Locus 2021

Sequence ID 3L_DroMel_CAF1
Location 5,562,577 – 5,562,708
Length 131
Max. P 0.898030
window3159 window3160

overview

Window 9

Location 5,562,577 – 5,562,673
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 92.81
Mean single sequence MFE -35.33
Consensus MFE -28.28
Energy contribution -29.28
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -1.89
Structure conservation index 0.80
SVM decision value 1.00
SVM RNA-class probability 0.898030
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5562577 96 + 23771897
UGGAAUCCCUUGCUCCUAUAGCGCCAUUGGAGGCAAUGCCAUCGAUGGCGGCUACGGCGUCAGGGAUGCCAGUGGCCGUACAAAAAGGAAACGUUU
(((.((((((.((.((..(((((((((((..(((...)))..))))))).)))).)).)).)))))).)))((..((.........))..)).... ( -40.60)
>DroSec_CAF1 26532 96 + 1
UGGAAUCCCUUGUUCCUAUAGCGCCAGUGGAGGCAAUGCCGUCGAUGACGGCCACGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUU
.(((((.....)))))...((((((......)))....((.......((((((((((((((...)))))).)))))))).......))....))). ( -35.64)
>DroSim_CAF1 26888 96 + 1
UGGAAUCCCUUGUUCCUAUAGCGCCAGUGGAGGCAAUGCCAUCGAUGGCGGCCACGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUU
.(((((.....)))))....((((((.((..(((...)))..)).))))((((((((((((...)))))).)))))))).......(....).... ( -38.80)
>DroEre_CAF1 26941 96 + 1
UAGAAUCCCUUGUUCCUAUAGCGCCAAUGGAGGCAAUUCCAUCGAUGGUGCCCUCGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUU
............(((((...((((((((((((....))))))...))))))((((((((((...)))))))).))..........)))))...... ( -31.80)
>DroYak_CAF1 28180 96 + 1
UAGAAUCCCUUGUUCCUAUAGCGCCAAUGGAGGCAAUGCCAUCGAUGGUGUCCUCGGCGUCUGUGAUGCCGGUGGCCGUACAAAAAGGUAACGUUU
...........((((((...((((((.((..(((...)))..)).))))))((((((((((...)))))))).))..........))).))).... ( -29.80)
>consensus
UGGAAUCCCUUGUUCCUAUAGCGCCAAUGGAGGCAAUGCCAUCGAUGGCGGCCACGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUU
...........((((((.....((((.((..(((...)))..)).))))((((((((((((...)))))).))))))........))).))).... (-28.28 = -29.28 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,562,609 – 5,562,708
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 80.07
Mean single sequence MFE -32.78
Consensus MFE -18.67
Energy contribution -19.08
Covariance contribution 0.41
Combinations/Pair 1.27
Mean z-score -1.77
Structure conservation index 0.57
SVM decision value 0.04
SVM RNA-class probability 0.551346
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5562609 99 + 23771897
GCAAUGCCAUCGAUGGCGGCUACGGCGUCAGGGAUGCCAGUGGCCGUACAAAAAGGAAACGUUUUGGAGAUAGUACCUUCUGGGGAGGAUAUACUGGAA
((...((((....))))((((((((((((...)))))).)))))))).(((((.(....).)))))....(((((((((.....))))...)))))... ( -35.70)
>DroVir_CAF1 30584 80 + 1
-------------------CCAUGGCGCCCGUUGUGCCUGUGGCCGUGCAAAAGGGAAAUGUGCUGGAAAUUGUGCCGUCUAUGGAGGCCGUCGUGGAG
-------------------(((((((((((.(((..(........)..)))..)))..................(((.((....))))))))))))).. ( -24.80)
>DroSec_CAF1 26564 99 + 1
GCAAUGCCGUCGAUGACGGCCACGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUUUGGAAAUAGUACCUUCUGGGGAGGAUAUACUGGAA
......((.((....((((((((((((((...)))))).)))))))).(((((.(....).)))))))...((((((((.....))))...)))))).. ( -36.40)
>DroSim_CAF1 26920 99 + 1
GCAAUGCCAUCGAUGGCGGCCACGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUUUGGAAAUAGUACCUUCUGGGGAGGAUAUACUGGAA
((...((((....))))((((((((((((...)))))).)))))))).(((((.(....).)))))....(((((((((.....))))...)))))... ( -38.00)
>DroEre_CAF1 26973 99 + 1
GCAAUUCCAUCGAUGGUGCCCUCGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUUUGGAGAUAGUACCUUCCGGUGAUGAUAUAAUGGAA
.......(((((..(((((((((((((((...)))))))).)).....(((((.(....).)))))......)))))...))))).............. ( -30.30)
>DroYak_CAF1 28212 99 + 1
GCAAUGCCAUCGAUGGUGUCCUCGGCGUCUGUGAUGCCGGUGGCCGUACAAAAAGGUAACGUUUUGGAAAUAGUACCUUCCGGUGAGGAUAUAAUGGAA
......((((.....((((((((((((((...))))))....((((......((((((..(((.....)))..)))))).)))))))))))).)))).. ( -31.50)
>consensus
GCAAUGCCAUCGAUGGCGGCCACGGCGUCAGUGAUGCCGGUGGCCGUACAAAAAGGAAACGUUUUGGAAAUAGUACCUUCUGGGGAGGAUAUACUGGAA
....(((((....))))).((((((((((...)))))).))))((...(((((.(....).)))))......(((((((.....)))).)))...)).. (-18.67 = -19.08 +   0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:37 2006