Locus 4514

Sequence ID X_DroMel_CAF1
Location 11,912,577 – 11,912,732
Length 155
Max. P 0.958391
window7423 window7424 window7425 window7426

overview

Window 3

Location 11,912,577 – 11,912,692
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.79
Mean single sequence MFE -26.28
Consensus MFE -19.74
Energy contribution -19.66
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -2.45
Structure conservation index 0.75
SVM decision value 1.08
SVM RNA-class probability 0.911723
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11912577 115 + 22224390
AAAUUGCUAAGCAGUUAUAAAUUUGAUCAAAGCCUAUUUGAUAAUUGGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCGGCGAUAACGAUAACCUG-----GCCAGUUAUGCAU
..........(((.............(((((.....)))))(((((((((((((((((.....))))))))..........((((.......)))).....)-----))))))))))).. ( -24.40)
>DroSec_CAF1 22434 115 + 1
AAAUUGCUAAGCAGUGAUAAAUUUGGUCAAAGCCUAUUUGAUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGCAUUGAUUAAUCGUCGAUAACGAUAACCUG-----GCCAGUUAUGCAC
....(((...)))(((((((...((((((............(((((((((((((((((.....))))))))).))))))))(((((.....)))))....))-----)))).)))).))) ( -27.40)
>DroSim_CAF1 20392 115 + 1
AAAUUGCUAAGCAGUGAUAAAUUUGGUCAAAGCCUAUUUGAUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGCAUUGAUUAAUCGUCGAUAACGAUAACCUG-----GCCAGUUAUGCAC
....(((...)))(((((((...((((((............(((((((((((((((((.....))))))))).))))))))(((((.....)))))....))-----)))).)))).))) ( -27.40)
>DroEre_CAF1 20683 111 + 1
AAAUUGCUAAGCAGUGAUAAAUUUGGGCAAAGCCUAUUUGGUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCAUCGAUAACGAUAACCUG-----GCCAGUUA----U
..(((((...)))))........(((((...))))).(((((((((((((((((((((.....))))))))).)))))))....((((....))))......-----)))))...----. ( -25.10)
>DroYak_CAF1 23616 120 + 1
AAAUUGCUAAGCAGUGAUAAAUUUGGCCAAAGCCUAUUUGAUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCAUCGAUAACGAUAAUAUGUUAUAGCCAGCUACGCAC
....(((..(((.(((((((((..(((....))).))))..(((((((((((((((((.....))))))))).)))))))))))))..((((((......)))))).....)))..))). ( -27.10)
>consensus
AAAUUGCUAAGCAGUGAUAAAUUUGGUCAAAGCCUAUUUGAUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCGUCGAUAACGAUAACCUG_____GCCAGUUAUGCAC
..(((((...))))).......(((((............(((((((((((((((((((.....))))))))).))))))).)))((((....))))...........)))))........ (-19.74 = -19.66 +  -0.08)

alignment

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secondary structure

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Window 4

Location 11,912,577 – 11,912,692
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.79
Mean single sequence MFE -23.20
Consensus MFE -18.04
Energy contribution -18.68
Covariance contribution 0.64
Combinations/Pair 1.16
Mean z-score -1.68
Structure conservation index 0.78
SVM decision value 0.38
SVM RNA-class probability 0.710850
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11912577 115 - 22224390
AUGCAUAACUGGC-----CAGGUUAUCGUUAUCGCCGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACCAAUUAUCAAAUAGGCUUUGAUCAAAUUUAUAACUGCUUAGCAAUUU
.(((((((.(((.-----..((((((((.......))).)))))....(((((((((.....))))))))).))).))))....(((((..(((......))).....)))))))).... ( -22.10)
>DroSec_CAF1 22434 115 - 1
GUGCAUAACUGGC-----CAGGUUAUCGUUAUCGACGAUUAAUCAAUGCAUUUCAUUUGUAUAAUGAAAUGACUAAUUAUCAAAUAGGCUUUGACCAAAUUUAUCACUGCUUAGCAAUUU
.(((((((.(((.-----..((((((((((...))))).)))))....(((((((((.....))))))))).))).))))....(((((..(((.........)))..)))))))).... ( -23.90)
>DroSim_CAF1 20392 115 - 1
GUGCAUAACUGGC-----CAGGUUAUCGUUAUCGACGAUUAAUCAAUGCAUUUCAUUUGUAUAAUGAAAUGACUAAUUAUCAAAUAGGCUUUGACCAAAUUUAUCACUGCUUAGCAAUUU
.(((((((.(((.-----..((((((((((...))))).)))))....(((((((((.....))))))))).))).))))....(((((..(((.........)))..)))))))).... ( -23.90)
>DroEre_CAF1 20683 111 - 1
A----UAACUGGC-----CAGGUUAUCGUUAUCGAUGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACUAAUUACCAAAUAGGCUUUGCCCAAAUUUAUCACUGCUUAGCAAUUU
.----.....(((-----(.((((((((....))))))))........(((((((((.....)))))))))...............))))((((...................))))... ( -21.21)
>DroYak_CAF1 23616 120 - 1
GUGCGUAGCUGGCUAUAACAUAUUAUCGUUAUCGAUGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACUAAUUAUCAAAUAGGCUUUGGCCAAAUUUAUCACUGCUUAGCAAUUU
.(((..(((((((((...(..(((((((....))))))).........(((((((((.....)))))))))...............)....))))))...........)))..))).... ( -24.90)
>consensus
GUGCAUAACUGGC_____CAGGUUAUCGUUAUCGACGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACUAAUUAUCAAAUAGGCUUUGACCAAAUUUAUCACUGCUUAGCAAUUU
.(((((((.(((........((((((((((...))))).)))))....(((((((((.....))))))))).))).))))....(((((..(((.........)))..)))))))).... (-18.04 = -18.68 +   0.64)

alignment

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secondary structure

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Window 5

Location 11,912,617 – 11,912,732
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.31
Mean single sequence MFE -21.89
Consensus MFE -15.84
Energy contribution -15.48
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -2.14
Structure conservation index 0.72
SVM decision value 1.49
SVM RNA-class probability 0.958391
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11912617 115 + 22224390
AUAAUUGGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCGGCGAUAACGAUAACCUG-----GCCAGUUAUGCAUUCGACGAGAUAUAUUCAAAAGUCGGACACAAAUGCUGCAU
.((((..(((((((((((.....))))))))).))..))))((((.......))))......-----((.(((..((..((((((..((.....))....))))))..))...))))).. ( -27.40)
>DroSec_CAF1 22474 93 + 1
AUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGCAUUGAUUAAUCGUCGAUAACGAUAACCUG-----GCCAGUUAUGCACUCGA----------------------CACAAAUGCUGCAU
.(((((((((((((((((.....))))))))).))))))))...(((((.....(((((...-----....)))))....))))----------------------)............. ( -20.90)
>DroSim_CAF1 20432 93 + 1
AUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGCAUUGAUUAAUCGUCGAUAACGAUAACCUG-----GCCAGUUAUGCACUCGA----------------------CACAAAUGCUGCAU
.(((((((((((((((((.....))))))))).))))))))...(((((.....(((((...-----....)))))....))))----------------------)............. ( -20.90)
>DroEre_CAF1 20723 111 + 1
GUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCAUCGAUAACGAUAACCUG-----GCCAGUUA----UUCAAAGAGAUAUAUUAAACAGUCGGGCACAAAUGCUGCAU
.(((((((((((((((((.....))))))))).))))))))...((((....))))..((((-----((...(((----.((.....)).....)))...)))))).............. ( -21.60)
>DroYak_CAF1 23656 107 + 1
AUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCAUCGAUAACGAUAAUAUGUUAUAGCCAGCUACGCACUCAAUGAGAUAUAUU-------------CAAAUGCUGCAU
.(((((((((((((((((.....))))))))).))))))))...((((....))))...........((.(((......................-------------.....))))).. ( -18.63)
>consensus
AUAAUUAGUCAUUUCAUUAUACAAAUGAAAUGUAUUGAUUAAUCGUCGAUAACGAUAACCUG_____GCCAGUUAUGCACUCGA_GAGAUAUAUU___________CACAAAUGCUGCAU
.(((((((((((((((((.....))))))))).))))))))...((((....))))...........((.(((........................................))))).. (-15.84 = -15.48 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,912,617 – 11,912,732
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.31
Mean single sequence MFE -22.00
Consensus MFE -16.67
Energy contribution -16.55
Covariance contribution -0.12
Combinations/Pair 1.21
Mean z-score -1.50
Structure conservation index 0.76
SVM decision value 0.33
SVM RNA-class probability 0.692995
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11912617 115 - 22224390
AUGCAGCAUUUGUGUCCGACUUUUGAAUAUAUCUCGUCGAAUGCAUAACUGGC-----CAGGUUAUCGUUAUCGCCGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACCAAUUAU
.....(((((((....(((..(........)..))).)))))))((((.(((.-----..((((((((.......))).)))))....(((((((((.....))))))))).))).)))) ( -23.70)
>DroSec_CAF1 22474 93 - 1
AUGCAGCAUUUGUG----------------------UCGAGUGCAUAACUGGC-----CAGGUUAUCGUUAUCGACGAUUAAUCAAUGCAUUUCAUUUGUAUAAUGAAAUGACUAAUUAU
..(((..(((..((----------------------((((..((((((((...-----..)))))).))..))))))...)))...)))((((((((.....)))))))).......... ( -21.70)
>DroSim_CAF1 20432 93 - 1
AUGCAGCAUUUGUG----------------------UCGAGUGCAUAACUGGC-----CAGGUUAUCGUUAUCGACGAUUAAUCAAUGCAUUUCAUUUGUAUAAUGAAAUGACUAAUUAU
..(((..(((..((----------------------((((..((((((((...-----..)))))).))..))))))...)))...)))((((((((.....)))))))).......... ( -21.70)
>DroEre_CAF1 20723 111 - 1
AUGCAGCAUUUGUGCCCGACUGUUUAAUAUAUCUCUUUGAA----UAACUGGC-----CAGGUUAUCGUUAUCGAUGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACUAAUUAC
..........((.(((.(..(((((((.........)))))----)).).)))-----))((((((((....))))))))........(((((((((.....)))))))))......... ( -21.40)
>DroYak_CAF1 23656 107 - 1
AUGCAGCAUUUG-------------AAUAUAUCUCAUUGAGUGCGUAGCUGGCUAUAACAUAUUAUCGUUAUCGAUGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACUAAUUAU
.....(((((..-------------(..........)..)))))((((....)))).....(((((((....))))))).........(((((((((.....)))))))))......... ( -21.50)
>consensus
AUGCAGCAUUUGUG___________AAUAUAUCUC_UCGAGUGCAUAACUGGC_____CAGGUUAUCGUUAUCGACGAUUAAUCAAUACAUUUCAUUUGUAUAAUGAAAUGACUAAUUAU
.....(((((((.........................)))))))((((.(((........((((((((((...))))).)))))....(((((((((.....))))))))).))).)))) (-16.67 = -16.55 +  -0.12)

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 11:27:03 2006