Locus 915

Sequence ID 2R_DroMel_CAF1
Location 4,057,955 – 4,058,097
Length 142
Max. P 0.999428
window1615 window1616 window1617 window1618

overview

Window 5

Location 4,057,955 – 4,058,057
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.95
Mean single sequence MFE -30.80
Consensus MFE -26.68
Energy contribution -26.72
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.80
Structure conservation index 0.87
SVM decision value 3.59
SVM RNA-class probability 0.999428
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4057955 102 + 20766785
------------CAAAGCCAAAGCCAUAG------CAAACCGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAUGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUU
------------.........((((((.(------(...(((((.(((...(..((((((((....(((......))).))))))))..).)))..)))))(((....))))).)))))) ( -31.60)
>DroSec_CAF1 40651 106 + 1
--------AAGCCAAAGCCAAAGCCAUAG------CAAACCGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUU
--------.............((((((.(------(...(((((.(((...(..((((((((.....((......))..))))))))..).)))..)))))(((....))))).)))))) ( -30.90)
>DroSim_CAF1 46837 106 + 1
--------AAGCCAAAGCCAAAGCCAUAG------CAAACCGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUU
--------.............((((((.(------(...(((((.(((...(..((((((((.....((......))..))))))))..).)))..)))))(((....))))).)))))) ( -30.90)
>DroEre_CAF1 41474 116 + 1
GAAAGCCAAAGCCAAAGCCAAAGCCAAAGCAAGACCAAACCGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGG----GCUCGCAAUGGUU
...(((((..((...((((...((....)).........(((((.(((...(..((((((((.....((......))..))))))))..).)))..))))).)----))).))..))))) ( -31.70)
>DroYak_CAF1 44193 112 + 1
--------AAGCCAAAGCCAAAGCCAAAGCAAGACCAAACCGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUU
--------.............(((((..((.........(((((.(((...(..((((((((.....((......))..))))))))..).)))..)))))(((....)))))..))))) ( -28.90)
>consensus
________AAGCCAAAGCCAAAGCCAUAG______CAAACCGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUU
...............(((((..((...............(((((.(((...(..((((((((.(((......)))....))))))))..).)))..)))))(((....)))))..))))) (-26.68 = -26.72 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,057,955 – 4,058,057
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.95
Mean single sequence MFE -26.77
Consensus MFE -20.05
Energy contribution -20.45
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.75
SVM decision value 0.54
SVM RNA-class probability 0.774126
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4057955 102 - 20766785
AACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCAUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCGGUUUG------CUAUGGCUUUGGCUUUG------------
...((..(((((((.((..(((((..(((....((((((((.................))))))))......))).)))))...)------)...)))))..))..))------------ ( -22.93)
>DroSec_CAF1 40651 106 - 1
AACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCGGUUUG------CUAUGGCUUUGGCUUUGGCUU--------
..(((..(((((((.((..(((((..(((....((((((((.................))))))))......))).)))))...)------)...)))))..))..)))...-------- ( -26.83)
>DroSim_CAF1 46837 106 - 1
AACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCGGUUUG------CUAUGGCUUUGGCUUUGGCUU--------
..(((..(((((((.((..(((((..(((....((((((((.................))))))))......))).)))))...)------)...)))))..))..)))...-------- ( -26.83)
>DroEre_CAF1 41474 116 - 1
AACCAUUGCGAGC----CCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCGGUUUGGUCUUGCUUUGGCUUUGGCUUUGGCUUUGGCUUUC
...((..((((((----(.(((((..(((....((((((((.................))))))))......))).)))))...)).)))))..))(((..(((....)))..))).... ( -31.13)
>DroYak_CAF1 44193 112 - 1
AACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCGGUUUGGUCUUGCUUUGGCUUUGGCUUUGGCUU--------
..(((..(((((((.....(((((..(((....((((((((.................))))))))......))).)))))...)).)))))..)))....(((....))).-------- ( -26.13)
>consensus
AACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCGGUUUG______CUAUGGCUUUGGCUUUGGCUU________
..(((..(((((....)))(((((..(((....((((((((.................))))))))......))).)))))...............))..)))................. (-20.05 = -20.45 +   0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,057,977 – 4,058,097
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.33
Mean single sequence MFE -34.90
Consensus MFE -32.50
Energy contribution -32.74
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.41
Structure conservation index 0.93
SVM decision value 0.91
SVM RNA-class probability 0.880422
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4057977 120 + 20766785
CGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAUGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUUGACUGCAUAAACCGCACUGCAUGGCCACUAACAAGUGCCG
....((((...(..((((((((....(((......))).))))))))((((((((...((((((....)))(((.........))).....)))...))))).))).....)...)))). ( -35.60)
>DroSec_CAF1 40677 120 + 1
CGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUUGACUGCAUAAACCUCACUGCAUGGCCACUAACAAGUGCCG
....((((...(..((((((((.....((......))..))))))))((((((((....(.(((....))).)...((((.........))))....))))).))).....)...)))). ( -33.50)
>DroSim_CAF1 46863 120 + 1
CGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUUGACUGCAUAAACCGCACUGCAUGGCCACUAACAAGUGCCG
....((((...(..((((((((.....((......))..))))))))((((((((...((((((....)))(((.........))).....)))...))))).))).....)...)))). ( -34.90)
>DroEre_CAF1 41514 116 + 1
CGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGG----GCUCGCAAUGGUUGACUGCAUAAACCGCACUGCAUGGCCACUAACCAGUGCCG
....((((..((..((((((((.....((......))..))))))))((((((((...(((..----((...((.....))...)).....)))...))))).))).....))..)))). ( -35.60)
>DroYak_CAF1 44225 120 + 1
CGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUUGACUGCAUAAACCGCACUGCAUGGCCACUAACAAGUGCCG
....((((...(..((((((((.....((......))..))))))))((((((((...((((((....)))(((.........))).....)))...))))).))).....)...)))). ( -34.90)
>consensus
CGAAGGCAAGGGAAAUAUUUGCAUAUGUCAAAGUGGAAGGCAAAUAUGGCAUGCAAUUCGGGAGCAAGCUCGCAAUGGUUGACUGCAUAAACCGCACUGCAUGGCCACUAACAAGUGCCG
....((((...(..((((((((.(((......)))....))))))))((((((((...((((((....)))(((.........))).....)))...))))).))).....)...)))). (-32.50 = -32.74 +   0.24)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,057,977 – 4,058,097
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -34.75
Consensus MFE -32.55
Energy contribution -33.15
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.94
SVM decision value 2.81
SVM RNA-class probability 0.997165
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4057977 120 - 20766785
CGGCACUUGUUAGUGGCCAUGCAGUGCGGUUUAUGCAGUCAACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCAUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCG
.((((.......(((((.(((((((.(((.....(((((.....)))))(((....)))))).))))))))))))((((((.................))))))........)))).... ( -35.13)
>DroSec_CAF1 40677 120 - 1
CGGCACUUGUUAGUGGCCAUGCAGUGAGGUUUAUGCAGUCAACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCG
.((((.......(((((.(((((((..((.....(((((.....)))))(((....)))))..))))))))))))((((((.................))))))........)))).... ( -33.83)
>DroSim_CAF1 46863 120 - 1
CGGCACUUGUUAGUGGCCAUGCAGUGCGGUUUAUGCAGUCAACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCG
.((((.......(((((.(((((((.(((.....(((((.....)))))(((....)))))).))))))))))))((((((.................))))))........)))).... ( -35.13)
>DroEre_CAF1 41514 116 - 1
CGGCACUGGUUAGUGGCCAUGCAGUGCGGUUUAUGCAGUCAACCAUUGCGAGC----CCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCG
.((((..((...(((((.(((((((.(((....((((((.....))))))...----..))).))))))))))))((((((.................))))))....))..)))).... ( -34.53)
>DroYak_CAF1 44225 120 - 1
CGGCACUUGUUAGUGGCCAUGCAGUGCGGUUUAUGCAGUCAACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCG
.((((.......(((((.(((((((.(((.....(((((.....)))))(((....)))))).))))))))))))((((((.................))))))........)))).... ( -35.13)
>consensus
CGGCACUUGUUAGUGGCCAUGCAGUGCGGUUUAUGCAGUCAACCAUUGCGAGCUUGCUCCCGAAUUGCAUGCCAUAUUUGCCUUCCACUUUGACAUAUGCAAAUAUUUCCCUUGCCUUCG
.((((.......(((((.(((((((.(((.....(((((.....)))))(((....)))))).))))))))))))((((((.................))))))........)))).... (-32.55 = -33.15 +   0.60)

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 09:51:17 2006