Locus 1482

Sequence ID X_DroMel_CAF1
Location 4,417,350 – 4,417,620
Length 270
Max. P 0.999020
window2372 window2373 window2374 window2375

overview

Window 2

Location 4,417,350 – 4,417,463
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.43
Mean single sequence MFE -21.26
Consensus MFE -19.04
Energy contribution -19.36
Covariance contribution 0.32
Combinations/Pair 1.13
Mean z-score -1.74
Structure conservation index 0.90
SVM decision value 1.86
SVM RNA-class probability 0.980181
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4417350 113 + 22224390
AUGGGCAAAGUUGCCAAAUGCAACGAGCUAACAACCGCAUCUAGUGGUGCAUCAUGCAAUCUUCCUCUUCAAUUUCCAUUUA-------CCAUUUGCCGCAUUCAUAAAACAAACAAAAU
((((((((((((((.....)))))(((......(((((.....)))))((.....)).......)))...............-------...)))))).))).................. ( -23.80)
>DroSec_CAF1 19771 120 + 1
AUGGACAAAGUUGCCAAAUGCAACGAGCUAACAACCGCAUCUAGUGGUGCAUCAUGCAAUCUUCCUCUUCAACUUCCAUUUUCCAUUUUCCUUUUGCCGCAUUCAUAAAAUAAACAAAAU
..((.(((((((((.....)))))(((......(((((.....)))))((.....)).......))).........................))))))...................... ( -19.30)
>DroSim_CAF1 21217 120 + 1
AUGGCCAAAGUUGCCAAAUGCAACGAGCUAACAACCGCAUCUAGUGGUGCAUCAUGCAAUCUUCCUCUUCAACUUCCAUUUUCCAUUUUCCAUUUGCUGCAUUCAUAAAACAAACAAAAU
.((((.......))))((((((.((((......(((((.....)))))((.....))...................................)))).))))))................. ( -18.80)
>DroEre_CAF1 20820 113 + 1
AUGGGCAAAGUUGCCAAAUGCAACGAGCAAACAACCGCAUCUAGUGGUGCAUCAUGCAAUCUUCCUCUUCAAUUUCCAUUUU-------CCAUUUGCCGCAGUCAUAAAACAAACAAAAU
.(((((((((((((.....)))))(((......(((((.....)))))((.....)).......)))...............-------...)))))).))................... ( -23.70)
>DroYak_CAF1 20482 113 + 1
AUGGGCAGAGUUGCCAAAUGCAGCGACCAAACAACCGCAUCUAGUGGUGCAUCAUGCAAUCUUCCUCUUCAAUUUCCAUUUU-------CCAAUUGCCGCAUUCAAAAAACAAACAAAAU
...(((......))).(((((.((((.......(((((.....)))))((.....)).........................-------....)))).)))))................. ( -20.70)
>consensus
AUGGGCAAAGUUGCCAAAUGCAACGAGCUAACAACCGCAUCUAGUGGUGCAUCAUGCAAUCUUCCUCUUCAAUUUCCAUUUU_______CCAUUUGCCGCAUUCAUAAAACAAACAAAAU
.(((((((((((((.....)))))(((......(((((.....)))))((.....)).......))).........................)))))).))................... (-19.04 = -19.36 +   0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,417,430 – 4,417,543
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.51
Mean single sequence MFE -22.27
Consensus MFE -22.34
Energy contribution -22.40
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.24
Structure conservation index 1.00
SVM decision value 0.33
SVM RNA-class probability 0.693501
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4417430 113 - 22224390
UUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUUUUUCAUUUUUCUCUUUUGUAUUUUGUUUGUUUUAUGAAUGCGGCAAAUGG-------UA
(((((((((((((.(((((((..........)))))))...(((......)))..........................................)))))))))))))...-------.. ( -22.70)
>DroSec_CAF1 19851 113 - 1
UUUGUUGCAUUUAUGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUU-------UCUCUCUUUUGUAUUUUGUUUAUUUUAUGAAUGCGGCAAAAGGAAAAUGGAA
(((((((((((((((((((((..........)))))))...(((......)))........-------..........................))))))))))))))............ ( -23.80)
>DroSim_CAF1 21297 113 - 1
UUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUU-------UCUCUCUUUUGUAUUUUGUUUGUUUUAUGAAUGCAGCAAAUGGAAAAUGGAA
(((((((((((((.(((((((..........)))))))...(((......)))........-------...........................)))))))))))))............ ( -23.50)
>DroEre_CAF1 20900 108 - 1
UUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUUUU-----UUUCUCUUUUGUAUUUUGUUUGUUUUAUGACUGCGGCAAAUGG-------AA
(((((((((..((((((((((..........)))))))...(((......)))..........-----..........)))........(((....))))))))))))...-------.. ( -19.10)
>consensus
UUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUU_______UCUCUCUUUUGUAUUUUGUUUGUUUUAUGAAUGCGGCAAAUGG_______AA
(((((((((((((.(((((((..........)))))))...(((......)))..........................................)))))))))))))............ (-22.34 = -22.40 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,417,463 – 4,417,583
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.69
Mean single sequence MFE -33.28
Consensus MFE -31.28
Energy contribution -31.72
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.94
SVM decision value 3.33
SVM RNA-class probability 0.999020
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4417463 120 - 22224390
GGCAGCAGCAGCCGGUUGCUAGUUGCGCAUGCGCCUCAAAUUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUUUUUCAUUUUUCUCUUUUGU
(((.((((((((.....))).)))))(((.(.(((((......((.......))(((((((..........))))))).))))).).))))))........................... ( -32.30)
>DroSec_CAF1 19891 113 - 1
GGCAACAGCAGCCGGUUGCAGGUUGCGCAUGCGCCUCAAAUUUGUUGCAUUUAUGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUU-------UCUCUCUUUUGU
(((....((((((.......))))))(((.(.(((((.......(((((....)))))((.(((......))).))...))))).).))))))........-------............ ( -31.70)
>DroSim_CAF1 21337 113 - 1
GGCAACAGCAGCCGGUUGCAGGUUGCGCAUGCGCCUCAAAUUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUU-------UCUCUCUUUUGU
(((....((((((.......))))))(((.(.(((((......((.......))(((((((..........))))))).))))).).))))))........-------............ ( -32.90)
>DroEre_CAF1 20933 115 - 1
GGCAGCAGCAGCCGGUUGCUGGUUGCGCAUGCGCCUCAAAUUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUUUU-----UUUCUCUUUUGU
(((....((((((((...))))))))(((.(.(((((......((.......))(((((((..........))))))).))))).).))))))..........-----............ ( -34.40)
>DroYak_CAF1 20595 115 - 1
GGCAACAGCAGCCGGUUGCUGGUUGCGCAUGCGCCUCAAAUUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUUUGCGCCGUUUUAUUUU-----UUUCUCUUUUGU
(((....((((((((...))))))))(((...(((((......((.......))(((((((..........))))))).)))))...))))))..........-----............ ( -35.10)
>consensus
GGCAACAGCAGCCGGUUGCUGGUUGCGCAUGCGCCUCAAAUUUGUUGCAUUUACGCGAGAUAUUUAUUAUGAUUUCGCCGAGGUUUCUGCGCCGUUUUAUUUU_____UUUCUCUUUUGU
(((....((((((((...))))))))(((...(((((......((.......))(((((((..........))))))).)))))...))))))........................... (-31.28 = -31.72 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,417,503 – 4,417,620
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.47
Mean single sequence MFE -27.58
Consensus MFE -24.92
Energy contribution -25.52
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.90
SVM decision value 2.04
SVM RNA-class probability 0.986327
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4417503 117 + 22224390
CGGCGAAAUCAUAAUAAAUAUCUCGCGUAAAUGCAACAAAUUUGAGGCGCAUGCGCAACUAGCAACCGGCUGCUGCUGCCGUGUAAUUAACAAAAACAACAGAGAAGCC---CACCACCA
.((((....)..........(((((((((..(((..((....))..)))..)))))........((((((.......)))).)).................)))).)))---........ ( -26.20)
>DroSec_CAF1 19924 120 + 1
CGGCGAAAUCAUAAUAAAUAUCUCGCAUAAAUGCAACAAAUUUGAGGCGCAUGCGCAACCUGCAACCGGCUGCUGUUGCCGUGUAAUUAACAAAAACAACAGAGAAGCCAACCACCACCA
.((((....)..........(((((((....))).......((((...(((((.(((((..(((......))).))))))))))..))))...........)))).)))........... ( -27.10)
>DroSim_CAF1 21370 120 + 1
CGGCGAAAUCAUAAUAAAUAUCUCGCGUAAAUGCAACAAAUUUGAGGCGCAUGCGCAACCUGCAACCGGCUGCUGUUGCCGUGUAAUUAACAAAAACAACAGAGAAGCCAACCACCACCA
.((.(...................(((((..(((..((....))..)))..)))))...........((((.((((((...(((.....)))....))))))...))))...).)).... ( -28.80)
>DroEre_CAF1 20968 117 + 1
CGGCGAAAUCAUAAUAAAUAUCUCGCGUAAAUGCAACAAAUUUGAGGCGCAUGCGCAACCAGCAACCGGCUGCUGCUGCCGUGUAAUUAACAAAAACAACAGAGAAGCC---CACCACCA
.((((....)..........((((((.(((((.......)))))..))(((((.(((..(((((......))))).)))))))).................)))).)))---........ ( -26.30)
>DroYak_CAF1 20630 117 + 1
CGGCGAAAUCAUAAUAAAUAUCUCGCGUAAAUGCAACAAAUUUGAGGCGCAUGCGCAACCAGCAACCGGCUGCUGUUGCCGUGUAAUUAACAAAAACAACAGAGAAGCC---CAUCACCA
.((.((..................(((((..(((..((....))..)))..)))))...........((((.((((((...(((.....)))....))))))...))))---..)).)). ( -29.50)
>consensus
CGGCGAAAUCAUAAUAAAUAUCUCGCGUAAAUGCAACAAAUUUGAGGCGCAUGCGCAACCAGCAACCGGCUGCUGUUGCCGUGUAAUUAACAAAAACAACAGAGAAGCC___CACCACCA
.((.(...................(((((..(((..((....))..)))..)))))...........((((.((((((...(((.....)))....))))))...))))......).)). (-24.92 = -25.52 +   0.60)

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 10:10:38 2006