Locus 4675

Sequence ID 3R_DroMel_CAF1
Location 12,326,907 – 12,327,099
Length 192
Max. P 0.984351
window7673 window7674 window7675 window7676 window7677

overview

Window 3

Location 12,326,907 – 12,327,027
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -40.63
Consensus MFE -38.82
Energy contribution -38.60
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.65
Structure conservation index 0.96
SVM decision value 1.55
SVM RNA-class probability 0.963438
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12326907 120 + 27905053
UCGGGCUCUUGCCCAACGUUGAUUAGCCUGCUCGAGGGGAAGUUACGUUUAUUGGUAGCAAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGGUUCACGCCC
..((((....))))..(((.((...(((((.((..((((((((((.(((..(((((.((((....(((......)))...)))))))))..))).))))))))))))))))))))))... ( -40.60)
>DroSec_CAF1 18060 119 + 1
UCGGGCUCUUGCCCAACGUUGAUUAGCCUGCUCGAGGGGAAGUUACGUUUAUUGGUAGCGAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGG-UCACGCCC
..((((....))))...........((.((((((.((((((((((.(((..(((((.((((....(((......)))...)))))))))..))).))))))))))..))))-.)).)).. ( -40.80)
>DroSim_CAF1 14113 118 + 1
UCGGGCUCUUGCCCAACGUUGAUUAGC-UGCUCGAGGGGAAGUUACGUUUAUUGGUAGCAAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGG-UCACGCCC
..((((....))))...........((-((((((.((((((((((.(((..(((((.((((....(((......)))...)))))))))..))).))))))))))..))))-.)).)).. ( -40.50)
>consensus
UCGGGCUCUUGCCCAACGUUGAUUAGCCUGCUCGAGGGGAAGUUACGUUUAUUGGUAGCAAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGG_UCACGCCC
..((((....))))...........((.((((((.((((((((((.(((..(((((.((((....(((......)))...)))))))))..))).))))))))))..))))..)).)).. (-38.82 = -38.60 +  -0.22)

alignment

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secondary structure

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Window 4

Location 12,326,947 – 12,327,067
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -41.13
Consensus MFE -39.65
Energy contribution -39.43
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.77
Structure conservation index 0.96
SVM decision value 1.74
SVM RNA-class probability 0.975108
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12326947 120 + 27905053
AGUUACGUUUAUUGGUAGCAAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGGUUCACGCCCACAAAAGUGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGG
.(((((........)))))...............((((((((((....).))))..((((((((.((((((....(((((((....))))))))))))).)))))))))))))....... ( -43.80)
>DroSec_CAF1 18100 119 + 1
AGUUACGUUUAUUGGUAGCGAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGG-UCACGCCCACAAAAGGGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGG
.(((((........)))))...............((((((((((....).))))..((((((((.((((((-...(((((........))))))))))).)))))))))))))....... ( -39.80)
>DroSim_CAF1 14152 119 + 1
AGUUACGUUUAUUGGUAGCAAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGG-UCACGCCCACAAAAGGGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGG
.(((((........)))))...............((((((((((....).))))..((((((((.((((((-...(((((........))))))))))).)))))))))))))....... ( -39.80)
>consensus
AGUUACGUUUAUUGGUAGCAAAAUACAAUUCCCUUUGCCAUUGCACCAGACAAUUUGAUUUCCCCGACGGG_UCACGCCCACAAAAGGGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGG
((((..(((...((((.((((....(((......)))...)))))))))))...(..(((((((.((((((....(((((........))))))))))).)))))))..).))))..... (-39.65 = -39.43 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,326,947 – 12,327,067
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -47.57
Consensus MFE -45.00
Energy contribution -45.33
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.94
Structure conservation index 0.95
SVM decision value 1.84
SVM RNA-class probability 0.979447
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12326947 120 - 27905053
CCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCACUUUUGUGGGCGUGAACCCGUCGGGGAAAUCAAAUUGUCUGGUGCAAUGGCAAAGGGAAUUGUAUUUUGCUACCAAUAAACGUAACU
.....((((((..((((((((((((.((((((((....)))))))).....))))))))))))....((((.((((((((..((((......))))...)))).))))))))..)))))) ( -51.10)
>DroSec_CAF1 18100 119 - 1
CCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCCCUUUUGUGGGCGUGA-CCCGUCGGGGAAAUCAAAUUGUCUGGUGCAAUGGCAAAGGGAAUUGUAUUUCGCUACCAAUAAACGUAACU
..((...(((((.((((((((((((.((((((.(....).))))))..-..))))))))))))...(((((.....))))))))))((.(((......))).)).))............. ( -44.60)
>DroSim_CAF1 14152 119 - 1
CCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCCCUUUUGUGGGCGUGA-CCCGUCGGGGAAAUCAAAUUGUCUGGUGCAAUGGCAAAGGGAAUUGUAUUUUGCUACCAAUAAACGUAACU
.....((((((..((((((((((((.((((((.(....).))))))..-..))))))))))))....((((.((((((((..((((......))))...)))).))))))))..)))))) ( -47.00)
>consensus
CCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCCCUUUUGUGGGCGUGA_CCCGUCGGGGAAAUCAAAUUGUCUGGUGCAAUGGCAAAGGGAAUUGUAUUUUGCUACCAAUAAACGUAACU
.....((((((..((((((((((((.((((((.(....).)))))).....))))))))))))....((((.((((((((..((((......))))...)))).))))))))..)))))) (-45.00 = -45.33 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,326,987 – 12,327,099
Length 112
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 97.61
Mean single sequence MFE -44.20
Consensus MFE -42.13
Energy contribution -42.47
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.23
Structure conservation index 0.95
SVM decision value 1.97
SVM RNA-class probability 0.984351
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12326987 112 + 27905053
UUGCACCAGACAAUUUGAUUUCCCCGACGGGUUCACGCCCACAAAAGUGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGGCGAAAGUGUCGCUGCUACUGGGGAUUUCUUAA
.....((((.....(..(((((((.((((((....(((((((....))))))))))))).)))))))..).......((((((.....))))))...))))........... ( -47.60)
>DroSec_CAF1 18140 111 + 1
UUGCACCAGACAAUUUGAUUUCCCCGACGGG-UCACGCCCACAAAAGGGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGGCGAAAGUGUCGCUGCUACUGGGAAUUUCUUAA
.....((((.....(..(((((((.((((((-...(((((........))))))))))).)))))))..).......((((((.....))))))...))))........... ( -43.60)
>DroSim_CAF1 14192 111 + 1
UUGCACCAGACAAUUUGAUUUCCCCGACGGG-UCACGCCCACAAAAGGGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGGCGAAAGUGUCGCUUCUACUGGGAAUUUCUUAA
.....((((.....(..(((((((.((((((-...(((((........))))))))))).)))))))..)........(((((.....)))))....))))........... ( -41.40)
>consensus
UUGCACCAGACAAUUUGAUUUCCCCGACGGG_UCACGCCCACAAAAGGGGGCGCUCGUCAGGGAAAUUGGCAACUUCCGGCGAAAGUGUCGCUGCUACUGGGAAUUUCUUAA
.....((((.....(..(((((((.((((((....(((((........))))))))))).)))))))..).......((((((.....))))))...))))........... (-42.13 = -42.47 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,326,987 – 12,327,099
Length 112
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 97.61
Mean single sequence MFE -43.03
Consensus MFE -40.33
Energy contribution -40.33
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.98
Structure conservation index 0.94
SVM decision value 1.69
SVM RNA-class probability 0.972470
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12326987 112 - 27905053
UUAAGAAAUCCCCAGUAGCAGCGACACUUUCGCCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCACUUUUGUGGGCGUGAACCCGUCGGGGAAAUCAAAUUGUCUGGUGCAA
.................(((((((.....))))((((..(((...((((((((((((.((((((((....)))))))).....)))))))))))))))....)))).))).. ( -46.10)
>DroSec_CAF1 18140 111 - 1
UUAAGAAAUUCCCAGUAGCAGCGACACUUUCGCCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCCCUUUUGUGGGCGUGA-CCCGUCGGGGAAAUCAAAUUGUCUGGUGCAA
.................(((((((.....))))((((..(((...((((((((((((.((((((.(....).))))))..-..)))))))))))))))....)))).))).. ( -42.00)
>DroSim_CAF1 14192 111 - 1
UUAAGAAAUUCCCAGUAGAAGCGACACUUUCGCCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCCCUUUUGUGGGCGUGA-CCCGUCGGGGAAAUCAAAUUGUCUGGUGCAA
..............................(((((((..(((...((((((((((((.((((((.(....).))))))..-..)))))))))))))))....)))))))... ( -41.00)
>consensus
UUAAGAAAUUCCCAGUAGCAGCGACACUUUCGCCGGAAGUUGCCAAUUUCCCUGACGAGCGCCCCCUUUUGUGGGCGUGA_CCCGUCGGGGAAAUCAAAUUGUCUGGUGCAA
..............................(((((((..(((...((((((((((((.((((((.(....).)))))).....)))))))))))))))....)))))))... (-40.33 = -40.33 +   0.00)

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 11:36:09 2006