Locus 4366

Sequence ID 3R_DroMel_CAF1
Location 11,516,773 – 11,516,877
Length 104
Max. P 0.993789
window7138 window7139

overview

Window 8

Location 11,516,773 – 11,516,877
Length 104
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 79.87
Mean single sequence MFE -27.48
Consensus MFE -13.70
Energy contribution -15.45
Covariance contribution 1.75
Combinations/Pair 1.17
Mean z-score -2.79
Structure conservation index 0.50
SVM decision value 0.84
SVM RNA-class probability 0.864598
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11516773 104 + 27905053
GGUUG-------UGCCAAAGAUAUAUGUAUGUAUAUGUACAUAUACAUACAUGCAUAUACUCGUAUGCCGGCGCUAAGAAAACCAACUUAAUUAUUUUCUCAAGGCGGAAG
(((((-------((((........((((((((((((....))))))))))))((((((....)))))).)))))......))))............((((......)))). ( -29.50)
>DroSec_CAF1 50419 96 + 1
GGUUG-------UGCCAAGGAUAUAUGUACAUAU--G------UACAUAUAUGCAUAUACUCGUAUGCCGGCGCUAAGAAAAACAACUUAAUUAUUUUCUCAGGGCGGAAG
.....-------.(((....((((((((((....--)------)))))))))((((((....)))))).)))(((.((((((............))))))...)))..... ( -26.40)
>DroSim_CAF1 52706 96 + 1
GGUUG-------UGCCAAGGAUAUAUGUAUGUAC--A------UAUGUAUAUGCAUAUACUCGUAUGCCGGCGCUAAGAAAAACAACUUAAUUAUUUUCUCAGGGCGGAAG
((...-------..))..(..(((((((((((((--.------...)))))))))))))..).....(((.(.((.((((((............)))))).))).)))... ( -27.80)
>DroYak_CAF1 48849 95 + 1
GGUUGUGGGUCCUGCCAAGGAUAUAUGUAAAUGC--A------UACAUAUA--CAU----ACGUAUGCCAGCCUUAAGAAA-ACAACUUAAUUAUUUUCUCAGGGCUGAG-
....(((.(((((....))))).)))......((--(------(((.....--...----..))))))(((((((.(((((-(.((.....)).)))))).)))))))..- ( -26.20)
>consensus
GGUUG_______UGCCAAGGAUAUAUGUAUAUAC__A______UACAUAUAUGCAUAUACUCGUAUGCCGGCGCUAAGAAAAACAACUUAAUUAUUUUCUCAGGGCGGAAG
(((..........)))...(((((((((((((((............))))))))))))).))......(.((.((.((((((............)))))).)).)).)... (-13.70 = -15.45 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 11,516,773 – 11,516,877
Length 104
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 79.87
Mean single sequence MFE -27.62
Consensus MFE -14.47
Energy contribution -15.71
Covariance contribution 1.25
Combinations/Pair 1.10
Mean z-score -3.73
Structure conservation index 0.52
SVM decision value 2.42
SVM RNA-class probability 0.993789
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11516773 104 - 27905053
CUUCCGCCUUGAGAAAAUAAUUAAGUUGGUUUUCUUAGCGCCGGCAUACGAGUAUAUGCAUGUAUGUAUAUGUACAUAUACAUACAUAUAUCUUUGGCA-------CAACC
.....((..(((((((((..........)))))))))))(((((((((......)))))((((((((((((....)))))))))))).......)))).-------..... ( -30.40)
>DroSec_CAF1 50419 96 - 1
CUUCCGCCCUGAGAAAAUAAUUAAGUUGUUUUUCUUAGCGCCGGCAUACGAGUAUAUGCAUAUAUGUA------C--AUAUGUACAUAUAUCCUUGGCA-------CAACC
........(((((((((((((...)))).))))))))).(((((((((......)))))(((((((((------(--....))))))))))...)))).-------..... ( -27.10)
>DroSim_CAF1 52706 96 - 1
CUUCCGCCCUGAGAAAAUAAUUAAGUUGUUUUUCUUAGCGCCGGCAUACGAGUAUAUGCAUAUACAUA------U--GUACAUACAUAUAUCCUUGGCA-------CAACC
.....((((((((((((((((...)))).)))))))))....((.(((...((((.((((((....))------)--))).))))...)))))..))).-------..... ( -20.60)
>DroYak_CAF1 48849 95 - 1
-CUCAGCCCUGAGAAAAUAAUUAAGUUGU-UUUCUUAAGGCUGGCAUACGU----AUG--UAUAUGUA------U--GCAUUUACAUAUAUCCUUGGCAGGACCCACAACC
-..(((((.((((((((((((...)))))-))))))).)))))((((((((----(..--..))))))------)--))...........((((....))))......... ( -32.40)
>consensus
CUUCCGCCCUGAGAAAAUAAUUAAGUUGUUUUUCUUAGCGCCGGCAUACGAGUAUAUGCAUAUAUGUA______C__AUACAUACAUAUAUCCUUGGCA_______CAACC
........(((((((((((((...)))).))))))))).(((((((((......)))))(((((((((..............)))))))))...))))............. (-14.47 = -15.71 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:24 2006