Locus 973

Sequence ID 3R_DroMel_CAF1
Location 3,159,223 – 3,159,380
Length 157
Max. P 0.980266
window1561 window1562 window1563 window1564

overview

Window 1

Location 3,159,223 – 3,159,343
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.81
Mean single sequence MFE -33.01
Consensus MFE -31.65
Energy contribution -31.52
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -2.49
Structure conservation index 0.96
SVM decision value 1.66
SVM RNA-class probability 0.970592
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3159223 120 + 27905053
GUGUGUGUUUGCAGGCUACUCAAAUGUGAUAAAUACGUGCAACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUUCUCUCUGAGCCUAAGCAAACAGGAUAACUUC
((.(.((((((((((((........(((((...((((.............)))).))))).......(((((((((....))))))))).......)))))..))))))).)...))... ( -32.82)
>DroSec_CAF1 7094 120 + 1
GUGUGUGUUUGCAGGCUACUCAAAUGUGAUAAAUACGUGCAACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUGCUCUCCGAGCCUAAGCAAACAGGAUAACUUC
((.(.((((((((((((......(((((.....)))))((..((((....))))..............((((((((....))))))))))......)))))..))))))).)...))... ( -34.10)
>DroSim_CAF1 9275 120 + 1
GUGUGUGUUUGCAGGCUACUCAAAUGUGAUAAAUACGUGCAACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUGCUCUCCGAGCCUAAGCAAACAGGAUAACUUC
((.(.((((((((((((......(((((.....)))))((..((((....))))..............((((((((....))))))))))......)))))..))))))).)...))... ( -34.10)
>DroYak_CAF1 8636 120 + 1
GUGUGUGCUUGCAGGCUACUCAAAUGUGAUAAAUACGUGCAAAAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUUCUCACUGGGCCUAAGCAAACAGGAUAGCUUC
.(((.(((((..(((((........((((.........((((.......))))..............(((((((((....))))))))).))))..)))))))))).))).......... ( -31.00)
>consensus
GUGUGUGUUUGCAGGCUACUCAAAUGUGAUAAAUACGUGCAACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUGCUCUCCGAGCCUAAGCAAACAGGAUAACUUC
((.(.((((((((((((........(((((...((((.............)))).)))))........((((((((....))))))))........)))))..))))))).)...))... (-31.65 = -31.52 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,159,223 – 3,159,343
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.81
Mean single sequence MFE -33.22
Consensus MFE -31.66
Energy contribution -31.98
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -2.46
Structure conservation index 0.95
SVM decision value 1.60
SVM RNA-class probability 0.966477
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3159223 120 - 27905053
GAAGUUAUCCUGUUUGCUUAGGCUCAGAGAGAAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUUGCACGUAUUUAUCACAUUUGAGUAGCCUGCAAACACACAC
..........(((((((....(((((((((((((((((((....))))))))))))..................((((.....)))).........))))))).....)))))))..... ( -35.50)
>DroSec_CAF1 7094 120 - 1
GAAGUUAUCCUGUUUGCUUAGGCUCGGAGAGCAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUUGCACGUAUUUAUCACAUUUGAGUAGCCUGCAAACACACAC
..........(((((((....((((((((((.((((((((....)))))))).)))..................((((.....)))).........))))))).....)))))))..... ( -30.80)
>DroSim_CAF1 9275 120 - 1
GAAGUUAUCCUGUUUGCUUAGGCUCGGAGAGCAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUUGCACGUAUUUAUCACAUUUGAGUAGCCUGCAAACACACAC
..........(((((((....((((((((((.((((((((....)))))))).)))..................((((.....)))).........))))))).....)))))))..... ( -30.80)
>DroYak_CAF1 8636 120 - 1
GAAGCUAUCCUGUUUGCUUAGGCCCAGUGAGAAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUUUUGCACGUAUUUAUCACAUUUGAGUAGCCUGCAAGCACACAC
..........(((((((..((((..(((((((((((((((....)))))))))))))))..........................((((((.......)))))))))))))))))..... ( -35.80)
>consensus
GAAGUUAUCCUGUUUGCUUAGGCUCAGAGAGAAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUUGCACGUAUUUAUCACAUUUGAGUAGCCUGCAAACACACAC
..........(((((((..((((.....((((((((((((....)))))))))))).............................((((((.......)))))))))))))))))..... (-31.66 = -31.98 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,159,263 – 3,159,380
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.66
Mean single sequence MFE -32.08
Consensus MFE -28.90
Energy contribution -29.15
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.70
Structure conservation index 0.90
SVM decision value 1.86
SVM RNA-class probability 0.980266
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3159263 117 + 27905053
AACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUUCUCUCUGAGCCUAAGCAAACAGGAUAACUUCGUCCUGGAAGUCCAUUCCGUUCUGGCGAA---AACAUUUC
..........(((...((.........(((((((((....)))))))))........(((..(((....(((((......)))))((((.....)))))))..))))).---.))).... ( -32.70)
>DroSec_CAF1 7134 117 + 1
AACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUGCUCUCCGAGCCUAAGCAAACAGGAUAACUUCGUCCUGGAAGUCCAUUCCGUUCUUGCGAA---AACAUUUC
..........(((...((..........((((((((....))))))))((((...))))....(((((((((((......)))))((((.....))))))..)))))).---.))).... ( -30.70)
>DroSim_CAF1 9315 117 + 1
AACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUGCUCUCCGAGCCUAAGCAAACAGGAUAACUUCGUCCUGGAAGUCCAUUCCGUUCUGGCGAA---AACAUUUC
..........(((...((..........((((((((....)))))))).........(((..(((....(((((......)))))((((.....)))))))..))))).---.))).... ( -32.40)
>DroYak_CAF1 8676 120 + 1
AAAAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUUCUCACUGGGCCUAAGCAAACAGGAUAGCUUCGUCCUGGAAGUCCAUUCCGUUCUGGCGAACGAACCGUUUC
...........((((............(((((((((....))))))))).))))...(((..(((....(((((......)))))((((.....)))))))..)))(((((...))))). ( -32.52)
>consensus
AACAUAAAAUUGUGAAUCAUUAAUAAAAAUGGGGGUUGCAACCCCCAUGCUCUCCGAGCCUAAGCAAACAGGAUAACUUCGUCCUGGAAGUCCAUUCCGUUCUGGCGAA___AACAUUUC
................((..........((((((((....)))))))).........(((..(((....(((((......)))))((((.....)))))))..)))))............ (-28.90 = -29.15 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,159,263 – 3,159,380
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.66
Mean single sequence MFE -35.03
Consensus MFE -30.29
Energy contribution -30.85
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.99
Structure conservation index 0.86
SVM decision value 0.76
SVM RNA-class probability 0.844432
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3159263 117 - 27905053
GAAAUGUU---UUCGCCAGAACGGAAUGGACUUCCAGGACGAAGUUAUCCUGUUUGCUUAGGCUCAGAGAGAAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUU
....(((.---.(((((.(((((((...((((((......)))))).))).)))).....))).....((((((((((((....))))))))))))......))...))).......... ( -34.00)
>DroSec_CAF1 7134 117 - 1
GAAAUGUU---UUCGCAAGAACGGAAUGGACUUCCAGGACGAAGUUAUCCUGUUUGCUUAGGCUCGGAGAGCAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUU
((((((((---(((....(((((((...((((((......)))))).))).))))((....))...))))))))((((((....))))))..............)))............. ( -32.40)
>DroSim_CAF1 9315 117 - 1
GAAAUGUU---UUCGCCAGAACGGAAUGGACUUCCAGGACGAAGUUAUCCUGUUUGCUUAGGCUCGGAGAGCAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUU
((((((((---((((((.(((((((...((((((......)))))).))).)))).....)))...))))))))((((((....))))))..............)))............. ( -33.90)
>DroYak_CAF1 8676 120 - 1
GAAACGGUUCGUUCGCCAGAACGGAAUGGACUUCCAGGACGAAGCUAUCCUGUUUGCUUAGGCCCAGUGAGAAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUUUU
.....(..(((((.(((.((((((.((((.((((......)))))))).)))))).....)))..(((((((((((((((....))))))))))))))))))))..)............. ( -39.80)
>consensus
GAAAUGUU___UUCGCCAGAACGGAAUGGACUUCCAGGACGAAGUUAUCCUGUUUGCUUAGGCUCAGAGAGAAUGGGGGUUGCAACCCCCAUUUUUAUUAAUGAUUCACAAUUUUAUGUU
(((...........(((.((((((.((((.((((......)))))))).)))))).....))).....((((((((((((....))))))))))))........)))............. (-30.29 = -30.85 +   0.56)

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 09:57:06 2006