Locus 4022

Sequence ID X_DroMel_CAF1
Location 10,635,199 – 10,635,333
Length 134
Max. P 0.999332
window6608 window6609 window6610 window6611

overview

Window 8

Location 10,635,199 – 10,635,303
Length 104
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 77.52
Mean single sequence MFE -18.03
Consensus MFE -11.05
Energy contribution -12.55
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -3.17
Structure conservation index 0.61
SVM decision value 3.52
SVM RNA-class probability 0.999332
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10635199 104 + 22224390
CAAAAUGAUAUACACAACAACAAAAUUAUA-AAAUAAUCAAAGUAAAU---AAGCGGGAAUCGU---AGAUUGAUUCCCA--------UAUGGGUAGUAAGAUAUCAACGGAAGAUAAA
.....((((((..((.((............-...........((....---..))((((((((.---....)))))))).--------.....)).))...)))))).(....)..... ( -19.40)
>DroEre_CAF1 17565 93 + 1
CAAAAUGAUAUACACAACAACAAAAUUAUA-AAAUAAUCAAAGUAAAU---AAGCGGGAAUCGC---AGAUUGAUUCCCA--------UAUGGGUAGUACGAUAUCAA-----------
.....((((((..((.((............-...........((....---..))((((((((.---....)))))))).--------.....)).))...)))))).----------- ( -17.30)
>DroYak_CAF1 17200 93 + 1
CAAAAUGAUAUACACAACAACAAAAUUAUA-AAAUAAUCAAAGUAAAU---AAGCGGGAAUCGC---AGAUUGAUUCCCA--------UAUGGGUUGUAAGAUAUCAA-----------
.....((((((..(((((............-...........((....---..))((((((((.---....)))))))).--------.....)))))...)))))).----------- ( -21.40)
>DroAna_CAF1 25114 105 + 1
CUAAAUGAAAUACACAACAAAAAAAUUAAACAAAUAAUCAAAGUAAAUAGUAAAGGGGAAUCAUCGGUGACGAAGUCCCAUCAUCUCCUAUGGAUA---CAAAAUCAA-----------
..........................................(((.((((.....((((....(((....)))..))))........))))...))---)........----------- ( -14.02)
>consensus
CAAAAUGAUAUACACAACAACAAAAUUAUA_AAAUAAUCAAAGUAAAU___AAGCGGGAAUCGC___AGAUUGAUUCCCA________UAUGGGUAGUAAGAUAUCAA___________
.....((((((.............(((((....))))).................((((((((........))))))))......................))))))............ (-11.05 = -12.55 +   1.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,635,199 – 10,635,303
Length 104
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 77.52
Mean single sequence MFE -16.79
Consensus MFE -11.19
Energy contribution -12.00
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -1.58
Structure conservation index 0.67
SVM decision value 0.03
SVM RNA-class probability 0.549636
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10635199 104 - 22224390
UUUAUCUUCCGUUGAUAUCUUACUACCCAUA--------UGGGAAUCAAUCU---ACGAUUCCCGCUU---AUUUACUUUGAUUAUUU-UAUAAUUUUGUUGUUGUGUAUAUCAUUUUG
............((((((..(((.((.....--------.(((((((.....---..)))))))....---....((...((((((..-.))))))..)).)).))).))))))..... ( -16.60)
>DroEre_CAF1 17565 93 - 1
-----------UUGAUAUCGUACUACCCAUA--------UGGGAAUCAAUCU---GCGAUUCCCGCUU---AUUUACUUUGAUUAUUU-UAUAAUUUUGUUGUUGUGUAUAUCAUUUUG
-----------.((((((.............--------.(((((((.....---..)))))))....---.................-((((((......)))))).))))))..... ( -15.60)
>DroYak_CAF1 17200 93 - 1
-----------UUGAUAUCUUACAACCCAUA--------UGGGAAUCAAUCU---GCGAUUCCCGCUU---AUUUACUUUGAUUAUUU-UAUAAUUUUGUUGUUGUGUAUAUCAUUUUG
-----------.((((((..((((((.....--------.(((((((.....---..)))))))....---....((...((((((..-.))))))..)).)))))).))))))..... ( -20.70)
>DroAna_CAF1 25114 105 - 1
-----------UUGAUUUUG---UAUCCAUAGGAGAUGAUGGGACUUCGUCACCGAUGAUUCCCCUUUACUAUUUACUUUGAUUAUUUGUUUAAUUUUUUUGUUGUGUAUUUCAUUUAG
-----------.........---..........((((((.((((..(((((...))))).))))...(((..........(((((......)))))..........)))..)))))).. ( -14.25)
>consensus
___________UUGAUAUCGUACUACCCAUA________UGGGAAUCAAUCU___ACGAUUCCCGCUU___AUUUACUUUGAUUAUUU_UAUAAUUUUGUUGUUGUGUAUAUCAUUUUG
............((((((......................(((((((..........))))))).........................((((((......)))))).))))))..... (-11.19 = -12.00 +   0.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,635,238 – 10,635,333
Length 95
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 86.86
Mean single sequence MFE -18.80
Consensus MFE -14.29
Energy contribution -14.73
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -2.29
Structure conservation index 0.76
SVM decision value 0.46
SVM RNA-class probability 0.744014
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10635238 95 + 22224390
AAGUAAAUAAGCGGGAAUCGUAGAUUGAUUCCCAUAUGGGUAGUAAGAUAUCAACGGAAGAUAAAACGGAAAUCAUUUUUCAAUAUGCCAAAUAA
............((((((((.....)))))))).....((((............(....).......(((((....)))))....))))...... ( -20.10)
>DroEre_CAF1 17604 84 + 1
AAGUAAAUAAGCGGGAAUCGCAGAUUGAUUCCCAUAUGGGUAGUACGAUAUCAA-----------UCGGAAAUCAUUUUUCAAUAUGCCAAAUAA
............((((((((.....)))))))).....((((...((((....)-----------)))((((.....))))....))))...... ( -19.90)
>DroYak_CAF1 17239 84 + 1
AAGUAAAUAAGCGGGAAUCGCAGAUUGAUUCCCAUAUGGGUUGUAAGAUAUCAA-----------UCGGAGAUAAUUUUUAAAUAUGCCAAAUAA
..........((((((((((.....)))))))).....(((((........)))-----------))...................))....... ( -16.40)
>consensus
AAGUAAAUAAGCGGGAAUCGCAGAUUGAUUCCCAUAUGGGUAGUAAGAUAUCAA___________UCGGAAAUCAUUUUUCAAUAUGCCAAAUAA
............((((((((.....)))))))).....((((....(....)...............(((((....)))))....))))...... (-14.29 = -14.73 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,635,238 – 10,635,333
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 86.86
Mean single sequence MFE -15.70
Consensus MFE -12.40
Energy contribution -12.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.79
SVM decision value 0.13
SVM RNA-class probability 0.600253
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10635238 95 - 22224390
UUAUUUGGCAUAUUGAAAAAUGAUUUCCGUUUUAUCUUCCGUUGAUAUCUUACUACCCAUAUGGGAAUCAAUCUACGAUUCCCGCUUAUUUACUU
......(((((((..(.....(((.........))).....)..))))..............(((((((.......))))))))))......... ( -16.20)
>DroEre_CAF1 17604 84 - 1
UUAUUUGGCAUAUUGAAAAAUGAUUUCCGA-----------UUGAUAUCGUACUACCCAUAUGGGAAUCAAUCUGCGAUUCCCGCUUAUUUACUU
......(((..........(((((.((...-----------..)).)))))...........(((((((.......))))))))))......... ( -16.30)
>DroYak_CAF1 17239 84 - 1
UUAUUUGGCAUAUUUAAAAAUUAUCUCCGA-----------UUGAUAUCUUACAACCCAUAUGGGAAUCAAUCUGCGAUUCCCGCUUAUUUACUU
......(((............((((.....-----------..))))...............(((((((.......))))))))))......... ( -14.60)
>consensus
UUAUUUGGCAUAUUGAAAAAUGAUUUCCGA___________UUGAUAUCUUACUACCCAUAUGGGAAUCAAUCUGCGAUUCCCGCUUAUUUACUU
......(((.((((....))))........................................(((((((.......))))))))))......... (-12.40 = -12.73 +   0.33)

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 11:14:27 2006