Locus 8135

Sequence ID X_DroMel_CAF1
Location 20,244,767 – 20,244,923
Length 156
Max. P 0.991407
window13369 window13370 window13371

overview

Window 9

Location 20,244,767 – 20,244,887
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -33.61
Consensus MFE -32.34
Energy contribution -32.67
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.07
Structure conservation index 0.96
SVM decision value 1.93
SVM RNA-class probability 0.982945
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20244767 120 - 22224390
CACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGUAGUAGUUAUUCACAUUUUUGCUGCAUACUUUUCGGCUGCUCCUCCCCCU
.......((((((((((((((((..............))))))))))).))).)).((((....((.(((((((((..((....))..)))))))))))....))))............. ( -33.84)
>DroSim_CAF1 362 120 - 1
CACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGUAGUAGUUAUUCACAUUUUUGCUGCAUACUUUUCGGCUGCUCCUCCCUCU
.......((((((((((((((((..............))))))))))).))).)).((((....((.(((((((((..((....))..)))))))))))....))))............. ( -33.84)
>DroYak_CAF1 1550 120 - 1
CACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGAAGUAGUUAUUCACAUUUUUGCUGCAUACUUUUCGGCUGCUCCUUCCUCU
.....((((((((((((((((((..............))))))))))).))).))(((.((.....((((((.......)))))).....)).)))........)).............. ( -33.14)
>consensus
CACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGUAGUAGUUAUUCACAUUUUUGCUGCAUACUUUUCGGCUGCUCCUCCCUCU
.......((((((((((((((((..............))))))))))).))).)).((((....((.(((((((((..((....))..)))))))))))....))))............. (-32.34 = -32.67 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,244,807 – 20,244,923
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.10
Mean single sequence MFE -34.02
Consensus MFE -28.67
Energy contribution -29.33
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.84
SVM decision value 0.60
SVM RNA-class probability 0.794307
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20244807 116 + 22224390
AUAACUACUACACAACAAAGCAGCAGCAUCAUCACACACACUCUGUUGUUGUUAUAUAAGUGUGUGCGUGAGCGGGAGUGUGUGCGUGCGUAGUAGUAAAAAUGUAGCAAAACUGC----
...((((((((.((.....((....)).....(.((((((((((.((((......)))).....(((....))))))))))))).))).))))))))......((((.....))))---- ( -35.30)
>DroSim_CAF1 402 113 + 1
AUAACUACUACACAACAAAGCAGCAGCAUCAUCACACACACUCUGUUGUUGUUAUAUAAGUGUGUGCGUGAGCGGGAGUGUGUGCGCGCAUAGUAGUAAAAAUGUAGCAAAA---C----
.....((((((.......((((((((((...............)))))))))).......((((((((((.((....))...))))))))))))))))..............---.---- ( -31.86)
>DroYak_CAF1 1590 120 + 1
AUAACUACUUCACAACAAAGCAGCAGCAUCAUCACACACACUCUGUUGUUGUUAUAUAAGUGUGUGCGUGAGCGGGAGUGUGUGCGUGCGUAGUAGUAAAAAUGUAGCAAAACUACAAUU
...((((((.(((......((....)).......((((((((((.((((......)))).....(((....))))))))))))).)))...)))))).....(((((.....)))))... ( -34.90)
>consensus
AUAACUACUACACAACAAAGCAGCAGCAUCAUCACACACACUCUGUUGUUGUUAUAUAAGUGUGUGCGUGAGCGGGAGUGUGUGCGUGCGUAGUAGUAAAAAUGUAGCAAAACU_C____
...((((((((.(......((....)).....(.(((((((((((((..(((.((((....)))))))..))).)))))))))).).).))))))))....................... (-28.67 = -29.33 +   0.67)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,244,807 – 20,244,923
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.10
Mean single sequence MFE -34.17
Consensus MFE -32.78
Energy contribution -32.67
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -3.20
Structure conservation index 0.96
SVM decision value 2.27
SVM RNA-class probability 0.991407
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20244807 116 - 22224390
----GCAGUUUUGCUACAUUUUUACUACUACGCACGCACACACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGUAGUAGUUAU
----((......)).........(((((((((((.(((....(..(.((((((((((((((((..............))))))))))).))).)).)..)...))))))))))))))... ( -35.94)
>DroSim_CAF1 402 113 - 1
----G---UUUUGCUACAUUUUUACUACUAUGCGCGCACACACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGUAGUAGUUAU
----.---..(((((((((....((......(((.(((.........((((((((((((((((..............))))))))))).))).))))))))...)).))))))))).... ( -31.64)
>DroYak_CAF1 1590 120 - 1
AAUUGUAGUUUUGCUACAUUUUUACUACUACGCACGCACACACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGAAGUAGUUAU
...(((((.....))))).....((((((.((((.(((....(..(.((((((((((((((((..............))))))))))).))).)).)..)...))))))).))))))... ( -34.94)
>consensus
____G_AGUUUUGCUACAUUUUUACUACUACGCACGCACACACUCCCGCUCACGCACACACUUAUAUAACAACAACAGAGUGUGUGUGAUGAUGCUGCUGCUUUGUUGUGUAGUAGUUAU
.......................(((((((((((.(((....(..(.((((((((((((((((..............))))))))))).))).)).)..)...))))))))))))))... (-32.78 = -32.67 +  -0.11)

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 12:56:42 2006