Locus 1490

Sequence ID X_DroMel_CAF1
Location 4,421,512 – 4,421,663
Length 151
Max. P 0.978835
window2385 window2386 window2387 window2388

overview

Window 5

Location 4,421,512 – 4,421,623
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.06
Mean single sequence MFE -31.88
Consensus MFE -26.16
Energy contribution -26.36
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.82
SVM decision value 1.00
SVM RNA-class probability 0.898225
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4421512 111 + 22224390
-------CAGCCCGCAGACCAAUCCAAUCCAAUACAAUACAAACCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGUCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCC
-------(((((((.............................((.((--(((((....)))).))).)).......((.(((((....)))))))..)))))))............... ( -31.40)
>DroSec_CAF1 24011 94 + 1
-------C-----------------AAUCCAAUACAAUACAAUCCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCC
-------.-----------------..................((.((--(((((....)))).))).)).......((((((((....))))))))..(((..(((......))).))) ( -28.20)
>DroSim_CAF1 25303 94 + 1
-------C-----------------AAUCCAAUACAAUACAAUCCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCC
-------.-----------------..................((.((--(((((....)))).))).)).......((((((((....))))))))..(((..(((......))).))) ( -28.20)
>DroEre_CAF1 24950 115 + 1
CAUCGCACAGUCCGCAGACC-----AAUCCAAUACAAUACAAUCCGAUCCGGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCC
.((((..(((((((......-----..........................((((....)))).(((((....)))))(((((((....)))))))..)))))))...))))........ ( -35.00)
>DroYak_CAF1 24542 109 + 1
----GCACAGCCCGCAGACC-----AAUCCAAUACAAUACAAUCCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCC
----((((((((((......-----..................((.((--(((((....)))).))).)).......((((((((....)))))))).)))))))........))).... ( -36.60)
>consensus
_______CAG_CCGCAGACC_____AAUCCAAUACAAUACAAUCCGAU__GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCC
...................................................((((....)))).(((((....)))))(((((((....)))))))...(((..(((......))).))) (-26.16 = -26.36 +   0.20)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,421,512 – 4,421,623
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.06
Mean single sequence MFE -38.08
Consensus MFE -30.74
Energy contribution -30.94
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.81
SVM decision value 0.57
SVM RNA-class probability 0.785663
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4421512 111 - 22224390
GGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGACCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGUUUGUAUUGUAUUGGAUUGGAUUGGUCUGCGGGCUG-------
.((.((((((((((.((..((((.(((((((....))))).))(((.(((((.(((.(((......))))--)).))))).)))....))))..)).))))))))))...)).------- ( -43.40)
>DroSec_CAF1 24011 94 - 1
GGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGAUUGUAUUGUAUUGGAUU-----------------G-------
.....(((..(((((((..((((.(((((((....)))))))(((((....))))).(((......))).--.))))..)))))))..)))....-----------------.------- ( -32.30)
>DroSim_CAF1 25303 94 - 1
GGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGAUUGUAUUGUAUUGGAUU-----------------G-------
.....(((..(((((((..((((.(((((((....)))))))(((((....))))).(((......))).--.))))..)))))))..)))....-----------------.------- ( -32.30)
>DroEre_CAF1 24950 115 - 1
GGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCCGGAUCGGAUUGUAUUGUAUUGGAUU-----GGUCUGCGGACUGUGCGAUG
........((((.(((((.(((.(((((........(((((.(((((....))))).))))).........((((.(((........))).))))-----))))).))).))))))))). ( -40.90)
>DroYak_CAF1 24542 109 - 1
GGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGAUUGUAUUGUAUUGGAUU-----GGUCUGCGGGCUGUGC----
..............((((((((.(((((........(((((.(((((....))))).)))))........--(((.(((........))).))).-----))))).))))))))..---- ( -41.50)
>consensus
GGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC__AUCGGAUUGUAUUGUAUUGGAUU_____GGUCUGCGG_CUG_______
.....(((..(((((((..((((.(((((((....)))))))(((((....))))).(((......)))....))))..)))))))..)))............................. (-30.74 = -30.94 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,421,545 – 4,421,663
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.19
Mean single sequence MFE -38.65
Consensus MFE -33.72
Energy contribution -33.92
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.87
SVM decision value 0.11
SVM RNA-class probability 0.586689
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4421545 118 + 22224390
AAACCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGUCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCCAGAAUUUUAAGUACUUGCCGAUCUGGCCGUCUGCCCAAAG
......((--(((((....)))).)))((((......((.(((((....)))))))...((((.((...((((.((....................)).))))..)).)))))))).... ( -34.05)
>DroSec_CAF1 24027 107 + 1
AAUCCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCCAGAAUUUUAAGUACUUGCCGAUCUGGCCG-----------
........--((((....((.((((((((....)))))(((((((....)))))))((.(((..(((......))).))).))............)))))....)))).----------- ( -35.20)
>DroSim_CAF1 25319 118 + 1
AAUCCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCCAGAAUUUUAAGUACUUGCCGAUCUGGCCGUCUGCCCAACG
.....(((--((((....((.((((((((....)))))(((((((....)))))))((.(((..(((......))).))).))............)))))....)))))))......... ( -40.20)
>DroEre_CAF1 24985 120 + 1
AAUCCGAUCCGGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCCAGAAUUUUAAGUACUUGCCGAUCUGGCCGGCUGCCCAAAG
...........((((....))))...(((((..((..((((((((....))))))))...(((((.((((.((((....)))).......((....)))))).)))))))..)))))... ( -41.60)
>DroYak_CAF1 24573 117 + 1
AAUCCGAU--GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCCAGAAUUUUAAGUACUUGCCGAUCUGGCCGGCUGCCCAAA-
......((--(((((....)))).)))((((..((..((((((((....))))))))...(((((.((((.((((....)))).......((....)))))).)))))))..))))...- ( -42.20)
>consensus
AAUCCGAU__GGCUUUUAUGAGCACAUGGGCUUCCAUGGGCCCAAAUAGUUGGGCCUCCGGGCUGCAUCGAUCUGCUCCCAGAAUUUUAAGUACUUGCCGAUCUGGCCGGCUGCCCAAAG
..........((((....((.((((((((....)))))(((((((....)))))))((.(((..(((......))).))).))............)))))....))))............ (-33.72 = -33.92 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,421,545 – 4,421,663
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.19
Mean single sequence MFE -42.12
Consensus MFE -35.42
Energy contribution -36.82
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.84
SVM decision value 1.82
SVM RNA-class probability 0.978835
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4421545 118 - 22224390
CUUUGGGCAGACGGCCAGAUCGGCAAGUACUUAAAAUUCUGGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGACCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGUUU
..((((((.....(((.....)))............(((((((.(((......)))..))))))))))))).....((((..(((((....)))))..))))...(((((--...))))) ( -39.40)
>DroSec_CAF1 24027 107 - 1
-----------CGGCCAGAUCGGCAAGUACUUAAAAUUCUGGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGAUU
-----------.(((...((.((((............((((((.(((......)))..))))))(((((((....)))))))(((((....))))))))).))....)))--........ ( -38.30)
>DroSim_CAF1 25319 118 - 1
CGUUGGGCAGACGGCCAGAUCGGCAAGUACUUAAAAUUCUGGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGAUU
.(((((((.....(((.....)))............(((((((.(((......)))..))))))))))))))....(((((.(((((....))))).)))))........--........ ( -44.30)
>DroEre_CAF1 24985 120 - 1
CUUUGGGCAGCCGGCCAGAUCGGCAAGUACUUAAAAUUCUGGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCCGGAUCGGAUU
.(((((....(((((...((.((((............((((((.(((......)))..))))))(((((((....)))))))(((((....))))))))).))....))))).))))).. ( -45.10)
>DroYak_CAF1 24573 117 - 1
-UUUGGGCAGCCGGCCAGAUCGGCAAGUACUUAAAAUUCUGGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC--AUCGGAUU
-.((((((.(((((.....)))))............(((((((.(((......)))..))))))))))))).....(((((.(((((....))))).)))))........--........ ( -43.50)
>consensus
CUUUGGGCAGACGGCCAGAUCGGCAAGUACUUAAAAUUCUGGGAGCAGAUCGAUGCAGCCCGGAGGCCCAACUAUUUGGGCCCAUGGAAGCCCAUGUGCUCAUAAAAGCC__AUCGGAUU
..((((((.....(((.....)))............(((((((.(((......)))..))))))))))))).....(((((.(((((....))))).))))).................. (-35.42 = -36.82 +   1.40)

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 10:10:50 2006