Locus 6657

Sequence ID 3L_DroMel_CAF1
Location 17,724,524 – 17,724,661
Length 137
Max. P 0.999834
window10825 window10826 window10827

overview

Window 5

Location 17,724,524 – 17,724,632
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.06
Mean single sequence MFE -36.64
Consensus MFE -30.82
Energy contribution -30.90
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -2.00
Structure conservation index 0.84
SVM decision value 1.51
SVM RNA-class probability 0.960324
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17724524 108 + 23771897
GUAGAAGCGGAUAGGGGUGCGG------------AUGCGGAUACGGCUGAGACAAACGAUUUGGCGUUUGUCGAGCUGAAAUUGCUGCAUUUGCCUAAUGAACAAAUGGAAGCGGGCACC
......(((..((..((.((((------------((((((...(((((..((((((((......)))))))).)))))......))))))))))))..))..)...((....)).))... ( -36.00)
>DroSec_CAF1 5853 99 + 1
---------GAUAGGGGUGCGG------------AUGCGAAUACGGCUGAGACAAACGAUUUGGCGUUUGUCGAGCUGAAAUUGCUGCAUUUGCCUAAUGAACAAACGGAAGCGGGCACC
---------......(((((((------------(((((....(((((..((((((((......)))))))).))))).......)))))))..............((....)).))))) ( -31.50)
>DroSim_CAF1 6072 108 + 1
GUAGAAGCGGAUAGGGGUGCGG------------AUGCGGAUACGGCUGAGACAAACGAUUUGGCGUUUGUCGAGCUGAAAUUGCUGCAUUUGCCUAAUGAACAAACGGAAGCGGGCACC
......(((..((..((.((((------------((((((...(((((..((((((((......)))))))).)))))......))))))))))))..))..)...((....)).))... ( -38.20)
>DroEre_CAF1 20164 120 + 1
GUAAAAGCGGAUAGGGGUGCGGAAGCGUAUGCGGAUGCGGAUACGGCUGAGACAAACGAUUUGGCGUUUGUAGAGCUGAAAUUGCUGCAUUUGCCUAAUGAACAAACGGAAGCGGGCACC
......((...(((..(((((....)))))((((((((((...(((((...(((((((......)))))))..)))))......))))))))))))).........((....)).))... ( -37.80)
>DroYak_CAF1 20552 120 + 1
GUAAAAGCGAAUAGGGGUGCGGAUGCGAAUACGGAUGCGGAUACAGCUGAGACAAACGAUUUGGCGUUUGUCGAGCUGGAAUUGCUGCAUUUGCCUAAUGAACAAACGGAAGCGGGCACC
...............(((((...(((.....(((((((((...(((((..((((((((......)))))))).)))))......)))))))))((............))..))).))))) ( -39.70)
>consensus
GUAAAAGCGGAUAGGGGUGCGG____________AUGCGGAUACGGCUGAGACAAACGAUUUGGCGUUUGUCGAGCUGAAAUUGCUGCAUUUGCCUAAUGAACAAACGGAAGCGGGCACC
...............(((((..............((((((...(((((..((((((((......)))))))).)))))......))))))................((....)).))))) (-30.82 = -30.90 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,724,524 – 17,724,632
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.06
Mean single sequence MFE -30.36
Consensus MFE -28.48
Energy contribution -28.52
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.80
Structure conservation index 0.94
SVM decision value 4.20
SVM RNA-class probability 0.999834
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17724524 108 - 23771897
GGUGCCCGCUUCCAUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAUCCGCAU------------CCGCACCCCUAUCCGCUUCUAC
(((((..(((..((((((((.....)))))))).))).......(((.((((((((......))))))))..)))...........------------..)))))............... ( -29.80)
>DroSec_CAF1 5853 99 - 1
GGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAUUCGCAU------------CCGCACCCCUAUC---------
(((((..(((..((((((((.....)))))))).))).......(((.((((((((......))))))))..)))...........------------..)))))......--------- ( -29.40)
>DroSim_CAF1 6072 108 - 1
GGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAUCCGCAU------------CCGCACCCCUAUCCGCUUCUAC
(((((..(((..((((((((.....)))))))).))).......(((.((((((((......))))))))..)))...........------------..)))))............... ( -29.40)
>DroEre_CAF1 20164 120 - 1
GGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCUACAAACGCCAAAUCGUUUGUCUCAGCCGUAUCCGCAUCCGCAUACGCUUCCGCACCCCUAUCCGCUUUUAC
(((((..(((..((((((((.....)))))))).))).......(((..(((((((......)))))))...)))(((((.((....)).))))).....)))))............... ( -29.70)
>DroYak_CAF1 20552 120 - 1
GGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUCCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCUGUAUCCGCAUCCGUAUUCGCAUCCGCACCCCUAUUCGCUUUUAC
(((((..(((..((((((((.....)))))))).))).....(((((.((((((((......))))))))..))))).......................)))))............... ( -33.50)
>consensus
GGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAUCCGCAU____________CCGCACCCCUAUCCGCUUCUAC
(((((..(((..((((((((.....)))))))).))).......(((.((((((((......))))))))..))).........................)))))............... (-28.48 = -28.52 +   0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,724,552 – 17,724,661
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.59
Mean single sequence MFE -26.04
Consensus MFE -18.49
Energy contribution -19.85
Covariance contribution 1.36
Combinations/Pair 1.16
Mean z-score -1.54
Structure conservation index 0.71
SVM decision value 0.06
SVM RNA-class probability 0.565467
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17724552 109 - 23771897
UUUUGGCCUAAU------CCCUCAUCGCUGU-----CUACGGUGCCCGCUUCCAUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAU
....(((.....------........((((.-----....((...))(((..((((((((.....)))))))).))).....))))..((((((((......))))))))...))).... ( -28.80)
>DroVir_CAF1 6682 104 - 1
UUUUGAUUGGAUUGGAUCCCCUUGUGCCUAU-----CAACAGU--------UCGCCUUUUCAUUAACCAACUGUUUCAAUUGCAACUCCACAAACGCCAAGUCGUUUUU-GCUGCUG--U
...((((.((...((....)).....)).))-----))(((((--------(.(............).)))))).......(((.(..((.(((((......))))).)-)..).))--) ( -13.50)
>DroSec_CAF1 5872 114 - 1
UUUUGGCCUAAU------CCCUCAUCGCUGUCAUCUCUACGGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAU
....(((.....------........((((.((((.....))))...(((..((((((((.....)))))))).))).....))))..((((((((......))))))))...))).... ( -30.10)
>DroSim_CAF1 6100 114 - 1
UUUUGGCCUAAU------CCCUCAUCGCUGUCAUCUCUACGGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAU
....(((.....------........((((.((((.....))))...(((..((((((((.....)))))))).))).....))))..((((((((......))))))))...))).... ( -30.10)
>DroEre_CAF1 20204 114 - 1
UUUUGGCCCAAU------CCCUCAUCGUUGUCAUCUCUACGGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCUACAAACGCCAAAUCGUUUGUCUCAGCCGUAU
....(((.....------....((((((.(......).))))))...(((..((((((((.....)))))))).)))............(((((((......)))))))....))).... ( -24.20)
>DroYak_CAF1 20592 114 - 1
UUUUGGCCCAAU------CCCUCAUCGCUGUCAUCUCUACGGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUCCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCUGUAU
....(((((...------......................)).))).(((..((((((((.....)))))))).))).....(((((.((((((((......))))))))..)))))... ( -29.51)
>consensus
UUUUGGCCUAAU______CCCUCAUCGCUGUCAUCUCUACGGUGCCCGCUUCCGUUUGUUCAUUAGGCAAAUGCAGCAAUUUCAGCUCGACAAACGCCAAAUCGUUUGUCUCAGCCGUAU
.....................................((((((....(((..((((((((.....)))))))).)))...........((((((((......))))))))...)))))). (-18.49 = -19.85 +   1.36)

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 12:26:43 2006