Locus 668

Sequence ID 2L_DroMel_CAF1
Location 1,966,846 – 1,966,998
Length 152
Max. P 0.952710
window1095 window1096

overview

Window 5

Location 1,966,846 – 1,966,958
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.44
Mean single sequence MFE -27.57
Consensus MFE -18.04
Energy contribution -18.23
Covariance contribution 0.20
Combinations/Pair 1.28
Mean z-score -2.93
Structure conservation index 0.65
SVM decision value 1.42
SVM RNA-class probability 0.952710
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966846 112 + 22407834
UUUUCGCCACAUGAAA--GCCAGAAGCAAAUGAGAAAAUAAAUAACACAA---A-UAAA-AAAGCGAAC-UCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCA
.....(((((......--((.....)).......................---.-....-...(((...-..(....).((((((...((.......)).))))))))).....))))). ( -24.00)
>DroSec_CAF1 9316 113 + 1
UUUUCGCCACAUGAAA--GCCAGAAGCAAAUGAGAAAAUAAAUAACACAA---A-UAAAAAAAGGGAAC-CCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCA
.....(((((......--((.....)).......................---.-.......((((...-))))..((.((((((...((.......)).))))))))......))))). ( -25.20)
>DroSim_CAF1 13467 113 + 1
UUUUCGCCACAUGAAA--GCCAGAAGCAAAUGAGAAAAUAAAUAACACAA---A-UAAAAAAAGGGAAC-CCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCA
.....(((((......--((.....)).......................---.-.......((((...-))))..((.((((((...((.......)).))))))))......))))). ( -25.20)
>DroEre_CAF1 18403 113 + 1
UUUUCGCCACAUGAAA--GGCAGAGGCAACGUGGAAAAUAAAUAAC--AAGG-C-UGAAAAAAGGGAAC-CCCUAACGAGCGCUGGAAUUAUUUUUAGAGCAGUGCCGCAAAAAGUGGCA
.....(((((......--((((..(....)((.((((((((....(--(..(-(-(......((((...-))))....)))..))...))))))))...))..)))).......))))). ( -28.42)
>DroYak_CAF1 16331 120 + 1
UUUUCGCCACAUGAACGGGGCAGAAGCAACUGCGAAACUAAAUAAUACAAAGUGUACAAAAAAGCAAACCCCCCAACGAGCGCUGAAAUUAUUUUUAGAGCAGCGCCGCAAAAAGUGGCA
.....(((((......(((((((......))))............(((.....)))...............)))..((.((((((...(((....)))..))))))))......))))). ( -32.60)
>DroAna_CAF1 40044 100 + 1
UUUGCGCCACAGGAAA--A--------AAAUGUAGAGA-----GGCACAG---A-GAAGGAAAAAAGAC-CCUUAACGAGCUCUAAAAUUAUUUUUAGAGCAGUGCCGCAAAAAGUGGCA
.....(((((.(....--.--------...).....(.-----(((((.(---.-.((((.........-))))..)..(((((((((....))))))))).))))).).....))))). ( -30.00)
>consensus
UUUUCGCCACAUGAAA__GCCAGAAGCAAAUGAGAAAAUAAAUAACACAA___A_UAAAAAAAGGGAAC_CCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCA
.....(((((.....................................................(((.....)))..((.((((((...((.......)).))))))))......))))). (-18.04 = -18.23 +   0.20)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 1,966,884 – 1,966,998
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.80
Mean single sequence MFE -31.77
Consensus MFE -21.88
Energy contribution -21.47
Covariance contribution -0.41
Combinations/Pair 1.25
Mean z-score -3.27
Structure conservation index 0.69
SVM decision value 0.03
SVM RNA-class probability 0.547846
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966884 114 + 22407834
AAUAACACAA---A-UAAA-AAAGCGAAC-UCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCAAGUAAUGCAAAUAUCUAAGCCUGCAAGUGGCUCGGGGAAA
..........---.-....-.........-((((..(((((........(((((((((.((..((((((.....)))))).(.....)..........)))))))))))))))))))).. ( -31.00)
>DroSec_CAF1 9354 115 + 1
AAUAACACAA---A-UAAAAAAAGGGAAC-CCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCAAGUAAUGCAAAUAUCUAAGCCUGCAAGUGGCUCGGGGAAA
..........---.-.............(-(((....((((........(((((((((.((..((((((.....)))))).(.....)..........)))))))))))))))))))... ( -31.60)
>DroSim_CAF1 13505 115 + 1
AAUAACACAA---A-UAAAAAAAGGGAAC-CCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCAAGUAAUGCAAAUAUCUAAGCCUGCAAGUGGCUCGGGGAAA
..........---.-.............(-(((....((((........(((((((((.((..((((((.....)))))).(.....)..........)))))))))))))))))))... ( -31.60)
>DroEre_CAF1 18441 115 + 1
AAUAAC--AAGG-C-UGAAAAAAGGGAAC-CCCUAACGAGCGCUGGAAUUAUUUUUAGAGCAGUGCCGCAAAAAGUGGCAAAUAAUGCAAGUAUCUAAGCCUGCAAGUGGCGCGGGGAAA
......--....-.-.............(-(((......((.((((((....)))))).)).(((((((.....((.....))..((((.((......)).)))).)))))))))))... ( -31.20)
>DroYak_CAF1 16371 120 + 1
AAUAAUACAAAGUGUACAAAAAAGCAAACCCCCCAACGAGCGCUGAAAUUAUUUUUAGAGCAGCGCCGCAAAAAGUGGCAAGUAAUGCAAAUAUCUAAGCCUGCAAGUGGCGCGGGGAAA
..............................((((.....((.((((((....)))))).)).(((((((.......(((...................))).....)))))))))))... ( -32.11)
>DroAna_CAF1 40072 112 + 1
---GGCACAG---A-GAAGGAAAAAAGAC-CCUUAACGAGCUCUAAAAUUAUUUUUAGAGCAGUGCCGCAAAAAGUGGCAAAUAAUGCAAAUAUCUAAGCAUGCAAGUGGCGCGAGGAAA
---(((((.(---.-.((((.........-))))..)..(((((((((....))))))))).))))).......(((.((....((((..........)))).....)).)))....... ( -33.10)
>consensus
AAUAACACAA___A_UAAAAAAAGGGAAC_CCCUAACGAGCGCUGAAAUCAUUUGUAGAGCAGUGCCGCAAAAAGUGGCAAGUAAUGCAAAUAUCUAAGCCUGCAAGUGGCGCGGGGAAA
..............................((((.....((((((...((.......)).))))(((((.....))))).......))..........(((.......)))..))))... (-21.88 = -21.47 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:28 2006