Locus 5136

Sequence ID 2R_DroMel_CAF1
Location 16,714,670 – 16,714,761
Length 91
Max. P 0.975030
window8213 window8214

overview

Window 3

Location 16,714,670 – 16,714,761
Length 91
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 83.03
Mean single sequence MFE -27.90
Consensus MFE -21.76
Energy contribution -21.96
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.78
SVM decision value 0.23
SVM RNA-class probability 0.645926
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16714670 91 + 20766785
GCAGCACCACAAUCCCAGCCAGAAUCACAGCCAGGACAAUGGGAAUGCGGAUGCAGCUGCGC------------------AUGAGAAUGAUAGCACGAUUGCAAAUGCA--------
(((...((.((.(((((.((.............))....))))).)).)).(((((((((.(------------------((....)))...))).).)))))..))).-------- ( -26.02)
>DroSec_CAF1 22712 99 + 1
GCAGCACCACAAUCCCAGCCAGAAUCACAGCCAGGACAAUGGGAACGCGGAUGCAGCUGCGA------------------AUGAGACCGAUUGCACGAUUGCAAAUGCAAAUGCAAA
(((((.......(((((.((.............))....)))))..((....)).)))))..------------------..........(((((...((((....)))).))))). ( -26.42)
>DroSim_CAF1 24353 91 + 1
GCAGCACCACAAUCCCAGCCAGAAUCACAGCCAGGACAAUGGGAAUGCGGAUGCAGCUGCGA------------------AUGAGAACGAUAGCACGAUUGCAAAUGCA--------
((((((((.((.(((((.((.............))....))))).)).)).))).((((((.------------------.......)).))))...........))).-------- ( -25.42)
>DroEre_CAF1 22841 117 + 1
GCAGCACCACAAUCCCAGCCAGAAUCACAGCCAGGACAAUGGGAAUGCGGAUGCAGCUGCGAUUGCGAAUGAGAUUGAAAAUGAGAAUGAUAGCACGAUUGCAAAUGCAAAUGCAAG
((((((((.((.(((((.((.............))....))))).)).)).)))...((((.((((((.((..(((............)))..))...)))))).))))..)))... ( -29.82)
>DroYak_CAF1 22798 117 + 1
GCAGCACCACAAUCCCAGCCAGAAUCACAGCCAGGACAAUGGGAAUGCGGAUGCGACUGCGAUUGCGAAUGAGAUUGAAAAUGAGAACGAUAGCACGAUUGCAAAUGCAAAUGCAAA
((((((((.((.(((((.((.............))....))))).)).)).)))...((((.((((((.((..((((..........))))..))...)))))).))))..)))... ( -31.82)
>consensus
GCAGCACCACAAUCCCAGCCAGAAUCACAGCCAGGACAAUGGGAAUGCGGAUGCAGCUGCGA__________________AUGAGAACGAUAGCACGAUUGCAAAUGCAAAUGCAA_
((((((((.((.(((((.((.............))....))))).)).)).)))......................................(((....)))...)))......... (-21.76 = -21.96 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,714,670 – 16,714,761
Length 91
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 83.03
Mean single sequence MFE -32.82
Consensus MFE -29.26
Energy contribution -29.10
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -2.19
Structure conservation index 0.89
SVM decision value 1.74
SVM RNA-class probability 0.975030
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16714670 91 - 20766785
--------UGCAUUUGCAAUCGUGCUAUCAUUCUCAU------------------GCGCAGCUGCAUCCGCAUUCCCAUUGUCCUGGCUGUGAUUCUGGCUGGGAUUGUGGUGCUGC
--------.((((..(((....)))..........))------------------))((((((((....)))...((((.((((..(((........)))..)))).)))).))))) ( -30.20)
>DroSec_CAF1 22712 99 - 1
UUUGCAUUUGCAUUUGCAAUCGUGCAAUCGGUCUCAU------------------UCGCAGCUGCAUCCGCGUUCCCAUUGUCCUGGCUGUGAUUCUGGCUGGGAUUGUGGUGCUGC
.((((((((((....))))..))))))..........------------------..(((((.((....))....((((.((((..(((........)))..)))).)))).))))) ( -35.80)
>DroSim_CAF1 24353 91 - 1
--------UGCAUUUGCAAUCGUGCUAUCGUUCUCAU------------------UCGCAGCUGCAUCCGCAUUCCCAUUGUCCUGGCUGUGAUUCUGGCUGGGAUUGUGGUGCUGC
--------.((((........))))............------------------..((((((((....)))...((((.((((..(((........)))..)))).)))).))))) ( -30.00)
>DroEre_CAF1 22841 117 - 1
CUUGCAUUUGCAUUUGCAAUCGUGCUAUCAUUCUCAUUUUCAAUCUCAUUCGCAAUCGCAGCUGCAUCCGCAUUCCCAUUGUCCUGGCUGUGAUUCUGGCUGGGAUUGUGGUGCUGC
...((((((((....))))..))))................................((((((((....)))...((((.((((..(((........)))..)))).)))).))))) ( -34.30)
>DroYak_CAF1 22798 117 - 1
UUUGCAUUUGCAUUUGCAAUCGUGCUAUCGUUCUCAUUUUCAAUCUCAUUCGCAAUCGCAGUCGCAUCCGCAUUCCCAUUGUCCUGGCUGUGAUUCUGGCUGGGAUUGUGGUGCUGC
...((((((((....))))..)))).........((((..((((((((..((.(((((((((((.....(((.......)))..))))))))))).))..)))))))).)))).... ( -33.80)
>consensus
_UUGCAUUUGCAUUUGCAAUCGUGCUAUCGUUCUCAU__________________UCGCAGCUGCAUCCGCAUUCCCAUUGUCCUGGCUGUGAUUCUGGCUGGGAUUGUGGUGCUGC
.........((((........))))................................(((((.((....))....((((.((((..(((........)))..)))).)))).))))) (-29.26 = -29.10 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:28 2006