Locus 4206

Sequence ID X_DroMel_CAF1
Location 11,027,542 – 11,027,669
Length 127
Max. P 0.898269
window6911 window6912 window6913

overview

Window 1

Location 11,027,542 – 11,027,648
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.78
Mean single sequence MFE -24.60
Consensus MFE -20.15
Energy contribution -20.40
Covariance contribution 0.25
Combinations/Pair 1.08
Mean z-score -2.69
Structure conservation index 0.82
SVM decision value 1.00
SVM RNA-class probability 0.898269
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11027542 106 - 22224390
G-----CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUACAU---GG------CAAAUGCUCAACAUUAAAACCAGAUUA
(-----(.(((....))).)).(((((((.(((.....)))(((((((.(((((......))))).)))))))........(---((------(....)).)).)))))))......... ( -23.90)
>DroSec_CAF1 19994 106 - 1
G-----CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUACAC---GG------CAAAUGCUCAACAUUAAAACCAGAUAC
(-----((.((....))((((((...(((((((.....)))))))(((.(((((......))))).))))))))).......---))------).((((.....))))............ ( -24.00)
>DroSim_CAF1 11749 106 - 1
G-----CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUACAC---GG------CAAAUGCUCAACAUUAAAACCAGAUUA
(-----((.((....))((((((...(((((((.....)))))))(((.(((((......))))).))))))))).......---))------).((((.....))))............ ( -24.00)
>DroEre_CAF1 14275 106 - 1
G-----CCUGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUACAU---GG------CAAAUGCUGAACAUUAAAACCAGAUUA
(-----((...(((...((((((...(((((((.....)))))))(((.(((((......))))).)))))))))...))).---))------).....(((...........))).... ( -24.10)
>DroYak_CAF1 15737 106 - 1
G-----CCUGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUACAU---GG------CAAAUGCUGAACAUUAAAACCAGAUUA
(-----((...(((...((((((...(((((((.....)))))))(((.(((((......))))).)))))))))...))).---))------).....(((...........))).... ( -24.10)
>DroMoj_CAF1 18357 118 - 1
GGAUAUCCUGUUGCUGC-UGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAU-UUCUACAAUUUUAUUAUGCACUUUACAGCCUGACGCGCUCCGAUGCUCAGCAUUAAAAUCAGAUUA
((....))...(((((.-.(((((....((((.........(((((((.((((-(.....))))).)))))))......(.....)..))))...))))).))))).............. ( -27.50)
>consensus
G_____CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUACAU___GG______CAAAUGCUCAACAUUAAAACCAGAUUA
...........(((((...((((((.....(((.....)))(((((((.(((((......))))).))))))).....................)))))).))))).............. (-20.15 = -20.40 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,027,573 – 11,027,669
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.13
Mean single sequence MFE -27.82
Consensus MFE -18.91
Energy contribution -19.02
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.76
Structure conservation index 0.68
SVM decision value 0.90
SVM RNA-class probability 0.876770
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11027573 96 + 22224390
GUAAAGUGCAUAAUAAAAUUGUAGAAAAUUUAAUUAUGCGCAAUUAAUGCGCAUUAAAUGCACGCAACAGCGGG-----CGGCGAAUGAUCCUGGG-------------------CGUCA
.....(((((((((.(((((......))))).))))))))).......((((((...)))).(((....))).)-----)((((..(......)..-------------------)))). ( -26.10)
>DroSec_CAF1 20025 96 + 1
GUAAAGUGCAUAAUAAAAUUGUAGAAAAUUUAAUUAUGCGCAAUUAAUGCGCAUUAAAUGCACGCAACAGCGGG-----CGGCGAAUGAUCCUGGG-------------------CGUAA
.....(((((((((.(((((......))))).)))))))))......(((((.......((.(((....))).)-----)((........))...)-------------------)))). ( -26.90)
>DroSim_CAF1 11780 96 + 1
GUAAAGUGCAUAAUAAAAUUGUAGAAAAUUUAAUUAUGCGCAAUUAAUGCGCAUUAAAUGCACGCAACAGCGGG-----CGGCGAAUGAUCCUGGG-------------------CGUAA
.....(((((((((.(((((......))))).)))))))))......(((((.......((.(((....))).)-----)((........))...)-------------------)))). ( -26.90)
>DroEre_CAF1 14306 115 + 1
GUAAAGUGCAUAAUAAAAUUGUAGAAAAUUUAAUUAUGCGCAAUUAAUGCGCAUUAAAUGCACGCAACAGCAGG-----CGGCAAAUGAUCCUGUCGCGGAGAAGGGGCGGUCUUCGAAA
.....(((((((((.(((((......))))).)))(((((((.....)))))))...))))))((....))..(-----(((((........))))))(((((........))))).... ( -32.00)
>DroYak_CAF1 15768 104 + 1
GUAAAGUGCAUAAUAAAAUUGUAGAAAAUUUAAUUAUGCGCAAUUAAUGCGCAUUAAAUGCACGCAACAGCAGG-----CGGCAAGUGAUCCUGGCCCG-CGAAGUGGG----------G
.....(((((((((.(((((......))))).)))))))))......(((((((...)))).(((........)-----)))))...........((((-(...)))))----------. ( -29.10)
>DroMoj_CAF1 18397 100 + 1
GUAAAGUGCAUAAUAAAAUUGUAGAA-AUUUAAUUAUGCGCAAUUAAUGCGCAUUAAAUGCA-GCAGCAACAGGAUAUCCAGCGAGUGAGUC--GCCAG----------------CCAAA
.....(((((((((.(((((.....)-)))).)))))))))......(((((((...)))).-)))((....((....)).((((.....))--))..)----------------).... ( -25.90)
>consensus
GUAAAGUGCAUAAUAAAAUUGUAGAAAAUUUAAUUAUGCGCAAUUAAUGCGCAUUAAAUGCACGCAACAGCAGG_____CGGCGAAUGAUCCUGGC___________________CGUAA
.....(((((((((.(((((......))))).)))))))))......(((((((...))))..((....))..........))).................................... (-18.91 = -19.02 +   0.11)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,027,573 – 11,027,669
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.13
Mean single sequence MFE -24.33
Consensus MFE -17.16
Energy contribution -17.35
Covariance contribution 0.19
Combinations/Pair 1.04
Mean z-score -2.60
Structure conservation index 0.71
SVM decision value 0.87
SVM RNA-class probability 0.871598
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11027573 96 - 22224390
UGACG-------------------CCCAGGAUCAUUCGCCG-----CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUAC
....(-------------------(...((........))(-----(.(((....))).)).......))(((.....)))(((((((.(((((......))))).)))))))....... ( -21.20)
>DroSec_CAF1 20025 96 - 1
UUACG-------------------CCCAGGAUCAUUCGCCG-----CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUAC
....(-------------------(...((........))(-----(.(((....))).)).......))(((.....)))(((((((.(((((......))))).)))))))....... ( -21.20)
>DroSim_CAF1 11780 96 - 1
UUACG-------------------CCCAGGAUCAUUCGCCG-----CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUAC
....(-------------------(...((........))(-----(.(((....))).)).......))(((.....)))(((((((.(((((......))))).)))))))....... ( -21.20)
>DroEre_CAF1 14306 115 - 1
UUUCGAAGACCGCCCCUUCUCCGCGACAGGAUCAUUUGCCG-----CCUGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUAC
....((((.......))))...(((((((.(..........-----..).)))))))((((((...(((((((.....)))))))(((.(((((......))))).)))))))))..... ( -28.80)
>DroYak_CAF1 15768 104 - 1
C----------CCCACUUCG-CGGGCCAGGAUCACUUGCCG-----CCUGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUAC
.----------........(-(((((((((....))))..)-----)))))......((((((...(((((((.....)))))))(((.(((((......))))).)))))))))..... ( -29.80)
>DroMoj_CAF1 18397 100 - 1
UUUGG----------------CUGGC--GACUCACUCGCUGGAUAUCCUGUUGCUGC-UGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAU-UUCUACAAUUUUAUUAUGCACUUUAC
...((----------------(.(((--(((.........((....)).))))))))-)(((.(((((....))))).)))(((((((.((((-(.....))))).)))))))....... ( -23.80)
>consensus
UUACG___________________CCCAGGAUCAUUCGCCG_____CCCGCUGUUGCGUGCAUUUAAUGCGCAUUAAUUGCGCAUAAUUAAAUUUUCUACAAUUUUAUUAUGCACUUUAC
.................................................((....))((((((...(((((((.....)))))))(((.(((((......))))).)))))))))..... (-17.16 = -17.35 +   0.19)

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 11:19:09 2006