Locus 4377

Sequence ID 2R_DroMel_CAF1
Location 14,387,684 – 14,387,775
Length 91
Max. P 0.924275
window7001 window7002

overview

Window 1

Location 14,387,684 – 14,387,775
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 83.23
Mean single sequence MFE -29.77
Consensus MFE -16.52
Energy contribution -16.27
Covariance contribution -0.25
Combinations/Pair 1.20
Mean z-score -2.58
Structure conservation index 0.55
SVM decision value 0.46
SVM RNA-class probability 0.743651
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14387684 91 + 20766785
UUUGCGUGCCUGGGCAUUGUCUAAAUGGUUUGGUGUGAGGAGGGGGGGUGGGGGGUGGGGGGAUCCUCUCCAUUUUCCAACCCACUUUGUG
....((..((..(.((((.....)))).)..))..))(.((((.(((.(((..(((((((((...)))))))))..))).))).)))).). ( -38.00)
>DroSec_CAF1 19864 74 + 1
UUUGCGUGCCUGGGCAUUGUCUAAAUGGUUUGGUG-----------------GGUUGGGGGGAUCCCCUCCAUUUUCCAACCCACUUUGUG
.....((((....))))..............((((-----------------(((((((((....)))........))))))))))..... ( -24.60)
>DroSim_CAF1 23121 74 + 1
UUUGCGUGCCUGGGCAUUGUCUAAAUGCUUUGGUG-----------------GGUUGGGGGGAUCCCCUCCAUUUUCCAACCCACUUUGUG
.......(((..((((((.....))))))..)))(-----------------(((((((((....)))........)))))))........ ( -27.40)
>DroEre_CAF1 21635 72 + 1
UUUGCGUGCCUGGGCAUUGUCUAAAUGGUCUGGGG-----------------GG--AGGGGGAUCCCCCUCAUUUUCCAACCCACUUGGUG
.....((((....))))...((((.(((..(((..-----------------((--(((((....))))))..)..)))..))).)))).. ( -29.10)
>consensus
UUUGCGUGCCUGGGCAUUGUCUAAAUGGUUUGGUG_________________GGUUGGGGGGAUCCCCUCCAUUUUCCAACCCACUUUGUG
.....(((((.((.((((.....)))).)).))...................((.(((((((...)))))))....))....)))...... (-16.52 = -16.27 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 14,387,684 – 14,387,775
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 83.23
Mean single sequence MFE -22.75
Consensus MFE -13.56
Energy contribution -13.62
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -2.78
Structure conservation index 0.60
SVM decision value 1.16
SVM RNA-class probability 0.924275
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14387684 91 - 20766785
CACAAAGUGGGUUGGAAAAUGGAGAGGAUCCCCCCACCCCCCACCCCCCCUCCUCACACCAAACCAUUUAGACAAUGCCCAGGCACGCAAA
....((((((.((((.....((((.((...................)).)))).....)))).))))))......(((....)))...... ( -20.41)
>DroSec_CAF1 19864 74 - 1
CACAAAGUGGGUUGGAAAAUGGAGGGGAUCCCCCCAACC-----------------CACCAAACCAUUUAGACAAUGCCCAGGCACGCAAA
......(((((((((........(((....)))))))))-----------------)))................(((....)))...... ( -22.70)
>DroSim_CAF1 23121 74 - 1
CACAAAGUGGGUUGGAAAAUGGAGGGGAUCCCCCCAACC-----------------CACCAAAGCAUUUAGACAAUGCCCAGGCACGCAAA
......(((((((((........(((....)))))))))-----------------)))................(((....)))...... ( -22.70)
>DroEre_CAF1 21635 72 - 1
CACCAAGUGGGUUGGAAAAUGAGGGGGAUCCCCCU--CC-----------------CCCCAGACCAUUUAGACAAUGCCCAGGCACGCAAA
....((((((.((((.....((((((....)))))--).-----------------..)))).))))))......(((....)))...... ( -25.20)
>consensus
CACAAAGUGGGUUGGAAAAUGGAGGGGAUCCCCCCAACC_________________CACCAAACCAUUUAGACAAUGCCCAGGCACGCAAA
......((((.((((........((((....)))).............................((((.....)))).)))).).)))... (-13.56 = -13.62 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:10 2006