Locus 126

Sequence ID 4_DroMel_CAF1
Location 858,081 – 858,263
Length 182
Max. P 0.925160
window203 window204 window205 window206

overview

Window 3

Location 858,081 – 858,183
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 96.27
Mean single sequence MFE -29.55
Consensus MFE -26.31
Energy contribution -25.95
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -1.55
Structure conservation index 0.89
SVM decision value 1.09
SVM RNA-class probability 0.914133
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 858081 102 + 1281640
UUUGCUUGGUAAUGACAGUAUGAUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGACGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUU
.(((.((((((.((......(((.((.(..((((((((((...((((((.....))))))..)).))))))))..).)).)))....)).)))))))))... ( -27.80)
>DroSec_CAF1 38304 102 + 1
UUUGCUUGGUAAUGACAGUAUGAUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUU
.(((.((((((..(((((..(((.....)))..)))))(((..((((((.....))))))...((((((((.....)))))))).)))..)))))))))... ( -28.00)
>DroSim_CAF1 33399 102 + 1
UUUGCUUGGUAAUGACAGUAUGAUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUU
.(((.((((((..(((((..(((.....)))..)))))(((..((((((.....))))))...((((((((.....)))))))).)))..)))))))))... ( -28.00)
>DroEre_CAF1 38116 102 + 1
UUUGUUUGGUAAUGACUGUAUGAUGAGUUUGAGUCGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUU
.((((((((((((((((..............)))))))).)).((((((.....))))))...((((((((.....))))))))))))))............ ( -30.34)
>DroYak_CAF1 40240 102 + 1
UUUGUUUGGUAAUGACUGUAUGAUGAGUUUGAGUCGUUGUCCUUGCCGAAGUGGUUGGUGUAACUGAGGACUUUUGGUCUUCAGAGACAAUAUCAACGAUUU
....((((((((.(((...(((((........))))).))).))))))))((.((((((((..((((((((.....)))))))).....)))))))).)).. ( -33.60)
>consensus
UUUGCUUGGUAAUGACAGUAUGAUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUU
.(((.(((((((((((................)))))((((..((((((.....))))))...((((((((.....)))))))).)))).)))))))))... (-26.31 = -25.95 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 858,081 – 858,183
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 96.27
Mean single sequence MFE -19.71
Consensus MFE -18.14
Energy contribution -18.30
Covariance contribution 0.16
Combinations/Pair 1.05
Mean z-score -1.46
Structure conservation index 0.92
SVM decision value 1.17
SVM RNA-class probability 0.925160
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 858081 102 - 1281640
AAAUCGUUGAUAUUGUCUCUGAAGACCAGGAGUCGUCAGUUACGCCAACCACUUCGGCGAGGACAACAACUCAAACUCAUCAUACUGUCAUUACCAAGCAAA
.....((((...((((((((((.(((.....))).))))...((((.........)))).))))))))))................................ ( -20.00)
>DroSec_CAF1 38304 102 - 1
AAAUCGUUGAUAUUGUCUCUGAAGACCAGGAGUCCUCAGUUACGCCAACCACUUCGGCGAGGACAACAACUCAAACUCAUCAUACUGUCAUUACCAAGCAAA
.....((((...((((((((((.(((.....))).))))...((((.........)))).))))))))))................................ ( -20.00)
>DroSim_CAF1 33399 102 - 1
AAAUCGUUGAUAUUGUCUCUGAAGACCAGGAGUCCUCAGUUACGCCAACCACUUCGGCGAGGACAACAACUCAAACUCAUCAUACUGUCAUUACCAAGCAAA
.....((((...((((((((((.(((.....))).))))...((((.........)))).))))))))))................................ ( -20.00)
>DroEre_CAF1 38116 102 - 1
AAAUCGUUGAUAUUGUCUCUGAAGACCAGGAGUCCUCAGUUACGCCAACCACUUCGGCGAGGACAACGACUCAAACUCAUCAUACAGUCAUUACCAAACAAA
.....(((....((((((((((.(((.....))).))))...((((.........)))).)))))).((((..............)))).......)))... ( -20.24)
>DroYak_CAF1 40240 102 - 1
AAAUCGUUGAUAUUGUCUCUGAAGACCAAAAGUCCUCAGUUACACCAACCACUUCGGCAAGGACAACGACUCAAACUCAUCAUACAGUCAUUACCAAACAAA
...((((((....(((..((((.(((.....))).))))..)))((..((.....))...)).))))))................................. ( -18.30)
>consensus
AAAUCGUUGAUAUUGUCUCUGAAGACCAGGAGUCCUCAGUUACGCCAACCACUUCGGCGAGGACAACAACUCAAACUCAUCAUACUGUCAUUACCAAGCAAA
.....((((...((((((((((.(((.....))).))))...((((.........)))).))))))))))................................ (-18.14 = -18.30 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 858,103 – 858,223
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.61
Mean single sequence MFE -40.45
Consensus MFE -29.31
Energy contribution -31.23
Covariance contribution 1.92
Combinations/Pair 1.15
Mean z-score -1.96
Structure conservation index 0.72
SVM decision value 0.64
SVM RNA-class probability 0.808446
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 858103 120 + 1281640
AUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGACGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCG
.((((((..((((((((.....(((((.....)))))((..((((.(((.....))).))))..)).....))))))))..))).)))...((((((.(((......)))...)))))). ( -41.90)
>DroGri_CAF1 67216 90 + 1
CUGUGUCUGUGUGGCAACC-U--------------------------GCCCAUCAUCUUC---CACAAUGUCCACAAUUUGCACAUCGGGCGCCAGCAGCGAGGCAACAUCAAAUUGCCU
..(((((((((((.(((..-(--------------------------(.....(((....---....)))....))..))))))).)))))))........((((((.......)))))) ( -20.90)
>DroSec_CAF1 38326 120 + 1
AUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACGUCGGGUGCCAGUAGCGAAGCCACAUCAAACUGGCG
.((((((..((((((((.....(((((.....)))))((..((((((((.....))))))))..)).....))))))))..))).)))...((((((...((.......))..)))))). ( -43.00)
>DroSim_CAF1 33421 120 + 1
AUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACGUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCG
.((((((..((((((((.....(((((.....)))))((..((((((((.....))))))))..)).....))))))))..))).)))...((((((.(((......)))...)))))). ( -45.70)
>DroEre_CAF1 38138 120 + 1
AUGAGUUUGAGUCGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCG
.((((((..((((((((.....(((((.....)))))((..((((((((.....))))))))..)).....))))))))..))).)))...((((((.(((......)))...)))))). ( -47.80)
>DroYak_CAF1 40262 120 + 1
AUGAGUUUGAGUCGUUGUCCUUGCCGAAGUGGUUGGUGUAACUGAGGACUUUUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGUGAAGCCACGUCAAAUUGGCG
.((((((..((((((((.((..(((.....))).))(((..((((((((.....))))))))..)))....))))))))..))).)))...((((((.(((....))).....)))))). ( -43.40)
>consensus
AUGAGUUUGAGUUGUUGUCCUCGCCGAAGUGGUUGGCGUAACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCG
....(((..((((((((....((((((.....))))))...((((((((.....)))))))).........))))))))..))).......((((((...((.......))..)))))). (-29.31 = -31.23 +   1.92)

alignment

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secondary structure

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dotplot

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Window 6

Location 858,143 – 858,263
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 87.28
Mean single sequence MFE -45.12
Consensus MFE -34.84
Energy contribution -36.82
Covariance contribution 1.97
Combinations/Pair 1.14
Mean z-score -3.56
Structure conservation index 0.77
SVM decision value 1.09
SVM RNA-class probability 0.914142
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 858143 120 + 1281640
ACUGACGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCGCUUCCGCGUCUGCGAAAACAUAUUCGCGAUUGUUGUUGUC
.((((.(((.....))).)))).(((((...((((((((.((((..(((((((((((.(((......)))...))))))))..))).))))(((((......)))))))))))))))))) ( -44.60)
>DroGri_CAF1 67236 110 + 1
-------GCCCAUCAUCUUC---CACAAUGUCCACAAUUUGCACAUCGGGCGCCAGCAGCGAGGCAACAUCAAAUUGCCUUUUGCGCGUCUGCGAAUAAAGAUUCGCAAUUGUUGUCGUC
-------.............---....(((.(.((((((........((((((..((((.(((((((.......)))))))))))))))))((((((....)))))))))))).).))). ( -31.40)
>DroSec_CAF1 38366 120 + 1
ACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACGUCGGGUGCCAGUAGCGAAGCCACAUCAAACUGGCGCUUUCGCGUCUGCGAAAACAUAUUCGCGAUAGUUGUUGUC
.((((((((.....)))))))).(((((...((((.....((((((.((((((((((...((.......))..))))))))))..))))))(((((......)))))....))))))))) ( -46.00)
>DroSim_CAF1 33461 120 + 1
ACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACGUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCGCUUUCGCGUCUGCGAAAACAUAUUCGCGAUAGUUGUUGUC
.((((((((.....)))))))).(((((...((((.....((((((.((((((((((.(((......)))...))))))))))..))))))(((((......)))))....))))))))) ( -48.70)
>DroEre_CAF1 38178 120 + 1
ACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCGCUUCCGUGUCUGCGAAAACAUAUUCGCGAUUGUUGUUGUC
.((((((((.....)))))))).(((((...((((((((.(((((.(((((((((((.(((......)))...))))))))..))))))))(((((......)))))))))))))))))) ( -51.10)
>DroYak_CAF1 40302 120 + 1
ACUGAGGACUUUUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGUGAAGCCACGUCAAAUUGGCGCUUCCGUGUCUGCGAAAACAUAUUCGCGAUUGUUGUUGUC
.((((((((.....)))))))).(((((...((((((((.(((((.(((((((((((.(((....))).....))))))))..))))))))(((((......)))))))))))))))))) ( -48.90)
>consensus
ACUGAGGACUCCUGGUCUUCAGAGACAAUAUCAACGAUUUGGACAUCGGGUGCCAGUAGCGAAGCCACGUCAAACUGGCGCUUCCGCGUCUGCGAAAACAUAUUCGCGAUUGUUGUUGUC
.((((((((.....)))))))).(((((...((((((((.((((((.((((((((((...((.......))..))))))))))..))))))(((((......)))))))))))))))))) (-34.84 = -36.82 +   1.97)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:02 2006