Locus 4923

Sequence ID X_DroMel_CAF1
Location 12,823,983 – 12,824,143
Length 160
Max. P 0.981012
window8029 window8030 window8031 window8032

overview

Window 9

Location 12,823,983 – 12,824,103
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.82
Mean single sequence MFE -29.43
Consensus MFE -27.24
Energy contribution -27.55
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.08
Structure conservation index 0.93
SVM decision value 1.16
SVM RNA-class probability 0.924316
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12823983 120 + 22224390
UUUAAAGUUGAGCCAAUUUUCCGGUUAAUGUUUAUUUGCCAGUUCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCUCCGACAUUUCGCUUA
....((((((((..........(((.(((....))).)))......(((((..(((((((......))))))).)))))..))))(((((.(((......))).)))))......)))). ( -30.30)
>DroSec_CAF1 22040 119 + 1
U-UAAAGUUGAGCCAAUUUUCCGGUUAAUGUUUAUUUGCCAGUUCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAAUUCAUCGGAAACGGAAUCACGUCUCCGACAUUUCGCUUA
.-......(((((.........(((.(((....))).)))......(((((..(((((((......))))))).)))))......(((((.(((......))).)))))......))))) ( -29.40)
>DroEre_CAF1 30351 119 + 1
U-UAAAGUUGAGCCAAUUUUCCGGUUAAUGUUUCUCUGCCAGUCCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCCCCGACAUUUCGCUUA
.-......(((((.((...((.((....((((((............(((((..(((((((......))))))).))))).......((....))))))))....)).))...)).))))) ( -28.00)
>DroYak_CAF1 30680 119 + 1
U-UAAAGUUGAGCCAAUUUUCCGGUUAAUGUUUACUUGCCAGUUGAGGUAACUUUGUUUCGAAUUGGCAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCUCCGACAUUUCGCUUA
.-......(((((.........(((.(((......(((((((((((..((....))..)).)))))))))..))).)))......(((((.(((......))).)))))......))))) ( -30.00)
>consensus
U_UAAAGUUGAGCCAAUUUUCCGGUUAAUGUUUAUUUGCCAGUUCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCUCCGACAUUUCGCUUA
....((((((((..........(((............)))......(((((..(((((((......))))))).)))))..))))(((((.(((......))).)))))......)))). (-27.24 = -27.55 +   0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,823,983 – 12,824,103
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.82
Mean single sequence MFE -32.35
Consensus MFE -30.64
Energy contribution -30.82
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -2.47
Structure conservation index 0.95
SVM decision value 1.82
SVM RNA-class probability 0.978511
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12823983 120 - 22224390
UAAGCGAAAUGUCGGAGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGAACUGGCAAAUAAACAUUAACCGGAAAAUUGGCUCAACUUUAAA
..........((((((((((......))))))))))((((((((((.(((((((......)))))))..)))))....((((..(((....)))..))))......)))))......... ( -33.30)
>DroSec_CAF1 22040 119 - 1
UAAGCGAAAUGUCGGAGACGUGAUUCCGUUUCCGAUGAAUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGAACUGGCAAAUAAACAUUAACCGGAAAAUUGGCUCAACUUUA-A
..(((.((..((((((((((......)))))))))).....(((((.(((((((......)))))))..)))))....((((..(((....)))..))))....)).)))........-. ( -31.20)
>DroEre_CAF1 30351 119 - 1
UAAGCGAAAUGUCGGGGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGGACUGGCAGAGAAACAUUAACCGGAAAAUUGGCUCAACUUUA-A
..........(((((..(((......)))..)))))((((((((((.(((((((......)))))))..)))))....((((..((......))..))))......))))).......-. ( -32.80)
>DroYak_CAF1 30680 119 - 1
UAAGCGAAAUGUCGGAGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUGCCAAUUCGAAACAAAGUUACCUCAACUGGCAAGUAAACAUUAACCGGAAAAUUGGCUCAACUUUA-A
..........((((((((((......))))))))))((((((((((....)))))))))).....((((((.((....((((..(((....)))..))))......))...)))))).-. ( -32.10)
>consensus
UAAGCGAAAUGUCGGAGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGAACUGGCAAAUAAACAUUAACCGGAAAAUUGGCUCAACUUUA_A
..........((((((((((......))))))))))((((((((((.(((((((......)))))))..)))))....((((..(((....)))..))))......)))))......... (-30.64 = -30.82 +   0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,824,023 – 12,824,143
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -32.80
Consensus MFE -30.80
Energy contribution -31.30
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.43
Structure conservation index 0.94
SVM decision value 1.88
SVM RNA-class probability 0.981012
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12824023 120 + 22224390
AGUUCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCUCCGACAUUUCGCUUAGAUAGUUUUGACUUGUCUGCGAAGUUCAGUUUCAAAUUGC
......(((((..(((((((......))))))).)))))((((..(((((.(((......))).))))).(((((((..(((((((....)).))))))))))))..))))......... ( -33.50)
>DroSec_CAF1 22079 120 + 1
AGUUCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAAUUCAUCGGAAACGGAAUCACGUCUCCGACAUUUCGCUUAGAUAGUUUUGAGUUGUCUGCGAAGUUCAGUUUAAAAUUGC
......(((((..(((((((......))))))).)))))......(((((.(((......))).))))).(((((((..((((((.......)))))))))))))............... ( -32.80)
>DroEre_CAF1 30390 120 + 1
AGUCCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCCCCGACAUUUCGCUUAGAUAGUUUUGACUUGUCUGCGAAGUUAAGUUUCAAAUUGC
......(((((..(((((((......))))))).))))).......((....))(((((..(((...)))(((((((..(((((((....)).))))))))))))...)))))....... ( -32.30)
>DroYak_CAF1 30719 120 + 1
AGUUGAGGUAACUUUGUUUCGAAUUGGCAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCUCCGACAUUUCGCUUAGAUAGUUUCGACUUGUCUGCGAAGUUCAGAUUCCAAUUGC
(((((.((..((..((((((((((((....))))))..........((....)))))))).))..))((.(((((((..(((((((....)).))))))))))))))......))))).. ( -32.60)
>consensus
AGUUCAGGUAACUUUGUUUCGAAUUGGAAACAAUUUACCAACUCAUCGGAAACGGAAACACGUCUCCGACAUUUCGCUUAGAUAGUUUUGACUUGUCUGCGAAGUUCAGUUUCAAAUUGC
......(((((..(((((((......))))))).)))))......(((((.(((......))).))))).(((((((..((((((.......)))))))))))))............... (-30.80 = -31.30 +   0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,824,023 – 12,824,143
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -32.01
Consensus MFE -28.64
Energy contribution -28.95
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.31
Structure conservation index 0.89
SVM decision value 1.38
SVM RNA-class probability 0.947951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12824023 120 - 22224390
GCAAUUUGAAACUGAACUUCGCAGACAAGUCAAAACUAUCUAAGCGAAAUGUCGGAGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGAACU
.........((((....((((((((..(((....))).)))..)))))..((((((((((......)))))))))).))))(((((.(((((((......)))))))..)))))...... ( -32.80)
>DroSec_CAF1 22079 120 - 1
GCAAUUUUAAACUGAACUUCGCAGACAACUCAAAACUAUCUAAGCGAAAUGUCGGAGACGUGAUUCCGUUUCCGAUGAAUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGAACU
.................((((((((.............)))..)))))..((((((((((......)))))))))).....(((((.(((((((......)))))))..)))))...... ( -29.12)
>DroEre_CAF1 30390 120 - 1
GCAAUUUGAAACUUAACUUCGCAGACAAGUCAAAACUAUCUAAGCGAAAUGUCGGGGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGGACU
.........(((((...((((((((..(((....))).)))..)))))..(((((..(((......)))..))))))))))(((((.(((((((......)))))))..)))))...... ( -33.10)
>DroYak_CAF1 30719 120 - 1
GCAAUUGGAAUCUGAACUUCGCAGACAAGUCGAAACUAUCUAAGCGAAAUGUCGGAGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUGCCAAUUCGAAACAAAGUUACCUCAACU
......((.........((((((((..(((....))).)))..)))))..((((((((((......))))))))))((((((((((....))))))))))............))...... ( -33.00)
>consensus
GCAAUUUGAAACUGAACUUCGCAGACAAGUCAAAACUAUCUAAGCGAAAUGUCGGAGACGUGUUUCCGUUUCCGAUGAGUUGGUAAAUUGUUUCCAAUUCGAAACAAAGUUACCUGAACU
.................((((((((..(((....))).)))..)))))..((((((((((......)))))))))).....(((((.(((((((......)))))))..)))))...... (-28.64 = -28.95 +   0.31)

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 11:36:11 2006