Locus 4781

Sequence ID 2L_DroMel_CAF1
Location 13,652,331 – 13,652,523
Length 192
Max. P 0.954340
window7568 window7569 window7570 window7571 window7572

overview

Window 8

Location 13,652,331 – 13,652,451
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 76.59
Mean single sequence MFE -34.07
Consensus MFE -16.03
Energy contribution -17.15
Covariance contribution 1.12
Combinations/Pair 1.18
Mean z-score -2.96
Structure conservation index 0.47
SVM decision value 0.37
SVM RNA-class probability 0.709427
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13652331 120 + 22407834
CUUGGCGGUCAAACUCUUUGGCGAAUACAUCUCCAUCAUUCGCAGAUACAUUUGAACGUUUCAAUUUUCAAGUGUUGAGAUUGGCCCACUUGGAAGUGGCCUGAUGUUUCCUUCAAGACA
...(((((((((.(((....((((((...........))))))....(((((((((.((....)).))))))))).))).))))))((((....)))))))...(((((......))))) ( -32.30)
>DroPse_CAF1 20769 106 + 1
CUUGGCGGUCAG-------------GACAUCUACAUCAAUCGCACUCCCAUUUAAAGGUUUCAAUUUUCGAGUGCGCCUAUUGGCCCACUUCUGGG-CUCUUGAUGUCUCUUCCAAGACA
(((((.((...(-------------((((((.....(((((((((((((.......))...........)))))))...))))(((((....))))-)....))))))))).)))))... ( -33.90)
>DroPer_CAF1 21094 106 + 1
CUUGGCGGUCAG-------------GACAUCUACAUCAGUCGCACUCCCAUUUAAAGGUUUCAAUUUUCGAGUGCGCCUAUUGGCCCACUUCUGGG-CUCUUGAUGUCUCUUCCAAGACA
(((((.((...(-------------((((((..((..((.(((((((((.......))...........))))))).))..))(((((....))))-)....))))))))).)))))... ( -36.00)
>consensus
CUUGGCGGUCAG_____________GACAUCUACAUCAAUCGCACUCCCAUUUAAAGGUUUCAAUUUUCGAGUGCGCCUAUUGGCCCACUUCUGGG_CUCUUGAUGUCUCUUCCAAGACA
(((((.((.................((((((....((((((((((((......................)))))))...)))))(((......)))......)))))).)).)))))... (-16.03 = -17.15 +   1.12)

alignment

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secondary structure

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Window 9

Location 13,652,371 – 13,652,486
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -34.53
Consensus MFE -21.05
Energy contribution -19.28
Covariance contribution -1.77
Combinations/Pair 1.26
Mean z-score -1.94
Structure conservation index 0.61
SVM decision value 0.42
SVM RNA-class probability 0.730601
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13652371 115 + 22407834
CGCAGAUACAUUUGAACGUUUCAAUUUUCAAGUGUUGAGAUUGGCCCACUUGGAAGUGGCCUGAUGUUUCCUUCAAGACAGCUUUCAGCUUUGUGCCGGCCACAUUCCACU-----CGGC
.......(((((((((.((....)).)))))))))........(((....(((((((((((...(((((......)))))((.....))........)))))).)))))..-----.))) ( -30.80)
>DroPse_CAF1 20796 119 + 1
CGCACUCCCAUUUAAAGGUUUCAAUUUUCGAGUGCGCCUAUUGGCCCACUUCUGGG-CUCUUGAUGUCUCUUCCAAGACAACUCAAAGCCUUGUGUUGGCCACAUUCGUCUUGGCUUGGC
.((((((((.......))...........))))))(((...(((((.((....(((-((.(((((((((......)))))..)))))))))...)).))))).....((....))..))) ( -36.40)
>DroPer_CAF1 21121 119 + 1
CGCACUCCCAUUUAAAGGUUUCAAUUUUCGAGUGCGCCUAUUGGCCCACUUCUGGG-CUCUUGAUGUCUCUUCCAAGACAACUCAAAGCCUUGUGUUGGCCACAUUCGUCUUGGCUUGGC
.((((((((.......))...........))))))(((...(((((.((....(((-((.(((((((((......)))))..)))))))))...)).))))).....((....))..))) ( -36.40)
>consensus
CGCACUCCCAUUUAAAGGUUUCAAUUUUCGAGUGCGCCUAUUGGCCCACUUCUGGG_CUCUUGAUGUCUCUUCCAAGACAACUCAAAGCCUUGUGUUGGCCACAUUCGUCUUGGCUUGGC
.((((((......................))))))((..((((((((((....(((......(.(((((......))))).)......))).)))..))))).))..))........... (-21.05 = -19.28 +  -1.77)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,652,371 – 13,652,486
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -39.10
Consensus MFE -21.72
Energy contribution -22.50
Covariance contribution 0.78
Combinations/Pair 1.11
Mean z-score -2.81
Structure conservation index 0.56
SVM decision value 1.27
SVM RNA-class probability 0.937978
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13652371 115 - 22407834
GCCG-----AGUGGAAUGUGGCCGGCACAAAGCUGAAAGCUGUCUUGAAGGAAACAUCAGGCCACUUCCAAGUGGGCCAAUCUCAACACUUGAAAAUUGAAACGUUCAAAUGUAUCUGCG
(((.-----(.(((((.((((((((((....((.....)))))).(((.(....).))))))))))))))..).)))........(((.(((((..........))))).)))....... ( -34.70)
>DroPse_CAF1 20796 119 - 1
GCCAAGCCAAGACGAAUGUGGCCAACACAAGGCUUUGAGUUGUCUUGGAAGAGACAUCAAGAG-CCCAGAAGUGGGCCAAUAGGCGCACUCGAAAAUUGAAACCUUUAAAUGGGAGUGCG
(((...(((((((((....((((.......)))).....)))))))))............(.(-((((....))))))....)))((((((...........((.......)))))))). ( -41.30)
>DroPer_CAF1 21121 119 - 1
GCCAAGCCAAGACGAAUGUGGCCAACACAAGGCUUUGAGUUGUCUUGGAAGAGACAUCAAGAG-CCCAGAAGUGGGCCAAUAGGCGCACUCGAAAAUUGAAACCUUUAAAUGGGAGUGCG
(((...(((((((((....((((.......)))).....)))))))))............(.(-((((....))))))....)))((((((...........((.......)))))))). ( -41.30)
>consensus
GCCAAGCCAAGACGAAUGUGGCCAACACAAGGCUUUGAGUUGUCUUGGAAGAGACAUCAAGAG_CCCAGAAGUGGGCCAAUAGGCGCACUCGAAAAUUGAAACCUUUAAAUGGGAGUGCG
..................(((((.((.((((((........))))))...((....)).............)).))))).....(((((((...(.((((.....)))).)..))))))) (-21.72 = -22.50 +   0.78)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,652,411 – 13,652,523
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.83
Mean single sequence MFE -42.33
Consensus MFE -25.12
Energy contribution -24.80
Covariance contribution -0.32
Combinations/Pair 1.17
Mean z-score -2.52
Structure conservation index 0.59
SVM decision value 1.35
SVM RNA-class probability 0.944861
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13652411 112 + 22407834
UUGGCCCACUUGGAAGUGGCCUGAUGUUUCCUUCAAGACAGCUUUCAGCUUUGUGCCGGCCACAUUCCACU-----CGGCCAGAU-UGCUC--CGUGUGAAGGGCCAUAUAGCUGCAAUC
.(((((....(((((((((((...(((((......)))))((.....))........)))))).)))))..-----.)))))(((-(((.(--..((((......))))..)..)))))) ( -39.60)
>DroPse_CAF1 20836 119 + 1
UUGGCCCACUUCUGGG-CUCUUGAUGUCUCUUCCAAGACAACUCAAAGCCUUGUGUUGGCCACAUUCGUCUUGGCUUGGCCAGUUGUGCUCACAGUGUGAAGUGCCACACUGGUGCAACC
.((((((((....(((-((.(((((((((......)))))..))))))))).)))..(((((.........))))).)))))((((..(...(((((((......))))))))..)))). ( -45.90)
>DroPer_CAF1 21161 119 + 1
UUGGCCCACUUCUGGG-CUCUUGAUGUCUCUUCCAAGACAACUCAAAGCCUUGUGUUGGCCACAUUCGUCUUGGCUUGGCCAGUUGUGCUCACAGUGUGAAGUGCCACACUGGUGGAACC
.((((((((....(((-((.(((((((((......)))))..))))))))).)))..(((((.........))))).)))))(((.(((...(((((((......)))))))))).))). ( -41.50)
>consensus
UUGGCCCACUUCUGGG_CUCUUGAUGUCUCUUCCAAGACAACUCAAAGCCUUGUGUUGGCCACAUUCGUCUUGGCUUGGCCAGUUGUGCUCACAGUGUGAAGUGCCACACUGGUGCAACC
((((((.......(((......(.(((((......))))).)......)))((((.....)))).............))))))...(((...(((((((......)))))))..)))... (-25.12 = -24.80 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,652,411 – 13,652,523
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.83
Mean single sequence MFE -44.47
Consensus MFE -23.98
Energy contribution -25.77
Covariance contribution 1.78
Combinations/Pair 1.09
Mean z-score -3.12
Structure conservation index 0.54
SVM decision value 1.44
SVM RNA-class probability 0.954340
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13652411 112 - 22407834
GAUUGCAGCUAUAUGGCCCUUCACACG--GAGCA-AUCUGGCCG-----AGUGGAAUGUGGCCGGCACAAAGCUGAAAGCUGUCUUGAAGGAAACAUCAGGCCACUUCCAAGUGGGCCAA
((((((.(((....)))((.......)--).)))-)))(((((.-----(.(((((.((((((((((....((.....)))))).(((.(....).))))))))))))))..).))))). ( -46.50)
>DroPse_CAF1 20836 119 - 1
GGUUGCACCAGUGUGGCACUUCACACUGUGAGCACAACUGGCCAAGCCAAGACGAAUGUGGCCAACACAAGGCUUUGAGUUGUCUUGGAAGAGACAUCAAGAG-CCCAGAAGUGGGCCAA
((((...((((((((.(((........)))..))).)))))...))))..........(((((.((....((((((....((((((....))))))...))))-)).....)).))))). ( -43.20)
>DroPer_CAF1 21161 119 - 1
GGUUCCACCAGUGUGGCACUUCACACUGUGAGCACAACUGGCCAAGCCAAGACGAAUGUGGCCAACACAAGGCUUUGAGUUGUCUUGGAAGAGACAUCAAGAG-CCCAGAAGUGGGCCAA
(((.((((((((((((....)))))))).........((((.(...(((((((((....((((.......)))).....)))))))))..((....))....)-.))))..))))))).. ( -43.70)
>consensus
GGUUGCACCAGUGUGGCACUUCACACUGUGAGCACAACUGGCCAAGCCAAGACGAAUGUGGCCAACACAAGGCUUUGAGUUGUCUUGGAAGAGACAUCAAGAG_CCCAGAAGUGGGCCAA
...(((.(((((((((....)))))))).).)))....(((((.............((((.....))))..(((((......((((((........))))))......))))).))))). (-23.98 = -25.77 +   1.78)

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 11:27:16 2006