Locus 9720

Sequence ID 3R_DroMel_CAF1
Location 25,721,953 – 25,722,055
Length 102
Max. P 0.788979
window15528 window15529

overview

Window 8

Location 25,721,953 – 25,722,055
Length 102
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 80.95
Mean single sequence MFE -22.24
Consensus MFE -14.52
Energy contribution -14.48
Covariance contribution -0.04
Combinations/Pair 1.07
Mean z-score -1.93
Structure conservation index 0.65
SVM decision value 0.58
SVM RNA-class probability 0.788979
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25721953 102 + 27905053
AUAUUACA-------GAUUGAGAUUGAAAGGCCAAUCUUUCGAGAGCUGGCGAUCACUAUCUGUUCGAACUGUAAUCUACAAUUACUUUA-------UUCUCCCAGCUAUUUCUAA
........-------....((((((((((((....)))))))).(((((((((.((.....)).)))....(((((.....)))))....-------.....)))))).))))... ( -19.70)
>DroSec_CAF1 17334 102 + 1
AUAUUACA-------GAUUGAGAUUGAAAGGCCAAUCUUUCGAGAGCUGGCGAUCUCUAUCUGUUCAAGCUGUAAUCUACAAUUACUUUG-------UUCGCCUAACUAUUUCUAA
.....(((-------(((.(((((((...(((...((....))..)))..))))))).))))))...(((.(((((.....)))))...)-------))................. ( -22.10)
>DroSim_CAF1 17594 82 + 1
AUAUUACA-------GAUUGAGAUUGAAAGGCCAAUCUUUCGAGAGCUGGCGAUCUCUAUCUGUUCAAGCUGUAAUCCACAAUUAC---------------------------UAA
.....(((-------(((.(((((((...(((...((....))..)))..))))))).)))))).......(((((.....)))))---------------------------... ( -21.60)
>DroEre_CAF1 18544 109 + 1
AUAUUACA-------GAUUGCGAUUGAAAGGCCAAUCUUUCGAGAGCUUGCGAUCGCUAUCUGCUCGAACUAUAAUUUACAAUUACUUUGUACUUUGCUCGCCCAACUAUUUCUAA
......((-------(((.(((((((..((((...((....))..)))).))))))).)))))..(((....(((..(((((.....)))))..))).)))............... ( -22.50)
>DroYak_CAF1 18129 109 + 1
AUAUUACAGAUUACAGAUUGAGAUUGAAAGGCCAAUCUUUCGAGAGCUGGCGAUCUCUAUCUGUUCAAACUACAAUUUACAAUUACUUUG-------UUCGCCCAACUAUUUGUAA
...((((((((.((((((.(((((((...(((...((....))..)))..))))))).))))))..............((((.....)))-------)..........)))))))) ( -25.30)
>consensus
AUAUUACA_______GAUUGAGAUUGAAAGGCCAAUCUUUCGAGAGCUGGCGAUCUCUAUCUGUUCAAACUGUAAUCUACAAUUACUUUG_______UUCGCCCAACUAUUUCUAA
...............(((.(((((((...(((...((....))..)))..))))))).)))....................................................... (-14.52 = -14.48 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 25,721,953 – 25,722,055
Length 102
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 80.95
Mean single sequence MFE -24.23
Consensus MFE -13.37
Energy contribution -13.13
Covariance contribution -0.24
Combinations/Pair 1.14
Mean z-score -1.92
Structure conservation index 0.55
SVM decision value 0.07
SVM RNA-class probability 0.566951
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25721953 102 - 27905053
UUAGAAAUAGCUGGGAGAA-------UAAAGUAAUUGUAGAUUACAGUUCGAACAGAUAGUGAUCGCCAGCUCUCGAAAGAUUGGCCUUUCAAUCUCAAUC-------UGUAAUAU
......((((.(((((...-------.((((........((((((...((.....))..))))))(((((...((....)))))))))))...)))))..)-------)))..... ( -22.20)
>DroSec_CAF1 17334 102 - 1
UUAGAAAUAGUUAGGCGAA-------CAAAGUAAUUGUAGAUUACAGCUUGAACAGAUAGAGAUCGCCAGCUCUCGAAAGAUUGGCCUUUCAAUCUCAAUC-------UGUAAUAU
..........((((((...-------....((((((...)))))).))))))((((((.(((((.(((((...((....)))))))......))))).)))-------)))..... ( -24.40)
>DroSim_CAF1 17594 82 - 1
UUA---------------------------GUAAUUGUGGAUUACAGCUUGAACAGAUAGAGAUCGCCAGCUCUCGAAAGAUUGGCCUUUCAAUCUCAAUC-------UGUAAUAU
...---------------------------..........(((((((.((((...(((.((((..(((((...((....))))))).)))).))))))).)-------)))))).. ( -22.10)
>DroEre_CAF1 18544 109 - 1
UUAGAAAUAGUUGGGCGAGCAAAGUACAAAGUAAUUGUAAAUUAUAGUUCGAGCAGAUAGCGAUCGCAAGCUCUCGAAAGAUUGGCCUUUCAAUCGCAAUC-------UGUAAUAU
..........((((((........(((((.....))))).......))))))((((((.(((((.(.(((((.((....))..)).))).).))))).)))-------)))..... ( -26.66)
>DroYak_CAF1 18129 109 - 1
UUACAAAUAGUUGGGCGAA-------CAAAGUAAUUGUAAAUUGUAGUUUGAACAGAUAGAGAUCGCCAGCUCUCGAAAGAUUGGCCUUUCAAUCUCAAUCUGUAAUCUGUAAUAU
(((((.....(..(((..(-------(((..((....))..)))).)))..)((((((.(((((.(((((...((....)))))))......))))).))))))....)))))... ( -25.80)
>consensus
UUAGAAAUAGUUGGGCGAA_______CAAAGUAAUUGUAGAUUACAGUUUGAACAGAUAGAGAUCGCCAGCUCUCGAAAGAUUGGCCUUUCAAUCUCAAUC_______UGUAAUAU
........................................((((((.........(((.(((((.(((((...((....)))))))......))))).))).......)))))).. (-13.37 = -13.13 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:38 2006