Locus 3785

Sequence ID X_DroMel_CAF1
Location 10,025,436 – 10,025,634
Length 198
Max. P 0.983994
window6215 window6216 window6217 window6218

overview

Window 5

Location 10,025,436 – 10,025,556
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.40
Mean single sequence MFE -20.90
Consensus MFE -15.23
Energy contribution -15.47
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -1.65
Structure conservation index 0.73
SVM decision value 0.65
SVM RNA-class probability 0.811502
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10025436 120 - 22224390
AUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCUAGAUGCCCAAGUGGGCGGUGCCAGAAGAGGAAACAAGUAAAGUGUAUUAGAGAUACUCUGCACAGCAAGAGGCAUAUUUGG
..................((((....................(((((....)))))((((.(((...(....).........(((((...))))))))))))......))))........ ( -25.50)
>DroSim_CAF1 2763 96 - 1
AUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAA------------------------GCCAGCAGAGGAAACAACCAAAGUGUAUUAGAGAUACUCUGUACAGCAAGAGGCAUGUUUAA
....(((((((.(((((........)))))....------------------------(((.((...(....)........(((((.((((...)))))))))))....))).))))))) ( -14.30)
>DroEre_CAF1 32864 114 - 1
AUAAUUCAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCCACAUGCCCAACUGGGCGG------AAGAGGAAACAACUAAAGUGUAUUAGAGAUACUCUGUGCAGCAAGAGGCAUGUUUAA
.......................................((((((((..(((.((((------(...(....).........(((((...)))))))))).)))...).))))))).... ( -23.30)
>DroYak_CAF1 30140 108 - 1
AUAAUUAAAUAAAUUAAAGCCUAAGUUAAUCAGAAAGCCACAUGCUCAAUUGGGCGA------U------GUCAACUAAAGUGUAUUAGAGAUACUCUGUACAGCAAAAGGCAUGUUGAA
.............................((((...(((((((((((....)))).)------)------)).........(((((.((((...)))))))))......)))...)))). ( -20.50)
>consensus
AUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCCACAUGCCCAA_UGGGCGG______AAGAGGAAACAACUAAAGUGUAUUAGAGAUACUCUGUACAGCAAGAGGCAUGUUUAA
..................((((....................(((((....))))).........................(((((.((((...))))))))).....))))........ (-15.23 = -15.47 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,025,476 – 10,025,596
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.97
Mean single sequence MFE -27.48
Consensus MFE -17.84
Energy contribution -18.15
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.11
Structure conservation index 0.65
SVM decision value 1.46
SVM RNA-class probability 0.955778
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10025476 120 + 22224390
UUUACUUGUUUCCUCUUCUGGCACCGCCCACUUGGGCAUCUAGCUUUUUGAUUAAUUUAGGCUUUAAUUUAUUUAAUUAUAAGCCAAAGGCAUAGGGAAUUUUGUCACCUGUUGGCACCC
.......(((((((...........((((....)))).....(((((((((.....)))((((((((((.....))))).)))))))))))..)))))))..(((((.....)))))... ( -28.20)
>DroSim_CAF1 2803 96 + 1
UUUGGUUGUUUCCUCUGCUGGC------------------------UUUGAUUAAUUUAGGCUUUAAUUUAUUUAAUUAUAAGCCAAAGGCACAGGGAAUUUUGUCACCUGUUGGCACCC
...(((.(((((((.(((((((------------------------(((((((((..((((......)))).))))))).)))))...)))).)))))))...((((.....))))))). ( -24.20)
>DroEre_CAF1 32904 114 + 1
UUUAGUUGUUUCCUCUU------CCGCCCAGUUGGGCAUGUGGCUUUUUGAUUAAUUUAGGCUUUAAUUUAUUGAAUUAUAAGCCACAGGCAUAGGGAAUUUUGUCACCUGUUGGCAUCC
.......(((((((...------((((((....)))).((((((((......((((((((...........)))))))).))))))))))...)))))))..(((((.....)))))... ( -32.90)
>DroYak_CAF1 30180 108 + 1
UUUAGUUGAC------A------UCGCCCAAUUGAGCAUGUGGCUUUCUGAUUAACUUAGGCUUUAAUUUAUUUAAUUAUAAGCCCAAGGCAUAGGGAAUUUUAUCACCUGUUGGCAGCC
....((..((------.------..(((((...((((.....))))..)).........((((((((((.....))))).)))))...)))..(((((......)).)))))..)).... ( -24.60)
>consensus
UUUAGUUGUUUCCUCUU______CCGCCCA_UUGGGCAUGUGGCUUUUUGAUUAAUUUAGGCUUUAAUUUAUUUAAUUAUAAGCCAAAGGCAUAGGGAAUUUUGUCACCUGUUGGCACCC
.........................((((....))))......................((((((((((.....))))).)))))...(.((((((((......)).)))).)).).... (-17.84 = -18.15 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,025,476 – 10,025,596
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.97
Mean single sequence MFE -26.62
Consensus MFE -14.14
Energy contribution -14.70
Covariance contribution 0.56
Combinations/Pair 1.13
Mean z-score -2.76
Structure conservation index 0.53
SVM decision value 1.96
SVM RNA-class probability 0.983994
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10025476 120 - 22224390
GGGUGCCAACAGGUGACAAAAUUCCCUAUGCCUUUGGCUUAUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCUAGAUGCCCAAGUGGGCGGUGCCAGAAGAGGAAACAAGUAAA
.((..((...(((.((......)))))........(((((.(((((.....))))))))))......................((((....))))))..))......(....)....... ( -29.50)
>DroSim_CAF1 2803 96 - 1
GGGUGCCAACAGGUGACAAAAUUCCCUGUGCCUUUGGCUUAUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAA------------------------GCCAGCAGAGGAAACAACCAAA
.((((((....))).......((((((((..(((((((((.(((((.....))))))))))..........)))------------------------)...)))).))))...)))... ( -21.10)
>DroEre_CAF1 32904 114 - 1
GGAUGCCAACAGGUGACAAAAUUCCCUAUGCCUGUGGCUUAUAAUUCAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCCACAUGCCCAACUGGGCGG------AAGAGGAAACAACUAAA
....(((....))).......((((((...((((((((((..................................)))))))).((((....))))))------.)).))))......... ( -25.68)
>DroYak_CAF1 30180 108 - 1
GGCUGCCAACAGGUGAUAAAAUUCCCUAUGCCUUGGGCUUAUAAUUAAAUAAAUUAAAGCCUAAGUUAAUCAGAAAGCCACAUGCUCAAUUGGGCGA------U------GUCAACUAAA
((((..(...(((.((......)))))....(((((((((.(((((.....)))))))))))))).......)..))))((((((((....)))).)------)------))........ ( -30.20)
>consensus
GGGUGCCAACAGGUGACAAAAUUCCCUAUGCCUUUGGCUUAUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCCACAUGCCCAA_UGGGCGG______AAGAGGAAACAACUAAA
.(..(((....)))..)....((((..........(((((.(((((.....)))))))))).....................(((((....)))))...........))))......... (-14.14 = -14.70 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,025,516 – 10,025,634
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.17
Mean single sequence MFE -19.36
Consensus MFE -12.54
Energy contribution -12.85
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.05
Structure conservation index 0.65
SVM decision value 0.53
SVM RNA-class probability 0.770210
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10025516 118 - 22224390
AAAACCUUUCUCGCACAC--ACACACACACACGAAUUUUUGGGUGCCAACAGGUGACAAAAUUCCCUAUGCCUUUGGCUUAUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCUA
..................--............((...((((((((((((.((((...............)))))))))...(((((.....)))))..)))))))....))......... ( -16.96)
>DroSim_CAF1 2825 106 - 1
AAAAUCUUUCG------C--ACACACACACACGAAUUUUUGGGUGCCAACAGGUGACAAAAUUCCCUGUGCCUUUGGCUUAUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAA------
...........------.--............((...((((((((((((.((((.(((........))))))))))))...(((((.....)))))..)))))))....))...------ ( -19.60)
>DroEre_CAF1 32938 110 - 1
AAAACCCUUCGAGCACAC----------ACACAAUUUUUUGGAUGCCAACAGGUGACAAAAUUCCCUAUGCCUGUGGCUUAUAAUUCAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCCA
..................----------......((((((((......((((((...............))))))(((((.(((((.....))))))))))........))))))))... ( -17.36)
>DroYak_CAF1 30208 120 - 1
AAAACCUUUCGCCCACACACACACACACACACGAAUUUUUGGCUGCCAACAGGUGAUAAAAUUCCCUAUGCCUUGGGCUUAUAAUUAAAUAAAUUAAAGCCUAAGUUAAUCAGAAAGCCA
.....(((((......................(((((((...(.(((....))))..))))))).......(((((((((.(((((.....)))))))))))))).......)))))... ( -23.50)
>consensus
AAAACCUUUCGCGCACAC__ACACACACACACGAAUUUUUGGGUGCCAACAGGUGACAAAAUUCCCUAUGCCUUUGGCUUAUAAUUAAAUAAAUUAAAGCCUAAAUUAAUCAAAAAGCCA
...................................(((((((........(((.((......)))))........(((((.(((((.....))))))))))........))))))).... (-12.54 = -12.85 +   0.31)

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 11:08:27 2006