Locus 1335

Sequence ID 3R_DroMel_CAF1
Location 3,936,340 – 3,936,445
Length 105
Max. P 0.886066
window2182 window2183

overview

Window 2

Location 3,936,340 – 3,936,445
Length 105
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 90.92
Mean single sequence MFE -34.22
Consensus MFE -29.98
Energy contribution -30.48
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.88
SVM decision value 0.47
SVM RNA-class probability 0.748929
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3936340 105 + 27905053
CUAUGCCUCUGUGUGUGGCAUGACUCAUGCAACAGCAACAGAGGCCCCAGCAGACGAAUCCAAUCGAAACGAAACGAAAACGCUCCGCGGUGGUGGAGUAGGUGA
....((((((((.(((.(((((...))))).)))...))))))))..((.(...(((......)))...............(((((((....))))))).).)). ( -35.40)
>DroSec_CAF1 4516 100 + 1
CUAUGCCUCUGUGUGUGGCAUGACUCAUGCAACAGCAACAGAGGCCCCAGCAGACGAAUCCAAUCGAAACGA-----AAACGCUCCGCGGUGGUGGAGUAGGUGA
....((((((((.(((.(((((...))))).)))...))))))))..((.(...(((......)))......-----....(((((((....))))))).).)). ( -35.40)
>DroEre_CAF1 4691 100 + 1
CUAUGCCUCUGUGUGUGGCAUGACUCAUGCAACAGCAACAGAGGCCCCAGCAGACGAAUCCAAUCGAAA-----CGAAAACGCUGCGCGGCGGUGGCGCAGGAGG
....((((((((.(((.(((((...))))).)))...)))))))).((......(((......)))...-----........((((((.......))))))..)) ( -34.40)
>DroYak_CAF1 4755 105 + 1
CUAUGCCUCUGUGUGUGGCAUGACUCAUGCAACAACAACAGAGGCCCCAGCAGACGAAUCCAAUCGAAACGAAACGAAAACGCACCGCGGUGGUGGAGAAGAAGG
....((((((((.(((.(((((...))))).)))...)))))))).(((.((..(((......)))..............(((...))).)).)))......... ( -31.70)
>consensus
CUAUGCCUCUGUGUGUGGCAUGACUCAUGCAACAGCAACAGAGGCCCCAGCAGACGAAUCCAAUCGAAACGA__CGAAAACGCUCCGCGGUGGUGGAGUAGGAGA
((((((((((((.(((.(((((...))))).)))...)))))))).(((.(...(((......)))..............(((...)))..).))).)))).... (-29.98 = -30.48 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 3,936,340 – 3,936,445
Length 105
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 90.92
Mean single sequence MFE -36.80
Consensus MFE -31.00
Energy contribution -32.00
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.84
SVM decision value 0.94
SVM RNA-class probability 0.886066
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3936340 105 - 27905053
UCACCUACUCCACCACCGCGGAGCGUUUUCGUUUCGUUUCGAUUGGAUUCGUCUGCUGGGGCCUCUGUUGCUGUUGCAUGAGUCAUGCCACACACAGAGGCAUAG
............((.(.(((((.((..((((..(((...))).))))..))))))).)))((((((((.(.(((.(((((...))))).)))))))))))).... ( -37.10)
>DroSec_CAF1 4516 100 - 1
UCACCUACUCCACCACCGCGGAGCGUUU-----UCGUUUCGAUUGGAUUCGUCUGCUGGGGCCUCUGUUGCUGUUGCAUGAGUCAUGCCACACACAGAGGCAUAG
............((.(.(((((.((..(-----(((.......))))..))))))).)))((((((((.(.(((.(((((...))))).)))))))))))).... ( -35.90)
>DroEre_CAF1 4691 100 - 1
CCUCCUGCGCCACCGCCGCGCAGCGUUUUCG-----UUUCGAUUGGAUUCGUCUGCUGGGGCCUCUGUUGCUGUUGCAUGAGUCAUGCCACACACAGAGGCAUAG
...(((((((....).)))((((((..((((-----.......))))..)).)))).)))((((((((.(.(((.(((((...))))).)))))))))))).... ( -37.70)
>DroYak_CAF1 4755 105 - 1
CCUUCUUCUCCACCACCGCGGUGCGUUUUCGUUUCGUUUCGAUUGGAUUCGUCUGCUGGGGCCUCUGUUGUUGUUGCAUGAGUCAUGCCACACACAGAGGCAUAG
............((.(.((((.(((..((((..(((...))).))))..))))))).)))((((((((.((.((.(((((...))))).)))))))))))).... ( -36.50)
>consensus
CCACCUACUCCACCACCGCGGAGCGUUUUCG__UCGUUUCGAUUGGAUUCGUCUGCUGGGGCCUCUGUUGCUGUUGCAUGAGUCAUGCCACACACAGAGGCAUAG
............((.(.((((.(((..((((............))))..))))))).)))((((((((.(.(((.(((((...))))).)))))))))))).... (-31.00 = -32.00 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:02 2006