Locus 1983

Sequence ID 2R_DroMel_CAF1
Location 7,481,850 – 7,481,953
Length 103
Max. P 0.965195
window3279 window3280

overview

Window 9

Location 7,481,850 – 7,481,953
Length 103
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 85.47
Mean single sequence MFE -45.65
Consensus MFE -34.53
Energy contribution -34.65
Covariance contribution 0.12
Combinations/Pair 1.16
Mean z-score -2.28
Structure conservation index 0.76
SVM decision value 1.25
SVM RNA-class probability 0.935558
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7481850 103 + 20766785
------------GGCGCAACAGGAGUGGCUGGGGGAAAGGCCAGAGGAGGCGGUGGGCCAACGAUGGCCCCACCACUGGCCACCACUCCAGCCGCAAACAAUGCAACUGCGGUUA
------------..((((........((((((((....((((((.(....)(((((((((....))).)))))).))))))....))))))))(((.....)))...)))).... ( -50.50)
>DroSec_CAF1 98208 103 + 1
------------AGCGCAACAGGAGUGGCUGGGGGAAAGGCCCGAGGAGGCGGUGUGGCAACGAUGGCCCCACCACUGGCCACCAGUCCAGCCGCAAACAAUGCAACUGCGGUUA
------------..((((........(((((((((.....)))..((.(((((((.(((.......))).))))....))).))...))))))(((.....)))...)))).... ( -41.30)
>DroSim_CAF1 90554 103 + 1
------------AGCGCAACAGGAGUGGCUGGGGGAAAGGCCCGAGGAGGCGGUGGGCCAACGAUGGCCCCACCACUGGCCACCAGUCUAGCCGCAAACAAUGCAACUGCGGUUA
------------..((((...((...((((((.((..(((((......)))(((((((((....))).)))))).))..)).))))))...))(((.....)))...)))).... ( -46.30)
>DroYak_CAF1 96568 115 + 1
GGUUCGGGACCAGGAGCAACAGGAGUUGCUGGGGGAAAGAUCAGAGGAGGCAGUGGGCCAACAAUGUCCCCAGCACUGGCCGCCAGCCCAGCGGCAAACAAUGCAACUGCGGCCA
(((...((.((((.((((((....)))))).(((((.....((..(..(((.....)))..)..)))))))....))))))))).((((((..(((.....)))..))).))).. ( -44.50)
>consensus
____________AGCGCAACAGGAGUGGCUGGGGGAAAGGCCAGAGGAGGCGGUGGGCCAACGAUGGCCCCACCACUGGCCACCAGUCCAGCCGCAAACAAUGCAACUGCGGUUA
...............((..(((....(((((((((...((((((.((.(((.((.(.....).)).)))))....)))))).))..)))))))(((.....)))..)))..)).. (-34.53 = -34.65 +   0.12)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 7,481,850 – 7,481,953
Length 103
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 85.47
Mean single sequence MFE -46.55
Consensus MFE -34.76
Energy contribution -35.95
Covariance contribution 1.19
Combinations/Pair 1.10
Mean z-score -2.57
Structure conservation index 0.75
SVM decision value 1.58
SVM RNA-class probability 0.965195
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7481850 103 - 20766785
UAACCGCAGUUGCAUUGUUUGCGGCUGGAGUGGUGGCCAGUGGUGGGGCCAUCGUUGGCCCACCGCCUCCUCUGGCCUUUCCCCCAGCCACUCCUGUUGCGCC------------
....((((((((((.....)))))))((((((((((((((.((((((((((....)))))..)))))....)))))).........))))))))....)))..------------ ( -53.00)
>DroSec_CAF1 98208 103 - 1
UAACCGCAGUUGCAUUGUUUGCGGCUGGACUGGUGGCCAGUGGUGGGGCCAUCGUUGCCACACCGCCUCCUCGGGCCUUUCCCCCAGCCACUCCUGUUGCGCU------------
....(((((..(((.....)))((((((...((.((((.((((((.(((.......))).)))))).......))))...)).)))))).......)))))..------------ ( -41.60)
>DroSim_CAF1 90554 103 - 1
UAACCGCAGUUGCAUUGUUUGCGGCUAGACUGGUGGCCAGUGGUGGGGCCAUCGUUGGCCCACCGCCUCCUCGGGCCUUUCCCCCAGCCACUCCUGUUGCGCU------------
....((((((((((.....))))))).(((.((((((..((((((((.(((....)))))))))))......(((.......))).))))))...))))))..------------ ( -45.40)
>DroYak_CAF1 96568 115 - 1
UGGCCGCAGUUGCAUUGUUUGCCGCUGGGCUGGCGGCCAGUGCUGGGGACAUUGUUGGCCCACUGCCUCCUCUGAUCUUUCCCCCAGCAACUCCUGUUGCUCCUGGUCCCGAACC
.((((.((((.(((.....))).))))))))((.((((((....(((((((..(..(((.....)))..)..)).....))))).((((((....)))))).))))))))..... ( -46.20)
>consensus
UAACCGCAGUUGCAUUGUUUGCGGCUGGACUGGUGGCCAGUGGUGGGGCCAUCGUUGGCCCACCGCCUCCUCGGGCCUUUCCCCCAGCCACUCCUGUUGCGCC____________
....(((((..(((.....)))((((((...((((((((..((((....))))..)))).))))(((......))).......)))))).......))))).............. (-34.76 = -35.95 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:03 2006