Locus 784

Sequence ID 2R_DroMel_CAF1
Location 3,747,419 – 3,747,531
Length 112
Max. P 0.629805
window1375 window1376

overview

Window 5

Location 3,747,419 – 3,747,531
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.34
Mean single sequence MFE -46.43
Consensus MFE -30.76
Energy contribution -31.43
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.25
Structure conservation index 0.66
SVM decision value 0.20
SVM RNA-class probability 0.629805
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3747419 112 + 20766785
GCUCUCGUG--------CCAAGAAUUGGCACAGCUGCCGACUCCAUUCUCCCGGCUGCAUCCCCCGCCACUUCUUCGAGCCACGAGAACAAUGGACUUGGCCCGGACAAUGGUCGGCGCU
......(((--------(((.....))))))(((.(((((..(((((.(((.(((((..(((........((((.((.....))))))....)))..))))).))).))))))))))))) ( -41.40)
>DroSim_CAF1 10272 112 + 1
GCUCUCGUG--------CCAAGGAUUGGCACAGCUGCCGACUCCAUUCUCCCGGCUGCAUCCCCCGCCACUUCUUCGGGCCACCAGAACAAUGGACUUGGCCCGGACAAUGGUCGGCGCU
......(((--------(((.....))))))(((.(((((..(((((.(((.(((..........)))........(((((((((......)))...))))))))).))))))))))))) ( -48.20)
>DroYak_CAF1 10035 120 + 1
GCUCUCGUGCCAUCCUGCCAAGGAUUGGCACAUCUGCCGACUCCAUUCUCCCUGCUGCAUCCCCCGCCACUUCUUCGGGCCAUGUGAACAAUGCAUUUGGCCCGGACAAUGGUCGGCGCU
((....((((((((((....)))).))))))....(((((..(((((.(((.....((.......)).........((((((.(((.......))).))))))))).)))))))))))). ( -49.70)
>consensus
GCUCUCGUG________CCAAGGAUUGGCACAGCUGCCGACUCCAUUCUCCCGGCUGCAUCCCCCGCCACUUCUUCGGGCCACGAGAACAAUGGACUUGGCCCGGACAAUGGUCGGCGCU
((....(((........(((.....))))))....(((((..(((((.(((.(((..........)))........((((((...............))))))))).)))))))))))). (-30.76 = -31.43 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 3,747,419 – 3,747,531
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.34
Mean single sequence MFE -51.77
Consensus MFE -36.41
Energy contribution -36.19
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.58
Structure conservation index 0.70
SVM decision value 0.05
SVM RNA-class probability 0.556290
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3747419 112 - 20766785
AGCGCCGACCAUUGUCCGGGCCAAGUCCAUUGUUCUCGUGGCUCGAAGAAGUGGCGGGGGAUGCAGCCGGGAGAAUGGAGUCGGCAGCUGUGCCAAUUCUUGG--------CACGAGAGC
(((((((((((((.(((.(((...((((......(((((.(((......))).)))))))))...))).))).)))))..))))).)))((((((.....)))--------)))...... ( -53.00)
>DroSim_CAF1 10272 112 - 1
AGCGCCGACCAUUGUCCGGGCCAAGUCCAUUGUUCUGGUGGCCCGAAGAAGUGGCGGGGGAUGCAGCCGGGAGAAUGGAGUCGGCAGCUGUGCCAAUCCUUGG--------CACGAGAGC
(((((((((((((.(((((((((...(((......))))))))).......((((..........))))))).)))))..))))).)))((((((.....)))--------)))...... ( -50.90)
>DroYak_CAF1 10035 120 - 1
AGCGCCGACCAUUGUCCGGGCCAAAUGCAUUGUUCACAUGGCCCGAAGAAGUGGCGGGGGAUGCAGCAGGGAGAAUGGAGUCGGCAGAUGUGCCAAUCCUUGGCAGGAUGGCACGAGAGC
.((((((((((((.(((((((((..((.......))..))))))......((.(((.....))).))..))).)))))..)))))...(((((((.((((....)))))))))))...)) ( -51.40)
>consensus
AGCGCCGACCAUUGUCCGGGCCAAGUCCAUUGUUCUCGUGGCCCGAAGAAGUGGCGGGGGAUGCAGCCGGGAGAAUGGAGUCGGCAGCUGUGCCAAUCCUUGG________CACGAGAGC
.((((((((((((.(((((((((...............))))))......((.(((.....))).))..))).)))))..))))).............((((...........)))).)) (-36.41 = -36.19 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:18 2006