Locus 7314

Sequence ID 3R_DroMel_CAF1
Location 19,320,845 – 19,320,953
Length 108
Max. P 0.994610
window11829 window11830 window11831 window11832

overview

Window 9

Location 19,320,845 – 19,320,939
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.90
Mean single sequence MFE -26.17
Consensus MFE -21.93
Energy contribution -22.30
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -3.37
Structure conservation index 0.84
SVM decision value 1.68
SVM RNA-class probability 0.971873
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19320845 94 + 27905053
--------------------------CAAUGGCAGACAGUUUCCAACUAAUUAGGCGUGGUGCCUUUUAAUCAAAACGAUUAAAAUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAA
--------------------------...(((.(((...))))))....(((((((((((.((.((((((((.....)))))))).)).................))))))))))).... ( -24.17)
>DroPse_CAF1 135326 120 + 1
GUACAGGGGACAGCUAACAGAGGACAUAUAGGCAGACAGUUUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAA
.....((..((..((..(............)..))...))..)).....(((((((((((.(((((((((((.....)))))))).)))................))))))))))).... ( -31.23)
>DroWil_CAF1 167550 84 + 1
------------------------------------CAAUUUCCAACUAAUUAGGCUUGCUGGCUUUUAAUCAAAACGAUUAAAGUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAA
------------------------------------.............(((((((..(..(((((((((((.....)))))))).)))..)(((.........)))..))))))).... ( -18.80)
>DroMoj_CAF1 133503 86 + 1
----------------------------------GAAAACUUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCCGACAAUAUUUUUCCACGCCUAAUCAAA
----------------------------------...............(((((((((((.(((((((((((.....)))))))).)))................))))))))))).... ( -24.73)
>DroAna_CAF1 120925 91 + 1
-----------------------------AGGCACACAAUUUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAA
-----------------------------....................(((((((((((.(((((((((((.....)))))))).)))................))))))))))).... ( -24.73)
>DroPer_CAF1 135555 120 + 1
GGACAGGGGACAGGGGACAGAGGACAUAUAGGCAGACAGUUUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAA
.....((..((.(....)............(.....).))..)).....(((((((((((.(((((((((((.....)))))))).)))................))))))))))).... ( -33.33)
>consensus
_____________________________AGGCAGACAAUUUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAA
.................................................(((((((((((.(((((((((((.....)))))))).)))................))))))))))).... (-21.93 = -22.30 +   0.36)

alignment

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secondary structure

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Window 0

Location 19,320,845 – 19,320,939
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.90
Mean single sequence MFE -26.70
Consensus MFE -23.98
Energy contribution -24.48
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.90
SVM decision value 1.70
SVM RNA-class probability 0.972765
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19320845 94 - 27905053
UUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGGCACCACGCCUAAUUAGUUGGAAACUGUCUGCCAUUG--------------------------
.((((((((((((((.......((....))..((.((((((((.....)))))))).)).))))))))))))))..(....)............-------------------------- ( -28.90)
>DroPse_CAF1 135326 120 - 1
UUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAAACUGUCUGCCUAUAUGUCCUCUGUUAGCUGUCCCCUGUAC
.((((((((((((((............(....)..((((((((.....))))))))....))))))))))))))..((..((.((..((.............))..)).))..))..... ( -29.52)
>DroWil_CAF1 167550 84 - 1
UUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCACUUUAAUCGUUUUGAUUAAAAGCCAGCAAGCCUAAUUAGUUGGAAAUUG------------------------------------
.((((((((((.(((.........((.(....).))(((((((.....)))))))..)))....))))))))))..........------------------------------------ ( -19.80)
>DroMoj_CAF1 133503 86 - 1
UUUGAUUAGGCGUGGAAAAAUAUUGUCGGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAAGUUUUC----------------------------------
.((((((((((((((........(((......)))((((((((.....))))))))....))))))))))))))............---------------------------------- ( -26.50)
>DroAna_CAF1 120925 91 - 1
UUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAAAUUGUGUGCCU-----------------------------
.((((((((((((((............(....)..((((((((.....))))))))....)))))))))))))).................----------------------------- ( -27.10)
>DroPer_CAF1 135555 120 - 1
UUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAAACUGUCUGCCUAUAUGUCCUCUGUCCCCUGUCCCCUGUCC
.((((((((((((((............(....)..((((((((.....))))))))....))))))))))))))..(((...(((......)))..)))..................... ( -28.40)
>consensus
UUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAAACUGUCUGCCU_____________________________
.((((((((((((((........(((......)))((((((((.....))))))))....)))))))))))))).............................................. (-23.98 = -24.48 +   0.50)

alignment

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secondary structure

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Window 1

Location 19,320,859 – 19,320,953
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.56
Mean single sequence MFE -24.18
Consensus MFE -19.78
Energy contribution -20.48
Covariance contribution 0.70
Combinations/Pair 1.05
Mean z-score -3.55
Structure conservation index 0.82
SVM decision value 1.65
SVM RNA-class probability 0.970101
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19320859 94 + 27905053
UUCCAACUAAUUAGGCGUGGUGCCUUUUAAUCAAAACGAUUAAAAUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAAGACUUUAUGCCAUU--------------------------
.........(((((((((((.((.((((((((.....)))))))).)).................)))))))))))..................-------------------------- ( -23.87)
>DroVir_CAF1 132531 94 + 1
UUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCCGACAAUAUUUUUCCACGCCUAAUCAAAGACUUUAUGCCAUU--------------------------
.........(((((((((((.(((((((((((.....)))))))).)))................)))))))))))..................-------------------------- ( -24.73)
>DroGri_CAF1 126240 94 + 1
UUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCCGACAAUAUUUUUCGACGCCUAAUCAAAGACUUAAUACCAUU--------------------------
.........(((((((((((.(((((((((((.....)))))))).)))..))((.........)).)))))))))..................-------------------------- ( -21.90)
>DroSim_CAF1 117945 94 + 1
UUCCAACUAAUUAGGCGUGGUGCCUUUUAAUCAAAACGAUUAAAAUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAAGACUUUAUGCCAUU--------------------------
.........(((((((((((.((.((((((((.....)))))))).)).................)))))))))))..................-------------------------- ( -23.87)
>DroWil_CAF1 167554 120 + 1
UUCCAACUAAUUAGGCUUGCUGGCUUUUAAUCAAAACGAUUAAAGUGCUUUCGGACAAUAUUUUUCCACGCCUAAUCAAAGAGUUUCGGUUUUUUCGAUGUGGUUGUUGUUGUAGUUUUA
...(((((((((((((..(..(((((((((((.....)))))))).)))..)(((.........)))..))))))).........((((.....))))..)))))).............. ( -26.00)
>DroMoj_CAF1 133509 94 + 1
UUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCCGACAAUAUUUUUCCACGCCUAAUCAAAGACUUUAUGCCAUU--------------------------
.........(((((((((((.(((((((((((.....)))))))).)))................)))))))))))..................-------------------------- ( -24.73)
>consensus
UUCCAACUAAUUAGGCGUGGUGGCUUUUAAUCAAAACGAUUAAAAUGCUUUCCGACAAUAUUUUUCCACGCCUAAUCAAAGACUUUAUGCCAUU__________________________
.........(((((((((((.(((((((((((.....)))))))).)))................)))))))))))............................................ (-19.78 = -20.48 +   0.70)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,320,859 – 19,320,953
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.56
Mean single sequence MFE -26.82
Consensus MFE -23.80
Energy contribution -24.47
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.39
Structure conservation index 0.89
SVM decision value 2.49
SVM RNA-class probability 0.994610
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19320859 94 - 27905053
--------------------------AAUGGCAUAAAGUCUUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGGCACCACGCCUAAUUAGUUGGAA
--------------------------...(((.....))).((((((((((((((.......((....))..((.((((((((.....)))))))).)).))))))))))))))...... ( -29.00)
>DroVir_CAF1 132531 94 - 1
--------------------------AAUGGCAUAAAGUCUUUGAUUAGGCGUGGAAAAAUAUUGUCGGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAA
--------------------------...(((.....))).((((((((((((((........(((......)))((((((((.....))))))))....))))))))))))))...... ( -27.60)
>DroGri_CAF1 126240 94 - 1
--------------------------AAUGGUAUUAAGUCUUUGAUUAGGCGUCGAAAAAUAUUGUCGGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAA
--------------------------............((((((((((((((((((......)))..((...((.((((((((.....))))))))))..))))))))))))))..))). ( -23.00)
>DroSim_CAF1 117945 94 - 1
--------------------------AAUGGCAUAAAGUCUUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGGCACCACGCCUAAUUAGUUGGAA
--------------------------...(((.....))).((((((((((((((.......((....))..((.((((((((.....)))))))).)).))))))))))))))...... ( -29.00)
>DroWil_CAF1 167554 120 - 1
UAAAACUACAACAACAACCACAUCGAAAAAACCGAAACUCUUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCACUUUAAUCGUUUUGAUUAAAAGCCAGCAAGCCUAAUUAGUUGGAA
...........((((.......(((.......))).......(((((((((.(((.........((.(....).))(((((((.....)))))))..)))....)))))))))))))... ( -24.70)
>DroMoj_CAF1 133509 94 - 1
--------------------------AAUGGCAUAAAGUCUUUGAUUAGGCGUGGAAAAAUAUUGUCGGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAA
--------------------------...(((.....))).((((((((((((((........(((......)))((((((((.....))))))))....))))))))))))))...... ( -27.60)
>consensus
__________________________AAUGGCAUAAAGUCUUUGAUUAGGCGUGGAAAAAUAUUGUCCGAAAGCAUUUUAAUCGUUUUGAUUAAAAGCCACCACGCCUAAUUAGUUGGAA
......................................(((((((((((((((((........(((......)))((((((((.....))))))))....))))))))))))))..))). (-23.80 = -24.47 +   0.67)

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 12:42:54 2006