Locus 7224

Sequence ID X_DroMel_CAF1
Location 18,065,850 – 18,066,088
Length 238
Max. P 0.913741
window11812 window11813 window11814 window11815

overview

Window 2

Location 18,065,850 – 18,065,968
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.57
Mean single sequence MFE -32.54
Consensus MFE -32.07
Energy contribution -31.19
Covariance contribution -0.88
Combinations/Pair 1.14
Mean z-score -1.78
Structure conservation index 0.99
SVM decision value 1.09
SVM RNA-class probability 0.913741
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18065850 118 + 22224390
AAGCCAUUCAGCGGAGCUGCGAAUAGCAAAUUGGGUGCCUAGCAAUGUAUAUGGGGCCAAUAGAAG--AAAAAAAGGGGUGGUUGGAGGUUUAACGGGUGUGAAGAGAUUCGCAGCGCGU
(((((.((((((.(..((((.....))......(((.((.............)).)))........--.......))..).))))))))))).((((.((((((....)))))).).))) ( -30.72)
>DroSec_CAF1 3686 115 + 1
AAGCCAUUCAGCGGAGCUGCGAAUAGCAAAUUGGGUGCCUAGCAAU--AUAUGGGGCCAACAAGAA---AAAAAAGGGGUGGUUGGAGGUUUAAUAGGUGCGGGGAGAUUCGCAGCGCGU
..........(((..(((((((((..(....(((....)))(((..--.(((..((((..(((...---.............)))..))))..)))..)))...)..))))))))).))) ( -30.39)
>DroSim_CAF1 6823 118 + 1
AAGCCAUUCAGCGGAGCUGCGAAUAGCAAAUUGGGUGCCUAGCAAU--AUAUGGGGCCAACAAAAAAAAAAAAAAGGGGUGGUUGGAGGUUUAAUGGGUGCGAGGAGACUCGCAGCGCGU
(((((.((((((.(..((((.....))......(((.((.......--....)).))).................))..).))))))))))).((((.((((((....)))))).).))) ( -36.50)
>consensus
AAGCCAUUCAGCGGAGCUGCGAAUAGCAAAUUGGGUGCCUAGCAAU__AUAUGGGGCCAACAAAAA__AAAAAAAGGGGUGGUUGGAGGUUUAAUGGGUGCGAGGAGAUUCGCAGCGCGU
(((((.((((((.(..((((.....))......(((.((.............)).))).................))..).)))))))))))....(.((((((....)))))).).... (-32.07 = -31.19 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,065,850 – 18,065,968
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.57
Mean single sequence MFE -22.43
Consensus MFE -20.65
Energy contribution -21.10
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.65
Structure conservation index 0.92
SVM decision value 0.24
SVM RNA-class probability 0.649331
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18065850 118 - 22224390
ACGCGCUGCGAAUCUCUUCACACCCGUUAAACCUCCAACCACCCCUUUUUUU--CUUCUAUUGGCCCCAUAUACAUUGCUAGGCACCCAAUUUGCUAUUCGCAGCUCCGCUGAAUGGCUU
....(((((((((.......................................--.......((((............))))((((.......)))))))))))))...(((....))).. ( -20.10)
>DroSec_CAF1 3686 115 - 1
ACGCGCUGCGAAUCUCCCCGCACCUAUUAAACCUCCAACCACCCCUUUUUU---UUCUUGUUGGCCCCAUAU--AUUGCUAGGCACCCAAUUUGCUAUUCGCAGCUCCGCUGAAUGGCUU
....(((((((((......(((..(((.......(((((............---.....)))))......))--).)))..((((.......)))))))))))))...(((....))).. ( -23.65)
>DroSim_CAF1 6823 118 - 1
ACGCGCUGCGAGUCUCCUCGCACCCAUUAAACCUCCAACCACCCCUUUUUUUUUUUUUUGUUGGCCCCAUAU--AUUGCUAGGCACCCAAUUUGCUAUUCGCAGCUCCGCUGAAUGGCUU
....((((((((....))))).............(((((....................)))))........--.......))).........(((((((((......)).))))))).. ( -23.55)
>consensus
ACGCGCUGCGAAUCUCCUCGCACCCAUUAAACCUCCAACCACCCCUUUUUUU__UUUUUGUUGGCCCCAUAU__AUUGCUAGGCACCCAAUUUGCUAUUCGCAGCUCCGCUGAAUGGCUU
....(((((((((......(((............(((((....................)))))............)))..((((.......)))))))))))))...(((....))).. (-20.65 = -21.10 +   0.45)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,065,890 – 18,066,008
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.33
Mean single sequence MFE -29.33
Consensus MFE -27.01
Energy contribution -26.35
Covariance contribution -0.66
Combinations/Pair 1.19
Mean z-score -1.84
Structure conservation index 0.92
SVM decision value 0.71
SVM RNA-class probability 0.831001
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18065890 118 + 22224390
AGCAAUGUAUAUGGGGCCAAUAGAAG--AAAAAAAGGGGUGGUUGGAGGUUUAACGGGUGUGAAGAGAUUCGCAGCGCGUAAAGCGGCUCAAAGGACCCUAAUUAAAGUAAAUCAUGUUU
........((((((.(((....)...--.......(((((..((.(((((((.((((.((((((....)))))).).))).))))..))).))..))))).......))...)))))).. ( -24.90)
>DroSec_CAF1 3726 115 + 1
AGCAAU--AUAUGGGGCCAACAAGAA---AAAAAAGGGGUGGUUGGAGGUUUAAUAGGUGCGGGGAGAUUCGCAGCGCGUAACGCGGCUCAAAGGAGCCUAAUUAAAGUAAAUCAUGUUU
......--((((((..(((((.....---............))))).(.((((((.(.((((((....)))))).)(((...)))(((((....)))))..)))))).)...)))))).. ( -27.23)
>DroSim_CAF1 6863 118 + 1
AGCAAU--AUAUGGGGCCAACAAAAAAAAAAAAAAGGGGUGGUUGGAGGUUUAAUGGGUGCGAGGAGACUCGCAGCGCGUAUCGCGGCUCAAAGGAGCCUAAUUAAAGCAAAUCAUGUUU
......--((((((..(((((....................))))).(.((((((.(.((((((....)))))).)(((...)))(((((....)))))..)))))).)...)))))).. ( -35.85)
>consensus
AGCAAU__AUAUGGGGCCAACAAAAA__AAAAAAAGGGGUGGUUGGAGGUUUAAUGGGUGCGAGGAGAUUCGCAGCGCGUAACGCGGCUCAAAGGAGCCUAAUUAAAGUAAAUCAUGUUU
........((((((..(((((....................))))).(.((((((.(.((((((....)))))).)((.....))(((((....)))))..)))))).)...)))))).. (-27.01 = -26.35 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,065,968 – 18,066,088
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -23.73
Consensus MFE -23.25
Energy contribution -23.37
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.74
Structure conservation index 0.98
SVM decision value 0.60
SVM RNA-class probability 0.795210
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18065968 120 + 22224390
AAAGCGGCUCAAAGGACCCUAAUUAAAGUAAAUCAUGUUUUUCAUAACGCACCCUAAUUAUUUCACUAUUCAAAUCGAACUUUUCAAGUUCCACGUUGCCCGAAGUAAUUGGAUUAAGUA
...(((.....((((((....(((......)))...)))))).....)))...(((((((((((......(((...(((((.....)))))....)))...)))))))))))........ ( -17.90)
>DroSec_CAF1 3801 120 + 1
AACGCGGCUCAAAGGAGCCUAAUUAAAGUAAAUCAUGUUUUUCAUAACGCACCCUAAUUACUUCACUAUUCAAAUCGAACUUUCCAAGUUCCACGUCGCCCGAAGUAAUUGGAUUAAGUA
...(((((((....))))).................(((......)))))...(((((((((((............(((((.....)))))...(.....))))))))))))........ ( -26.00)
>DroSim_CAF1 6941 120 + 1
AUCGCGGCUCAAAGGAGCCUAAUUAAAGCAAAUCAUGUUUUUCAUAACGCACCCUAAUUACUUCACUAUUCAAAUCGAACUUUCCAAGUUCCACGUCGCCCGAAGUAAUUGGAUUAAGUA
...(((((((....))))).....((((((.....)))))).......))...(((((((((((............(((((.....)))))...(.....))))))))))))........ ( -27.30)
>consensus
AACGCGGCUCAAAGGAGCCUAAUUAAAGUAAAUCAUGUUUUUCAUAACGCACCCUAAUUACUUCACUAUUCAAAUCGAACUUUCCAAGUUCCACGUCGCCCGAAGUAAUUGGAUUAAGUA
...(((((((....))))).................(((......)))))...(((((((((((............(((((.....)))))...(.....))))))))))))........ (-23.25 = -23.37 +   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 12:33:24 2006