Locus 1293

Sequence ID 2L_DroMel_CAF1
Location 3,423,018 – 3,423,183
Length 165
Max. P 0.997787
window2108 window2109 window2110 window2111 window2112 window2113

overview

Window 8

Location 3,423,018 – 3,423,112
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 89.89
Mean single sequence MFE -31.75
Consensus MFE -25.98
Energy contribution -25.60
Covariance contribution -0.38
Combinations/Pair 1.15
Mean z-score -2.36
Structure conservation index 0.82
SVM decision value 1.38
SVM RNA-class probability 0.947770
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423018 94 + 22407834
GCCGUAUAAGAGUCGCGUUCGAACUUCGAACGCAACGUGCUUGCUGCUCGUCUACGAGUUCGAACCGAACAACAACGGCAUCGAAUCGAACUCA
...(((........(((((((.....))))))).(((.((.....)).))).)))((((((((..(((.(......)...)))..)))))))). ( -31.50)
>DroSec_CAF1 11894 94 + 1
GUCGUAUAAGAGUCGCGUUCGAACUUCGAACGCAACGUGCUCGAUGCUCGUCUUCGAGUUCGAAGCGAACAACAACGGUAUUGAAUCGAACUCG
.........((((.(((((((.....)))))))..(((..((((.(((((....))))))))).)))........((((.....)))).)))). ( -31.20)
>DroSim_CAF1 12081 94 + 1
GUCGUAUAAGAGUCGCGUUCGAACUUCGAACGCAACAUGCUGGACGUUCGUCUUCGAGUUCGAAGCGAACAACAACGGUAUUGAAUCGAACUCG
.........((((((((((((.....)))))))...((((((...(((((.(((((....)))))))))).....))))))......).)))). ( -34.40)
>DroEre_CAF1 12129 94 + 1
GUCGUAUAAGAGUCGCGUUCGAACUUCGAACGCAACAUGUUGGACGCUCGUCUUCGAGUUCGAACCGAACCACUUCGGCAUUGCACCGAACUCG
.........((((((.(((((((((.((((..(((....)))(((....))))))))))))))))))).....(((((.......)))))))). ( -29.90)
>consensus
GUCGUAUAAGAGUCGCGUUCGAACUUCGAACGCAACAUGCUGGACGCUCGUCUUCGAGUUCGAACCGAACAACAACGGCAUUGAAUCGAACUCG
.........((((((((((((.....)))))))..(((((((.....(((....)))(((((...))))).....))))).))....).)))). (-25.98 = -25.60 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,423,018 – 3,423,112
Length 94
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 89.89
Mean single sequence MFE -36.90
Consensus MFE -30.10
Energy contribution -29.98
Covariance contribution -0.13
Combinations/Pair 1.13
Mean z-score -3.47
Structure conservation index 0.82
SVM decision value 2.01
SVM RNA-class probability 0.985503
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423018 94 - 22407834
UGAGUUCGAUUCGAUGCCGUUGUUGUUCGGUUCGAACUCGUAGACGAGCAGCAAGCACGUUGCGUUCGAAGUUCGAACGCGACUCUUAUACGGC
...............((((((((((((((...((....))....))))))))).....((((((((((.....))))))))))......))))) ( -36.80)
>DroSec_CAF1 11894 94 - 1
CGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCGAAGACGAGCAUCGAGCACGUUGCGUUCGAAGUUCGAACGCGACUCUUAUACGAC
((.((((((..((((...)))).(((((((((((....))))).))))))))))))..((((((((((.....)))))))))).......)).. ( -38.20)
>DroSim_CAF1 12081 94 - 1
CGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCGAAGACGAACGUCCAGCAUGUUGCGUUCGAAGUUCGAACGCGACUCUUAUACGAC
.....(((..........((((.(((((((((((....))))).))))))..))))..((((((((((.....)))))))))).......))). ( -36.20)
>DroEre_CAF1 12129 94 - 1
CGAGUUCGGUGCAAUGCCGAAGUGGUUCGGUUCGAACUCGAAGACGAGCGUCCAACAUGUUGCGUUCGAAGUUCGAACGCGACUCUUAUACGAC
(((((((((......((((((....)))))))))))))))..(((....)))......((((((((((.....))))))))))........... ( -36.40)
>consensus
CGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCGAAGACGAGCAUCCAGCACGUUGCGUUCGAAGUUCGAACGCGACUCUUAUACGAC
(((((((((......((((........)))))))))))))..................((((((((((.....))))))))))........... (-30.10 = -29.98 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,423,041 – 3,423,143
Length 102
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 84.66
Mean single sequence MFE -33.17
Consensus MFE -27.33
Energy contribution -27.82
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -3.47
Structure conservation index 0.82
SVM decision value 2.93
SVM RNA-class probability 0.997787
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423041 102 + 22407834
CUUCGAACGCAACGUGCUUGCUGCUCGUCUACGAGUUCGAACCGAACAACAACGGCAUCGAAUCGAACUCAAAGAUAAAAAGUUGUAAGGGAAU---------UUCUGUUA
........((((((.((.....)).)((((..((((((((..(((.(......)...)))..))))))))..)))).....)))))((.((...---------..)).)). ( -23.50)
>DroSec_CAF1 11917 102 + 1
CUUCGAACGCAACGUGCUCGAUGCUCGUCUUCGAGUUCGAAGCGAACAACAACGGUAUUGAAUCGAACUCGAAGAUAAGAAGUUGUAACAGAAU---------UUCUGUUA
((((....(((.((....)).)))..((((((((((((((..(((((.......)).)))..))))))))))))))..))))...((((((...---------..)))))) ( -36.00)
>DroSim_CAF1 12104 102 + 1
CUUCGAACGCAACAUGCUGGACGUUCGUCUUCGAGUUCGAAGCGAACAACAACGGUAUUGAAUCGAACUCGAAGAUAAGAAGUUGUAACAGAAU---------UUCUGUUA
(((((((((...(.....)..)))))((((((((((((((..(((((.......)).)))..))))))))))))))..))))...((((((...---------..)))))) ( -36.70)
>DroEre_CAF1 12152 111 + 1
CUUCGAACGCAACAUGUUGGACGCUCGUCUUCGAGUUCGAACCGAACCACUUCGGCAUUGCACCGAACUCGAAGAUAACAAGUUUUAACAGAACUUUUUCUAGUUCUGUUA
..((.((((.....)))).)).....(((((((((((((..(((((....)))))........))))))))))))).........((((((((((......)))))))))) ( -36.50)
>consensus
CUUCGAACGCAACAUGCUGGACGCUCGUCUUCGAGUUCGAACCGAACAACAACGGCAUUGAAUCGAACUCGAAGAUAAGAAGUUGUAACAGAAU_________UUCUGUUA
........(((((..((.....))..((((((((((((((..(((.(......)...)))..)))))))))))))).....)))))(((((((..........))))))). (-27.33 = -27.82 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,423,041 – 3,423,143
Length 102
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 84.66
Mean single sequence MFE -36.05
Consensus MFE -28.46
Energy contribution -29.65
Covariance contribution 1.19
Combinations/Pair 1.12
Mean z-score -3.95
Structure conservation index 0.79
SVM decision value 2.92
SVM RNA-class probability 0.997750
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423041 102 - 22407834
UAACAGAA---------AUUCCCUUACAACUUUUUAUCUUUGAGUUCGAUUCGAUGCCGUUGUUGUUCGGUUCGAACUCGUAGACGAGCAGCAAGCACGUUGCGUUCGAAG
........---------...................(((.(((((((((..(((.((....))...)))..))))))))).)))(((((.((((.....)))))))))... ( -28.10)
>DroSec_CAF1 11917 102 - 1
UAACAGAA---------AUUCUGUUACAACUUCUUAUCUUCGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCGAAGACGAGCAUCGAGCACGUUGCGUUCGAAG
((((((..---------...))))))......((..(((((((((((((..(((((....)))))......)))))))))))))..))..((((((.......)))))).. ( -35.90)
>DroSim_CAF1 12104 102 - 1
UAACAGAA---------AUUCUGUUACAACUUCUUAUCUUCGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCGAAGACGAACGUCCAGCAUGUUGCGUUCGAAG
((((((..---------...))))))...((((...(((((((((((((..(((((....)))))......))))))))))))).((((((..........)))))))))) ( -35.50)
>DroEre_CAF1 12152 111 - 1
UAACAGAACUAGAAAAAGUUCUGUUAAAACUUGUUAUCUUCGAGUUCGGUGCAAUGCCGAAGUGGUUCGGUUCGAACUCGAAGACGAGCGUCCAACAUGUUGCGUUCGAAG
((((((((((......))))))))))..........(((((((((((((......((((((....)))))))))))))))))))((((((..(((....)))))))))... ( -44.70)
>consensus
UAACAGAA_________AUUCUGUUACAACUUCUUAUCUUCGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCGAAGACGAGCAUCCAGCACGUUGCGUUCGAAG
((((((((..........))))))))..........(((((((((((((......((((........)))))))))))))))))(((((((..........)))))))... (-28.46 = -29.65 +   1.19)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,423,072 – 3,423,183
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.63
Mean single sequence MFE -29.80
Consensus MFE -21.16
Energy contribution -21.44
Covariance contribution 0.28
Combinations/Pair 1.15
Mean z-score -3.13
Structure conservation index 0.71
SVM decision value 2.31
SVM RNA-class probability 0.992161
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423072 111 + 22407834
CGAGUUCGAACCGAACAACAACGGCAUCGAAUCGAACUCAAAGAUAAAAAGUUGUAAGGGAAU---------UUCUGUUAUUUGUCUAAUUGGAAUAGAAAUUGGAAUUUAUCUAAUUUA
.((((((((..(((.(......)...)))..))))))))..(((((((.....((((.((...---------..)).))))...(((((((........))))))).)))))))...... ( -25.90)
>DroSec_CAF1 11948 111 + 1
CGAGUUCGAAGCGAACAACAACGGUAUUGAAUCGAACUCGAAGAUAAGAAGUUGUAACAGAAU---------UUCUGUUAUUUGUCUAAUUGGAAUAGAAAUUGAAAUUGAACAGAUUUA
(((((((((..(((((.......)).)))..)))))))))..............((((((...---------..))))))(((((.(((((..(((....)))..))))).))))).... ( -25.10)
>DroSim_CAF1 12135 111 + 1
CGAGUUCGAAGCGAACAACAACGGUAUUGAAUCGAACUCGAAGAUAAGAAGUUGUAACAGAAU---------UUCUGUUAUUUGUCCAAUUGGAAUAUAAAUUGGAAUUGAACUAAUUUA
(((((((((..(((((.......)).)))..))))))))).........(((((((((((...---------..)))))))...(((((((........)))))))....))))...... ( -30.10)
>DroEre_CAF1 12183 120 + 1
CGAGUUCGAACCGAACCACUUCGGCAUUGCACCGAACUCGAAGAUAACAAGUUUUAACAGAACUUUUUCUAGUUCUGUUAUUUGUCCAAUUGGAAUAGCAGUUGGAAUCGAACUUAUUUA
((((((((..(((((....)))))........))))))))........((((((((((((((((......))))))))))....((((((((......))))))))...))))))..... ( -38.40)
>DroYak_CAF1 13342 120 + 1
CGAGUUCGAAGCGAACCACUCCGGCAUUGAAUCAAACUCGAAGAUAAAAAGUUUUAACAGAACUUUUUCUAGUUCUGUUAUCUGUCUAAUUGGAAUGUAAAUUGGAAUUGAACUAAGUUA
((((((.((..(((.((.....))..)))..)).)))))).........(((((((((((((((......))))))))))....(((((((........)))))))...)))))...... ( -29.50)
>consensus
CGAGUUCGAAGCGAACAACAACGGCAUUGAAUCGAACUCGAAGAUAAAAAGUUGUAACAGAAU_________UUCUGUUAUUUGUCUAAUUGGAAUAGAAAUUGGAAUUGAACUAAUUUA
(((((((((..(((............)))..)))))))))..............((((((((..........))))))))....(((((((........))))))).............. (-21.16 = -21.44 +   0.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,423,072 – 3,423,183
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.63
Mean single sequence MFE -26.23
Consensus MFE -16.90
Energy contribution -16.58
Covariance contribution -0.32
Combinations/Pair 1.21
Mean z-score -2.85
Structure conservation index 0.64
SVM decision value 1.53
SVM RNA-class probability 0.961331
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3423072 111 - 22407834
UAAAUUAGAUAAAUUCCAAUUUCUAUUCCAAUUAGACAAAUAACAGAA---------AUUCCCUUACAACUUUUUAUCUUUGAGUUCGAUUCGAUGCCGUUGUUGUUCGGUUCGAACUCG
......(((((((....(((((((....................))))---------)))............)))))))..((((((((..(((.((....))...)))..)))))))). ( -19.34)
>DroSec_CAF1 11948 111 - 1
UAAAUCUGUUCAAUUUCAAUUUCUAUUCCAAUUAGACAAAUAACAGAA---------AUUCUGUUACAACUUCUUAUCUUCGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCG
......(((..((((..(((....)))..))))..)))..((((((..---------...))))))..............(((((((((..(((((....)))))......))))))))) ( -21.10)
>DroSim_CAF1 12135 111 - 1
UAAAUUAGUUCAAUUCCAAUUUAUAUUCCAAUUGGACAAAUAACAGAA---------AUUCUGUUACAACUUCUUAUCUUCGAGUUCGAUUCAAUACCGUUGUUGUUCGCUUCGAACUCG
.......((((((((..(((....)))..))))))))...((((((..---------...))))))..............(((((((((..(((((....)))))......))))))))) ( -25.40)
>DroEre_CAF1 12183 120 - 1
UAAAUAAGUUCGAUUCCAACUGCUAUUCCAAUUGGACAAAUAACAGAACUAGAAAAAGUUCUGUUAAAACUUGUUAUCUUCGAGUUCGGUGCAAUGCCGAAGUGGUUCGGUUCGAACUCG
......(((((((..(((((..((..(((....)))....((((((((((......))))))))))..(((((.......)))))(((((.....)))))))..))).)).))))))).. ( -39.30)
>DroYak_CAF1 13342 120 - 1
UAACUUAGUUCAAUUCCAAUUUACAUUCCAAUUAGACAGAUAACAGAACUAGAAAAAGUUCUGUUAAAACUUUUUAUCUUCGAGUUUGAUUCAAUGCCGGAGUGGUUCGCUUCGAACUCG
.......((..((((..(((....)))..))))..))...((((((((((......))))))))))..............(((((((((..(...(((.....)))..)..))))))))) ( -26.00)
>consensus
UAAAUUAGUUCAAUUCCAAUUUCUAUUCCAAUUAGACAAAUAACAGAA_________AUUCUGUUACAACUUCUUAUCUUCGAGUUCGAUUCAAUGCCGUUGUUGUUCGCUUCGAACUCG
........................................((((((((..........))))))))..............(((((((((......((.......)).....))))))))) (-16.90 = -16.58 +  -0.32)

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 09:58:49 2006