Locus 674

Sequence ID 2R_DroMel_CAF1
Location 3,343,889 – 3,344,027
Length 138
Max. P 0.993711
window1189 window1190 window1191 window1192

overview

Window 9

Location 3,343,889 – 3,344,009
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.20
Mean single sequence MFE -38.10
Consensus MFE -26.27
Energy contribution -28.90
Covariance contribution 2.63
Combinations/Pair 1.09
Mean z-score -2.98
Structure conservation index 0.69
SVM decision value 2.42
SVM RNA-class probability 0.993711
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3343889 120 + 20766785
AAGCUAUUGAGCGCAAGCUAAAUCUAACUGGAAUUAAGGCAGUUGGCCGUAACUAAGCACAGGUGAACCUAUCGACAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCU
..(((....(((....)))...(((....))).....)))((((((((((.(((..((((..((((...(((((.....)))))...))))(....)))))...))).)))))))))).. ( -43.50)
>DroSim_CAF1 15502 120 + 1
AAGCUAUUUAGCACAAGCUAGAUCUAACUGGAAUUAAGGCAGUUGGCCGUAACUAAUCACAGUUAAACCUAUCGACAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCU
..(((.((((((....))))))(((....))).....)))((((((((((.(((...............(((((.....)))))(((.((((....))))))).))).)))))))))).. ( -39.20)
>DroEre_CAF1 15616 112 + 1
--------GAAAGCAAGCCAGAUCUAUCUGGAAAUAAAGCAGUUGGCCGAUAGUACGCACAGUUAAACCUAUCGACAAUCGAUAACGUCGCGGUGUCGUGCGUAAGUGAUGGCCAACUCU
--------....((...(((((....))))).......))(((((((((.((.(((((((((......))...((((..((((...))))...)))))))))))..)).))))))))).. ( -38.10)
>DroYak_CAF1 16241 117 + 1
AGG-ACCAAAGAGCAAGCCAGAUUUAACUGGAAAUAAGGCCAAU-ACCAAUAGCA-AUACAGUUAAACCUAUCGUCAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCU
...-.....((((....((((......))))......(((((.(-((...((((.-.....))))....(((((.....)))))(((.((((....)))))))..))).)))))..)))) ( -31.60)
>consensus
AAG_UAUUGAGAGCAAGCCAGAUCUAACUGGAAAUAAGGCAGUUGGCCGAAACUAAGCACAGUUAAACCUAUCGACAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCU
.................((((......))))......((.((((((((((((((...............(((((.....)))))(((.((((....))))))).)))))))))))))))) (-26.27 = -28.90 +   2.63)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,343,889 – 3,344,009
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.20
Mean single sequence MFE -36.52
Consensus MFE -22.85
Energy contribution -24.73
Covariance contribution 1.87
Combinations/Pair 1.17
Mean z-score -2.24
Structure conservation index 0.63
SVM decision value 0.85
SVM RNA-class probability 0.866257
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3343889 120 - 20766785
AGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGUCGAUAGGUUCACCUGUGCUUAGUUACGGCCAACUGCCUUAAUUCCAGUUAGAUUUAGCUUGCGCUCAAUAGCUU
..((((((((...(((...((((((.(((.(((((........)))))...)))....))))))..)))...))))))))...........(((((.....(((....)))...))))). ( -37.40)
>DroSim_CAF1 15502 120 - 1
AGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGUCGAUAGGUUUAACUGUGAUUAGUUACGGCCAACUGCCUUAAUUCCAGUUAGAUCUAGCUUGUGCUAAAUAGCUU
..((((((((...(((....(((((.(((.(((((........)))))...)))....)))))...)))...))))))))...........(((((....((((....))))..))))). ( -36.90)
>DroEre_CAF1 15616 112 - 1
AGAGUUGGCCAUCACUUACGCACGACACCGCGACGUUAUCGAUUGUCGAUAGGUUUAACUGUGCGUACUAUCGGCCAACUGCUUUAUUUCCAGAUAGAUCUGGCUUGCUUUC--------
..((((((((......((((((((..(((.(((((........)))))...))).....)))))))).....))))))))((.......(((((....)))))...))....-------- ( -38.30)
>DroYak_CAF1 16241 117 - 1
AGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGACGAUAGGUUUAACUGUAU-UGCUAUUGGU-AUUGGCCUUAUUUCCAGUUAAAUCUGGCUUGCUCUUUGGU-CCU
(((((.((((........(((........))).(((((.....)))))..(((((((((((((.-.((((.....-..))))..))....))))))))))))))).))))).....-... ( -33.50)
>consensus
AGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGUCGAUAGGUUUAACUGUGCUUACUAACGGCCAACUGCCUUAAUUCCAGUUAGAUCUAGCUUGCGCUCAAUA_CUU
..((((((((...(((...((((((.(((.(((((........)))))...)))....))))))..)))...)))))))).........((((......))))................. (-22.85 = -24.73 +   1.87)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,343,929 – 3,344,027
Length 98
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 89.63
Mean single sequence MFE -29.83
Consensus MFE -22.99
Energy contribution -25.55
Covariance contribution 2.56
Combinations/Pair 1.04
Mean z-score -1.63
Structure conservation index 0.77
SVM decision value 0.23
SVM RNA-class probability 0.644343
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3343929 98 + 20766785
AGUUGGCCGUAACUAAGCACAGGUGAACCUAUCGACAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCUAGCUGGAUGUAACCAUUG
((((((((((.(((..((((..((((...(((((.....)))))...))))(....)))))...))).)))))))))).....(((......)))... ( -35.50)
>DroSim_CAF1 15542 98 + 1
AGUUGGCCGUAACUAAUCACAGUUAAACCUAUCGACAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCUAGCUGGAUGUAACCAUUG
((((((((((.(((...............(((((.....)))))(((.((((....))))))).))).)))))))))).....(((......)))... ( -31.90)
>DroEre_CAF1 15648 98 + 1
AGUUGGCCGAUAGUACGCACAGUUAAACCUAUCGACAAUCGAUAACGUCGCGGUGUCGUGCGUAAGUGAUGGCCAACUCUAGCUGGAUGUAACGAUUG
(((((((((.((.(((((((((......))...((((..((((...))))...)))))))))))..)).))))))))).................... ( -31.30)
>DroYak_CAF1 16280 96 + 1
CAAU-ACCAAUAGCA-AUACAGUUAAACCUAUCGUCAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCUAGCUGGAUGUAACCAUUG
....-.....((((.-.....))))....(((((.....)))))(((((.(((((((((((....)).)))))........)))))))))........ ( -20.60)
>consensus
AGUUGGCCGAAACUAAGCACAGUUAAACCUAUCGACAAUCGAUAACGUCGCGGUGCCGUGCGUAAGUGAUGGCCAACUCUAGCUGGAUGUAACCAUUG
.(((((((((((((...............(((((.....)))))(((.((((....))))))).)))))))))))))..................... (-22.99 = -25.55 +   2.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,343,929 – 3,344,027
Length 98
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 89.63
Mean single sequence MFE -30.38
Consensus MFE -22.29
Energy contribution -23.85
Covariance contribution 1.56
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 0.73
SVM decision value 0.52
SVM RNA-class probability 0.766657
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3343929 98 - 20766785
CAAUGGUUACAUCCAGCUAGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGUCGAUAGGUUCACCUGUGCUUAGUUACGGCCAACU
...(((......))).....((((((((...(((...((((((.(((.(((((........)))))...)))....))))))..)))...)))))))) ( -34.70)
>DroSim_CAF1 15542 98 - 1
CAAUGGUUACAUCCAGCUAGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGUCGAUAGGUUUAACUGUGAUUAGUUACGGCCAACU
...(((......))).....((((((((...(((....(((((.(((.(((((........)))))...)))....)))))...)))...)))))))) ( -32.00)
>DroEre_CAF1 15648 98 - 1
CAAUCGUUACAUCCAGCUAGAGUUGGCCAUCACUUACGCACGACACCGCGACGUUAUCGAUUGUCGAUAGGUUUAACUGUGCGUACUAUCGGCCAACU
....................((((((((......((((((((..(((.(((((........)))))...))).....)))))))).....)))))))) ( -32.20)
>DroYak_CAF1 16280 96 - 1
CAAUGGUUACAUCCAGCUAGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGACGAUAGGUUUAACUGUAU-UGCUAUUGGU-AUUG
(((((((((((.(((((....))))).....((((((((........))).(((((.....))))).))))).....)))).-.)))))))..-.... ( -22.60)
>consensus
CAAUGGUUACAUCCAGCUAGAGUUGGCCAUCACUUACGCACGGCACCGCGACGUUAUCGAUUGUCGAUAGGUUUAACUGUGCUUACUAACGGCCAACU
...(((((......)))))..(((((((...(((...((((((.(((.(((((........)))))...)))....))))))..)))...))))))). (-22.29 = -23.85 +   1.56)

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 09:44:20 2006