Locus 3081

Sequence ID 2R_DroMel_CAF1
Location 10,548,258 – 10,548,436
Length 178
Max. P 0.684641
window5084 window5085

overview

Window 4

Location 10,548,258 – 10,548,370
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 70.92
Mean single sequence MFE -22.92
Consensus MFE -12.73
Energy contribution -12.98
Covariance contribution 0.25
Combinations/Pair 1.07
Mean z-score -1.64
Structure conservation index 0.56
SVM decision value 0.31
SVM RNA-class probability 0.684641
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10548258 112 + 20766785
AAACAAAUACUUAACUCCUAGUUUUCAAACAGUAACUGA--------GCAGACAACUGCGAAAGUAAAAAUGAAGUGCGGCUAAUGAAAGCCAAAUGCAGCCCAAACAUUCUGCACGAAC
.......(((((......(((((..........))))).--------((((....))))..)))))........((((((((......)))).((((.........))))..)))).... ( -20.20)
>DroSec_CAF1 46079 90 + 1
AAACGA---------UCC---UUUUCGAUCAGUAACUCA--------GCAGAAAACUGCAAAAGUGAAAAUGGAGUGCGGCUAAUGAAAGCCAAAUGCAGACCAAACAUU----------
....((---------((.---.....)))).(((((((.--------((((....))))....((....)).))))..((((......))))...)))............---------- ( -19.20)
>DroSim_CAF1 37877 100 + 1
AAACGA---------UCC---UUUUCGAUCAGUAACUCA--------GCAGAAAACUGCAAAAGCGAAAAUGGAGUGCGGCUAAUGAAAGCCAAAUGCAGACCAAACAUUCUGCACGAGG
....((---------((.---.....)))).....(((.--------((((((...(((....)))....(((..(((((((......))))....)))..)))....))))))..))). ( -25.90)
>DroYak_CAF1 42637 110 + 1
AAGCGAAUGCCCAACUCUUGCAUUUCGCACAGUAACUCAGUCACACGGCAGAGUCCUGCGAAAGGGAAAAUGAAGUGCGGCCAAUGAAAGCCAACUGCAGCUCAAAAGCC----------
..((((((((.........))).))))).((((..........(((..((...((((......))))...))..))).(((........))).))))..(((....))).---------- ( -26.40)
>consensus
AAACGA_________UCC___UUUUCGAACAGUAACUCA________GCAGAAAACUGCAAAAGUGAAAAUGAAGUGCGGCUAAUGAAAGCCAAAUGCAGACCAAACAUU__________
...............................................((((....))))...........(((..(((((((......))))....)))..)))................ (-12.73 = -12.98 +   0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,548,330 – 10,548,436
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.29
Mean single sequence MFE -32.73
Consensus MFE -23.68
Energy contribution -26.01
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.72
SVM decision value 0.02
SVM RNA-class probability 0.543002
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10548330 106 + 20766785
CUAAUGAAAGCCAAAUGCAGCCCAAACAUUCUGCACGAACAGACGCUUAGUAAUUCAGGCAUCUCUGGGUCCUGCGU--------------CCGGCCAGGACCUGCAGAGCUCGAAAACU
....(((..(((...(((((..........))))).(((...((.....))..))).)))..((((((((((((.(.--------------....))))))))..))))).)))...... ( -29.50)
>DroSec_CAF1 46139 107 + 1
CUAAUGAAAGCCAAAUGCAGACCAAACAUU-------------CGCUUAGUAAUUCAGGCAUCUCUGGGUCCUGCGUCCUGCUUCCUGCUUCCGGCCAGGACCUGCAGAGCUCGAAAACU
.......((((..((((.........))))-------------.)))).....(((..((.(((.(((((((((.(((..((.....))....)))))))))))).)))))..))).... ( -30.40)
>DroSim_CAF1 37937 113 + 1
CUAAUGAAAGCCAAAUGCAGACCAAACAUUCUGCACGAGGAGUCGCUUAGUAAUUCAGGCAUCUCUGGGUCCUGCGUCCUG-------CUUCCGGCCAGGACCUGCAGAGCUCGAAAACU
(((((((...((...((((((........))))))...))..))).))))...(((..((.(((.(((((((((.(((...-------.....)))))))))))).)))))..))).... ( -38.30)
>consensus
CUAAUGAAAGCCAAAUGCAGACCAAACAUUCUGCACGA__AG_CGCUUAGUAAUUCAGGCAUCUCUGGGUCCUGCGUCCUG_______CUUCCGGCCAGGACCUGCAGAGCUCGAAAACU
.......((((....((((((........)))))).........)))).....(((..((.(((.(((((((((.(((...............)))))))))))).)))))..))).... (-23.68 = -26.01 +   2.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:02 2006