Locus 3827

Sequence ID X_DroMel_CAF1
Location 10,164,431 – 10,164,572
Length 141
Max. P 0.998279
window6295 window6296 window6297

overview

Window 5

Location 10,164,431 – 10,164,536
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.33
Mean single sequence MFE -29.58
Consensus MFE -14.56
Energy contribution -14.95
Covariance contribution 0.39
Combinations/Pair 1.23
Mean z-score -2.90
Structure conservation index 0.49
SVM decision value 1.34
SVM RNA-class probability 0.943522
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10164431 105 + 22224390
AUCAAACGACCAAUCGCGUUUAUCAAUAUA-UUUUGGCGCCAAAAAAUCGCGC--------GUAAGCUC------GGAAAGCUUUUCGAAUGCGAAGAAGCUUUCGCCAAGCUUAGCAAC
...(((((........))))).........-.((((((..........((.((--------....)).)------)((((((((((((....)).))))))))))))))))......... ( -29.30)
>DroPse_CAF1 32973 110 + 1
AACUAACGCCGCAAAACAUUCAACAAUCUUUUUUUGGCGCCAAAAAAUCGCGUAAGCGUAGGAAAGCUCCCUAGAGCAAAGCUUUUCACAAAACAAAAAGCUCGCGGCAG----------
.......(((((......(((........(((((((....))))))).(((....)))...))).((((....))))..(((((((.........))))))).)))))..---------- ( -31.00)
>DroSec_CAF1 10419 105 + 1
AUUAAACGACCAAUCCCGUUUAUCAAUAUA-UUUUGGCGCCAAAAAAUCGCGU--------GUAAGCUC------GAAAAGCUUUUGGAAUGCGAAGAAGCUUUCACCGAGCUUAGCAAC
..((((((........))))))........-(((((....)))))....((..--------.(((((((------(.(((((((((.........)))))))))...))))))))))... ( -26.70)
>DroSim_CAF1 12855 105 + 1
AUCAAACGACCAAUCCCGUUUAUCAAUAUA-UUUUGGCGCCAAAAAAUCGCGU--------GUAAGCUC------GAAAAGCUUUUGGAAUGCGAAGAAGCUUUCGCCGAGCUUAGCAAC
...(((((........))))).........-(((((....)))))....((..--------.(((((((------(.(((((((((.........)))))))))...))))))))))... ( -25.60)
>DroEre_CAF1 32329 105 + 1
ACCAAACGACCAAUCCCGUUUAUCAAUGUA-UUUUGGCGCCAAAAAAUCGUGC--------GUAAGCUC------GGAAAGCUUUUCGAUUACGAAGAAGCUUUCGCCGAGCUUAGCAAC
...(((((........))))).........-(((((....))))).....(((--------.(((((((------((.((((((((((....)).))))))))...)))))))))))).. ( -33.20)
>DroYak_CAF1 13505 105 + 1
AUCAAACGACCAAUCCCGUUUAUCAAUACA-UUUUGGCGCCAAAAAACCGUGC--------GUAAGCUC------GGAAAGCUUUUCGAAUGCGAAAAAGCUUUCGCCGAGCUUAGUAAC
...(((((........))))).....(((.-.....((((.........))))--------.(((((((------((.((((((((((....)).))))))))...)))))))))))).. ( -31.70)
>consensus
AUCAAACGACCAAUCCCGUUUAUCAAUAUA_UUUUGGCGCCAAAAAAUCGCGC________GUAAGCUC______GGAAAGCUUUUCGAAUGCGAAGAAGCUUUCGCCGAGCUUAGCAAC
...(((((........)))))...............((((.........)))).........(((((((......((((.((((((.........))))))))))...)))))))..... (-14.56 = -14.95 +   0.39)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,164,470 – 10,164,572
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 91.37
Mean single sequence MFE -31.08
Consensus MFE -25.58
Energy contribution -26.26
Covariance contribution 0.68
Combinations/Pair 1.14
Mean z-score -2.92
Structure conservation index 0.82
SVM decision value 3.05
SVM RNA-class probability 0.998279
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10164470 102 + 22224390
CAAAAAAUCGCGCGUAAGCUCGGAAAGCUUUUCGAAUGCGAAGAAGCUUUCGCCAAGCUUAGCAACAACUGCAGCGGAACGAAAUGGCAAUGGGAACAGGCC
.......((.(((.((((((.((.((((((((((....)).))))))))...)).))))))(((.....))).))))).......(((..((....)).))) ( -30.70)
>DroSec_CAF1 10458 102 + 1
CAAAAAAUCGCGUGUAAGCUCGAAAAGCUUUUGGAAUGCGAAGAAGCUUUCACCGAGCUUAGCAACAACUGCAGCGGAACGAAAUGGCAAUGGAAACACGAC
.......((((...((((((((.(((((((((.........)))))))))...))))))))(((.....))).)))).............((....)).... ( -28.60)
>DroSim_CAF1 12894 102 + 1
CAAAAAAUCGCGUGUAAGCUCGAAAAGCUUUUGGAAUGCGAAGAAGCUUUCGCCGAGCUUAGCAACAACUGCAGCGGAACGAAAUGGCAAUGGAAACACGAC
.......((((...((((((((.(((((((((.........)))))))))...))))))))(((.....))).)))).............((....)).... ( -28.60)
>DroEre_CAF1 32368 102 + 1
CAAAAAAUCGUGCGUAAGCUCGGAAAGCUUUUCGAUUACGAAGAAGCUUUCGCCGAGCUUAGCAACAACUGCAGCGGAACGAAAUGGCAAUGGGAACAAGCC
.......((((.(((((((((((.((((((((((....)).))))))))...)))))))).(((.....))).)))..))))...(((..((....)).))) ( -35.50)
>DroYak_CAF1 13544 102 + 1
CAAAAAACCGUGCGUAAGCUCGGAAAGCUUUUCGAAUGCGAAAAAGCUUUCGCCGAGCUUAGUAACAACCGCAGCGGAACGAAAUGGAAAUGAAAAGAAGCC
.......((((((((((((((((.((((((((((....)).))))))))...)))))))))((....)))))).)))......................... ( -32.00)
>consensus
CAAAAAAUCGCGCGUAAGCUCGGAAAGCUUUUCGAAUGCGAAGAAGCUUUCGCCGAGCUUAGCAACAACUGCAGCGGAACGAAAUGGCAAUGGAAACAAGCC
.......((((...((((((((((((((((((((....)).)))))))))..)))))))))(((.....))).)))).............((....)).... (-25.58 = -26.26 +   0.68)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,164,470 – 10,164,572
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 91.37
Mean single sequence MFE -29.51
Consensus MFE -24.00
Energy contribution -23.80
Covariance contribution -0.20
Combinations/Pair 1.14
Mean z-score -2.04
Structure conservation index 0.81
SVM decision value 1.53
SVM RNA-class probability 0.961445
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10164470 102 - 22224390
GGCCUGUUCCCAUUGCCAUUUCGUUCCGCUGCAGUUGUUGCUAAGCUUGGCGAAAGCUUCUUCGCAUUCGAAAAGCUUUCCGAGCUUACGCGCGAUUUUUUG
(((.((....))..)))...............((((((.(((((((((((..(((((((.((((....)))))))))))))))))))).))))))))..... ( -29.80)
>DroSec_CAF1 10458 102 - 1
GUCGUGUUUCCAUUGCCAUUUCGUUCCGCUGCAGUUGUUGCUAAGCUCGGUGAAAGCUUCUUCGCAUUCCAAAAGCUUUUCGAGCUUACACGCGAUUUUUUG
(((((((....................((.((....)).))((((((((..((((((((.............)))))))))))))))).)))))))...... ( -26.12)
>DroSim_CAF1 12894 102 - 1
GUCGUGUUUCCAUUGCCAUUUCGUUCCGCUGCAGUUGUUGCUAAGCUCGGCGAAAGCUUCUUCGCAUUCCAAAAGCUUUUCGAGCUUACACGCGAUUUUUUG
(((((((....................((.((....)).))((((((((..((((((((.............)))))))))))))))).)))))))...... ( -26.12)
>DroEre_CAF1 32368 102 - 1
GGCUUGUUCCCAUUGCCAUUUCGUUCCGCUGCAGUUGUUGCUAAGCUCGGCGAAAGCUUCUUCGUAAUCGAAAAGCUUUCCGAGCUUACGCACGAUUUUUUG
(((.((....))..)))...............((((((.(((((((((((..(((((((.((((....)))))))))))))))))))).))))))))..... ( -34.30)
>DroYak_CAF1 13544 102 - 1
GGCUUCUUUUCAUUUCCAUUUCGUUCCGCUGCGGUUGUUACUAAGCUCGGCGAAAGCUUUUUCGCAUUCGAAAAGCUUUCCGAGCUUACGCACGGUUUUUUG
.........................(((.((((((....))(((((((((..(((((((((.((....)))))))))))))))))))))))))))....... ( -31.20)
>consensus
GGCGUGUUUCCAUUGCCAUUUCGUUCCGCUGCAGUUGUUGCUAAGCUCGGCGAAAGCUUCUUCGCAUUCGAAAAGCUUUCCGAGCUUACGCGCGAUUUUUUG
....................((((...((.((....)).))(((((((((..(((((((.((((....))))))))))))))))))))...))))....... (-24.00 = -23.80 +  -0.20)

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 11:09:41 2006