Locus 1324

Sequence ID X_DroMel_CAF1
Location 3,953,387 – 3,953,530
Length 143
Max. P 0.814187
window2112 window2113 window2114

overview

Window 2

Location 3,953,387 – 3,953,491
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.69
Mean single sequence MFE -22.42
Consensus MFE -20.23
Energy contribution -20.42
Covariance contribution 0.19
Combinations/Pair 1.18
Mean z-score -1.28
Structure conservation index 0.90
SVM decision value -0.04
SVM RNA-class probability 0.510683
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3953387 104 - 22224390
AAUCUUUGUUCUGAUAAUGCUGCU--GAAUUGCUCACAAUUCUUUAUCGGUACCAAAAUAACAGCAAUGAGCCAAUAAUGAGAAAACGGCAACUGAACAAUAAAGA--------------
.....((((((.(....(((((..--((((((....))))))......(....).......)))))....(((..............)))..).))))))......-------------- ( -18.64)
>DroSim_CAF1 3822 120 - 1
AAUCUUUGUUCUGAUAAUUCUGCUGUGAAUUGCUCACAAUUCUUUAUCGGGACCAAAAUAACAGCGGUGAGCCAAUAAUUAGAAAACGGCAACUGAACAAUAAAGAAUAUCUGCUCCAGA
..(((((((((((((((......(((((.....))))).....))))))))))...........((((..(((..............))).))))......)))))...((((...)))) ( -24.84)
>DroEre_CAF1 3803 118 - 1
AAUCUUUGUCCUGAUAAUGCUGAU--GAAUUGCCCACAAUUCUUUAUCAGCACCAAAAUAACAGCGGUGAGCCAAUAAUAAGAAAACGGCAACUGAACAAUAAAGAAUAUCUGCUCUAGA
..(((((((..((....(((((((--((((((....))))))...)))))))............((((..(((..............))).))))..))))))))).............. ( -23.84)
>DroYak_CAF1 3713 118 - 1
AGUCUUUGUUCUGAUAAUGCCAAU--GAAUUGGCCACAAUUCUUUAUCGGUACCAAAAUAACAGCGGUGAGCCAAUAAUGAGAAAACGGCAACUGAACAAUAAAGAAUAUCUGCUCUAGA
..((((((((.......((((...--((((((....)))))).((((.((((((...........)))..))).)))).........)))).......)))))))).............. ( -22.34)
>consensus
AAUCUUUGUUCUGAUAAUGCUGAU__GAAUUGCCCACAAUUCUUUAUCGGUACCAAAAUAACAGCGGUGAGCCAAUAAUGAGAAAACGGCAACUGAACAAUAAAGAAUAUCUGCUCUAGA
..((((((((.......(((((((..((((((....))))))...)))))))............((((..(((..............))).))))...)))))))).............. (-20.23 = -20.42 +   0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,953,413 – 3,953,530
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.75
Mean single sequence MFE -26.72
Consensus MFE -18.19
Energy contribution -18.75
Covariance contribution 0.56
Combinations/Pair 1.25
Mean z-score -1.75
Structure conservation index 0.68
SVM decision value 0.31
SVM RNA-class probability 0.683814
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3953413 117 + 22224390
CAUUAUUGGCUCAUUGCUGUUAUUUUGGUACCGAUAAAGAAUUGUGAGCAAUUC--AGCAGCAUUAUCAGAACAAAGAUUGGCGGGCCAAAUAAUGUUGAAUUAAUCAUCA-UCACUUAC
((((((((((((..(((((((...(((....)))....((((((....))))))--)))))))..(((........)))....))))).)))))))...............-........ ( -28.40)
>DroSim_CAF1 3862 119 + 1
AAUUAUUGGCUCACCGCUGUUAUUUUGGUCCCGAUAAAGAAUUGUGAGCAAUUCACAGCAGAAUUAUCAGAACAAAGAUUAGCGGGCCAAAUAAUGUUGAAUUAAUCAUCA-UCAGUUGC
.....(((((...((((((...(((((.((..(((((....(((((((...))))))).....))))).)).)))))..)))))))))))...(((.(((.....))).))-)....... ( -26.90)
>DroEre_CAF1 3843 107 + 1
UAUUAUUGGCUCACCGCUGUUAUUUUGGUGCUGAUAAAGAAUUGUGGGCAAUUC--AUCAGCAUUAUCAGGACAAAGAUUAGCGAGUC-----------AAUUAAUCAUCAGUUAAUACC
....((((((((.((..((((....((((((((((...((((((....))))))--))))))))))....))))..)....).)))))-----------))).................. ( -28.40)
>DroYak_CAF1 3753 118 + 1
CAUUAUUGGCUCACCGCUGUUAUUUUGGUACCGAUAAAGAAUUGUGGCCAAUUC--AUUGGCAUUAUCAGAACAAAGACUAGCGAACCAAAUAAUGUUUAAUUAAUCAUCAGUUAAAUAC
(((((((((.....(((((((.(((((((((((((...((((((....))))))--)))))...))))))))....))).))))..)).)))))))(((((((.......)))))))... ( -23.20)
>consensus
CAUUAUUGGCUCACCGCUGUUAUUUUGGUACCGAUAAAGAAUUGUGAGCAAUUC__AGCAGCAUUAUCAGAACAAAGAUUAGCGAGCCAAAUAAUGUUGAAUUAAUCAUCA_UCAAUUAC
.....(((((((...((((((.(((((((((((((...((((((....))))))..)))))...))))))))....))).)))))))))).............................. (-18.19 = -18.75 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,953,413 – 3,953,530
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.75
Mean single sequence MFE -26.77
Consensus MFE -18.58
Energy contribution -19.82
Covariance contribution 1.25
Combinations/Pair 1.23
Mean z-score -1.93
Structure conservation index 0.69
SVM decision value 0.66
SVM RNA-class probability 0.814187
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3953413 117 - 22224390
GUAAGUGA-UGAUGAUUAAUUCAACAUUAUUUGGCCCGCCAAUCUUUGUUCUGAUAAUGCUGCU--GAAUUGCUCACAAUUCUUUAUCGGUACCAAAAUAACAGCAAUGAGCCAAUAAUG
..((((((-((.(((.....))).))))))))(((.........((((..(((((((.......--((((((....)))))).)))))))...))))....((....)).)))....... ( -23.40)
>DroSim_CAF1 3862 119 - 1
GCAACUGA-UGAUGAUUAAUUCAACAUUAUUUGGCCCGCUAAUCUUUGUUCUGAUAAUUCUGCUGUGAAUUGCUCACAAUUCUUUAUCGGGACCAAAAUAACAGCGGUGAGCCAAUAAUU
.....(((-((.(((.....))).))))).((((((((((....(((((((((((((......(((((.....))))).....))))))))).)))).....)))))...)))))..... ( -32.50)
>DroEre_CAF1 3843 107 - 1
GGUAUUAACUGAUGAUUAAUU-----------GACUCGCUAAUCUUUGUCCUGAUAAUGCUGAU--GAAUUGCCCACAAUUCUUUAUCAGCACCAAAAUAACAGCGGUGAGCCAAUAAUA
..................(((-----------(.((((((.(((........)))..(((((((--((((((....))))))...))))))).............)))))).)))).... ( -23.70)
>DroYak_CAF1 3753 118 - 1
GUAUUUAACUGAUGAUUAAUUAAACAUUAUUUGGUUCGCUAGUCUUUGUUCUGAUAAUGCCAAU--GAAUUGGCCACAAUUCUUUAUCGGUACCAAAAUAACAGCGGUGAGCCAAUAAUG
........................(((((((.((((((((.((..(((((.((....((((...--((((((....))))))......)))).)).)))))..))))))))))))))))) ( -27.50)
>consensus
GUAAUUAA_UGAUGAUUAAUUCAACAUUAUUUGGCCCGCUAAUCUUUGUUCUGAUAAUGCUGAU__GAAUUGCCCACAAUUCUUUAUCGGUACCAAAAUAACAGCGGUGAGCCAAUAAUG
..............................((((((((((.(((........)))..(((((((..((((((....))))))...))))))).............))))))))))..... (-18.58 = -19.82 +   1.25)

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 10:06:34 2006