Locus 6417

Sequence ID 2R_DroMel_CAF1
Location 20,057,225 – 20,057,393
Length 168
Max. P 0.959224
window10240 window10241 window10242

overview

Window 0

Location 20,057,225 – 20,057,327
Length 102
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 74.43
Mean single sequence MFE -21.64
Consensus MFE -12.01
Energy contribution -12.35
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.56
SVM decision value 0.07
SVM RNA-class probability 0.568152
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20057225 102 + 20766785
UUCCGACUCAAACUUUGACUCAAAGCU--GGCUGCAAAGAGCCUCGCUGCAAAACA---ACAACACAUACAUAUGCAUACGAAAGCCGCACUGAGUCGAGUAUGAUA
.......(((.((((.((((((..((.--((((((.....)).(((.((((.....---..............))))..))).))))))..)))))))))).))).. ( -24.91)
>DroEre_CAF1 17313 80 + 1
UUCCGACUCAAACUUUGGCUCAAAGC----------------CUCGCUGCAAAACA---GAAAC--------ACAUAUACGAAACCCGCACUGAGUCGAGCAUGAUA
...(((((((......(((.....))----------------)...(((.....))---)....--------...................)))))))......... ( -15.80)
>DroYak_CAF1 17334 96 + 1
UUCCGACUCAAACUUUGGCUCAAAGCUCUGG-----------CUGGCUGCAAAACAACAGCAACACAUAUACACAUGUACGAAAGCCGCACUGAGUCGAGCAUGGUA
...(((((((......(((.....)))..((-----------((.((((........))))...((((......)))).....))))....)))))))......... ( -24.20)
>consensus
UUCCGACUCAAACUUUGGCUCAAAGCU__GG___________CUCGCUGCAAAACA___GCAACACAUA_A_ACAUAUACGAAAGCCGCACUGAGUCGAGCAUGAUA
...(((((((..(((((...)))))....................((.((..................................)).))..)))))))......... (-12.01 = -12.35 +   0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,057,225 – 20,057,327
Length 102
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 74.43
Mean single sequence MFE -28.00
Consensus MFE -19.97
Energy contribution -19.87
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.47
Structure conservation index 0.71
SVM decision value 0.90
SVM RNA-class probability 0.877002
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20057225 102 - 20766785
UAUCAUACUCGACUCAGUGCGGCUUUCGUAUGCAUAUGUAUGUGUUGU---UGUUUUGCAGCGAGGCUCUUUGCAGCC--AGCUUUGAGUCAAAGUUUGAGUCGGAA
..(((.(((.(((((((.((((((.....((((....))))((.((((---((.....)))))).)).......))))--.)).)))))))..))).)))....... ( -31.40)
>DroEre_CAF1 17313 80 - 1
UAUCAUGCUCGACUCAGUGCGGGUUUCGUAUAUGU--------GUUUC---UGUUUUGCAGCGAG----------------GCUUUGAGCCAAAGUUUGAGUCGGAA
........(((((((((.((.((((.((.....((--------.((.(---((.....))).)).----------------))..))))))...))))))))))).. ( -22.10)
>DroYak_CAF1 17334 96 - 1
UACCAUGCUCGACUCAGUGCGGCUUUCGUACAUGUGUAUAUGUGUUGCUGUUGUUUUGCAGCCAG-----------CCAGAGCUUUGAGCCAAAGUUUGAGUCGGAA
........(((((((.....((((....((((((....))))))..(((((......))))).))-----------)).((((((((...))))))))))))))).. ( -30.50)
>consensus
UAUCAUGCUCGACUCAGUGCGGCUUUCGUAUAUGU_U_UAUGUGUUGC___UGUUUUGCAGCGAG___________CC__AGCUUUGAGCCAAAGUUUGAGUCGGAA
........(((((((((((((.....)))))............(((((.........)))))...................((((((...)))))).)))))))).. (-19.97 = -19.87 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,057,295 – 20,057,393
Length 98
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.56
Mean single sequence MFE -27.07
Consensus MFE -20.80
Energy contribution -20.58
Covariance contribution -0.22
Combinations/Pair 1.16
Mean z-score -3.03
Structure conservation index 0.77
SVM decision value 1.50
SVM RNA-class probability 0.959224
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20057295 98 + 20766785
CAUAC-------GAAAGCCGCACU-GAGUCGAGUAUGAUAAUUUGGC--AUGCAUUUGGAAAACGAGCUGAAACCAGUUCGCC---AUGCUAAAUUGUUUUGCUUUCAAUU
.....-------((((((...(((-......)))..(((((((((((--(((...((....))(((((((....))))))).)---)))))))))))))..)))))).... ( -30.50)
>DroSec_CAF1 16900 82 + 1
-----------------------U-GAGUCGAGUAUGAUAAUUUGGC--AUGCAUUUGGAAAACGAGCUGAAACCAGUUCGCC---AUGCUAAAUUGUUUUGCUUUCAAUU
-----------------------(-((...(((((.(((((((((((--(((...((....))(((((((....))))))).)---))))))))))))).))))))))... ( -28.50)
>DroSim_CAF1 17382 82 + 1
-----------------------U-GAGUCGAGUAUGAUAAUUUGGC--AUGCAUUUGGAAAACGAGCUGAAACCAGUUCGCC---AUGCUAAAUUGUUUUGCUUUCAAUU
-----------------------(-((...(((((.(((((((((((--(((...((....))(((((((....))))))).)---))))))))))))).))))))))... ( -28.50)
>DroEre_CAF1 17361 98 + 1
UAUAC-------GAAACCCGCACU-GAGUCGAGCAUGAUAAUUUGGC--AUGCAUUUGGAAAACGAGCUGAAACCAGUUCGCC---AUGCUAAAUUGUUUUGCUUUCAAUU
.....-------...........(-((...(((((.(((((((((((--(((...((....))(((((((....))))))).)---))))))))))))).))))))))... ( -30.60)
>DroWil_CAF1 17463 109 + 1
UCUACAUCCUCCGUUUGCCGU--UGCCAUCGAGUAUGAUAAUUUAGUUGAAGCAUUUGGAAAACGAGUCGAAACCAGUUCGCCAUCAUGCUAAAUUGUUUUGCUUUCAAUU
.....................--.......(((((.((((((((((((((......(((..(((..((....))..)))..)))))).))))))))))).)))))...... ( -19.20)
>DroAna_CAF1 18913 84 + 1
---------------------ACU-GCAUCGAGUAUGAUAAUUUGGC--GUGCGUUUGGAAAACAAGCUGAAACCAGUUCGCC---AUGCUAAAUUGUUUUGCUUUCAAUU
---------------------...-.....(((((.(((((((((((--(((((((((.....))))).(((.....)))).)---))))))))))))).)))))...... ( -25.10)
>consensus
_______________________U_GAGUCGAGUAUGAUAAUUUGGC__AUGCAUUUGGAAAACGAGCUGAAACCAGUUCGCC___AUGCUAAAUUGUUUUGCUUUCAAUU
..............................(((((.(((((((((((....((....(.....)((((((....))))))))......))))))))))).)))))...... (-20.80 = -20.58 +  -0.22)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:31 2006