Locus 1720

Sequence ID X_DroMel_CAF1
Location 4,790,931 – 4,791,064
Length 133
Max. P 0.985985
window2824 window2825 window2826 window2827

overview

Window 4

Location 4,790,931 – 4,791,024
Length 93
Sequences 3
Columns 93
Reading direction forward
Mean pairwise identity 84.53
Mean single sequence MFE -17.07
Consensus MFE -15.50
Energy contribution -15.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 0.91
SVM decision value 2.03
SVM RNA-class probability 0.985985
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4790931 93 + 22224390
AGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGCUCUGCUGCCUUUUCAAAUUUUCAAUCC
.((((............(((....)))....(((((((((((((.....)))))))))......))))........))))............. ( -18.20)
>DroSec_CAF1 36721 75 + 1
AGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAU-----------------UA-AAUUUUCAAUCC
.((((.....(((.((.(((....))).)).))).(((((((((.....)))))))))...-----------------..-...))))..... ( -15.50)
>DroSim_CAF1 23174 92 + 1
AGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGCACUGCUGCCCAUUC-AAUUUUCAGUCC
.((((.....(((.((.(((....))).)).))).(((((((((.....)))))))))....((((...)))).......-...))))..... ( -17.50)
>consensus
AGAAAUCAUAUUCAAAUUGCAUAUGCACUUCGAGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGC_CUGCUGCC__UUC_AAUUUUCAAUCC
.((((.....(((.((.(((....))).)).))).(((((((((.....)))))))))..........................))))..... (-15.50 = -15.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,790,931 – 4,791,024
Length 93
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 84.53
Mean single sequence MFE -20.70
Consensus MFE -18.20
Energy contribution -18.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.88
SVM decision value 1.02
SVM RNA-class probability 0.900828
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4790931 93 - 22224390
GGAUUGAAAAUUUGAAAAGGCAGCAGAGCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCU
.............((((...((((...))))....(((((((((.....)))))))))..(((((.(((....))).)))))......)))). ( -21.00)
>DroSec_CAF1 36721 75 - 1
GGAUUGAAAAUU-UA-----------------AUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCU
.....((((...-..-----------------...(((((((((.....)))))))))..(((((.(((....))).)))))......)))). ( -18.20)
>DroSim_CAF1 23174 92 - 1
GGACUGAAAAUU-GAAUGGGCAGCAGUGCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCU
............-....(((((((...))).....(((((((((.....)))))))))))))(((((.(((((.(.....).)))))))))). ( -22.90)
>consensus
GGAUUGAAAAUU_GAA__GGCAGCAG_GCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCUCGAAGUGCAUAUGCAAUUUGAAUAUGAUUUCU
.....((((..........................(((((((((.....)))))))))..(((((.(((....))).)))))......)))). (-18.20 = -18.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,790,963 – 4,791,064
Length 101
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 83.11
Mean single sequence MFE -22.70
Consensus MFE -19.29
Energy contribution -19.73
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.27
Structure conservation index 0.85
SVM decision value 1.40
SVM RNA-class probability 0.949971
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4790963 101 + 22224390
AGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGCUCUGCUGCCUUUUCAAAUUUUCAAUCCAUUUUCCGGACUACGAAUGUUUUCCAGCAUGAUCGGAAUC
.(.(((((((((.....))))))))))((((.(.(((((((.................(((.......)))....(((....)))))))).)).).)))). ( -21.70)
>DroSec_CAF1 36753 83 + 1
AGCGUAGGAAAAUCUGUUUUUCCUACCAU-----------------UA-AAUUUUCAAUCCAUUUUCCGGAUUCCGGAUGUUUUGCAGCAUGAUCGGAAUC
.(.(((((((((.....))))))))))..-----------------..-....................((((((((((((......))))..)))))))) ( -22.00)
>DroSim_CAF1 23206 100 + 1
AGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGCACUGCUGCCCAUUC-AAUUUUCAGUCCAUUUUCCGGAUUCCGGAUGUUUUCCAGCAUGAUCGGAAUC
.(.(((((((((.....))))))))))...((((...)))).......-....................((((((((((((......))))..)))))))) ( -24.40)
>consensus
AGCGUAGGAAAAUCUGUUUUUCCUACCAUUCAGC_CUGCUGCC__UUC_AAUUUUCAAUCCAUUUUCCGGAUUCCGGAUGUUUUCCAGCAUGAUCGGAAUC
.(.(((((((((.....))))))))))..........................................((((((((((((......))))..)))))))) (-19.29 = -19.73 +   0.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,790,963 – 4,791,064
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 83.11
Mean single sequence MFE -24.40
Consensus MFE -17.25
Energy contribution -17.37
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.03
Structure conservation index 0.71
SVM decision value 0.47
SVM RNA-class probability 0.750322
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4790963 101 - 22224390
GAUUCCGAUCAUGCUGGAAAACAUUCGUAGUCCGGAAAAUGGAUUGAAAAUUUGAAAAGGCAGCAGAGCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCU
..(((((.......)))))..(((((.(((((((.....)))))))............(((......))))))))(((((((((.....)))))))))... ( -27.00)
>DroSec_CAF1 36753 83 - 1
GAUUCCGAUCAUGCUGCAAAACAUCCGGAAUCCGGAAAAUGGAUUGAAAAUU-UA-----------------AUGGUAGGAAAAACAGAUUUUCCUACGCU
(((....)))..((..(((..(((((((...)))))...))..)))......-..-----------------...(((((((((.....))))))))))). ( -19.80)
>DroSim_CAF1 23206 100 - 1
GAUUCCGAUCAUGCUGGAAAACAUCCGGAAUCCGGAAAAUGGACUGAAAAUU-GAAUGGGCAGCAGUGCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCU
...((((.(((..(((((.....)))))..((((.....))))........)-)).))))((((...))))....(((((((((.....)))))))))... ( -26.40)
>consensus
GAUUCCGAUCAUGCUGGAAAACAUCCGGAAUCCGGAAAAUGGAUUGAAAAUU_GAA__GGCAGCAG_GCUGAAUGGUAGGAAAAACAGAUUUUCCUACGCU
.....(((((....((.....))((((.....)))).....))))).............................(((((((((.....)))))))))... (-17.25 = -17.37 +   0.11)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:29 2006