Locus 6549

Sequence ID 3L_DroMel_CAF1
Location 17,299,925 – 17,300,066
Length 141
Max. P 0.994145
window10653 window10654 window10655 window10656

overview

Window 3

Location 17,299,925 – 17,300,036
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.81
Mean single sequence MFE -33.83
Consensus MFE -26.07
Energy contribution -27.82
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.77
SVM decision value 1.06
SVM RNA-class probability 0.908921
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17299925 111 + 23771897
CCAGUUGAAGUUGGAAAACUGCUGCUCCUGCUG---------CCCGCCCAAUAGCAAAAUGGUAAAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUU
(((((...((((....))))...))((((((((---------((.((......)).....)))....(((((....))))))))).)))........(((((((....)))))))))).. ( -31.30)
>DroSim_CAF1 423 120 + 1
CCAGUUGAAGUUGGAAAACUGCUGCUCCUGCUGCUACUGCUGUCCGCCCAAUAGCAAAAUGGCAAAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUU
(((((...((((....))))...))(((((((((((.((((((.......))))))...))))....(((((....))))))))).)))........(((((((....)))))))))).. ( -38.50)
>DroEre_CAF1 4139 99 + 1
CCAGUUGAAGUUGGAAAACUGCUGCUCCUGCUG-------------UCCAAUAGCA--------AAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUU
(((..(((((((....))))..(((((..((((-------------(....((((.--------.....)))).))))).))))).(....))))..(((((((....)))))))))).. ( -32.80)
>DroYak_CAF1 4475 99 + 1
CCAGUUGAAGUUGGAAAACUGCUGCUCCUGCAG-------------CCCAAUAGCA--------AAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUU
.((((((.((((....))))(((((....))))-------------)....((((.--------.....))))..))))))(((..(....).....(((((((....)))))))..))) ( -32.70)
>consensus
CCAGUUGAAGUUGGAAAACUGCUGCUCCUGCUG_____________CCCAAUAGCA________AAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUU
(((..(((((((....))))..(((((.(((((..................)))))............((((....))))))))).(....))))..(((((((....)))))))))).. (-26.07 = -27.82 +   1.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,299,925 – 17,300,036
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.81
Mean single sequence MFE -32.02
Consensus MFE -25.52
Energy contribution -25.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.80
SVM decision value 0.80
SVM RNA-class probability 0.852993
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17299925 111 - 23771897
AACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUUUACCAUUUUGCUAUUGGGCGGG---------CAGCAGGAGCAGCAGUUUUCCAACUUCAACUGG
.....(((((((....))))))).....(((((..(((((((((....)))).............(((....))))))---------))...)))))..(((((..........))))). ( -32.00)
>DroSim_CAF1 423 120 - 1
AACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUUUGCCAUUUUGCUAUUGGGCGGACAGCAGUAGCAGCAGGAGCAGCAGUUUUCCAACUUCAACUGG
.....(((((((....))))))).....(((.((.((((..((((((..(((..((((((............)))))).))))))))))))))))))..(((((..........))))). ( -36.00)
>DroEre_CAF1 4139 99 - 1
AACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUU--------UGCUAUUGGA-------------CAGCAGGAGCAGCAGUUUUCCAACUUCAACUGG
..((.(((((((....)))))))....((((....(((((.(((.((((((.....--------.))...))))-------------.)))..)))))(.((((....)))).))))))) ( -28.70)
>DroYak_CAF1 4475 99 - 1
AACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUU--------UGCUAUUGGG-------------CUGCAGGAGCAGCAGUUUUCCAACUUCAACUGG
..((((((((((....)))))))..(((((......))))).......(((.....--------.)))..)))(-------------((((....)))))......(((........))) ( -31.40)
>consensus
AACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUU________UGCUAUUGGG_____________CAGCAGGAGCAGCAGUUUUCCAACUUCAACUGG
..((.(((((((....)))))))....((((....(((((((((....))))............(((......................))).)))))(.((((....)))).))))))) (-25.52 = -25.53 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,299,958 – 17,300,066
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.16
Mean single sequence MFE -30.60
Consensus MFE -26.45
Energy contribution -26.45
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.86
SVM decision value 0.11
SVM RNA-class probability 0.587146
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17299958 108 + 23771897
--CCCGCCCAAUAGCAAAAUGGUAAAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUUUGCGGAGUAACAAGGCGGAGAGUUGGC----------AGU
--.(((((...................(((((....))))).((.((.(((((....(((((((....))))))).))))).))..)).....))))).........----------... ( -31.30)
>DroSim_CAF1 463 110 + 1
UGUCCGCCCAAUAGCAAAAUGGCAAAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUUUGCGGAGUAACAAGGCGGAGAGUUGGC----------AGU
(.((((((...((((.....(((......))).....)))).((.((.(((((....(((((((....))))))).))))).))..)).....)))))).)......----------... ( -34.70)
>DroEre_CAF1 4172 106 + 1
------UCCAAUAGCA--------AAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUUUGCGGAGUAACAAGGCGGAGAGUUGGUAGGGGUUGCUAGU
------(((....((.--------...(((((....))))).))..(.(((((....(((((((....))))))).))))).))))(((((...((.((...)).))....))))).... ( -29.70)
>DroYak_CAF1 4508 96 + 1
------CCCAAUAGCA--------AAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUUUGCGGAGUAACAAGGCGGAGAGUUGGU----------AGU
------.((((((((.--------.....))).....(((..((.((.(((((....(((((((....))))))).))))).))..)).....))).....))))).----------... ( -26.70)
>consensus
______CCCAAUAGCA________AAAUAGCUGAAUAGCUGAGCAUGGAAACUCAUUUCGGCCAUUAAUGGCCGAUGGUUUGCGGAGUAACAAGGCGGAGAGUUGGC__________AGU
.......(((((.((............(((((....))))).((.((.(((((....(((((((....))))))).))))).))..))......)).....))))).............. (-26.45 = -26.45 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,299,958 – 17,300,066
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.16
Mean single sequence MFE -29.98
Consensus MFE -24.24
Energy contribution -24.24
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.21
Structure conservation index 0.81
SVM decision value 2.45
SVM RNA-class probability 0.994145
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17299958 108 - 23771897
ACU----------GCCAACUCUCCGCCUUGUUACUCCGCAAACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUUUACCAUUUUGCUAUUGGGCGGG--
...----------.........((((((.((......(((((...(((((((....)))))))...((((......))))((((....))))..........))))).)).)))))).-- ( -32.50)
>DroSim_CAF1 463 110 - 1
ACU----------GCCAACUCUCCGCCUUGUUACUCCGCAAACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUUUGCCAUUUUGCUAUUGGGCGGACA
...----------........(((((((.((......(((((...(((((((....)))))))...((((......))))((((....))))..)))))......))....))))))).. ( -35.80)
>DroEre_CAF1 4172 106 - 1
ACUAGCAACCCCUACCAACUCUCCGCCUUGUUACUCCGCAAACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUU--------UGCUAUUGGA------
..............((((...................((......(((((((....)))))))..(((((......))))))).....(((.....--------.))).)))).------ ( -25.70)
>DroYak_CAF1 4508 96 - 1
ACU----------ACCAACUCUCCGCCUUGUUACUCCGCAAACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUU--------UGCUAUUGGG------
...----------.((((...................((......(((((((....)))))))..(((((......))))))).....(((.....--------.))).)))).------ ( -25.90)
>consensus
ACU__________ACCAACUCUCCGCCUUGUUACUCCGCAAACCAUCGGCCAUUAAUGGCCGAAAUGAGUUUCCAUGCUCAGCUAUUCAGCUAUUU________UGCUAUUGGG______
..............((((...................((......(((((((....)))))))..(((((......))))))).....(((..............))).))))....... (-24.24 = -24.24 +   0.00)

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 12:23:59 2006