Locus 7214

Sequence ID X_DroMel_CAF1
Location 18,057,734 – 18,057,932
Length 198
Max. P 0.979079
window11786 window11787 window11788 window11789

overview

Window 6

Location 18,057,734 – 18,057,852
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.84
Mean single sequence MFE -25.30
Consensus MFE -21.34
Energy contribution -21.57
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -2.63
Structure conservation index 0.84
SVM decision value 1.50
SVM RNA-class probability 0.959072
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18057734 118 + 22224390
CUGUGCCACAUUUUUUGUUUUUUUUUUUUCAUUCGUGCACUUCUAUUUCUUGUGACGAGUUUUUAAUCGAAAACUUAUCGCUGAGAGC--AGCGCCUGCGCUGCCCGAUUAAUUUUCAAU
..((((.((.........................)))))).......((((((((..(((((((....)))))))..)))).))))((--((((....))))))................ ( -28.11)
>DroSec_CAF1 2358 104 + 1
--------CAAU-------UUUU-UUUUUGUUUCGUGCUCUUCUAUUGCUUGUGACGAGUUUUUAAUCGAAAACUUAUCGCUGAUAACUGAGCGCCUGCGCUGUCCGAUUAAUUUUCAAU
--------....-------....-.....((...((((((...((((....((((..(((((((....)))))))..)))).))))...))))))..))..................... ( -21.70)
>DroSim_CAF1 2375 103 + 1
--------CAAU-------UUUUUUUUUUGUUUCGUGCACUUCUAUUUCUUGUGACGAGUUUUUAAUCGAAAACUUAUCGCUGAGAGC--AGCGCCUGCGCUGCCCGAUUAAUUUUCAAU
--------....-------.............(((............((((((((..(((((((....)))))))..)))).))))((--((((....)))))).)))............ ( -26.10)
>consensus
________CAAU_______UUUUUUUUUUGUUUCGUGCACUUCUAUUUCUUGUGACGAGUUUUUAAUCGAAAACUUAUCGCUGAGAGC__AGCGCCUGCGCUGCCCGAUUAAUUUUCAAU
................................(((.((........(((((((((..(((((((....)))))))..)))).)))))...((((....)))))).)))............ (-21.34 = -21.57 +   0.23)

alignment

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secondary structure

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Window 7

Location 18,057,734 – 18,057,852
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.84
Mean single sequence MFE -24.20
Consensus MFE -20.31
Energy contribution -20.20
Covariance contribution -0.11
Combinations/Pair 1.04
Mean z-score -2.60
Structure conservation index 0.84
SVM decision value 1.44
SVM RNA-class probability 0.954399
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18057734 118 - 22224390
AUUGAAAAUUAAUCGGGCAGCGCAGGCGCU--GCUCUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGAAAUAGAAGUGCACGAAUGAAAAAAAAAAAACAAAAAAUGUGGCACAG
((((((((((.(((((((((((....))))--))).....)))).)))))))))).......(((((((...........))).))))................................ ( -27.70)
>DroSec_CAF1 2358 104 - 1
AUUGAAAAUUAAUCGGACAGCGCAGGCGCUCAGUUAUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGCAAUAGAAGAGCACGAAACAAAAA-AAAA-------AUUG--------
............(((....((....))((((..((((..((((..((((((......))))))..))....)).))))..)))).)))........-....-------....-------- ( -17.20)
>DroSim_CAF1 2375 103 - 1
AUUGAAAAUUAAUCGGGCAGCGCAGGCGCU--GCUCUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGAAAUAGAAGUGCACGAAACAAAAAAAAAA-------AUUG--------
((((((((((.(((((((((((....))))--))).....)))).)))))))))).......(((((((...........))).)))).............-------....-------- ( -27.70)
>consensus
AUUGAAAAUUAAUCGGGCAGCGCAGGCGCU__GCUCUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGAAAUAGAAGUGCACGAAACAAAAAAAAAA_______AUUG________
((((((((((.(((((((((((....))))..))).....)))).)))))))))).......(((((((...........))).))))................................ (-20.31 = -20.20 +  -0.11)

alignment

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secondary structure

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Window 8

Location 18,057,774 – 18,057,892
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.65
Mean single sequence MFE -32.37
Consensus MFE -31.61
Energy contribution -31.17
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -2.61
Structure conservation index 0.98
SVM decision value 1.83
SVM RNA-class probability 0.979079
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18057774 118 - 22224390
AACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGGCAGCGCAGGCGCU--GCUCUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGAAAUAGAA
..((((..((((((((((((.(.(((....)))(((((.......)))))....).))))))).))))).--((.....))((..((((((......))))))..)).))))........ ( -32.10)
>DroSec_CAF1 2382 120 - 1
AACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGACAGCGCAGGCGCUCAGUUAUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGCAAUAGAA
...(((((((((((((((((.(.(((....)))(((((.......)))))....).))))))).)))))..........(.((..((((((......))))))..)).).)))))..... ( -32.90)
>DroSim_CAF1 2400 118 - 1
AACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGGCAGCGCAGGCGCU--GCUCUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGAAAUAGAA
..((((..((((((((((((.(.(((....)))(((((.......)))))....).))))))).))))).--((.....))((..((((((......))))))..)).))))........ ( -32.10)
>consensus
AACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGGCAGCGCAGGCGCU__GCUCUCAGCGAUAAGUUUUCGAUUAAAAACUCGUCACAAGAAAUAGAA
..((((..((((((((((((.(.(((....)))(((((.......)))))....).))))))).)))))...((.....))((..((((((......))))))..)).))))........ (-31.61 = -31.17 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,057,814 – 18,057,932
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.21
Mean single sequence MFE -37.17
Consensus MFE -35.61
Energy contribution -35.50
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -2.25
Structure conservation index 0.96
SVM decision value 1.17
SVM RNA-class probability 0.926184
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18057814 118 - 22224390
CCGAGCGACAACGUCAACUGGUCAUGCCAAUUUAUGGCCAAACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGGCAGCGCAGGCGCU--GCUCUCAG
..(((((((...)))...((((((((......))))))))........((((((((((((.(.(((....)))(((((.......)))))....).))))))).))))).--)))).... ( -37.80)
>DroSec_CAF1 2422 120 - 1
CCGAGCGACAACGUCAACUGGUCAUGCCAAUUUAUGGCCAAACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGACAGCGCAGGCGCUCAGUUAUCAG
..((((....(((.(((.((((((((......))))))))...))).)))((((((((((.(.(((....)))(((((.......)))))....).))))))).)))))))......... ( -35.90)
>DroSim_CAF1 2440 118 - 1
CCGAGCGACAACGUCAACUGGUCAUGCCAAUUUAUGGCCAAACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGGCAGCGCAGGCGCU--GCUCUCAG
..(((((((...)))...((((((((......))))))))........((((((((((((.(.(((....)))(((((.......)))))....).))))))).))))).--)))).... ( -37.80)
>consensus
CCGAGCGACAACGUCAACUGGUCAUGCCAAUUUAUGGCCAAACUUGCUGUGCCGUGCUGUGCAUACAAAUGUAAAUUUAAAUUGAAAAUUAAUCGGGCAGCGCAGGCGCU__GCUCUCAG
..(((((((...)))...((((((((......))))))))........((((((((((((.(.(((....)))(((((.......)))))....).))))))).)))))...)))).... (-35.61 = -35.50 +  -0.11)

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 12:33:01 2006