACUAUUUCCCUCCACGAGAUGACCCCAUCCU
...(((.((((((....)))))).)))(((((((.(((((((.........)))).))).)))).))).................((((....)))).. ( -32.10)
>DroSec_CAF1 29569 98 + 1
GCUGGUGACCCCAUUUGUGGGGUGACCCCGCCAUGUGGUGACACCUUAACAGUUAGCCAAGUGGCCAGACU-UUUCCCUCCACGAGAUGACCCCAUCCU
...(((.((((((....)))))).)))..(((((.(((((((.........)))).))).)))))......-.............((((....)))).. ( -31.40)
>DroEre_CAF1 30783 95 + 1
----GUGACCCCAUUUGUGGGGUGACCCUGCCAUGUGGAGACACCUUUACUGUUAGCCAAAUGGCCAGACUUUCUCCCCCCAUGAGAUGACCCCAUCCU
----((.((((((....)))))).)).(((((((.(((.((((.......))))..))).)))).))).................((((....)))).. ( -28.00)
>DroYak_CAF1 29356 96 + 1
---GGUGACCCCAUUUAUGGGGUGACCCUGCCAUGUGGAGACACCUUUACAGUUAGCCAAAUGGCCAGACUUUCUCCCACCAUGAGAUGACCCCAUCCU
---(((.((((((....)))))).)))....((((.(((((.........((((.(((....)))..)))).)))))...)))).((((....)))).. ( -31.00)
>consensus
___GGUGACCCCAUUUGUGGGGUGACCCUGCCAUGUGGAGACACCUUAACAGUUAGCCAAAUGGCCAGACUUUCUCCCUCCACGAGAUGACCCCAUCCU
...(((.((((((....)))))).)))..(((((.(((((((.........)))).))).)))))....................((((....)))).. (-27.77 = -28.27 +   0.50)

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 10:53:51 2006