Locus 3608

Sequence ID 3L_DroMel_CAF1
Location 10,625,149 – 10,625,241
Length 92
Max. P 0.939053
window5622 window5623

overview

Window 2

Location 10,625,149 – 10,625,241
Length 92
Sequences 6
Columns 92
Reading direction forward
Mean pairwise identity 77.18
Mean single sequence MFE -25.92
Consensus MFE -17.26
Energy contribution -18.35
Covariance contribution 1.09
Combinations/Pair 1.09
Mean z-score -1.52
Structure conservation index 0.67
SVM decision value 0.73
SVM RNA-class probability 0.835100
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10625149 92 + 23771897
GCCAUUGGACUUUCGCCCACAAUGGAAACGCGUGACGCUAUAAAACAGUUGAUGUCAUGCGUUUGGGCUACACGGAAAGGGGGGGGGGGGGG
.((......((..(.(((.......(((((((((((((.((......)).).)))))))))))).(......).....))).)..))..)). ( -28.00)
>DroSec_CAF1 507412 86 + 1
GCCAUUGGACUUUCGCCCACAAUGGAAACGCGUGACGCUAUAAAAUAGUUGAUGUCAUGCGUUUGUG--UCGCGGAG----GGGGGAAGGGG
.........(((((.(((.(.(((.((((((((((((((((...)))))....))))))))))).))--)....).)----)).)))))... ( -30.10)
>DroSim_CAF1 509216 86 + 1
GCCAUUGGACUUUCGCCCACAAUGGAAACGCGUGACGCUAUAAAAUAGUUGAUGUCAUGCGUUUGUG--ACGCGGAG----GGGGGAAGGGG
.((......(((((((.(((((.....((((((((((((((...)))))....))))))))))))))--..))))))----).......)). ( -29.32)
>DroEre_CAF1 515473 74 + 1
GCAAUUGGACUUUCGCCCACAAUGGAAACGCGUGACGCUGUAAAAUAGUUGAUGUCAUGCGUUUUCG--AAGC----------GA------G
((...(((........)))...(((((((((((((((((((...)))))....))))))))))))))--..))----------..------. ( -24.70)
>DroYak_CAF1 517769 77 + 1
GCCAGCGGACUUUCGCCCACAAUGGAAACGCGUGACGCUAUAAAAUAGUUGAUGUCAUGCGUUUUCG--CGGG----------GAGAA---G
...........(((.(((....(((((((((((((((((((...)))))....))))))))))))))--..))----------).)))---. ( -28.10)
>DroPer_CAF1 571835 77 + 1
--GAUCGGACUUUCGCCCACAAUGGAAACGCGUGACGCUAUCAAAUAGUUUCUCUCAUGUGUUUUGCCUCUACAGAAG-------------G
--.......(((((..((.....))((((((((((.(((((...))))).....))))))))))..........))))-------------) ( -15.30)
>consensus
GCCAUUGGACUUUCGCCCACAAUGGAAACGCGUGACGCUAUAAAAUAGUUGAUGUCAUGCGUUUGCG__ACGCGGA_______GGGAA___G
.((((((............))))))((((((((((((((((...)))))....)))))))))))............................ (-17.26 = -18.35 +   1.09)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,625,149 – 10,625,241
Length 92
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 77.18
Mean single sequence MFE -21.01
Consensus MFE -17.25
Energy contribution -17.36
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -1.59
Structure conservation index 0.82
SVM decision value 1.27
SVM RNA-class probability 0.939053
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10625149 92 - 23771897
CCCCCCCCCCCCCCUUUCCGUGUAGCCCAAACGCAUGACAUCAACUGUUUUAUAGCGUCACGCGUUUCCAUUGUGGGCGAAAGUCCAAUGGC
........................(((.((((((.((((.................)))).))))))......(((((....)))))..))) ( -22.33)
>DroSec_CAF1 507412 86 - 1
CCCCUUCCCCC----CUCCGCGA--CACAAACGCAUGACAUCAACUAUUUUAUAGCGUCACGCGUUUCCAUUGUGGGCGAAAGUCCAAUGGC
...........----........--...((((((.((((.................)))).))))))((((..(((((....))))))))). ( -21.93)
>DroSim_CAF1 509216 86 - 1
CCCCUUCCCCC----CUCCGCGU--CACAAACGCAUGACAUCAACUAUUUUAUAGCGUCACGCGUUUCCAUUGUGGGCGAAAGUCCAAUGGC
...........----........--...((((((.((((.................)))).))))))((((..(((((....))))))))). ( -21.93)
>DroEre_CAF1 515473 74 - 1
C------UC----------GCUU--CGAAAACGCAUGACAUCAACUAUUUUACAGCGUCACGCGUUUCCAUUGUGGGCGAAAGUCCAAUUGC
.------..----------((..--.(.((((((.((((.................)))).)))))).)....(((((....)))))...)) ( -20.53)
>DroYak_CAF1 517769 77 - 1
C---UUCUC----------CCCG--CGAAAACGCAUGACAUCAACUAUUUUAUAGCGUCACGCGUUUCCAUUGUGGGCGAAAGUCCGCUGGC
.---.....----------.((.--.(.((((((.((((.................)))).)))))).)...((((((....)))))).)). ( -23.83)
>DroPer_CAF1 571835 77 - 1
C-------------CUUCUGUAGAGGCAAAACACAUGAGAGAAACUAUUUGAUAGCGUCACGCGUUUCCAUUGUGGGCGAAAGUCCGAUC--
.-------------((((....))))........(..(..(((((....((((...))))...)))))..)..)((((....))))....-- ( -15.50)
>consensus
C___UUCCC_______UCCGCGU__CAAAAACGCAUGACAUCAACUAUUUUAUAGCGUCACGCGUUUCCAUUGUGGGCGAAAGUCCAAUGGC
............................((((((.((((.................)))).))))))......(((((....)))))..... (-17.25 = -17.36 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:07 2006