Locus 901

Sequence ID 2R_DroMel_CAF1
Location 4,047,018 – 4,047,298
Length 280
Max. P 0.999411
window1576 window1577 window1578 window1579 window1580

overview

Window 6

Location 4,047,018 – 4,047,138
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.83
Mean single sequence MFE -42.74
Consensus MFE -40.82
Energy contribution -40.62
Covariance contribution -0.20
Combinations/Pair 1.06
Mean z-score -2.50
Structure conservation index 0.96
SVM decision value 3.40
SVM RNA-class probability 0.999143
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4047018 120 + 20766785
UUUUGGCAAGUGGGAAACUUUGUCCUGCUGCCAUGACAAUAAUCGUGGUAAUGGGCUGUCUCAUAAUAAUGCUAAUGAUGCCUCUGGGUGCGGGUCUGGACCCGACACGCCCAGCGAAUU
..((((((.((((((......((((...((((((((......))))))))..))))..)))))).....))))))......(.((((((((((((....)))))...))))))).).... ( -44.20)
>DroSec_CAF1 29768 120 + 1
UUUUGGCAAGUGGGAAACUUUGUCCUGCUGCCAUGACAAUAAUCGUGGUAAUGGGCUGUCUCAUAAUAAUGCUAAUGAUGCCUCUGGGUACGGGUCUGGACCCGACACGCCCAGCGAAUU
..((.((.((..(((.......)))..))(((((((......)))))))..(((((((((..................((((....)))).((((....)))))))).))))))).)).. ( -42.10)
>DroSim_CAF1 34439 120 + 1
UUUUGGCAAGUGGGAAACUUUGUCCUGCUGCCAUGACAAUAAUCGUGGUAAUGGGCUGUCUCAUAAUAAUGCUAAUGAUGCCUCUGGGUACGGGUCUGGACCCGACACGCCCAGCGAAUU
..((.((.((..(((.......)))..))(((((((......)))))))..(((((((((..................((((....)))).((((....)))))))).))))))).)).. ( -42.10)
>DroEre_CAF1 29112 120 + 1
UUUUGGCAAGUGGGAAACUUUGUCCUGCUGCCAUGACAAUAAUCGUGGUAAUGGGCUGUCUCAUAAUAAUGCUAAUGAUGCCUCUGGGUACGGGUCUGGACCCGACACGCCCAGCAAAUU
....(((((..((....))))))).(((((((((((......)))))))).(((((((((..................((((....)))).((((....)))))))).)))))))).... ( -42.10)
>DroYak_CAF1 32907 120 + 1
UUUUGCCAAGUGGGAAACUUUGUCCUGCUGCCAUGACAAUAAUCGUGGUAAUGGGCUGUCUCAUAAUAAUGCUAAUGAUGCCUCUGGGUACGGGUCUGGACCCGACACGCCCAGCAAAUU
.(((((..((..(((.......)))..))(((((((......)))))))..(((((((((..................((((....)))).((((....)))))))).)))))))))).. ( -43.20)
>consensus
UUUUGGCAAGUGGGAAACUUUGUCCUGCUGCCAUGACAAUAAUCGUGGUAAUGGGCUGUCUCAUAAUAAUGCUAAUGAUGCCUCUGGGUACGGGUCUGGACCCGACACGCCCAGCGAAUU
....(((((..((....))))))).(((((((((((......)))))))).(((((((((..................((((....)))).((((....)))))))).)))))))).... (-40.82 = -40.62 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,047,138 – 4,047,258
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.92
Mean single sequence MFE -37.70
Consensus MFE -33.20
Energy contribution -33.28
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.78
Structure conservation index 0.88
SVM decision value 1.81
SVM RNA-class probability 0.978141
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4047138 120 + 20766785
AUAACUGCCUCCGGAGCAAUGGCGAAAUUAGAGUUUCAAUUUCCUCUGCGAAUCCGGCUGCCGAAGGCGGGGAAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUU
......((((.((((((...((......(((((..........))))).....)).))).))).))))((((((((..((((((......)))))).))))))))............... ( -38.70)
>DroSec_CAF1 29888 120 + 1
AUAACUGCCUCCGGUGCGAUGGUGAAAUUAGAGUUUCAAUUUCCUCUGCGAAUCCGGCAGCCAAAGGCGGGGCAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUU
....(((((.....((((..((((((((....))))))....))..)))).....)))))...(((((((((.(((..((((((......)))))).))).)))).((....)).))))) ( -35.40)
>DroSim_CAF1 34559 120 + 1
AUAACUGCCUCCGGCGCGAUGGUGAAAUUAGAGUUUCAAUUUCCUCUGCGAAUCCGGCUGCCAAAGGCGGGGCAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUU
......((..((((((((..((((((((....))))))....))..))))...))))..))..(((((((((.(((..((((((......)))))).))).)))).((....)).))))) ( -35.50)
>DroEre_CAF1 29232 120 + 1
AUAACAGCCUCCGGCGCAAUGGCGAAAUUAGAGUUUCAAUUUCCGCAGCGAAUCCGGCUGCCAAAAGCGGGGAAAGCGGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUU
............((((.....(((((((....))))).......(((((.......))))).....))((((((((..((((((......)))))).)))))))).........)))).. ( -39.70)
>DroYak_CAF1 33027 120 + 1
AUGACUGCCUCCGGCGCAAUGGCGAAAUUAGAGUUUCAAUUUCCGCAGCGAAUCCGGCUGCCAAAGGCGGGGAAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUU
.(((..((((..(((((....((((((((.(.....)))))).)))..((....)))).)))..))))((((((((..((((((......)))))).))))))))....)))........ ( -39.20)
>consensus
AUAACUGCCUCCGGCGCAAUGGCGAAAUUAGAGUUUCAAUUUCCUCUGCGAAUCCGGCUGCCAAAGGCGGGGAAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUU
............(((((..(((((((((....)))))..........((.......)).))))...))((((((((..((((((......)))))).))))))))..........))).. (-33.20 = -33.28 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,047,138 – 4,047,258
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.92
Mean single sequence MFE -39.84
Consensus MFE -35.62
Energy contribution -35.94
Covariance contribution 0.32
Combinations/Pair 1.09
Mean z-score -1.58
Structure conservation index 0.89
SVM decision value 1.43
SVM RNA-class probability 0.953040
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4047138 120 - 20766785
AAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUUCCCCGCCUUCGGCAGCCGGAUUCGCAGAGGAAAUUGAAACUCUAAUUUCGCCAUUGCUCCGGAGGCAGUUAU
..(((..........(((.((((((((((........))))).))))).)))((((((((.(((.((......((((..........)))).......))...))))))))))).))).. ( -39.92)
>DroSec_CAF1 29888 120 - 1
AAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUGCCCCGCCUUUGGCUGCCGGAUUCGCAGAGGAAAUUGAAACUCUAAUUUCACCAUCGCACCGGAGGCAGUUAU
((((((((....)))(((..(((((((((........))))).))))..))))))))((((((((......((.((.(((((((......)))))))....))))......)))))))). ( -38.10)
>DroSim_CAF1 34559 120 - 1
AAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUGCCCCGCCUUUGGCAGCCGGAUUCGCAGAGGAAAUUGAAACUCUAAUUUCACCAUCGCGCCGGAGGCAGUUAU
..(((..........(((..(((((((((........))))).))))..)))(((((((((.((.......)).(..(((((((......)))))))..).....))))))))).))).. ( -39.30)
>DroEre_CAF1 29232 120 - 1
AAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCCGCUUUCCCCGCUUUUGGCAGCCGGAUUCGCUGCGGAAAUUGAAACUCUAAUUUCGCCAUUGCGCCGGAGGCUGUUAU
((((((.........((((((.(((((((........)))).)))))))))))))))((((((((.....(((.(((.((((((......)))))))))....))).....)))))))). ( -39.00)
>DroYak_CAF1 33027 120 - 1
AAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUUCCCCGCCUUUGGCAGCCGGAUUCGCUGCGGAAAUUGAAACUCUAAUUUCGCCAUUGCGCCGGAGGCAGUCAU
..(((..........(((.((((((((((........))))).))))).)))((((((((((((.......)))(((.((((((......)))))))))......))))))))).))).. ( -42.90)
>consensus
AAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUUCCCCGCCUUUGGCAGCCGGAUUCGCAGAGGAAAUUGAAACUCUAAUUUCGCCAUUGCGCCGGAGGCAGUUAU
..(((..........(((.((((((((((........))))).))))).)))(((((((((.((.......))....(((((((......)))))))........))))))))).))).. (-35.62 = -35.94 +   0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,047,178 – 4,047,298
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.50
Mean single sequence MFE -35.42
Consensus MFE -32.22
Energy contribution -32.62
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.17
Structure conservation index 0.91
SVM decision value 2.95
SVM RNA-class probability 0.997873
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4047178 120 + 20766785
UUCCUCUGCGAAUCCGGCUGCCGAAGGCGGGGAAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUUAAAGCGAAAACUUUUUAAUUGUGCCACAACAACCGGAGCU
.......((...(((((.((.....(((((((((((..((((((......)))))).)))))))).........(((......)))................)))....)).))))))). ( -36.70)
>DroSec_CAF1 29928 120 + 1
UUCCUCUGCGAAUCCGGCAGCCAAAGGCGGGGCAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUUAAAGCGAAAACUUUUUAAUUGUGCCACAACAACCGGAGCU
((((.((((.......)))).....(((((((.(((..((((((......)))))).))).)))).........(((......)))................))).........)))).. ( -31.30)
>DroSim_CAF1 34599 120 + 1
UUCCUCUGCGAAUCCGGCUGCCAAAGGCGGGGCAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUUAAAGCGAAAACUUUUUAAUUGUGCCACAACAACCGGAGCU
.......((...(((((.((.....(((((((.(((..((((((......)))))).))).)))).........(((......)))................)))....)).))))))). ( -32.80)
>DroEre_CAF1 29272 120 + 1
UUCCGCAGCGAAUCCGGCUGCCAAAAGCGGGGAAAGCGGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUUAAAGCGAAAACUUUUUAAUUGUGCCACAACAAGCGGAGCU
((((((.((......(((.((.....))((((((((..((((((......)))))).))))))))..........))).....)).............((((......)))))))))).. ( -38.60)
>DroYak_CAF1 33067 120 + 1
UUCCGCAGCGAAUCCGGCUGCCAAAGGCGGGGAAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUUAAAGCAAAAACUUUUUAAUUGUGCCACAACAACCGGAGCU
(((((((((.......)))))....(((((((((((..((((((......)))))).))))))))..........((......)).................))).........)))).. ( -37.70)
>consensus
UUCCUCUGCGAAUCCGGCUGCCAAAGGCGGGGAAAGCAGCACAUAACUGAGUGUGCACUUUUCCCAUUAUCAAACGCCUUAAAGCGAAAACUUUUUAAUUGUGCCACAACAACCGGAGCU
((((...((......(((.((.....))((((((((..((((((......)))))).))))))))..........))).....)).............((((......))))..)))).. (-32.22 = -32.62 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,047,178 – 4,047,298
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -40.94
Consensus MFE -40.20
Energy contribution -40.52
Covariance contribution 0.32
Combinations/Pair 1.08
Mean z-score -2.06
Structure conservation index 0.98
SVM decision value 3.58
SVM RNA-class probability 0.999411
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4047178 120 - 20766785
AGCUCCGGUUGUUGUGGCACAAUUAAAAAGUUUUCGCUUUAAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUUCCCCGCCUUCGGCAGCCGGAUUCGCAGAGGAA
.(((((((((((((.(((...........(((..((((....))))...)))...(((.((((((((((........))))).))))).))))))..)))))))))))...))....... ( -45.50)
>DroSec_CAF1 29928 120 - 1
AGCUCCGGUUGUUGUGGCACAAUUAAAAAGUUUUCGCUUUAAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUGCCCCGCCUUUGGCUGCCGGAUUCGCAGAGGAA
.((((((((.((((.(((...........(((..((((....))))...)))...(((..(((((((((........))))).))))..))))))..)))).))))))...))....... ( -38.60)
>DroSim_CAF1 34599 120 - 1
AGCUCCGGUUGUUGUGGCACAAUUAAAAAGUUUUCGCUUUAAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUGCCCCGCCUUUGGCAGCCGGAUUCGCAGAGGAA
.(((((((((((((.(((...........(((..((((....))))...)))...(((..(((((((((........))))).))))..))))))..)))))))))))...))....... ( -42.40)
>DroEre_CAF1 29272 120 - 1
AGCUCCGCUUGUUGUGGCACAAUUAAAAAGUUUUCGCUUUAAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCCGCUUUCCCCGCUUUUGGCAGCCGGAUUCGCUGCGGAA
...(((((.((.(.((((...........(((..((((....))))...)))...(((.((((((((((........)))).)))))).)))((.....)).)))).)..))..))))). ( -36.20)
>DroYak_CAF1 33067 120 - 1
AGCUCCGGUUGUUGUGGCACAAUUAAAAAGUUUUUGCUUUAAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUUCCCCGCCUUUGGCAGCCGGAUUCGCUGCGGAA
((((((((((((((.(((...((((((..(((((......))))).))))))...(((.((((((((((........))))).))))).))))))..)))))))))))...)))...... ( -42.00)
>consensus
AGCUCCGGUUGUUGUGGCACAAUUAAAAAGUUUUCGCUUUAAGGCGUUUGAUAAUGGGAAAAGUGCACACUCAGUUAUGUGCUGCUUUCCCCGCCUUUGGCAGCCGGAUUCGCAGAGGAA
.(((((((((((((.(((...........(((..((((....))))...)))...(((.((((((((((........))))).))))).))))))..)))))))))))...))....... (-40.20 = -40.52 +   0.32)

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 09:50:39 2006