Locus 1822

Sequence ID 2R_DroMel_CAF1
Location 6,818,752 – 6,818,912
Length 160
Max. P 0.750015
window3025 window3026 window3027

overview

Window 5

Location 6,818,752 – 6,818,872
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.89
Mean single sequence MFE -31.00
Consensus MFE -28.20
Energy contribution -28.33
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.38
Structure conservation index 0.91
SVM decision value 0.10
SVM RNA-class probability 0.583126
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6818752 120 + 20766785
AAAAAAAAACCAAACUCAAAACCCACCACUAGUUGCGGUGGUCUUUGGCAAUCAAUCGUGGCUUGGCCAAAUACUAGACGAGUAUUUAGGGCCAGCGAAGCGAAGAUCACAAGAAGCUGA
................((((..(((((.(.....).)))))..))))((......((((.(((.((((.((((((.....))))))...)))))))...))))...((....)).))... ( -32.80)
>DroSec_CAF1 20687 119 + 1
CCAG-AAAACCAAACUUAAAACCCACCACUAGUUGCGGUGGUCUUUGGCAAUCAAUCGUGGUUUGGCCAAAUACUAGACGAGUAGUUAGGGCCAGCAAAGCGAAGAUCACAAGAAGCUGA
.(((-.................(((((.(.....).)))))((((.(...(((..((((.(((.((((...((((.....)))).....)))))))...)))).)))..)))))..))). ( -29.80)
>DroSim_CAF1 21226 119 + 1
CCAG-AAAACCAAACUCAAAACCCACCACUAGUUGCGGUGGUCUUUGGCAAUCAAUCGUGGUUUGGCCAAAUACUAGACGAGUAUUUAGGGCCAGCAAAGCGAAGAUCACAAGAAGCUGA
.(((-..........(((((..(((((.(.....).)))))..))))).........(((((((((((.((((((.....))))))...)))).((...))..)))))))......))). ( -33.40)
>DroEre_CAF1 20430 119 + 1
CCGG-AAAACCAAACUCAAAACCCACCACUAGUUGGGGCGGUCUUUGGCAAUUAAUGGUGGUUUGGCCAAAUACUAGACGAGUAUUUAGGGUCAGCAAGGCGAAGAUCACAUAAAGCUGA
.(((-................((((.(....).))))(.((((((((.((((((....)))))(((((.((((((.....))))))...)))))....).)))))))).)......))). ( -28.00)
>consensus
CCAG_AAAACCAAACUCAAAACCCACCACUAGUUGCGGUGGUCUUUGGCAAUCAAUCGUGGUUUGGCCAAAUACUAGACGAGUAUUUAGGGCCAGCAAAGCGAAGAUCACAAGAAGCUGA
.............................(((((...((((((((((((........)).(((.((((.((((((.....))))))...)))))))....))))))))))....))))). (-28.20 = -28.33 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,818,752 – 6,818,872
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.89
Mean single sequence MFE -33.90
Consensus MFE -30.91
Energy contribution -31.10
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -1.55
Structure conservation index 0.91
SVM decision value 0.47
SVM RNA-class probability 0.750015
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6818752 120 - 20766785
UCAGCUUCUUGUGAUCUUCGCUUCGCUGGCCCUAAAUACUCGUCUAGUAUUUGGCCAAGCCACGAUUGAUUGCCAAAGACCACCGCAACUAGUGGUGGGUUUUGAGUUUGGUUUUUUUUU
..((((.((.(..(((.(((....(((((((..(((((((.....))))))))))).)))..)))..)))..)(((((.(((((((.....))))))).)))))))...))))....... ( -37.50)
>DroSec_CAF1 20687 119 - 1
UCAGCUUCUUGUGAUCUUCGCUUUGCUGGCCCUAACUACUCGUCUAGUAUUUGGCCAAACCACGAUUGAUUGCCAAAGACCACCGCAACUAGUGGUGGGUUUUAAGUUUGGUUUU-CUGG
.(((..(((((..(((.(((......(((((...((((......))))....))))).....)))..)))..)..))))(((((((.....))))))).................-))). ( -31.80)
>DroSim_CAF1 21226 119 - 1
UCAGCUUCUUGUGAUCUUCGCUUUGCUGGCCCUAAAUACUCGUCUAGUAUUUGGCCAAACCACGAUUGAUUGCCAAAGACCACCGCAACUAGUGGUGGGUUUUGAGUUUGGUUUU-CUGG
.(((......(..(((.(((......(((((..(((((((.....)))))))))))).....)))..)))..)(((((.(((((((.....))))))).)))))...........-))). ( -35.90)
>DroEre_CAF1 20430 119 - 1
UCAGCUUUAUGUGAUCUUCGCCUUGCUGACCCUAAAUACUCGUCUAGUAUUUGGCCAAACCACCAUUAAUUGCCAAAGACCGCCCCAACUAGUGGUGGGUUUUGAGUUUGGUUUU-CCGG
(((((.....(((.....)))...)))))(((((((((((.....)))))))))((((((...((.....)).(((((.(((((.(.....).))))).))))).))))))....-..)) ( -30.40)
>consensus
UCAGCUUCUUGUGAUCUUCGCUUUGCUGGCCCUAAAUACUCGUCUAGUAUUUGGCCAAACCACGAUUGAUUGCCAAAGACCACCGCAACUAGUGGUGGGUUUUGAGUUUGGUUUU_CUGG
(((((.....(((.....)))...)))))..(((((((((.....)))))))))((((((((........)).(((((.(((((((.....))))))).))))).))))))......... (-30.91 = -31.10 +   0.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,818,792 – 6,818,912
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -34.00
Consensus MFE -32.14
Energy contribution -32.33
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -1.53
Structure conservation index 0.95
SVM decision value 0.36
SVM RNA-class probability 0.705818
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6818792 120 + 20766785
GUCUUUGGCAAUCAAUCGUGGCUUGGCCAAAUACUAGACGAGUAUUUAGGGCCAGCGAAGCGAAGAUCACAAGAAGCUGACUGGGCGACAUAGCUGCAAUUGAGUGAGUAAAAUGACUGA
((((((..((.(((((.(..((((((((.((((((.....))))))...)))))..(..((..((.(((........)))))..))..)..)))..).))))).))....))).)))... ( -32.70)
>DroSec_CAF1 20726 120 + 1
GUCUUUGGCAAUCAAUCGUGGUUUGGCCAAAUACUAGACGAGUAGUUAGGGCCAGCAAAGCGAAGAUCACAAGAAGCUGACUGGGCGACAUAGCUGCGAUUGAGUGAGCAAAAUGACUGA
(((((((.((.(((((((..((((((((...((((.....)))).....))))).....((..((.(((........)))))..)).....)))..))))))).))..))))..)))... ( -35.60)
>DroSim_CAF1 21265 120 + 1
GUCUUUGGCAAUCAAUCGUGGUUUGGCCAAAUACUAGACGAGUAUUUAGGGCCAGCAAAGCGAAGAUCACAAGAAGCUGACUGGGCGACAUAGCUGCGAUUGAGUGAGUAAAAUGACUGA
((((((..((.(((((((..((((((((.((((((.....))))))...))))).....((..((.(((........)))))..)).....)))..))))))).))....))).)))... ( -35.90)
>DroEre_CAF1 20469 120 + 1
GUCUUUGGCAAUUAAUGGUGGUUUGGCCAAAUACUAGACGAGUAUUUAGGGUCAGCAAGGCGAAGAUCACAUAAAGCUGACUGGGCGACAUAGCUGCGAUUGAGUGAAUAAAAUGACUGA
((((((..((.(((((.(..((((.((((((((((.....)))))))..(((((((...(.(.....).).....))))))).))).)...)))..).))))).))....))).)))... ( -31.80)
>consensus
GUCUUUGGCAAUCAAUCGUGGUUUGGCCAAAUACUAGACGAGUAUUUAGGGCCAGCAAAGCGAAGAUCACAAGAAGCUGACUGGGCGACAUAGCUGCGAUUGAGUGAGUAAAAUGACUGA
((((((..((.(((((((..((((((((.((((((.....))))))...))))).....((..((.(((........)))))..)).....)))..))))))).))....))).)))... (-32.14 = -32.33 +   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 10:14:01 2006