Locus 466

Sequence ID 3R_DroMel_CAF1
Location 1,753,674 – 1,753,816
Length 142
Max. P 0.998576
window754 window755 window756 window757

overview

Window 4

Location 1,753,674 – 1,753,790
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 81.16
Mean single sequence MFE -37.24
Consensus MFE -35.01
Energy contribution -35.57
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -3.07
Structure conservation index 0.94
SVM decision value 3.15
SVM RNA-class probability 0.998576
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1753674 116 + 27905053
GAUAGUUAAAAGAUCUUAAAAGAUUAAAAGAUAUCAGGCAGUCCAUCCGUCGCCAGGUGGCUCUCUUGUGCAAUUACUGUGGCGCACUCCGUAGAAGAGCCACCUGGCGUUAAAUG
((((.......(((((....)))))......))))........(((....(((((((((((((((((((((.((....)).)))))......)).))))))))))))))....))) ( -40.12)
>DroSec_CAF1 63000 97 + 1
-----------GAUCUUA--------AAAGAUAUUAUGCAGUCCCUCCGUCGCCAGGUGGCUCUCUUGCGUAAUUACUGUGGCGCACCCAGUAGAAGACCCACCUGGCGUUAGGUA
-----------.((((..--------..))))..............((..((((((((((.((((((((((.((....)).)))))......)).))).))))))))))...)).. ( -32.60)
>DroSim_CAF1 65373 97 + 1
-----------GAUCUUA--------AAAGAUAUUAUGCAGUCCAUCCGUCGCCAGGUGGCUCUCUUGCGUAAUUACAGUGGCGCACCCAGUAGAAGAGCCACCUGGCGUUAGGUA
-----------.((((..--------..))))..............((..(((((((((((((((((((((.((....)).)))))......)).))))))))))))))...)).. ( -39.00)
>consensus
___________GAUCUUA________AAAGAUAUUAUGCAGUCCAUCCGUCGCCAGGUGGCUCUCUUGCGUAAUUACUGUGGCGCACCCAGUAGAAGAGCCACCUGGCGUUAGGUA
............(((((..........)))))..............((..(((((((((((((((((((((.((....)).)))))......)).))))))))))))))...)).. (-35.01 = -35.57 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,753,674 – 1,753,790
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 81.16
Mean single sequence MFE -38.70
Consensus MFE -31.60
Energy contribution -31.93
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.61
Structure conservation index 0.82
SVM decision value 2.94
SVM RNA-class probability 0.997817
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1753674 116 - 27905053
CAUUUAACGCCAGGUGGCUCUUCUACGGAGUGCGCCACAGUAAUUGCACAAGAGAGCCACCUGGCGACGGAUGGACUGCCUGAUAUCUUUUAAUCUUUUAAGAUCUUUUAACUAUC
(((((..((((((((((((((((....))(((((..........)))))...))))))))))))))..)))))..............((((((....))))))............. ( -40.80)
>DroSec_CAF1 63000 97 - 1
UACCUAACGCCAGGUGGGUCUUCUACUGGGUGCGCCACAGUAAUUACGCAAGAGAGCCACCUGGCGACGGAGGGACUGCAUAAUAUCUUU--------UAAGAUC-----------
..(((..((((((((((.(((..(((((((....)).)))))....(....)))).))))))))))....)))...........((((..--------..)))).----------- ( -38.50)
>DroSim_CAF1 65373 97 - 1
UACCUAACGCCAGGUGGCUCUUCUACUGGGUGCGCCACUGUAAUUACGCAAGAGAGCCACCUGGCGACGGAUGGACUGCAUAAUAUCUUU--------UAAGAUC-----------
..((...((((((((((((((..(((..((....))...)))....(....)))))))))))))))..))..............((((..--------..)))).----------- ( -36.80)
>consensus
UACCUAACGCCAGGUGGCUCUUCUACUGGGUGCGCCACAGUAAUUACGCAAGAGAGCCACCUGGCGACGGAUGGACUGCAUAAUAUCUUU________UAAGAUC___________
.......(((((((((((((((........(((......))).........)))))))))))))))..................(((((..........)))))............ (-31.60 = -31.93 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,753,710 – 1,753,816
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.78
Mean single sequence MFE -43.31
Consensus MFE -37.11
Energy contribution -38.33
Covariance contribution 1.23
Combinations/Pair 1.06
Mean z-score -3.40
Structure conservation index 0.86
SVM decision value 2.50
SVM RNA-class probability 0.994637
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1753710 106 + 27905053
GGCAGUCCAUCCGUCGCCAGGUGGCUCUCUUGUGCAAUUACUGUGGCGCACUCCGUAGAAGAGCCACCUGGCGUUAAAUG-ACAAACUGGA------UAUGUUCCAUGGCCUA-------
(((.(((.......(((((((((((((((((((((.((....)).)))))......)).))))))))))))))......)-))....((((------.....))))..)))..------- ( -46.82)
>DroSec_CAF1 63017 120 + 1
UGCAGUCCCUCCGUCGCCAGGUGGCUCUCUUGCGUAAUUACUGUGGCGCACCCAGUAGAAGACCCACCUGGCGUUAGGUAUACAAACUGUACAGUAAUCUGUUCCAUGAAUUAGUUUUAA
.(((((....((..((((((((((.((((((((((.((....)).)))))......)).))).))))))))))...)).......)))))((((....)))).................. ( -38.30)
>DroSim_CAF1 65390 120 + 1
UGCAGUCCAUCCGUCGCCAGGUGGCUCUCUUGCGUAAUUACAGUGGCGCACCCAGUAGAAGAGCCACCUGGCGUUAGGUAUACGAACUGUACAGUAAUCUGUUCCAUGAAUUAGUUUUAA
.((((((...((..(((((((((((((((((((((.((....)).)))))......)).))))))))))))))...)).....).)))))((((....)))).................. ( -44.80)
>consensus
UGCAGUCCAUCCGUCGCCAGGUGGCUCUCUUGCGUAAUUACUGUGGCGCACCCAGUAGAAGAGCCACCUGGCGUUAGGUAUACAAACUGUACAGUAAUCUGUUCCAUGAAUUAGUUUUAA
((((((....((..(((((((((((((((((((((.((....)).)))))......)).))))))))))))))...)).......))))))............................. (-37.11 = -38.33 +   1.23)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,753,710 – 1,753,816
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -46.33
Consensus MFE -36.36
Energy contribution -36.36
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -4.15
Structure conservation index 0.78
SVM decision value 2.46
SVM RNA-class probability 0.994260
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1753710 106 - 27905053
-------UAGGCCAUGGAACAUA------UCCAGUUUGU-CAUUUAACGCCAGGUGGCUCUUCUACGGAGUGCGCCACAGUAAUUGCACAAGAGAGCCACCUGGCGACGGAUGGACUGCC
-------..(((...(((.....------)))((((..(-(......((((((((((((((((....))(((((..........)))))...))))))))))))))...))..))))))) ( -49.30)
>DroSec_CAF1 63017 120 - 1
UUAAAACUAAUUCAUGGAACAGAUUACUGUACAGUUUGUAUACCUAACGCCAGGUGGGUCUUCUACUGGGUGCGCCACAGUAAUUACGCAAGAGAGCCACCUGGCGACGGAGGGACUGCA
..................((((....)))).((((((.(...((...((((((((((.(((..(((((((....)).)))))....(....)))).))))))))))..))).)))))).. ( -43.00)
>DroSim_CAF1 65390 120 - 1
UUAAAACUAAUUCAUGGAACAGAUUACUGUACAGUUCGUAUACCUAACGCCAGGUGGCUCUUCUACUGGGUGCGCCACUGUAAUUACGCAAGAGAGCCACCUGGCGACGGAUGGACUGCA
..................((((....)))).((((((((...((...((((((((((((((..(((..((....))...)))....(....)))))))))))))))..)))))))))).. ( -46.70)
>consensus
UUAAAACUAAUUCAUGGAACAGAUUACUGUACAGUUUGUAUACCUAACGCCAGGUGGCUCUUCUACUGGGUGCGCCACAGUAAUUACGCAAGAGAGCCACCUGGCGACGGAUGGACUGCA
...............................((((((((...((...(((((((((((((((........(((......))).........)))))))))))))))..)))))))))).. (-36.36 = -36.36 +   0.01)

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 09:43:54 2006