Locus 8248

Sequence ID 3L_DroMel_CAF1
Location 21,662,726 – 21,662,872
Length 146
Max. P 0.995602
window13490 window13491 window13492

overview

Window 0

Location 21,662,726 – 21,662,838
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.22
Mean single sequence MFE -29.00
Consensus MFE -17.61
Energy contribution -19.43
Covariance contribution 1.81
Combinations/Pair 1.05
Mean z-score -2.42
Structure conservation index 0.61
SVM decision value 2.59
SVM RNA-class probability 0.995602
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21662726 112 + 23771897
ACCA------CUUUGCUCACUGAAAUCGCAGACGUGUGGCAACACUC-AAGCCGCCAGAAAGAUCUGGCAUCUCUCAUACUUA-ACACGCGCAUGCAAAAUAUUUAAGAAAUAAAUAUUA
....------.................(((..((((((((.......-..)))((((((....))))))..............-..)))))..)))..((((((((.....)))))))). ( -27.50)
>DroEre_CAF1 39024 114 + 1
ACCA------CUUUACGCACUGAAACAGUAGUGGUGUGGCAACGCUCGAAGCCGCCAGAAAGAUCUGGCAUCGCCGAAUCUUAAACACGCGCAAGCAAAAUAUUUAAGAAAUGGAAAUUA
((((------((......((((...))))))))))(((....)))........((((((....))))))....(((..(((((((...((....))......)))))))..)))...... ( -31.90)
>DroYak_CAF1 48015 114 + 1
ACCA------CUUUGCACACUGAAACCGCAGUGGUGUGGCAACGCCCGAAGCCGCCAGAAAGGUCUGGCAACGCUGAUUCUUAAACACGCGCAAGCAAAAUAUUUAAGAAAUGGAAAUCA
.(((------.......(((((......)))))(((((((..(....)..)))((((((....)))))).))))...((((((((...((....))......)))))))).)))...... ( -34.40)
>DroAna_CAF1 38727 117 + 1
ACCCUUAUCUUUUCCAACACUGUCAUUGCAAAGAUAUGGCAGCACC-AAAGCCGCGAAAGAGAUAUGGCAGCAUUGAUUUAGAAACACGCGCAAGCUAAAUAUUAAACAAAUGAGAAA--
..((.((((((((.(..((.((((........))))))((.((...-...)).))).)))))))).))...((((..(((((......((....))......)))))..)))).....-- ( -22.20)
>consensus
ACCA______CUUUGCACACUGAAACCGCAGAGGUGUGGCAACACCCGAAGCCGCCAGAAAGAUCUGGCAUCGCUGAUUCUUAAACACGCGCAAGCAAAAUAUUUAAGAAAUGAAAAUUA
.................(((((......)))))(((((((..........)))((((((....))))))...............))))((....))........................ (-17.61 = -19.43 +   1.81)

alignment

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secondary structure

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dotplot

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Window 1

Location 21,662,760 – 21,662,872
Length 112
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 74.82
Mean single sequence MFE -21.38
Consensus MFE -13.50
Energy contribution -14.00
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.63
SVM decision value 0.68
SVM RNA-class probability 0.820652
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21662760 112 + 23771897
AACACUC-AAGCCGCCAGAAAGAUCUGGCAUCUCUCAUACUUA-ACACGCGCAUGCAAAAUAUUUAAGAAAUAAAUAUUAGUCGCUAAC---AGUUUAAAUAUAAUAAAAUUCUGCU
.......-.(((.((((((....))))))..............-....(((.((....((((((((.....)))))))).)))))....---......................))) ( -17.40)
>DroEre_CAF1 39058 117 + 1
AACGCUCGAAGCCGCCAGAAAGAUCUGGCAUCGCCGAAUCUUAAACACGCGCAAGCAAAAUAUUUAAGAAAUGGAAAUUAGUAGCUAACAAUAGUUUAAAUAUUAUAAUAUUCUGCU
...((.....)).((((((....))))))...((.((((.(((.....((....))..(((((((((..(((....)))....((((....))))))))))))).))).)))).)). ( -26.10)
>DroYak_CAF1 48049 117 + 1
AACGCCCGAAGCCGCCAGAAAGGUCUGGCAACGCUGAUUCUUAAACACGCGCAAGCAAAAUAUUUAAGAAAUGGAAAUCAGUAGCUAACAAUAGUGUAAAUAUUAUAAUAUUCUGCU
...((....(((.((((((....))))))...(((((((((((((...((....))......))))))).......)))))).)))....((((((....))))))........)). ( -26.11)
>DroAna_CAF1 38767 105 + 1
AGCACC-AAAGCCGCGAAAGAGAUAUGGCAGCAUUGAUUUAGAAACACGCGCAAGCUAAAUAUUAAACAAAUGAGAAA---UAGCUAAU--------AAAUACUAUUUAAAACGCUU
(((...-...(((((....).....))))..((((..(((((......((....))......)))))..))))..(((---(((.....--------.....)))))).....))). ( -15.90)
>consensus
AACACCCGAAGCCGCCAGAAAGAUCUGGCAUCGCUGAUUCUUAAACACGCGCAAGCAAAAUAUUUAAGAAAUGAAAAUUAGUAGCUAAC___AGUUUAAAUAUUAUAAAAUUCUGCU
.........(((.((((((....))))))...................((....))...........................)))............................... (-13.50 = -14.00 +   0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,662,760 – 21,662,872
Length 112
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 74.82
Mean single sequence MFE -26.58
Consensus MFE -15.04
Energy contribution -17.60
Covariance contribution 2.56
Combinations/Pair 1.12
Mean z-score -1.85
Structure conservation index 0.57
SVM decision value 0.37
SVM RNA-class probability 0.706640
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21662760 112 - 23771897
AGCAGAAUUUUAUUAUAUUUAAACU---GUUAGCGACUAAUAUUUAUUUCUUAAAUAUUUUGCAUGCGCGUGU-UAAGUAUGAGAGAUGCCAGAUCUUUCUGGCGGCUU-GAGUGUU
(((...(((((.(((((((((((((---((..((((..((((((((.....))))))))))))..))).)).)-))))))))))))))((((((....)))))).))).-....... ( -28.70)
>DroEre_CAF1 39058 117 - 1
AGCAGAAUAUUAUAAUAUUUAAACUAUUGUUAGCUACUAAUUUCCAUUUCUUAAAUAUUUUGCUUGCGCGUGUUUAAGAUUCGGCGAUGCCAGAUCUUUCUGGCGGCUUCGAGCGUU
.((.((((((....))))))......(((..((((....(((.((...((((((((((...((....))))))))))))...)).)))((((((....)))))))))).)))))... ( -29.70)
>DroYak_CAF1 48049 117 - 1
AGCAGAAUAUUAUAAUAUUUACACUAUUGUUAGCUACUGAUUUCCAUUUCUUAAAUAUUUUGCUUGCGCGUGUUUAAGAAUCAGCGUUGCCAGACCUUUCUGGCGGCUUCGGGCGUU
.((.((((((....))))))................((((.......(((((((((((...((....))))))))))))).....(((((((((....))))))))).))))))... ( -29.50)
>DroAna_CAF1 38767 105 - 1
AAGCGUUUUAAAUAGUAUUU--------AUUAGCUA---UUUCUCAUUUGUUUAAUAUUUAGCUUGCGCGUGUUUCUAAAUCAAUGCUGCCAUAUCUCUUUCGCGGCUUU-GGUGCU
..((((...(((((((....--------....))))---))).......(((........)))..))))..........(((((.(((((.(........).))))).))-)))... ( -18.40)
>consensus
AGCAGAAUAUUAUAAUAUUUAAACU___GUUAGCUACUAAUUUCCAUUUCUUAAAUAUUUUGCUUGCGCGUGUUUAAGAAUCAGCGAUGCCAGAUCUUUCUGGCGGCUUCGAGCGUU
................................(((............(((((((((((...((....))))))))))))).....(((((((((....)))))))))....)))... (-15.04 = -17.60 +   2.56)

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 13:10:29 2006