Locus 1821

Sequence ID X_DroMel_CAF1
Location 5,042,552 – 5,042,709
Length 157
Max. P 0.681808
window2964 window2965

overview

Window 4

Location 5,042,552 – 5,042,670
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.06
Mean single sequence MFE -18.96
Consensus MFE -14.44
Energy contribution -14.28
Covariance contribution -0.16
Combinations/Pair 1.07
Mean z-score -1.71
Structure conservation index 0.76
SVM decision value 0.31
SVM RNA-class probability 0.681808
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5042552 118 - 22224390
UUACCUUCCCAGUUGAUUGGCUAC--CAAAGCCAAAGGCCCAAUCAACCCAGCCCAGUCAGCCAACCAUCCCUGAAAACAUCGAACCAGCCAAAGGAACAACAUCCACGAUCCACCAUUA
...((((....(((((((((....--....(((...)))))))))))).........((((..........)))).................))))........................ ( -16.80)
>DroSec_CAF1 1448 105 - 1
UUACCUUCCCAGUUGAUUGGCUGC--CAAAGCCAAAGGCCCAAUCAGCC-------------CAACCAUCCCUGAAAACAUCGAACCAGCCAAAGGAGCAACAUCCACGAUCCACCAUUA
...........(((((((((..((--(.........)))))))))))).-------------................................(((......))).............. ( -18.30)
>DroSim_CAF1 1527 105 - 1
UUACCUUCCCAGUUGAUUGGCUGC--CAAAGCCAAAGGCCCAAUCAGCC-------------CAACCAUCCCUGAAAACGUCGAACCAGCCAAAGGAGCAACAUCCACGAUCCACCAUUA
...........(((((((((..((--(.........)))))))))))).-------------................................(((......))).............. ( -18.30)
>DroEre_CAF1 6617 103 - 1
UUACCUUCCCAGUUGAUUGGCUGCGUCAAACC---AGGCCCAAUCAGCC----------AGCCAACCACCCGG-GAAACAUCGCACCAGCCAAAGGA---ACAUCCACGAUCCACCAUUA
.....(((((.((((..((((((.(((.....---.))).....)))))----------)..)))).....))-))).....((....))....(((---.(......).)))....... ( -23.20)
>DroYak_CAF1 6499 101 - 1
UUACCUUCCCAGUUGAUUGGCUGC--CAAACC---AGGCCCAAUCAGCC----------AGCCAACCACCCCA-GAAACAUCGAACCAACCAAAGGA---ACAUCCACCAUCCACCGUUA
...((((....(((((((((..((--(.....---.)))))))))))).----------..............-((....))..........)))).---.................... ( -18.20)
>consensus
UUACCUUCCCAGUUGAUUGGCUGC__CAAAGCCAAAGGCCCAAUCAGCC__________AGCCAACCAUCCCUGAAAACAUCGAACCAGCCAAAGGA_CAACAUCCACGAUCCACCAUUA
...........(((((((((((..............)).)))))))))..............................................(((......))).............. (-14.44 = -14.28 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,042,592 – 5,042,709
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.43
Mean single sequence MFE -23.84
Consensus MFE -11.78
Energy contribution -12.39
Covariance contribution 0.61
Combinations/Pair 1.21
Mean z-score -1.78
Structure conservation index 0.49
SVM decision value 0.14
SVM RNA-class probability 0.601950
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5042592 117 - 22224390
AUUUGGCCU-UUUCGACUUUGAUUUCGUGGCUUACAAUUAUUACCUUCCCAGUUGAUUGGCUAC--CAAAGCCAAAGGCCCAAUCAACCCAGCCCAGUCAGCCAACCAUCCCUGAAAACA
..(((((..-....((((((((((..(.(((((.(((((...........))))).((((((..--...))))))))))))))))))........)))).)))))............... ( -22.70)
>DroPse_CAF1 1171 108 - 1
UUUUGGAUUUAUUCGAGUU-----GGGAGGCUUACAAUUAUUUC-GUCUUACUUGAUUGGACAC--CCAAUCAAAGUCCCCAAUAAACG-ACCCCACACAGAUUUC--CCCCC-GAGACC
((((((......(((.(((-----(((.(((((...........-(.....).(((((((....--))))))))))))))))))...))-).........(....)--...))-)))).. ( -23.30)
>DroSec_CAF1 1488 104 - 1
AUUUGGCCU-UUUCGACUUUGAUUUCGAGGCUUACAAUUAUUACCUUCCCAGUUGAUUGGCUGC--CAAAGCCAAAGGCCCAAUCAGCC-------------CAACCAUCCCUGAAAACA
....(((((-((((((........))))(((...((((((.............))))))...))--)......)))))))...((((..-------------.........))))..... ( -22.72)
>DroSim_CAF1 1567 104 - 1
AUUUGGCCU-UUUCGACUUUGAUUUCGAGGCUUACAAUUAUUACCUUCCCAGUUGAUUGGCUGC--CAAAGCCAAAGGCCCAAUCAGCC-------------CAACCAUCCCUGAAAACG
....(((((-((((((........))))(((...((((((.............))))))...))--)......)))))))...((((..-------------.........))))..... ( -22.72)
>DroEre_CAF1 6654 105 - 1
AUUUGGCCU-UUUUGACUUUGAUUUCGAGGCUUACAAUUAUUACCUUCCCAGUUGAUUGGCUGCGUCAAACC---AGGCCCAAUCAGCC----------AGCCAACCACCCGG-GAAACA
....(((((-(...((........)))))))).............(((((.((((..((((((.(((.....---.))).....)))))----------)..)))).....))-)))... ( -25.50)
>DroYak_CAF1 6536 103 - 1
AUUUGGCCU-UCUUGACAUUGAUUUCAAGGCUUACAAUUAUUACCUUCCCAGUUGAUUGGCUGC--CAAACC---AGGCCCAAUCAGCC----------AGCCAACCACCCCA-GAAACA
..(((((..-((((((........)))))).....................(((((((((..((--(.....---.)))))))))))).----------.)))))........-...... ( -26.10)
>consensus
AUUUGGCCU_UUUCGACUUUGAUUUCGAGGCUUACAAUUAUUACCUUCCCAGUUGAUUGGCUGC__CAAAGCCAAAGGCCCAAUCAGCC__________AGCCAACCACCCCU_AAAACA
....((((....((((........))))))))...................(((((((((((..............)).)))))))))................................ (-11.78 = -12.39 +   0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:34 2006