Locus 7691

Sequence ID 3L_DroMel_CAF1
Location 20,590,487 – 20,590,657
Length 170
Max. P 0.936094
window12499 window12500 window12501 window12502 window12503

overview

Window 9

Location 20,590,487 – 20,590,577
Length 90
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 89.81
Mean single sequence MFE -32.05
Consensus MFE -25.91
Energy contribution -26.60
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -2.08
Structure conservation index 0.81
SVM decision value 0.98
SVM RNA-class probability 0.893269
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20590487 90 + 23771897
AUCAUGCUGAAUGGAGGGGUGAUGUCAGGUAGUCCCGGUACGAGUUUUGGGCUCUAGAGGAUGGGCCAGGAUGGCAACUAAGUUGCCAUA
(((((.((.......)).)))))....(((.(((((.....((((.....))))..).))))..)))...((((((((...)))))))). ( -27.00)
>DroSec_CAF1 35225 90 + 1
AUCAUGCUGAAUGGAGGGGCGAUGUCAGGUAGCCCCGGUUCGGGUUUUGGGCUCUAGAGGAUGGGCCAGGAUGGCAACUAAGUUGCCAUA
......((((((...(((((...........))))).))))))......(((((........)))))...((((((((...)))))))). ( -34.70)
>DroSim_CAF1 28728 90 + 1
AUCAUGCUGAAUGGAGGGGCGAUGUCAGGUAGCCCCGGUUCGGGUUUUGGGCUCUAGAGGAUGGGCCAGGAUGGCAACUUAGUUGCCAUA
......((((((...(((((...........))))).))))))......(((((........)))))...((((((((...)))))))). ( -34.70)
>DroEre_CAF1 28390 86 + 1
AUGAAGCUGAAUGGAGG-GCGAUGCCAGGUAGCCUCUGUUCGAGAUUCGGGCUCUAGAG---AGGCCAGGAUGGCAACUAAGUUGCCAUG
..(((.(((((((((((-((........))..))))))))).)).)))((.(((....)---)).))...((((((((...)))))))). ( -31.80)
>consensus
AUCAUGCUGAAUGGAGGGGCGAUGUCAGGUAGCCCCGGUUCGAGUUUUGGGCUCUAGAGGAUGGGCCAGGAUGGCAACUAAGUUGCCAUA
......((((((...(((((...........))))).))))))......(((((........)))))...((((((((...)))))))). (-25.91 = -26.60 +   0.69)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,590,487 – 20,590,577
Length 90
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 89.81
Mean single sequence MFE -21.38
Consensus MFE -16.40
Energy contribution -15.59
Covariance contribution -0.81
Combinations/Pair 1.21
Mean z-score -1.71
Structure conservation index 0.77
SVM decision value 0.30
SVM RNA-class probability 0.678829
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20590487 90 - 23771897
UAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACUCGUACCGGGACUACCUGACAUCACCCCUCCAUUCAGCAUGAU
..(((((((...)))))))((((((..(........(((.......))))..))))))....((((..............))))...... ( -17.14)
>DroSec_CAF1 35225 90 - 1
UAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACCCGAACCGGGGCUACCUGACAUCGCCCCUCCAUUCAGCAUGAU
.((((((((...))))))))...(((.(........).)))........(((..(((((...........)))))....)))........ ( -22.00)
>DroSim_CAF1 28728 90 - 1
UAUGGCAACUAAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACCCGAACCGGGGCUACCUGACAUCGCCCCUCCAUUCAGCAUGAU
.((((((((...))))))))...(((.(........).)))........(((..(((((...........)))))....)))........ ( -22.00)
>DroEre_CAF1 28390 86 - 1
CAUGGCAACUUAGUUGCCAUCCUGGCCU---CUCUAGAGCCCGAAUCUCGAACAGAGGCUACCUGGCAUCGC-CCUCCAUUCAGCUUCAU
.((((((((...))))))))..((((((---((...(((.......)))....))))))))...(((...))-)................ ( -24.40)
>consensus
UAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACCCGAACCGGGGCUACCUGACAUCGCCCCUCCAUUCAGCAUGAU
.((((((((...))))))))...(((.(........).))).....(((.....))).....((((..............))))...... (-16.40 = -15.59 +  -0.81)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,590,497 – 20,590,617
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.86
Mean single sequence MFE -38.50
Consensus MFE -26.18
Energy contribution -27.66
Covariance contribution 1.48
Combinations/Pair 1.16
Mean z-score -2.40
Structure conservation index 0.68
SVM decision value 1.25
SVM RNA-class probability 0.936094
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20590497 120 - 23771897
UUCAGGCCUCCAUAACCUUGCGAAGGGGUUUAGGUUAGGGUAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACUCGUACCGGGACUACCUGACAUCACCCCUCCAU
.(((((..(((.......(((((..(((((((((...((((((((((((...))))))))....))))..)))...)))))).....)))))...)))...))))).............. ( -38.20)
>DroSec_CAF1 35235 120 - 1
UUCAGGCCUCCAUAACCUUGCGAAUGGGUUUAGGUUAGGGUAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACCCGAACCGGGGCUACCUGACAUCGCCCCUCCAU
(((.((..((((......)).)).((((((((((...((((((((((((...))))))))....))))..)))...)))))))...)).)))..(((((...........)))))..... ( -39.40)
>DroAna_CAF1 58281 104 - 1
UCCAGGCCUUUAUAACCUUGCGAAUG-GCUUAGGGAAGGGUAUGGCAACUUUGUUGCCAAUCU--------UUCUUGAUCC---AACGUGAAUA-GGCCUACCUGCCAUUGCUCC---AU
...((((((........(..((..((-(.((((((((((...(((((((...))))))).)))--------))))))).))---).))..)..)-)))))...............---.. ( -33.50)
>DroSim_CAF1 28738 120 - 1
UUCAGGCCUCCAUAACCUUGCGAAUGGGUUUAGGUUAGGGUAUGGCAACUAAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACCCGAACCGGGGCUACCUGACAUCGCCCCUCCAU
(((.((..((((......)).)).((((((((((...((((((((((((...))))))))....))))..)))...)))))))...)).)))..(((((...........)))))..... ( -39.40)
>DroEre_CAF1 28400 115 - 1
UUCAGGCCUCCAUAACCUUGCGAAUG-GUUUGGGUUAGGGCAUGGCAACUUAGUUGCCAUCCUGGCCU---CUCUAGAGCCCGAAUCUCGAACAGAGGCUACCUGGCAUCGC-CCUCCAU
....(((..(((.((((........)-))))))(((((((.((((((((...)))))))).)((((((---((...(((.......)))....))))))))))))))...))-)...... ( -42.00)
>consensus
UUCAGGCCUCCAUAACCUUGCGAAUGGGUUUAGGUUAGGGUAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGCCCAAAACCCGAACCGGGGCUACCUGACAUCGCCCCUCCAU
.(((((((((..((((((.((......))..))))))((((.(((((((...)))))))..((((........)))).))))............))))...))))).............. (-26.18 = -27.66 +   1.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,590,537 – 20,590,657
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.38
Mean single sequence MFE -32.88
Consensus MFE -24.08
Energy contribution -26.48
Covariance contribution 2.40
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.73
SVM decision value 0.29
SVM RNA-class probability 0.669419
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20590537 120 + 23771897
GCUCUAGAGGAUGGGCCAGGAUGGCAACUAAGUUGCCAUACCCUAACCUAAACCCCUUCGCAAGGUUAUGGAGGCCUGAAAAAAGAAAUUCUGAAUAAUUCGUGAUCUGCAGGCGCAAAA
.(((((((((.((((..(((((((((((...))))))))..)))..))))....))))(....)....)))))(((((.....(((...(((((.....))).))))).)))))...... ( -34.30)
>DroSec_CAF1 35275 120 + 1
GCUCUAGAGGAUGGGCCAGGAUGGCAACUAAGUUGCCAUACCCUAACCUAAACCCAUUCGCAAGGUUAUGGAGGCCUGAAAAAAGAAAUUCUGAAUAAUUCGUGAUCUGCAGGCGCAAAA
((.((...(((((((..(((((((((((...)))))))).......)))...)))))))(((.(((((((((.....(((........))).......)))))))))))).)).)).... ( -36.31)
>DroAna_CAF1 58314 111 + 1
GAUCAAGAA--------AGAUUGGCAACAAAGUUGCCAUACCCUUCCCUAAGC-CAUUCGCAAGGUUAUAAAGGCCUGGAAAAAGAAAUUCUGAAUAAUUCGUGAUCCGCAGGCGCAAAA
(((((.(((--------....(((((((...))))))).....((((....((-.....)).(((((.....))))))))).................))).))))).((....)).... ( -24.50)
>DroSim_CAF1 28778 120 + 1
GCUCUAGAGGAUGGGCCAGGAUGGCAACUUAGUUGCCAUACCCUAACCUAAACCCAUUCGCAAGGUUAUGGAGGCCUGAAAAAAGAAAUUCUGAAUAAUUCGUGAUCUGCAGGCGCAAAA
((.((...(((((((..(((((((((((...)))))))).......)))...)))))))(((.(((((((((.....(((........))).......)))))))))))).)).)).... ( -36.31)
>DroEre_CAF1 28439 116 + 1
GCUCUAGAG---AGGCCAGGAUGGCAACUAAGUUGCCAUGCCCUAACCCAAAC-CAUUCGCAAGGUUAUGGAGGCCUGAAAAAAGAAAUUCUGAAUAAUUCGUGAUCUGCAGGCGCAAAA
(((.((((.---(((((.((((((((((...)))))))).)).....((((((-(........)))).))).)))))............(((((.....))).))))))..)))...... ( -33.00)
>consensus
GCUCUAGAGGAUGGGCCAGGAUGGCAACUAAGUUGCCAUACCCUAACCUAAACCCAUUCGCAAGGUUAUGGAGGCCUGAAAAAAGAAAUUCUGAAUAAUUCGUGAUCUGCAGGCGCAAAA
.(((((.....((((..(((((((((((...))))))))..)))..)))).......((....))...)))))(((((.....(((...(((((.....))).))))).)))))...... (-24.08 = -26.48 +   2.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,590,537 – 20,590,657
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.38
Mean single sequence MFE -33.90
Consensus MFE -28.16
Energy contribution -28.00
Covariance contribution -0.16
Combinations/Pair 1.14
Mean z-score -1.80
Structure conservation index 0.83
SVM decision value 1.19
SVM RNA-class probability 0.928971
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20590537 120 - 23771897
UUUUGCGCCUGCAGAUCACGAAUUAUUCAGAAUUUCUUUUUUCAGGCCUCCAUAACCUUGCGAAGGGGUUUAGGUUAGGGUAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGC
......(((((.(((....(((((......)))))....))))))))............((..(((((....(((((((..((((((((...)))))))))))))))...)))))...)) ( -36.20)
>DroSec_CAF1 35275 120 - 1
UUUUGCGCCUGCAGAUCACGAAUUAUUCAGAAUUUCUUUUUUCAGGCCUCCAUAACCUUGCGAAUGGGUUUAGGUUAGGGUAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGC
......(((((.(((....(((((......)))))....))))))))(((...(((((.......)))))..(((((((..((((((((...))))))))))))))).........))). ( -33.50)
>DroAna_CAF1 58314 111 - 1
UUUUGCGCCUGCGGAUCACGAAUUAUUCAGAAUUUCUUUUUCCAGGCCUUUAUAACCUUGCGAAUG-GCUUAGGGAAGGGUAUGGCAACUUUGUUGCCAAUCU--------UUCUUGAUC
......(((((.(((....(((((......)))))....))))))))........(((.((.....-))..)))(((((((.(((((((...)))))))))))--------)))...... ( -30.80)
>DroSim_CAF1 28778 120 - 1
UUUUGCGCCUGCAGAUCACGAAUUAUUCAGAAUUUCUUUUUUCAGGCCUCCAUAACCUUGCGAAUGGGUUUAGGUUAGGGUAUGGCAACUAAGUUGCCAUCCUGGCCCAUCCUCUAGAGC
......(((((.(((....(((((......)))))....))))))))(((...(((((.......)))))..(((((((..((((((((...))))))))))))))).........))). ( -33.50)
>DroEre_CAF1 28439 116 - 1
UUUUGCGCCUGCAGAUCACGAAUUAUUCAGAAUUUCUUUUUUCAGGCCUCCAUAACCUUGCGAAUG-GUUUGGGUUAGGGCAUGGCAACUUAGUUGCCAUCCUGGCCU---CUCUAGAGC
......(((((.(((...((((((((((.(((........)))(((.........)))...)))))-)))))(((((((..((((((((...))))))))))))))))---)).))).)) ( -35.50)
>consensus
UUUUGCGCCUGCAGAUCACGAAUUAUUCAGAAUUUCUUUUUUCAGGCCUCCAUAACCUUGCGAAUGGGUUUAGGUUAGGGUAUGGCAACUUAGUUGCCAUCCUGGCCCAUCCUCUAGAGC
......(((((.(((....(((((......)))))....))))))))(((..((((((.((......))..))))))(((.((((((((...))))))))))).............))). (-28.16 = -28.00 +  -0.16)

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 12:54:00 2006