Locus 43

Sequence ID 3L_DroMel_CAF1
Location 172,994 – 173,194
Length 200
Max. P 0.744504
window51 window52 window53 window54

overview

Window 1

Location 172,994 – 173,114
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -39.03
Consensus MFE -36.27
Energy contribution -36.83
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.85
Structure conservation index 0.93
SVM decision value 0.43
SVM RNA-class probability 0.734589
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 172994 120 + 23771897
UAAGAGUGCUAAAAUUACUUGUCAAACGCUUUUUAGGUGGACAAGCCCUUCGGGUCAUUUCAUAACUGUAGUUUUGGCCCUCGUCAACGCUUGAAACACCUGAAGGUGUCUCGUUGGCCG
...(((.((((((((((((((((...((((.....)))))))))(.((....)).)...........))))))))))).)))(((((((......(((((....)))))..))))))).. ( -40.60)
>DroSec_CAF1 6700 120 + 1
UAAGAGUGCUAAAAUUGCUGGUCAAACGCUUUUUAGGUGGACAAGCCCUUCGGGUCAUCUCAUAACUGUAGUUUUGGCCCUCGUCGACGCUUGAAACACCUGAUGGUGUCUCGUUGGCCG
...(((.(((((((((((.((((...((((.....)))))))..(.((....)).).........).))))))))))).)))(((((((......(((((....)))))..))))))).. ( -39.10)
>DroYak_CAF1 6909 120 + 1
UAAGAGUGCUAUAAUUGCUUGUCAAACGCUUCUUUGGUGGACAAGCCCUUCGGGUCAUCUCAUAACUGUAGUUUUGGCCCUCGUCGACGCUUGAAACCCCUGAAGGUGUCUCGUUGGCCG
.......((((((...(((((((...((((.....)))))))))))((....))............))))))...((((..((..(((((((...........))))))).))..)))). ( -37.40)
>consensus
UAAGAGUGCUAAAAUUGCUUGUCAAACGCUUUUUAGGUGGACAAGCCCUUCGGGUCAUCUCAUAACUGUAGUUUUGGCCCUCGUCGACGCUUGAAACACCUGAAGGUGUCUCGUUGGCCG
...(((.((((((((((((((((...((((.....)))))))))((((...))))............))))))))))).)))(((((((......(((((....)))))..))))))).. (-36.27 = -36.83 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 173,034 – 173,154
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -41.00
Consensus MFE -36.93
Energy contribution -37.93
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.90
SVM decision value 0.46
SVM RNA-class probability 0.744504
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 173034 120 - 23771897
CACCAGGCCCCUAAGCUGAAGAUCAAAAUCAGGGGUUUGACGGCCAACGAGACACCUUCAGGUGUUUCAAGCGUUGACGAGGGCCAAAACUACAGUUAUGAAAUGACCCGAAGGGCUUGU
...(((((((.....((((.........))))(((((....((((...((((((((....))))))))...((....))..))))..(((....))).......)))))...))))))). ( -42.10)
>DroSec_CAF1 6740 120 - 1
CACCAGGCCCCCAAGCUGAAGAUCAAAAUCAGGGGGUUGACGGCCAACGAGACACCAUCAGGUGUUUCAAGCGUCGACGAGGGCCAAAACUACAGUUAUGAGAUGACCCGAAGGGCUUGU
...(((((((.....((((.........)))).(((((...((((...((((((((....))))))))...((....))..))))....((.((....))))..)))))...))))))). ( -42.70)
>DroYak_CAF1 6949 120 - 1
CACCAGGCCCCCAAGCUGAAGAUCAAAAUAAGGGGUUUGGCGGCCAACGAGACACCUUCAGGGGUUUCAAGCGUCGACGAGGGCCAAAACUACAGUUAUGAGAUGACCCGAAGGGCUUGU
.....((((.(((((((................))))))).)))).(((((...(((((.(((((((((.(.(((......))))..(((....))).))))))..)))))))).))))) ( -38.19)
>consensus
CACCAGGCCCCCAAGCUGAAGAUCAAAAUCAGGGGUUUGACGGCCAACGAGACACCUUCAGGUGUUUCAAGCGUCGACGAGGGCCAAAACUACAGUUAUGAGAUGACCCGAAGGGCUUGU
...(((((((.....((((.........))))(((((....((((...((((((((....))))))))...((....))..))))..(((....))).......)))))...))))))). (-36.93 = -37.93 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 173,074 – 173,194
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -41.15
Consensus MFE -38.29
Energy contribution -38.63
Covariance contribution 0.34
Combinations/Pair 1.07
Mean z-score -1.72
Structure conservation index 0.93
SVM decision value 0.21
SVM RNA-class probability 0.634237
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 173074 120 + 23771897
UCGUCAACGCUUGAAACACCUGAAGGUGUCUCGUUGGCCGUCAAACCCCUGAUUUUGAUCUUCAGCUUAGGGGCCUGGUGGUCAUCCUCGCUGCUUUCGAGAGUCUUACUGCGUCCUCGC
.((...((((..((.(((((....))))).))..(((((..((..(((((((..(((.....))).)))))))..))..)))))..((((.......)))).........))))...)). ( -38.60)
>DroSec_CAF1 6780 120 + 1
UCGUCGACGCUUGAAACACCUGAUGGUGUCUCGUUGGCCGUCAACCCCCUGAUUUUGAUCUUCAGCUUGGGGGCCUGGUGGUCAUCCUCACUGCUUUCGAGAGUCUUACUGCGUCCUCGC
.((..(((((......((((....))))(((((.(((((..((..((((..(..(((.....))).)..))))..))..))))).............)))))........)))))..)). ( -40.84)
>DroYak_CAF1 6989 120 + 1
UCGUCGACGCUUGAAACCCCUGAAGGUGUCUCGUUGGCCGCCAAACCCCUUAUUUUGAUCUUCAGCUUGGGGGCCUGGUGGUCAUCCUCACUGCUUUCGAGAGUCUUACUGCGUCCUCGC
.((..(((((.(((.((.(.(((((((((.....(((((((((..(((((....(((.....)))...)))))..))))))))).....)).))))))).).)).)))..)))))..)). ( -44.00)
>consensus
UCGUCGACGCUUGAAACACCUGAAGGUGUCUCGUUGGCCGUCAAACCCCUGAUUUUGAUCUUCAGCUUGGGGGCCUGGUGGUCAUCCUCACUGCUUUCGAGAGUCUUACUGCGUCCUCGC
.((..(((((.(((.((.(.(((((((((.....(((((((((..(((((((..(((.....))).)))))))..))))))))).....)).))))))).).)).)))..)))))..)). (-38.29 = -38.63 +   0.34)

alignment

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secondary structure

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dotplot

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Window 4

Location 173,074 – 173,194
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -40.70
Consensus MFE -36.74
Energy contribution -36.97
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -1.70
Structure conservation index 0.90
SVM decision value -0.02
SVM RNA-class probability 0.524676
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 173074 120 - 23771897
GCGAGGACGCAGUAAGACUCUCGAAAGCAGCGAGGAUGACCACCAGGCCCCUAAGCUGAAGAUCAAAAUCAGGGGUUUGACGGCCAACGAGACACCUUCAGGUGUUUCAAGCGUUGACGA
.((..(((((.((.....(((((.......))))).((.((..(((((((((.(..((.....))...).)))))))))..)).))))((((((((....))))))))..)))))..)). ( -41.70)
>DroSec_CAF1 6780 120 - 1
GCGAGGACGCAGUAAGACUCUCGAAAGCAGUGAGGAUGACCACCAGGCCCCCAAGCUGAAGAUCAAAAUCAGGGGGUUGACGGCCAACGAGACACCAUCAGGUGUUUCAAGCGUCGACGA
.((..(((((.((..(((((((.....((((..((..(.((....)))..))..))))..(((....))).)))))))....))....((((((((....))))))))..)))))..)). ( -39.60)
>DroYak_CAF1 6989 120 - 1
GCGAGGACGCAGUAAGACUCUCGAAAGCAGUGAGGAUGACCACCAGGCCCCCAAGCUGAAGAUCAAAAUAAGGGGUUUGGCGGCCAACGAGACACCUUCAGGGGUUUCAAGCGUCGACGA
.((..(((((.((....(((.(....)....)))..((.((.(((((((((.....((.....))......))))))))).)).))))(((((.((.....)))))))..)))))..)). ( -40.80)
>consensus
GCGAGGACGCAGUAAGACUCUCGAAAGCAGUGAGGAUGACCACCAGGCCCCCAAGCUGAAGAUCAAAAUCAGGGGUUUGACGGCCAACGAGACACCUUCAGGUGUUUCAAGCGUCGACGA
.((..(((((.((.....(((((.......))))).((.((..((((((((.....((.....))......))))))))..)).))))((((((((....))))))))..)))))..)). (-36.74 = -36.97 +   0.23)

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 09:30:43 2006