Locus 3539

Sequence ID 3L_DroMel_CAF1
Location 10,370,521 – 10,370,630
Length 109
Max. P 0.999044
window5525 window5526

overview

Window 5

Location 10,370,521 – 10,370,630
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.72
Mean single sequence MFE -33.08
Consensus MFE -20.96
Energy contribution -21.68
Covariance contribution 0.72
Combinations/Pair 1.13
Mean z-score -2.15
Structure conservation index 0.63
SVM decision value 1.80
SVM RNA-class probability 0.977881
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10370521 109 + 23771897
UUGUUGCAGGUUGCUACUGGGAUAUGAUGUUGCUUGCAGCUAGUUGCUUAUGAGUGCACUGAGAAAA--AUG--CAGCUUGCAGCUC-------UGACAUACAAAUGAUGUUAUCCUGUU
..((((((((((((..............((((....))))((((.((........))))))......--..)--)))))))))))..-------((((((.(....)))))))....... ( -29.50)
>DroSec_CAF1 244254 97 + 1
UAGUUGCAGGUUGCUACUGGGAUAUGUUGCUGCUUGCAGCUAGUUGCUCAUGGCUGCACUGAGAGAA--AUG--CAGCUUGCAGCUU-------UUACAU------------AUCCUGUU
.(((.((.....)).)))(((((((((.((((....)))).((((((....(((((((.(......)--.))--))))).)))))).-------..))))------------)))))... ( -37.40)
>DroSim_CAF1 254932 97 + 1
UUGUUGCAGGUUGCUACUGGGAUAUGUUGCUGCUUGCAGCUAGUUGCUCAUGGCUGCACUGAGAGAA--AUG--CAGCUUGCAGCUU-------UGACAU------------AUCCUGUU
..((.((.....)).)).((((((((((((((....)))).((((((....(((((((.(......)--.))--))))).)))))).-------.)))))------------)))))... ( -38.00)
>DroEre_CAF1 259107 109 + 1
UUGUUGCAGGUUGCUACUGGGAUAUGUUGCUGCUUGCAGCUAGUUGGCCGUGACUGCACUGCCAAAA--ACGCACAGUAUGUAGAUUGGGUUAC-AACAUAAAAAAUA--------UGUU
..(((((((((.((.((........)).)).)))))))))...(((((.(((....))).))))).(--((.(.((((......))))))))..-((((((.....))--------)))) ( -30.70)
>DroYak_CAF1 256747 120 + 1
UUGUUGCAGGUUGCUACUGGGAUAUGUUGCUGGUUGCGGCUAGUUGCUCAUGGCUGCACUGCCAAAAAAAAUCACACCUUGCAGCUAAGGUUACUUACAUUAACAAUACUUUAUCCUGUU
..(((((((((.((.((........)).))((((((((((((........))))))))..))))...........))).))))))((((....))))....................... ( -29.80)
>consensus
UUGUUGCAGGUUGCUACUGGGAUAUGUUGCUGCUUGCAGCUAGUUGCUCAUGGCUGCACUGAGAAAA__AUG__CAGCUUGCAGCUU_______UGACAU__A_A__A____AUCCUGUU
..(((((((((.((.((........)).)).)))))))))...........((((((((((.............)))..))))))).................................. (-20.96 = -21.68 +   0.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,370,521 – 10,370,630
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.72
Mean single sequence MFE -29.04
Consensus MFE -12.55
Energy contribution -13.67
Covariance contribution 1.12
Combinations/Pair 1.11
Mean z-score -2.96
Structure conservation index 0.43
SVM decision value 3.34
SVM RNA-class probability 0.999044
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10370521 109 - 23771897
AACAGGAUAACAUCAUUUGUAUGUCA-------GAGCUGCAAGCUG--CAU--UUUUCUCAGUGCACUCAUAAGCAACUAGCUGCAAGCAACAUCAUAUCCCAGUAGCAACCUGCAACAA
..((((.........((((.....))-------))(((((.((.((--(((--(......)))))))).....(((......)))..................)))))..))))...... ( -21.30)
>DroSec_CAF1 244254 97 - 1
AACAGGAU------------AUGUAA-------AAGCUGCAAGCUG--CAU--UUCUCUCAGUGCAGCCAUGAGCAACUAGCUGCAAGCAGCAACAUAUCCCAGUAGCAACCUGCAACUA
....((((------------((((..-------..(((((..((((--(((--(......))))))))..(((((.....))).)).))))).)))))))).(((.((.....)).))). ( -35.60)
>DroSim_CAF1 254932 97 - 1
AACAGGAU------------AUGUCA-------AAGCUGCAAGCUG--CAU--UUCUCUCAGUGCAGCCAUGAGCAACUAGCUGCAAGCAGCAACAUAUCCCAGUAGCAACCUGCAACAA
....((((------------((((..-------..(((((..((((--(((--(......))))))))..(((((.....))).)).))))).))))))))..((((....))))..... ( -34.90)
>DroEre_CAF1 259107 109 - 1
AACA--------UAUUUUUUAUGUU-GUAACCCAAUCUACAUACUGUGCGU--UUUUGGCAGUGCAGUCACGGCCAACUAGCUGCAAGCAGCAACAUAUCCCAGUAGCAACCUGCAACAA
....--------.........((((-(((.......((((...........--..(((((.(((....))).)))))...((((....))))...........)))).....))))))). ( -24.90)
>DroYak_CAF1 256747 120 - 1
AACAGGAUAAAGUAUUGUUAAUGUAAGUAACCUUAGCUGCAAGGUGUGAUUUUUUUUGGCAGUGCAGCCAUGAGCAACUAGCCGCAACCAGCAACAUAUCCCAGUAGCAACCUGCAACAA
..((((.................((((....))))(((((..((((((.........((((((((........)).))).)))((.....))..))))))...)))))..))))...... ( -28.50)
>consensus
AACAGGAU____U__U_U__AUGUAA_______AAGCUGCAAGCUG__CAU__UUUUCUCAGUGCAGCCAUGAGCAACUAGCUGCAAGCAGCAACAUAUCCCAGUAGCAACCUGCAACAA
..((((.............................(((((..((((.............)))))))))............(((((..................)))))..))))...... (-12.55 = -13.67 +   1.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:35 2006