Locus 2272

Sequence ID 3L_DroMel_CAF1
Location 6,345,535 – 6,345,630
Length 95
Max. P 0.880675
window3509 window3510

overview

Window 9

Location 6,345,535 – 6,345,630
Length 95
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 72.12
Mean single sequence MFE -16.00
Consensus MFE -8.80
Energy contribution -8.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.55
SVM decision value 0.57
SVM RNA-class probability 0.784235
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6345535 95 + 23771897
UUAGUAAAAAAAAAAACAUUGAGUUAUUUUUCCAAAA-UUAACAAGAACCGAAACUCUGGCUUUUUCUUCCAGUGCAGCUCUCUGCACUCCCCUGC
.........(((((..((..(((((....(((.....-.......)))....)))))))..))))).....(((((((....)))))))....... ( -12.60)
>DroSec_CAF1 110317 92 + 1
UUAGGGAC---AAAAACAUUGGGUUAUUUUUCAAAAU-UUCACAAUGACAAGAACUCUUGCCUUUUCUCCCAGUGCAGCUCUCUGCACUCCCCUGC
...((((.---((((.(((((.(..((((....))))-..).))))).((((....))))..)))).))))(((((((....)))))))....... ( -23.70)
>DroSim_CAF1 116249 80 + 1
UUUGUGAC---AAAAACAUUAAGUUAUUUUUCUAAAA-UUAACAAGGAC------------UUUUUCUCUCAGUGCAGCUCUCUGCACUCCCCUGC
..((.((.---(((((......((((.(((....)))-.))))......------------))))).)).))((((((....))))))........ ( -11.70)
>DroYak_CAF1 120784 81 + 1
GUA--UAU-CAUAACACUUAGAGUUAUGUUUCGAAAACUUCAGUUGCAG------------UUUUUCUCUCAGUGCAGCUCUCUGCACUCCCCUGC
...--...-((((((.......))))))....(((((((.(....).))------------))))).....(((((((....)))))))....... ( -16.00)
>consensus
UUAGUGAC___AAAAACAUUGAGUUAUUUUUCAAAAA_UUAACAAGGAC____________UUUUUCUCCCAGUGCAGCUCUCUGCACUCCCCUGC
.......................................................................(((((((....)))))))....... ( -8.80 =  -8.80 +  -0.00)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 6,345,535 – 6,345,630
Length 95
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 72.12
Mean single sequence MFE -22.38
Consensus MFE -11.25
Energy contribution -10.25
Covariance contribution -1.00
Combinations/Pair 1.38
Mean z-score -2.10
Structure conservation index 0.50
SVM decision value 0.91
SVM RNA-class probability 0.880675
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6345535 95 - 23771897
GCAGGGGAGUGCAGAGAGCUGCACUGGAAGAAAAAGCCAGAGUUUCGGUUCUUGUUAA-UUUUGGAAAAAUAACUCAAUGUUUUUUUUUUUACUAA
.......(((((((....)))))))((((((((((((..(((((....((((......-....))))....)))))...))))))))))))..... ( -25.10)
>DroSec_CAF1 110317 92 - 1
GCAGGGGAGUGCAGAGAGCUGCACUGGGAGAAAAGGCAAGAGUUCUUGUCAUUGUGAA-AUUUUGAAAAAUAACCCAAUGUUUUU---GUCCCUAA
...(((((((((((....))))))((((......((((((....))))))........-...((....))...))))........---.))))).. ( -28.60)
>DroSim_CAF1 116249 80 - 1
GCAGGGGAGUGCAGAGAGCUGCACUGAGAGAAAAA------------GUCCUUGUUAA-UUUUAGAAAAAUAACUUAAUGUUUUU---GUCACAAA
((((((((((((((....)))))))..........------------.)))))))...-......(((((((......)))))))---........ ( -16.90)
>DroYak_CAF1 120784 81 - 1
GCAGGGGAGUGCAGAGAGCUGCACUGAGAGAAAAA------------CUGCAACUGAAGUUUUCGAAACAUAACUCUAAGUGUUAUG-AUA--UAC
((((...(((((((....)))))))..........------------)))).................((((((.......))))))-...--... ( -18.92)
>consensus
GCAGGGGAGUGCAGAGAGCUGCACUGAGAGAAAAA____________GUCCUUGUGAA_UUUUAGAAAAAUAACUCAAUGUUUUU___GUCACUAA
...(((.(((((((....))))))).............................(((.....)))........))).................... (-11.25 = -10.25 +  -1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:20 2006