Locus 7711

Sequence ID X_DroMel_CAF1
Location 19,210,829 – 19,210,949
Length 120
Max. P 0.558782
window12645 window12646

overview

Window 5

Location 19,210,829 – 19,210,949
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.99
Mean single sequence MFE -33.40
Consensus MFE -20.89
Energy contribution -24.82
Covariance contribution 3.94
Combinations/Pair 1.21
Mean z-score -1.68
Structure conservation index 0.63
SVM decision value -0.05
SVM RNA-class probability 0.508374
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19210829 120 + 22224390
AUCCAAUAGUUGCAAUUGCAACCGCAUUGCAACAACGUGUGCAGCAGUGAAAACAGCAGAUCGCAAAUGAAUCUGGGUAUCUCGUGUUGGAUUAUUCGAGCCGUGUAUGUGUAUAUGUGU
........((((((((.((....)))))))))).(((((((((...((....))..(((((((....)).))))).((((..((.(((.((....)).))))).)))).))))))))).. ( -32.80)
>DroSec_CAF1 32137 119 + 1
AUGCAAUAGUUGCAUUUGCAACCGCAUUGCAACAACUUGUGCAGCAGUGAAAACAGCAGAUCGAAAAUGGAUCUG-GUAGCUCGAGUUGUAUUAUUCGAGCCCUGUGUGUGUGCAUGUGU
.((((((.(((((....)))))...))))))(((...((..((((((.(.......((((((.......))))))-...((((((((......)))))))))))))...))..))..))) ( -40.10)
>DroEre_CAF1 29273 107 + 1
UU-CAAUAGUUGCCAUUUCAACCGCAUUGCAAUAGCAUGUGC---AGUGGAAACAGGGGAUCGAAAAUGAAUCUG-GGGGCUCGUGUUGGAUUAUUCGAGCAGGAG--------AUGUGU
..-........((((((((..((.(((((((........)))---))))....((((...((......)).))))-)).(((((.((......)).)))))..)))--------))).)) ( -26.70)
>DroYak_CAF1 30032 107 + 1
AU-CAAUAGUUGCAUUUGCAACCGCAUUGCAAUAACAUGUGC---AGUGAAAACAGCAGAUCGAAAAUGGAUCUG-GCAGCUCGGGUUGGAUUAUUCGAGCAGGAG--------AUGUGU
..-.....(((((....)))))(((((..(.........(((---.((....))..((((((.......))))))-)))((((((((......))))))))..)..--------))))). ( -34.00)
>consensus
AU_CAAUAGUUGCAAUUGCAACCGCAUUGCAACAACAUGUGC___AGUGAAAACAGCAGAUCGAAAAUGAAUCUG_GUAGCUCGUGUUGGAUUAUUCGAGCAGGAG________AUGUGU
........((((((((.((....)))))))))).(((((((((.............((((((.......))))))....((((((((......))))))))........))))))))).. (-20.89 = -24.82 +   3.94)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,210,829 – 19,210,949
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.99
Mean single sequence MFE -26.77
Consensus MFE -16.19
Energy contribution -16.75
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.82
Structure conservation index 0.60
SVM decision value 0.05
SVM RNA-class probability 0.558782
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19210829 120 - 22224390
ACACAUAUACACAUACACGGCUCGAAUAAUCCAACACGAGAUACCCAGAUUCAUUUGCGAUCUGCUGUUUUCACUGCUGCACACGUUGUUGCAAUGCGGUUGCAAUUGCAACUAUUGGAU
............................((((((...((((....((((((.......))))))....))))...............((((((((((....)).))))))))..)))))) ( -23.60)
>DroSec_CAF1 32137 119 - 1
ACACAUGCACACACACAGGGCUCGAAUAAUACAACUCGAGCUAC-CAGAUCCAUUUUCGAUCUGCUGUUUUCACUGCUGCACAAGUUGUUGCAAUGCGGUUGCAAAUGCAACUAUUGCAU
......(((.....(((((((((((..........)))))))..-((((((.......))))))))))......)))((((..((((((((((((...))))))...))))))..)))). ( -34.70)
>DroEre_CAF1 29273 107 - 1
ACACAU--------CUCCUGCUCGAAUAAUCCAACACGAGCCCC-CAGAUUCAUUUUCGAUCCCCUGUUUCCACU---GCACAUGCUAUUGCAAUGCGGUUGAAAUGGCAACUAUUG-AA
....((--------((...(((((............)))))...-.)))).....((((((...(((((((.(((---(((..(((....))).)))))).))))))).....))))-)) ( -25.40)
>DroYak_CAF1 30032 107 - 1
ACACAU--------CUCCUGCUCGAAUAAUCCAACCCGAGCUGC-CAGAUCCAUUUUCGAUCUGCUGUUUUCACU---GCACAUGUUAUUGCAAUGCGGUUGCAAAUGCAACUAUUG-AU
......--------.....(((((............))))).((-((((((.......))))))..........(---(((........))))..))((((((....))))))....-.. ( -23.40)
>consensus
ACACAU________ACACGGCUCGAAUAAUCCAACACGAGCUAC_CAGAUCCAUUUUCGAUCUGCUGUUUUCACU___GCACAUGUUAUUGCAAUGCGGUUGCAAAUGCAACUAUUG_AU
...................(((((............)))))....((((((.......))))))..............(((...((....))..)))((((((....))))))....... (-16.19 = -16.75 +   0.56)

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 12:45:38 2006