Locus 864

Sequence ID X_DroMel_CAF1
Location 2,444,174 – 2,444,414
Length 240
Max. P 0.993847
window1394 window1395 window1396 window1397 window1398

overview

Window 4

Location 2,444,174 – 2,444,294
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -25.30
Consensus MFE -22.07
Energy contribution -22.40
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.74
Structure conservation index 0.87
SVM decision value 0.98
SVM RNA-class probability 0.893360
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2444174 120 + 22224390
AACAUAACUUAUAAUGAUCUUUCGGUGACGAGAAAACUAAAUUUAAGCGUAAAAGAUACAACAGGUGCUCGGGGCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAA
........((((((((.(((((((....)..................................((((((.((((.....)))))))))).)))))).))).))))).............. ( -25.80)
>DroSec_CAF1 5036 120 + 1
AACAAAACUUAUAAUGAUCUUUCGGUGACGAGAAAACUAAAUUUAAGCGAAACACAUACAACAGGUGCUCGGGGCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAA
........((((((((.(((((((....)..................................((((((.((((.....)))))))))).)))))).))).))))).............. ( -25.80)
>DroSim_CAF1 7219 120 + 1
AACAAAACUUACAAUGAUCUUUCGGUGACGAGAAAACUAAAUUUAAGUGAAACACAUACAACAGGUGCUCGGGUCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAA
.........((((......(((((....))))).......((((..(((...)))........((((((.(((.......))))))))).....)))).................)))). ( -24.30)
>consensus
AACAAAACUUAUAAUGAUCUUUCGGUGACGAGAAAACUAAAUUUAAGCGAAACACAUACAACAGGUGCUCGGGGCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAA
........((((((((.(((((((((.........))).........................((((((.(((.......))))))))).)))))).))).))))).............. (-22.07 = -22.40 +   0.33)

alignment

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secondary structure

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Window 5

Location 2,444,214 – 2,444,334
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -25.30
Consensus MFE -23.59
Energy contribution -23.37
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.92
Structure conservation index 0.93
SVM decision value 0.53
SVM RNA-class probability 0.772894
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2444214 120 + 22224390
AUUUAAGCGUAAAAGAUACAACAGGUGCUCGGGGCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCGGCGGCGCCCAAG
......((((....((.((....((((((.((((.....)))))))))).....................((((((....))))))................)).))....))))..... ( -27.30)
>DroSec_CAF1 5076 120 + 1
AUUUAAGCGAAACACAUACAACAGGUGCUCGGGGCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCAGCGGCGCCCAAA
......(((..............((((((.((((.....)))))))))).....................((((((....))))))..............((((....)))))))..... ( -25.30)
>DroSim_CAF1 7259 120 + 1
AUUUAAGUGAAACACAUACAACAGGUGCUCGGGUCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCAUCGGCGCCCAAG
......(((..............((((((.(((.......))))))))).....................((((((....))))))............)))((((.....))))...... ( -23.30)
>consensus
AUUUAAGCGAAACACAUACAACAGGUGCUCGGGGCAGAAUCCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCAGCGGCGCCCAAG
......(((..............((((((.(((.......))))))))).....................((((((....))))))..............(((......))))))..... (-23.59 = -23.37 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,444,254 – 2,444,374
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -28.00
Consensus MFE -28.03
Energy contribution -27.70
Covariance contribution -0.33
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 1.00
SVM decision value 0.59
SVM RNA-class probability 0.790852
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2444254 120 + 22224390
CCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCGGCGGCGCCCAAGUGUCCUUUCAACUUGCGCGCUUUUCGAGGCGAGACACUUA
............(((...............((((((....))))))...............((((((((.(((((.(((((.........))))).)))))..)))))))).....))). ( -29.10)
>DroSec_CAF1 5116 120 + 1
CCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCAGCGGCGCCCAAAUGUCCUUUCAACUUGCGCGCCUUUUGAGGCGAGACACUUA
............(((...............((((((....))))))...............((((((((.(((((.(((.((......))..))).)))))..)))))))).....))). ( -25.00)
>DroSim_CAF1 7299 120 + 1
CCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCAUCGGCGCCCAAGUGUCCUUUCAACUUGCGCGCCUUUUGAGGCGAGACACUUA
............(((...............((((((....))))))...............(((((((..(((((.(((((.........))))).)))))...))))))).....))). ( -29.90)
>consensus
CCCAGCGCCAGAAAGAAUAUAUAUAAAAUACGAAAUGUAAAUUUUGAAUAAAAGAAAACACCGUCUCAGCGGCGCCCAAGUGUCCUUUCAACUUGCGCGCCUUUUGAGGCGAGACACUUA
............(((...............((((((....))))))...............(((((((..(((((.(((((.........))))).)))))...))))))).....))). (-28.03 = -27.70 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,444,294 – 2,444,414
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.85
Mean single sequence MFE -31.93
Consensus MFE -31.83
Energy contribution -31.50
Covariance contribution -0.33
Combinations/Pair 1.07
Mean z-score -2.82
Structure conservation index 1.00
SVM decision value 2.43
SVM RNA-class probability 0.993847
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2444294 120 + 22224390
AUUUUGAAUAAAAGAAAACACCGUCUCGGCGGCGCCCAAGUGUCCUUUCAACUUGCGCGCUUUUCGAGGCGAGACACUUAAAUGUACAAAUUGCAUUUUAUUCACAUAAUAAGAGAAGUU
....(((((((((........((((((((.(((((.(((((.........))))).)))))..))))))))...........((((.....)))))))))))))................ ( -32.90)
>DroSec_CAF1 5156 118 + 1
AUUUUGAAUAAAAGAAAACACCGUCUCAGCGGCGCCCAAAUGUCCUUUCAACUUGCGCGCCUUUUGAGGCGAGACACUUAAAUGUACAAAUUGCAUUUUAUUCACUCAAUG--AGAAGUU
....(((((((((........((((((((.(((((.(((.((......))..))).)))))..))))))))...........((((.....)))))))))))))(((...)--))..... ( -29.20)
>DroSim_CAF1 7339 118 + 1
AUUUUGAAUAAAAGAAAACACCGUCUCAUCGGCGCCCAAGUGUCCUUUCAACUUGCGCGCCUUUUGAGGCGAGACACUUAAAUGUACAAAUUGCAUUUUAUUCACUCGAUA--AGAAGUU
....(((((((((........(((((((..(((((.(((((.........))))).)))))...)))))))...........((((.....))))))))))))).......--....... ( -33.70)
>consensus
AUUUUGAAUAAAAGAAAACACCGUCUCAGCGGCGCCCAAGUGUCCUUUCAACUUGCGCGCCUUUUGAGGCGAGACACUUAAAUGUACAAAUUGCAUUUUAUUCACUCAAUA__AGAAGUU
....(((((((((........(((((((..(((((.(((((.........))))).)))))...)))))))...........((((.....)))))))))))))................ (-31.83 = -31.50 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,444,294 – 2,444,414
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.85
Mean single sequence MFE -32.33
Consensus MFE -30.70
Energy contribution -31.37
Covariance contribution 0.67
Combinations/Pair 1.05
Mean z-score -1.92
Structure conservation index 0.95
SVM decision value 0.77
SVM RNA-class probability 0.846072
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2444294 120 - 22224390
AACUUCUCUUAUUAUGUGAAUAAAAUGCAAUUUGUACAUUUAAGUGUCUCGCCUCGAAAAGCGCGCAAGUUGAAAGGACACUUGGGCGCCGCCGAGACGGUGUUUUCUUUUAUUCAAAAU
................(((((((((.((((((((......)))))((((((...((....((((.(((((.(......)))))).)))))).))))))..)))....))))))))).... ( -29.10)
>DroSec_CAF1 5156 118 - 1
AACUUCU--CAUUGAGUGAAUAAAAUGCAAUUUGUACAUUUAAGUGUCUCGCCUCAAAAGGCGCGCAAGUUGAAAGGACAUUUGGGCGCCGCUGAGACGGUGUUUUCUUUUAUUCAAAAU
.......--..(((((((((.(((((((.......((((....))))..((.((((...(((((.(((((.(......)))))).)))))..)))).)))))))))..)))))))))... ( -33.60)
>DroSim_CAF1 7339 118 - 1
AACUUCU--UAUCGAGUGAAUAAAAUGCAAUUUGUACAUUUAAGUGUCUCGCCUCAAAAGGCGCGCAAGUUGAAAGGACACUUGGGCGCCGAUGAGACGGUGUUUUCUUUUAUUCAAAAU
.......--....(((((((.(((((((.......((((....))))..((.((((...(((((.(((((.(......)))))).)))))..)))).)))))))))..)))))))..... ( -34.30)
>consensus
AACUUCU__UAUUGAGUGAAUAAAAUGCAAUUUGUACAUUUAAGUGUCUCGCCUCAAAAGGCGCGCAAGUUGAAAGGACACUUGGGCGCCGCUGAGACGGUGUUUUCUUUUAUUCAAAAU
...........(((((((((.(((((((.......((((....))))..((.((((...(((((.(((((.(......)))))).)))))..)))).)))))))))..)))))))))... (-30.70 = -31.37 +   0.67)

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 09:55:40 2006