Locus 2931

Sequence ID X_DroMel_CAF1
Location 7,840,861 – 7,841,006
Length 145
Max. P 0.998392
window4799 window4800 window4801 window4802

overview

Window 9

Location 7,840,861 – 7,840,969
Length 108
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 73.65
Mean single sequence MFE -31.30
Consensus MFE -20.40
Energy contribution -21.07
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.65
SVM decision value 3.09
SVM RNA-class probability 0.998392
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7840861 108 + 22224390
CGUGCUAUUCGUUACGCGAUUUCUCUGACGAAAGCGUAGAAGCGCGCCAAAAAAAGCGCGCGCAAAAACAAAAAGCCAA---GCUAACGGGACAAAAGUCGCGCGCGACUC--
(((((...((((((.((...((((.((.(....))).))))((((((........))))))..................---))))))))(((....)))..)))))....-- ( -34.80)
>DroEre_CAF1 26275 110 + 1
CCUGCUCUCCGUCACGCGAUUUCCCUGCCGAAAGCGUAGAAACGCGCCAAAAAAAGCGCGCGCAAAAACAAAAAGCCAA---GCUAACGGGACAAAAGUCGCGCGCGACUCGC
..........(((.((((.((((..((((....).)))))))))))...........((((((............((..---......))(((....)))))))))))).... ( -31.80)
>DroAna_CAF1 13030 90 + 1
-CGGCUCUCCA--ACGCG-UCUCAUUGU------------UUGGCGCGGUAAAAAGCGCGCGCAAAAACAAAAAGCCAACUAACUAACGGGACAAAAGUCGCGCGC-------
-..(((.....--.((((-((.......------------..))))))......)))((((((............((...........))(((....)))))))))------- ( -27.30)
>consensus
CCUGCUCUCCGU_ACGCGAUUUCACUGACGAAAGCGUAGAAACGCGCCAAAAAAAGCGCGCGCAAAAACAAAAAGCCAA___GCUAACGGGACAAAAGUCGCGCGCGACUC__
..............(((..........................((((........))))((((..........(((......))).....(((....))))))))))...... (-20.40 = -21.07 +   0.67)

alignment

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secondary structure

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Window 0

Location 7,840,861 – 7,840,969
Length 108
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 73.65
Mean single sequence MFE -36.67
Consensus MFE -27.01
Energy contribution -27.46
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.74
SVM decision value 2.02
SVM RNA-class probability 0.985905
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7840861 108 - 22224390
--GAGUCGCGCGCGACUUUUGUCCCGUUAGC---UUGGCUUUUUGUUUUUGCGCGCGCUUUUUUUGGCGCGCUUCUACGCUUUCGUCAGAGAAAUCGCGUAACGAAUAGCACG
--((((...(((.(((....))).)))..))---)).(((.((((((..((((((((((......)))))))(((((((....))).)))).....))).)))))).)))... ( -36.20)
>DroEre_CAF1 26275 110 - 1
GCGAGUCGCGCGCGACUUUUGUCCCGUUAGC---UUGGCUUUUUGUUUUUGCGCGCGCUUUUUUUGGCGCGUUUCUACGCUUUCGGCAGGGAAAUCGCGUGACGGAGAGCAGG
((...((((((((((.((((.(.(((..(((---...((...........))(((((((......)))))))......)))..))).).)))).))))))).)))...))... ( -42.70)
>DroAna_CAF1 13030 90 - 1
-------GCGCGCGACUUUUGUCCCGUUAGUUAGUUGGCUUUUUGUUUUUGCGCGCGCUUUUUACCGCGCCAA------------ACAAUGAGA-CGCGU--UGGAGAGCCG-
-------(((((((((....)))..(((((....)))))...........))))))((((((((.(((((((.------------....)).).-)))).--))))))))..- ( -31.10)
>consensus
__GAGUCGCGCGCGACUUUUGUCCCGUUAGC___UUGGCUUUUUGUUUUUGCGCGCGCUUUUUUUGGCGCGAUUCUACGCUUUCGACAGAGAAAUCGCGU_ACGGAGAGCAGG
.......(((((((((....)))..(((((....)))))...........))))))(((((((...(((((........................)))))...)))))))... (-27.01 = -27.46 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,840,895 – 7,841,006
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.02
Mean single sequence MFE -33.58
Consensus MFE -25.42
Energy contribution -26.17
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.76
SVM decision value 1.10
SVM RNA-class probability 0.914519
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7840895 111 + 22224390
CGUAGAAGCGCGCCAAA-AAAAGCGCGCGCAAAAACAAAAAGCCAA---GCUAACGGGACAAAAGUCGCGCGCGACUC--GUAAGCUUGUUUACUUUGCCAUUAUAAAUCC---GGCGGG
.(((((.((((((....-....))))))...............(((---(((.(((.......(((((....))))))--)).))))))))))).(((((...........---))))). ( -34.31)
>DroEre_CAF1 26309 113 + 1
CGUAGAAACGCGCCAAA-AAAAGCGCGCGCAAAAACAAAAAGCCAA---GCUAACGGGACAAAAGUCGCGCGCGACUCGCGUAAGCUUGUUUACUUUGCCAUUAUAAAUCC---GGCGGG
.(((((..(((((....-....)))))................(((---(((.(((.((.....((((....)))))).))).))))))))))).(((((...........---))))). ( -32.50)
>DroYak_CAF1 21601 112 + 1
CGUAGAAGCGCGCCAAAAAAAAGCGCGCGCAAAAACAAAAAGCCAA---GCUAACGGGACAAAAGUCGCGCGCGACUC--GUAAGCUUGUUUACUUUGCCAUUAUAAAUCC---GGCGGG
.(((((.(((((((........).)))))).............(((---(((.(((.......(((((....))))))--)).))))))))))).(((((...........---))))). ( -34.31)
>DroAna_CAF1 13054 106 + 1
------UUGGCGCGGUA-AAAAGCGCGCGCAAAAACAAAAAGCCAACUAACUAACGGGACAAAAGUCGCGCGC-------GUAAGCUUGUUUACUUUGCCAUUAUAAAUCCGACGGCGGG
------.(((((.((((-((((((((((((............((...........))(((....)))))))))-------....)))).)))))).)))))........(((....))). ( -33.20)
>consensus
CGUAGAAGCGCGCCAAA_AAAAGCGCGCGCAAAAACAAAAAGCCAA___GCUAACGGGACAAAAGUCGCGCGCGACUC__GUAAGCUUGUUUACUUUGCCAUUAUAAAUCC___GGCGGG
..........((((.........(((((((..........(((......))).....(((....))))))))))......(((((....)))))....................)))).. (-25.42 = -26.17 +   0.75)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,840,895 – 7,841,006
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.02
Mean single sequence MFE -34.16
Consensus MFE -25.64
Energy contribution -26.26
Covariance contribution 0.62
Combinations/Pair 1.03
Mean z-score -1.46
Structure conservation index 0.75
SVM decision value 0.04
SVM RNA-class probability 0.555805
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7840895 111 - 22224390
CCCGCC---GGAUUUAUAAUGGCAAAGUAAACAAGCUUAC--GAGUCGCGCGCGACUUUUGUCCCGUUAGC---UUGGCUUUUUGUUUUUGCGCGCGCUUUU-UUUGGCGCGCUUCUACG
...(((---(.........))))...(((((((((((.((--((((((....))))).......))).)))---)))((.....)).)))))(((((((...-...)))))))....... ( -36.31)
>DroEre_CAF1 26309 113 - 1
CCCGCC---GGAUUUAUAAUGGCAAAGUAAACAAGCUUACGCGAGUCGCGCGCGACUUUUGUCCCGUUAGC---UUGGCUUUUUGUUUUUGCGCGCGCUUUU-UUUGGCGCGUUUCUACG
...(((---(.........))))...(((((((((((.(((.((((((....))))))......))).)))---)))((.....)).)))))(((((((...-...)))))))....... ( -34.80)
>DroYak_CAF1 21601 112 - 1
CCCGCC---GGAUUUAUAAUGGCAAAGUAAACAAGCUUAC--GAGUCGCGCGCGACUUUUGUCCCGUUAGC---UUGGCUUUUUGUUUUUGCGCGCGCUUUUUUUUGGCGCGCUUCUACG
...(((---(.........))))...(((((((((((.((--((((((....))))).......))).)))---)))((.....)).)))))(((((((.......)))))))....... ( -35.81)
>DroAna_CAF1 13054 106 - 1
CCCGCCGUCGGAUUUAUAAUGGCAAAGUAAACAAGCUUAC-------GCGCGCGACUUUUGUCCCGUUAGUUAGUUGGCUUUUUGUUUUUGCGCGCGCUUUU-UACCGCGCCAA------
.(((....)))........((((...(((((.((((....-------(((((((((....)))..(((((....)))))...........))))))))))))-)))...)))).------ ( -29.70)
>consensus
CCCGCC___GGAUUUAUAAUGGCAAAGUAAACAAGCUUAC__GAGUCGCGCGCGACUUUUGUCCCGUUAGC___UUGGCUUUUUGUUUUUGCGCGCGCUUUU_UUUGGCGCGCUUCUACG
.((......))..........((((((..((.(((((..........(((.(.(((....))))))).........))))).))..))))))(((((((.......)))))))....... (-25.64 = -26.26 +   0.62)

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 10:46:56 2006