Locus 746

Sequence ID 3R_DroMel_CAF1
Location 2,636,619 – 2,636,848
Length 229
Max. P 0.782261
window1184 window1185 window1186

overview

Window 4

Location 2,636,619 – 2,636,728
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.99
Mean single sequence MFE -35.49
Consensus MFE -25.04
Energy contribution -25.28
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.46
Structure conservation index 0.71
SVM decision value 0.56
SVM RNA-class probability 0.781055
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2636619 109 + 27905053
ACAC-----A------CAAGGGGUAGCAAGGACUUUGGAAGCAAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCAGCCAAAAGGCAGCUGGGACACAGUCGCGCUUGCCUCUGUGAUC
...(-----(------((.((((((((.....(((((........)))))............((((.(..((((.(.(((....))).)))))..)....)))))).))))))))))... ( -33.90)
>DroSec_CAF1 36935 109 + 1
ACAC-----A------CAGGGGGUAGCAAGGACUUUGGAAGCGAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCUGGCGAAAGGCAGCUGGGACAAAGUCGCGCUUGCCUCUGUGAUC
...(-----(------((((((..........(((((........))))).......((((.((((.(..((((.(((.(....).)))))))..)....)))).))))))))))))... ( -40.70)
>DroSim_CAF1 25146 109 + 1
ACAC-----A------CAAGGGGUAGCAAGGACUUUGGAAGCGAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCUGGCGAAAGGCAGCUGGGACAAAGUCGCGCUUGCCUCUGUGAUC
...(-----(------((.((((((((.....(((((........)))))............((((.(..((((.(((.(....).)))))))..)....)))))).))))))))))... ( -38.30)
>DroEre_CAF1 27640 119 + 1
ACACAAUCCACAUGCACAAGGGGUAGCAAGGACU-UGGAAGCGAAUAAAGAGUAAUAUAAGGGUGCAGGACCAGGCAGGCGAAAGGCAGCUGGGACAGAGUCGCAUUUGCCUCUGUGAUC
..............((((.(((((((....((((-(....(((.......(....).......))).(..((((.(.(.(....).).)))))..).)))))....)))))))))))... ( -31.74)
>DroYak_CAF1 18585 114 + 1
ACACAAUCCA------CAAGGGGUAGCAAGGACUUUGGAAGCGAGUGAAGAGUAAUAUAAGGGUGAAGGACCAGGCAGCCAAAAGGCAGCUGGGACAAAGUCGCAUUUGCCUCUGUGAUC
........((------((.(((((((....(((((((..(((...................(((.....))).....(((....))).)))....)))))))....)))))))))))... ( -32.80)
>consensus
ACAC_____A______CAAGGGGUAGCAAGGACUUUGGAAGCGAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCAGGCGAAAGGCAGCUGGGACAAAGUCGCGCUUGCCUCUGUGAUC
..................((((((((...((((((((..(((...................(((.....))).....(.(....).).)))....))))))).)..))))))))...... (-25.04 = -25.28 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,636,648 – 2,636,768
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.75
Mean single sequence MFE -41.04
Consensus MFE -32.78
Energy contribution -32.70
Covariance contribution -0.08
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.80
SVM decision value 0.56
SVM RNA-class probability 0.782261
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2636648 120 + 27905053
GCAAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCAGCCAAAAGGCAGCUGGGACACAGUCGCGCUUGCCUCUGUGAUCAUCCAGCUGAAGCUCGCUGCGAAGUGCUCCACUUUUCAGC
.........((((.......((((((....((.(((.(((....))).))).)).(((((..((....))..))))).)))))).......))))((((.((((((...)))))).)))) ( -41.64)
>DroSec_CAF1 36964 120 + 1
GCGAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCUGGCGAAAGGCAGCUGGGACAAAGUCGCGCUUGCCUCUGUGAUCAUCCAGCUGAAGCUCGCUGCGAAGUGCUCCACUUUUCAGC
.........((((.......((((((.(..((((.(((.(....).)))))))..)....(((((........))))))))))).......))))((((.((((((...)))))).)))) ( -41.84)
>DroSim_CAF1 25175 120 + 1
GCGAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCUGGCGAAAGGCAGCUGGGACAAAGUCGCGCUUGCCUCUGUGAUCAUCCAGCUGAAGCUCGCUGCGAAGUGCUCCACUUUUCAGC
.........((((.......((((((.(..((((.(((.(....).)))))))..)....(((((........))))))))))).......))))((((.((((((...)))))).)))) ( -41.84)
>DroEre_CAF1 27679 120 + 1
GCGAAUAAAGAGUAAUAUAAGGGUGCAGGACCAGGCAGGCGAAAGGCAGCUGGGACAGAGUCGCAUUUGCCUCUGUGAUCAUCCAGCUGAAGCUCGCUGCAAAGUGCUCCACUUUUCAAC
..................(((((((.((.((...((((.(((....((((((((((((((..((....)))))))).....))))))))....)))))))...)).)).))))))).... ( -40.90)
>DroYak_CAF1 18619 120 + 1
GCGAGUGAAGAGUAAUAUAAGGGUGAAGGACCAGGCAGCCAAAAGGCAGCUGGGACAAAGUCGCAUUUGCCUCUGUGAUCAUCCAGCCAAUGCUCGCUGCAAAGUGCUCCACUUUUCAGC
.........(((((......((((((.(..((((.(.(((....))).)))))..)....(((((........)))))))))))......)))))((((.((((((...)))))).)))) ( -39.00)
>consensus
GCGAAUAAAGAGUAAUAUAAGGGUGAAGGACCAGGCAGGCGAAAGGCAGCUGGGACAAAGUCGCGCUUGCCUCUGUGAUCAUCCAGCUGAAGCUCGCUGCGAAGUGCUCCACUUUUCAGC
.........((((.......((((((.(..((((.(.(.(....).).)))))..)....(((((........))))))))))).......))))((((.((((((...)))))).)))) (-32.78 = -32.70 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,636,728 – 2,636,848
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.50
Mean single sequence MFE -36.34
Consensus MFE -34.30
Energy contribution -33.78
Covariance contribution -0.52
Combinations/Pair 1.19
Mean z-score -1.13
Structure conservation index 0.94
SVM decision value 0.27
SVM RNA-class probability 0.660387
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2636728 120 - 27905053
CGUGGGUGCUGUUGGGCUGGGGUGAUGUAAUAUAUUUUGCGGACUUCGAUUUGGCAAGACGGCGAUAAUUUGGCAAAGGUGCUGAAAAGUGGAGCACUUCGCAGCGAGCUUCAGCUGGAU
......(((((((..((((((((..(((((......))))).))))).....)))..)))))))...(((..((..((((((((..(((((...)))))..))))..))))..))..))) ( -37.10)
>DroSec_CAF1 37044 120 - 1
CGGGGGUGCUGUUGGGCUGGGGUGAUGUAAUAUUUUUUGCGGACUUCGAUUUGGCAAGACGGCGAUAAUUUGGCAAAGGUGCUGAAAAGUGGAGCACUUCGCAGCGAGCUUCAGCUGGAU
......(((((((..((((((((..(((((......))))).))))).....)))..)))))))...(((..((..((((((((..(((((...)))))..))))..))))..))..))) ( -37.10)
>DroSim_CAF1 25255 120 - 1
CGGGGGUGCUGUUGGGCUGGGGUGAUGUAAUAUUUUUUGCGGUCUUCGAUUUGGCAAGACGGCGAUAAUUUGGCAAAGGUGCUGAAAAGUGGAGCACUUCGCAGCGAGCUUCAGCUGGAU
..........(((.(((((((((..(((...(((..((((.((((((......).))))).)))).)))...)))....(((((..(((((...)))))..))))).))))))))).))) ( -38.60)
>DroEre_CAF1 27759 120 - 1
CGGGGGUGCCGUUGCGCUGGGGUGAUGUAAUAUAUUUUGCGAAUUUCGAUUUGGCAAGACGGCGAUAAUUUGGCAAAGGUGUUGAAAAGUGGAGCACUUUGCAGCGAGCUUCAGCUGGAU
......(((((((..((..((.((((((((......)))))....))).))..))..)))))))...(((..((..((((((((.((((((...)))))).))))..))))..))..))) ( -35.60)
>DroYak_CAF1 18699 120 - 1
CGGGGUUGCUGAUGGGUUGAAAUGAUGUAAUAUAUUUUGCUGAUUUUGAUUUGGCAAGACGGCAAUAAUUUGGCAAAGGUGCUGAAAAGUGGAGCACUUUGCAGCGAGCAUUGGCUGGAU
....(((((((.((.(((.....))).)).....((((((..(.......)..))))))))))))).(((..((.....(((((.((((((...)))))).))))).......))..))) ( -33.30)
>consensus
CGGGGGUGCUGUUGGGCUGGGGUGAUGUAAUAUAUUUUGCGGACUUCGAUUUGGCAAGACGGCGAUAAUUUGGCAAAGGUGCUGAAAAGUGGAGCACUUCGCAGCGAGCUUCAGCUGGAU
......(((((((..((..((.((((((((......)))))....))).))..))..)))))))...(((..((..((((((((..(((((...)))))..))))..))))..))..))) (-34.30 = -33.78 +  -0.52)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:00 2006