Locus 4755

Sequence ID 2L_DroMel_CAF1
Location 13,573,510 – 13,573,710
Length 200
Max. P 0.995565
window7523 window7524 window7525

overview

Window 3

Location 13,573,510 – 13,573,630
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.14
Mean single sequence MFE -32.86
Consensus MFE -25.63
Energy contribution -26.28
Covariance contribution 0.65
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.78
SVM decision value 0.39
SVM RNA-class probability 0.716134
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13573510 120 + 22407834
AUAUGUAUGUAUGUACAUAGUUACGUAUAGUUAGUUGGCUGAGUGGGGUGCUGACUCUCGUAACUUUGAAGUGUUGCGAACUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACA
.......((((((((......))))))))....(((((((....(((((((..(...(((((((........)))))))..)..)))).)))....(((........)))..))))))). ( -36.40)
>DroSec_CAF1 6751 106 + 1
AUAUGUAU--AUAU-----GUUACGUAUAGUUAGUUGGCU----GGGCUGCUGACUCUCGUA--CUUGAAGU-UUGCGAACUUGGCGCACUUGAUGGCACUAAUUUAUGCCGGGCCAACA
(((((((.--....-----..))))))).....(((((((----.((((((.((((.(((..--..))))))-).)))...((((.((.(.....))).)))).....))).))))))). ( -34.30)
>DroSim_CAF1 6328 111 + 1
AUUUGUAUAUAUAU-----GUUACGUAUAGUUAGUUGGCU----GGGCUGCUGACUCUCGUAACUUUGAAGUGUUGCGAACUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACA
.........(((((-----(...))))))....(((((((----..((.((..(...(((((((........)))))))..)..))((.(.....)))..........))..))))))). ( -30.90)
>DroEre_CAF1 7205 107 + 1
AUAUGUAG---------UAGUUACGUAUAUUUAGUUGGCU----GGGCUGCUGACUCUCGUAACUUUGAAGUGUUGCGAACUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACA
((((((((---------...)))))))).....(((((((----..((.((..(...(((((((........)))))))..)..))((.(.....)))..........))..))))))). ( -32.80)
>DroYak_CAF1 3858 104 + 1
AUAUGUA------------GUUACGUAUAGUUAGUUCGCU----GGGGUGCUGACUCUCGUAACUUUGAAGUGUUGCGAACUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACA
...(((.------------(((..((((((((((((((..----(((((((..(...(((((((........)))))))..)..)))).)))..))).))))).))))))..)))..))) ( -29.90)
>consensus
AUAUGUAU__AU_U_____GUUACGUAUAGUUAGUUGGCU____GGGCUGCUGACUCUCGUAACUUUGAAGUGUUGCGAACUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACA
(((((((..............))))))).....(((((((.........((..(...(((((((........)))))))..)..))(((...(((.......)))..)))..))))))). (-25.63 = -26.28 +   0.65)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,573,590 – 13,573,710
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.33
Mean single sequence MFE -30.84
Consensus MFE -30.56
Energy contribution -30.56
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.30
Structure conservation index 0.99
SVM decision value 0.35
SVM RNA-class probability 0.699582
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13573590 120 + 22407834
CUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACAAUGCCACACCGCAUAAUCAUAAUCCAGACCGCGUGGCUAAUUUGUUUAUAAUUUUCAUAACUUAACGUGUGCGCUAAGCG
((((((((((.((.((((.((..........))))))((((.(((((...((....((........))..)))))))....))))....................)).)))))))))).. ( -30.60)
>DroSec_CAF1 6817 120 + 1
CUUGGCGCACUUGAUGGCACUAAUUUAUGCCGGGCCAACAAUGCCACACCGCAUAAUCAUAAUCCAGACCGCGUGGCUAAUUUGUUUAUAAUUUUCAUAACUUAACGUGUGCGCUAAGCG
((((((((((.((.(((((........)))))....(((((.(((((...((....((........))..)))))))....)))))...................)).)))))))))).. ( -31.80)
>DroSim_CAF1 6399 120 + 1
CUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACAAUGCCACACCGCAUAAUCAUAAUCCAGACCGCGUGGCUAAUUUGUUUAUAAUUUUCAUAACUUAACGUGUGCGCUAAGCG
((((((((((.((.((((.((..........))))))((((.(((((...((....((........))..)))))))....))))....................)).)))))))))).. ( -30.60)
>DroEre_CAF1 7272 120 + 1
CUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACAAUGCCACACCGCAUAAUCAUAAUCCAGACCGCGUGGCUAAUUUGUUUAUAAUUUUCAUAACUUAACGUGUGCGCUAAGCG
((((((((((.((.((((.((..........))))))((((.(((((...((....((........))..)))))))....))))....................)).)))))))))).. ( -30.60)
>DroYak_CAF1 3922 120 + 1
CUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACAAUGCCACACCGCAUAAUCAUGAUCCAGACCGCGUGGCUAAUUUGUUUAUAAUUUUCAUAACUUAACGUGUGCGCUAAGCG
((((((((((.((.((((.((..........))))))((((.(((((...((....((........))..)))))))....))))....................)).)))))))))).. ( -30.60)
>consensus
CUUGGCGCACUUGAUGGCACUAAUUUAUGCAGGGCCAACAAUGCCACACCGCAUAAUCAUAAUCCAGACCGCGUGGCUAAUUUGUUUAUAAUUUUCAUAACUUAACGUGUGCGCUAAGCG
((((((((((.((.((((.((..........))))))((((.(((((...((....((........))..)))))))....))))....................)).)))))))))).. (-30.56 = -30.56 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,573,590 – 13,573,710
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.33
Mean single sequence MFE -36.90
Consensus MFE -35.92
Energy contribution -36.12
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.97
SVM decision value 2.59
SVM RNA-class probability 0.995565
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13573590 120 - 22407834
CGCUUAGCGCACACGUUAAGUUAUGAAAAUUAUAAACAAAUUAGCCACGCGGUCUGGAUUAUGAUUAUGCGGUGUGGCAUUGUUGGCCCUGCAUAAAUUAGUGCCAUCAAGUGCGCCAAG
..(((.((((((...............................(((((((.((...(((....)))..)).))))))).(((.((((.(((.......))).)))).))))))))).))) ( -36.60)
>DroSec_CAF1 6817 120 - 1
CGCUUAGCGCACACGUUAAGUUAUGAAAAUUAUAAACAAAUUAGCCACGCGGUCUGGAUUAUGAUUAUGCGGUGUGGCAUUGUUGGCCCGGCAUAAAUUAGUGCCAUCAAGUGCGCCAAG
..(((.((((((..(((((.((((((...))))))........(((((((.((...(((....)))..)).)))))))....)))))..(((((......))))).....)))))).))) ( -37.40)
>DroSim_CAF1 6399 120 - 1
CGCUUAGCGCACACGUUAAGUUAUGAAAAUUAUAAACAAAUUAGCCACGCGGUCUGGAUUAUGAUUAUGCGGUGUGGCAUUGUUGGCCCUGCAUAAAUUAGUGCCAUCAAGUGCGCCAAG
..(((.((((((...............................(((((((.((...(((....)))..)).))))))).(((.((((.(((.......))).)))).))))))))).))) ( -36.60)
>DroEre_CAF1 7272 120 - 1
CGCUUAGCGCACACGUUAAGUUAUGAAAAUUAUAAACAAAUUAGCCACGCGGUCUGGAUUAUGAUUAUGCGGUGUGGCAUUGUUGGCCCUGCAUAAAUUAGUGCCAUCAAGUGCGCCAAG
..(((.((((((...............................(((((((.((...(((....)))..)).))))))).(((.((((.(((.......))).)))).))))))))).))) ( -36.60)
>DroYak_CAF1 3922 120 - 1
CGCUUAGCGCACACGUUAAGUUAUGAAAAUUAUAAACAAAUUAGCCACGCGGUCUGGAUCAUGAUUAUGCGGUGUGGCAUUGUUGGCCCUGCAUAAAUUAGUGCCAUCAAGUGCGCCAAG
..(((.((((((...............................(((((((.((...(((....)))..)).))))))).(((.((((.(((.......))).)))).))))))))).))) ( -37.30)
>consensus
CGCUUAGCGCACACGUUAAGUUAUGAAAAUUAUAAACAAAUUAGCCACGCGGUCUGGAUUAUGAUUAUGCGGUGUGGCAUUGUUGGCCCUGCAUAAAUUAGUGCCAUCAAGUGCGCCAAG
..(((.((((((...............................(((((((.((...(((....)))..)).))))))).(((.((((.(((.......))).)))).))))))))).))) (-35.92 = -36.12 +   0.20)

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 11:26:28 2006