Locus 3986

Sequence ID X_DroMel_CAF1
Location 10,558,874 – 10,559,001
Length 127
Max. P 0.935023
window6555 window6556 window6557

overview

Window 5

Location 10,558,874 – 10,558,967
Length 93
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 87.29
Mean single sequence MFE -11.70
Consensus MFE -9.49
Energy contribution -9.55
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -2.19
Structure conservation index 0.81
SVM decision value 1.24
SVM RNA-class probability 0.935023
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10558874 93 - 22224390
AAAUUUUGGUAAACUAAAAUGGAAUUUAGAUUUAAUUUUAGAUACACCAAAUCAAAUCUAAUACAACACACACGAUCAC----ACACACACACACCU
....((((((...(((((((.((((....)))).)))))))....))))))............................----.............. ( -10.00)
>DroSec_CAF1 85251 97 - 1
AAAUUUUGGUAAACUAAAAUGGAAUUUAGAUCUAGUUUUAGACACACCAAAUGAAAUCUAAUACAACACACACGAUCACGAUCACACACACACACCU
....((((((...((((((((((.......)))).))))))....))))))......................(((....))).............. ( -10.70)
>DroSim_CAF1 89945 97 - 1
AAAUUUUGGUAAACUAAAAUGGAAUUUAGAUUUAGUUUUAGACACACCAAAUCAAAUCUAAUACAACACACACGGUCACGAUCACACACACACACCU
....((((((...(((((((.((((....)))).)))))))....)))))).....................((....))................. ( -11.10)
>DroEre_CAF1 87041 88 - 1
GAAUUUUGGUAGACUAAAAUGGAAU-UAUAUUUCGUUUUAGACGCACCAAAUCAAAUCUAAUAACACACAC--------GAUCACACACACACACCU
....((((((.(.((((((((((((-...)))))))))))).)..))))))....................--------.................. ( -15.00)
>consensus
AAAUUUUGGUAAACUAAAAUGGAAUUUAGAUUUAGUUUUAGACACACCAAAUCAAAUCUAAUACAACACACACGAUCACGAUCACACACACACACCU
....((((((...(((((((.((((....)))).)))))))....)))))).............................................. ( -9.49 =  -9.55 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,558,895 – 10,559,001
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 91.31
Mean single sequence MFE -22.44
Consensus MFE -18.10
Energy contribution -19.14
Covariance contribution 1.04
Combinations/Pair 1.09
Mean z-score -1.79
Structure conservation index 0.81
SVM decision value 0.94
SVM RNA-class probability 0.886462
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10558895 106 + 22224390
UGUGUGUUGUAUUAGAUUUGAUUUGGUGUAUCUAAAAUUAAAUCUAAAUUCCAUUUUAGUUUACCAAAAUUUGCCACCGCUUUGGCUUACAAAUCAUUCAGCAUAG
..(((((((.....((((((.(((((((...(((((((..(((....)))..)))))))..)))))))....((((......))))...))))))...))))))). ( -27.70)
>DroSec_CAF1 85276 106 + 1
UGUGUGUUGUAUUAGAUUUCAUUUGGUGUGUCUAAAACUAGAUCUAAAUUCCAUUUUAGUUUACCAAAAUUUGCCACCGCUUUGGCUUACAAAUCAUUCAGCAUAG
..(((((((.....(((((..(((((((.(((((....)))))(((((......)))))..)))))))....((((......))))....)))))...))))))). ( -23.20)
>DroSim_CAF1 89970 106 + 1
UGUGUGUUGUAUUAGAUUUGAUUUGGUGUGUCUAAAACUAAAUCUAAAUUCCAUUUUAGUUUACCAAAAUUUGCCACCGCUUUGGCUUACAAAUCAUUCAGCAUAG
..(((((((.....((((((.(((((((...((((((...(((....)))...))))))..)))))))....((((......))))...))))))...))))))). ( -25.50)
>DroEre_CAF1 87059 104 + 1
-GUGUGUGUUAUUAGAUUUGAUUUGGUGCGUCUAAAACGAAAUAUA-AUUCCAUUUUAGUCUACCAAAAUUCGUCACCGCUUUGGCUUACAAAUCAUUCAGCAUAG
-...((((((....((((((.(((((((.(.((((((.(((.....-.)))..)))))).))))))))....((((......))))...))))))....)))))). ( -23.20)
>DroYak_CAF1 89332 105 + 1
UGUGUGUGUUAUUAAAUUUGAUUUGGUGUGUCUAAAAUUAAAUAUA-AUUCCAUUUCAGUUUACCAAAAUUUUUCACCGCUUUGGCUUACAAAUCAAUUAGUAUAG
.........((((((..(((((((((.(((...((((((......(-(((.......))))......)))))).))))((....))...))))))))))))))... ( -12.60)
>consensus
UGUGUGUUGUAUUAGAUUUGAUUUGGUGUGUCUAAAACUAAAUCUAAAUUCCAUUUUAGUUUACCAAAAUUUGCCACCGCUUUGGCUUACAAAUCAUUCAGCAUAG
..(((((((.....((((((.(((((((...((((((...(((....)))...))))))..)))))))....((((......))))...))))))...))))))). (-18.10 = -19.14 +   1.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,558,895 – 10,559,001
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 91.31
Mean single sequence MFE -20.32
Consensus MFE -15.46
Energy contribution -15.30
Covariance contribution -0.16
Combinations/Pair 1.12
Mean z-score -1.81
Structure conservation index 0.76
SVM decision value 0.42
SVM RNA-class probability 0.729376
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10558895 106 - 22224390
CUAUGCUGAAUGAUUUGUAAGCCAAAGCGGUGGCAAAUUUUGGUAAACUAAAAUGGAAUUUAGAUUUAAUUUUAGAUACACCAAAUCAAAUCUAAUACAACACACA
...........((((((...((((......))))....((((((...(((((((.((((....)))).)))))))....)))))).)))))).............. ( -20.30)
>DroSec_CAF1 85276 106 - 1
CUAUGCUGAAUGAUUUGUAAGCCAAAGCGGUGGCAAAUUUUGGUAAACUAAAAUGGAAUUUAGAUCUAGUUUUAGACACACCAAAUGAAAUCUAAUACAACACACA
..............(((((.((((......))))....((((((...((((((((((.......)))).))))))....))))))..........)))))...... ( -17.90)
>DroSim_CAF1 89970 106 - 1
CUAUGCUGAAUGAUUUGUAAGCCAAAGCGGUGGCAAAUUUUGGUAAACUAAAAUGGAAUUUAGAUUUAGUUUUAGACACACCAAAUCAAAUCUAAUACAACACACA
...........((((((...((((......))))....((((((...(((((((.((((....)))).)))))))....)))))).)))))).............. ( -20.60)
>DroEre_CAF1 87059 104 - 1
CUAUGCUGAAUGAUUUGUAAGCCAAAGCGGUGACGAAUUUUGGUAGACUAAAAUGGAAU-UAUAUUUCGUUUUAGACGCACCAAAUCAAAUCUAAUAACACACAC-
..........(((((((...((((((.((....))...))))))...((((((((((((-...))))))))))))......))))))).................- ( -25.60)
>DroYak_CAF1 89332 105 - 1
CUAUACUAAUUGAUUUGUAAGCCAAAGCGGUGAAAAAUUUUGGUAAACUGAAAUGGAAU-UAUAUUUAAUUUUAGACACACCAAAUCAAAUUUAAUAACACACACA
.........(((((((....((....))((((.....(((..(....)..)))((((((-((....))))))))....)))))))))))................. ( -17.20)
>consensus
CUAUGCUGAAUGAUUUGUAAGCCAAAGCGGUGGCAAAUUUUGGUAAACUAAAAUGGAAUUUAGAUUUAGUUUUAGACACACCAAAUCAAAUCUAAUACAACACACA
...........((((((...(((.....))).......((((((...(((((((.((((....)))).)))))))....)))))).)))))).............. (-15.46 = -15.30 +  -0.16)

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 11:13:38 2006