Locus 234

Sequence ID 2R_DroMel_CAF1
Location 1,587,042 – 1,587,202
Length 160
Max. P 0.838984
window511 window512 window513

overview

Window 1

Location 1,587,042 – 1,587,162
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.28
Mean single sequence MFE -46.93
Consensus MFE -27.67
Energy contribution -28.53
Covariance contribution 0.87
Combinations/Pair 1.31
Mean z-score -1.92
Structure conservation index 0.59
SVM decision value 0.74
SVM RNA-class probability 0.838984
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1587042 120 + 20766785
CGCAAGUCACAGCCAGCACGCACAGCAACUUGCUGAGUCUUGUUAUCAAACUGAAAGUCGCAGUUGGGCUGACAAGCAUGCUCCAUCAUGCAGGCCUGCCGGAACAACCCGCUGAGUUCC
.(((.(((.(((((((((.((.((((.....)))).))..))))....(((((.......))))).)))))....(((((......))))).))).))).(((((..........))))) ( -37.30)
>DroVir_CAF1 794 120 + 1
UUCAUAUCGCAGCCGGCGCGUACCGCAAUGCGCUGCGUGGCGGAAUCGAACUGAAAGUAGCAGUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGCCGAAAGAGUCCGCUCAGCUCC
((((..(((...(((.((((((.(((...))).)))))).)))...)))..))))......((((((((.(((((((.(((........))).)))))))((.....)).)))))))).. ( -54.60)
>DroGri_CAF1 809 120 + 1
UUCAGAUCGCAGCCGGCGCGCACAGCAAUCCGUUGCGUGGCCGCAUCGAAUUGAAAGUAGCAAUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGCCGAAAGACGCCGCUCAGCUCC
(((((.(((..((.(((.(((.((((.....)))).))))))))..))).)))))..........((((((((((((.(((........))).))))))(....)........)))))). ( -49.00)
>DroWil_CAF1 809 120 + 1
UUCAAAUUGCAACCGGCUCGCACUGCAAUCUGCUGGGUGGCCGCAUCGAAUGUGAAAUAACAAUUCGGUUGACAGGCAUGCUCCAUCAUGCAAGCCUGCCGGAAUAGGCCACUCAAUUCC
..((.((((((....(....)..)))))).)).(((((((((..(((((((((......)).)))))))((.(((((.(((........))).))))).)).....)))))))))..... ( -41.70)
>DroMoj_CAF1 791 120 + 1
UUCAGGUCGCAGCCCGCACGCACCGCAAUGCGUUGUGUGGCUGCAUCGAACUGGAAGUAGCAAUUUGGCUGGCAGGCGUGCUCCAUCAUACAGGCUUGCCGGAAGAGACCGCUCAACUCU
....((((((((((((((((((......)))).)))).)))))).(((((.((.......)).)))))(((((((((.((..........)).)))))))))....)))).......... ( -48.20)
>DroAna_CAF1 806 120 + 1
UGCAGGUCACACCCUGCCCGCACAGUGAUCUGCUGGGUGAAGGCGUCGAACUGGAAGUAGCAGUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGUCGGAACAGACCACUCAGCUCC
.(((((((((....((....))..))))))))).((((..((..(((.(((((.......)))))(..(((((((((.(((........))).)))))))))..).)))..))..)))). ( -50.80)
>consensus
UUCAGAUCGCAGCCGGCACGCACAGCAAUCCGCUGCGUGGCGGCAUCGAACUGAAAGUAGCAAUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGCCGGAAGAGACCGCUCAGCUCC
...............((.......)).....((((.((((.....((.(((((.......))))).))(((((((((.(((........))).)))))))))......)))).))))... (-27.67 = -28.53 +   0.87)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,587,082 – 1,587,202
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.39
Mean single sequence MFE -41.45
Consensus MFE -27.72
Energy contribution -28.80
Covariance contribution 1.09
Combinations/Pair 1.34
Mean z-score -1.56
Structure conservation index 0.67
SVM decision value 0.33
SVM RNA-class probability 0.693061
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1587082 120 + 20766785
UGUUAUCAAACUGAAAGUCGCAGUUGGGCUGACAAGCAUGCUCCAUCAUGCAGGCCUGCCGGAACAACCCGCUGAGUUCCACGCCACUCGGGAGUUCGAUAACCAUAAAGUUUGUUUCGA
.((((((.((((..........((((..(((.((.((.(((........))).)).)).)))..))))...((((((........)))))).)))).))))))................. ( -31.40)
>DroVir_CAF1 834 120 + 1
CGGAAUCGAACUGAAAGUAGCAGUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGCCGAAAGAGUCCGCUCAGCUCCACACCCGUCGCCAGCUCGAUGACCAUGUAGUUGGUCUCUA
.((((((((.(((...(..((.(((((((((((((((.(((........))).)))))))....(((....)))))).))).))..))..)))).)))))(((((......)))))))). ( -49.50)
>DroGri_CAF1 849 120 + 1
CCGCAUCGAAUUGAAAGUAGCAAUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGCCGAAAGACGCCGCUCAGCUCCACGCCCGUUGCUAGCUCGAUGACCAUGUAGUUAGUCUCAA
..((((.(.(((((...(((((((.((((((((((((.(((........))).))))))))...((.((......))))...)))))))))))..)))))..).))))............ ( -44.50)
>DroWil_CAF1 849 120 + 1
CCGCAUCGAAUGUGAAAUAACAAUUCGGUUGACAGGCAUGCUCCAUCAUGCAAGCCUGCCGGAAUAGGCCACUCAAUUCCACUCCAGUGGGCAAUUCGAUGACCAUGUAAUUGGUCUCAA
....(((((((............(((((....(((((.(((........))).))))))))))...(.(((((............))))).).)))))))(((((......))))).... ( -37.90)
>DroMoj_CAF1 831 120 + 1
CUGCAUCGAACUGGAAGUAGCAAUUUGGCUGGCAGGCGUGCUCCAUCAUACAGGCUUGCCGGAAGAGACCGCUCAACUCUAUGCCCGUGGCCAGCUCGAUGACCAUAUAGUUGGUCUCAA
....(((((.((((.....(((......(((((((((.((..........)).)))))))))..(((....))).......)))......)))).)))))(((((......))))).... ( -41.10)
>DroAna_CAF1 846 120 + 1
AGGCGUCGAACUGGAAGUAGCAGUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGUCGGAACAGACCACUCAGCUCCACUCCCGAAGGCAGCUCGAUGACCAUAUAGUUGGUUUCAA
.((((((....(((.(((.(.(((((((..(((((((.(((........))).)))))))((......)).)))))))).))).)))..))).))).((.(((((......))))))).. ( -44.30)
>consensus
CGGCAUCGAACUGAAAGUAGCAAUUGGGCUGGCAGGCGUGCUCCAUCAUGCAGGCCUGCCGGAAGAGACCGCUCAGCUCCACGCCCGUCGCCAGCUCGAUGACCAUAUAGUUGGUCUCAA
....(((((.(((.........((.((((((((((((.(((........))).)))))))((......))....))))).)).........))).)))))(((((......))))).... (-27.72 = -28.80 +   1.09)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,587,082 – 1,587,202
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.39
Mean single sequence MFE -44.28
Consensus MFE -31.71
Energy contribution -30.64
Covariance contribution -1.07
Combinations/Pair 1.47
Mean z-score -1.74
Structure conservation index 0.72
SVM decision value 0.68
SVM RNA-class probability 0.820907
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1587082 120 - 20766785
UCGAAACAAACUUUAUGGUUAUCGAACUCCCGAGUGGCGUGGAACUCAGCGGGUUGUUCCGGCAGGCCUGCAUGAUGGAGCAUGCUUGUCAGCCCAACUGCGACUUUCAGUUUGAUAACA
.................(((((((((((...((((.((..(((((..........)))))(((.(((..(((((......)))))..))).))).....)).))))..))))))))))). ( -41.70)
>DroVir_CAF1 834 120 - 1
UAGAGACCAACUACAUGGUCAUCGAGCUGGCGACGGGUGUGGAGCUGAGCGGACUCUUUCGGCAGGCCUGCAUGAUGGAGCACGCCUGCCAGCCCAACUGCUACUUUCAGUUCGAUUCCG
....(((((......)))))((((((((((.....(((.(((.((((((....)))....(((((((.(((........))).)))))))))))))...)))....)))))))))).... ( -49.60)
>DroGri_CAF1 849 120 - 1
UUGAGACUAACUACAUGGUCAUCGAGCUAGCAACGGGCGUGGAGCUGAGCGGCGUCUUUCGGCAGGCCUGCAUGAUGGAGCACGCCUGCCAGCCCAAUUGCUACUUUCAAUUCGAUGCGG
(((((((((......)))))...(((.((((((.(((((.((((((....))).)))..)(((((((.(((........))).))))))).))))..))))))))))))).......... ( -45.40)
>DroWil_CAF1 849 120 - 1
UUGAGACCAAUUACAUGGUCAUCGAAUUGCCCACUGGAGUGGAAUUGAGUGGCCUAUUCCGGCAGGCUUGCAUGAUGGAGCAUGCCUGUCAACCGAAUUGUUAUUUCACAUUCGAUGCGG
(((((((((......))))).))))..(((((((....)))).((((((((.........(((((((.(((........))).)))))))....(((.......))).))))))))))). ( -40.90)
>DroMoj_CAF1 831 120 - 1
UUGAGACCAACUAUAUGGUCAUCGAGCUGGCCACGGGCAUAGAGUUGAGCGGUCUCUUCCGGCAAGCCUGUAUGAUGGAGCACGCCUGCCAGCCAAAUUGCUACUUCCAGUUCGAUGCAG
....(((((......)))))((((((((((.....((((.....(((.((((......))((((.((.(((........))).)).)))).)))))..))))....)))))))))).... ( -44.10)
>DroAna_CAF1 846 120 - 1
UUGAAACCAACUAUAUGGUCAUCGAGCUGCCUUCGGGAGUGGAGCUGAGUGGUCUGUUCCGACAGGCCUGCAUGAUGGAGCACGCCUGCCAGCCCAACUGCUACUUCCAGUUCGACGCCU
................(((..((((((((((....))(((((.((((.(((((.(((((((.((.(....).)).))))))).))).)))))))).)))........)))))))).))). ( -44.00)
>consensus
UUGAGACCAACUACAUGGUCAUCGAGCUGCCCACGGGCGUGGAGCUGAGCGGCCUCUUCCGGCAGGCCUGCAUGAUGGAGCACGCCUGCCAGCCCAACUGCUACUUCCAGUUCGAUGCCG
....(((((......)))))((((((((......(((.((((......((((......))(((((((.(((........))).))))))).)).......)))).))))))))))).... (-31.71 = -30.64 +  -1.07)

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 09:33:10 2006