Locus 1643

Sequence ID 3L_DroMel_CAF1
Location 4,766,226 – 4,766,323
Length 97
Max. P 0.984084
window2543 window2544

overview

Window 3

Location 4,766,226 – 4,766,323
Length 97
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 87.80
Mean single sequence MFE -32.89
Consensus MFE -27.50
Energy contribution -27.12
Covariance contribution -0.38
Combinations/Pair 1.14
Mean z-score -2.65
Structure conservation index 0.84
SVM decision value 1.96
SVM RNA-class probability 0.984084
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4766226 97 + 23771897
AAUGUUUCGCAGGCCGGCGAAACGUGCAACUGCAACAACAA-----------AAGUAGCAGCUGUAGUAAAUGUUGUUGCUGCCACUACCUCUUGCUGCACUUUGUUU
...(((((((......)))))))(((((...((((......-----------..((((((((..((.....))..)))))))).........)))))))))....... ( -29.73)
>DroSec_CAF1 29027 97 + 1
AAUGUUUCGCAGGCCGGCGAGACGUGCAACUGCAACAACAA-----------GAGCAGCAGCUGCAGUAAAUGUUGUUGCUGCAACUACCUCUUGCUGCACUUUGUUU
...(((((((......)))))))(((((...((((......-----------..((((((((.(((.....))).)))))))).........)))))))))....... ( -34.93)
>DroSim_CAF1 27975 97 + 1
AAUGUUUCGCAGGCCGGCGAGACGUGCAACUGCAACAACAA-----------GAGCAGCAGCUGCAGUAAAUGUUGUUGCUGCAACUACCUCUUUCUGCACUUUGUUU
...(((((((......)))))))(((((.((.........)-----------).((((((((.(((.....))).)))))))).............)))))....... ( -32.90)
>DroYak_CAF1 25274 107 + 1
AAUGUUUCGCAGGCCGGCGAAACGUGCAACUGCAGCAACU-GCAACAACAGAAAGCAGCAGCUGCAUUAAACGUUGUUGCUGCCACUACCUAUUGCUUCACUUUGUUU
.(((((((((......)))))))))((((.((.(((((((-(......)))...((((((((.((.......)).)))))))).........))))).))..)))).. ( -34.00)
>consensus
AAUGUUUCGCAGGCCGGCGAAACGUGCAACUGCAACAACAA___________AAGCAGCAGCUGCAGUAAAUGUUGUUGCUGCAACUACCUCUUGCUGCACUUUGUUU
.(((((((((......)))))))))((....)).....................((((((((..((.....))..))))))))......................... (-27.50 = -27.12 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,766,226 – 4,766,323
Length 97
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 87.80
Mean single sequence MFE -36.52
Consensus MFE -27.85
Energy contribution -29.85
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -3.40
Structure conservation index 0.76
SVM decision value 1.91
SVM RNA-class probability 0.982317
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4766226 97 - 23771897
AAACAAAGUGCAGCAAGAGGUAGUGGCAGCAACAACAUUUACUACAGCUGCUACUU-----------UUGUUGUUGCAGUUGCACGUUUCGCCGGCCUGCGAAACAUU
.....((.((((((((.(((.(((((((((................))))))))))-----------)).)))))))).))....(((((((......)))))))... ( -36.99)
>DroSec_CAF1 29027 97 - 1
AAACAAAGUGCAGCAAGAGGUAGUUGCAGCAACAACAUUUACUGCAGCUGCUGCUC-----------UUGUUGUUGCAGUUGCACGUCUCGCCGGCCUGCGAAACAUU
.......((((((((((((((((((((((.((......)).))))))))))..)))-----------))((....)).)))))))((.((((......)))).))... ( -35.80)
>DroSim_CAF1 27975 97 - 1
AAACAAAGUGCAGAAAGAGGUAGUUGCAGCAACAACAUUUACUGCAGCUGCUGCUC-----------UUGUUGUUGCAGUUGCACGUCUCGCCGGCCUGCGAAACAUU
.......((((((.(((((((((((((((.((......)).))))))))))..)))-----------))((....))..))))))((.((((......)))).))... ( -31.90)
>DroYak_CAF1 25274 107 - 1
AAACAAAGUGAAGCAAUAGGUAGUGGCAGCAACAACGUUUAAUGCAGCUGCUGCUUUCUGUUGUUGC-AGUUGCUGCAGUUGCACGUUUCGCCGGCCUGCGAAACAUU
............(((((..((((..((.(((((((((......((((...))))....)))))))))-.))..)))).)))))..(((((((......)))))))... ( -41.40)
>consensus
AAACAAAGUGCAGCAAGAGGUAGUGGCAGCAACAACAUUUACUGCAGCUGCUGCUC___________UUGUUGUUGCAGUUGCACGUCUCGCCGGCCUGCGAAACAUU
.......(((((((....(((((((((((.((......)).))))))))))).................((....)).)))))))(((((((......)))))))... (-27.85 = -29.85 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:42 2006