Locus 2984

Sequence ID 2R_DroMel_CAF1
Location 10,288,746 – 10,288,887
Length 141
Max. P 0.930234
window4930 window4931 window4932

overview

Window 0

Location 10,288,746 – 10,288,850
Length 104
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.70
Mean single sequence MFE -34.92
Consensus MFE -21.67
Energy contribution -22.65
Covariance contribution 0.98
Combinations/Pair 1.28
Mean z-score -1.72
Structure conservation index 0.62
SVM decision value 0.38
SVM RNA-class probability 0.713671
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10288746 104 + 20766785
UUGGGGCCU--GCCAAU-----------AGCCUCAUUUAGUAGUAAUAUUAUUUGGUUGACGUCACCAGUUG---GGUGCUAUAGCCCUGUGUAUUGCAGGUGGGCAGGGCGAAGGGAUU
....(.(((--(((.((-----------(((((((..(((((....))))).(((((.(....)))))).))---)).)))))..((((((.....))))).))))))).)......... ( -35.70)
>DroVir_CAF1 8903 109 + 1
UCGGAGCCUGGGCCAAC-----------AGCUUCCCUUAAUAAUAAUAUUAUUUGGUUGAUGUCACCAGCUGACUGGUGCUAUAGCCCUGUGUGUUGCAGGUGGGCAGGGCGAAUGGGUU
(((..((((..(((..(-----------((((.....(((((....)))))...)))))(((.((((((....)))))).)))..((((((.....))))).)))).))))...)))... ( -33.30)
>DroGri_CAF1 4912 109 + 1
CAAGAGCAGUGGCCAAU-----------AGCCUCAUUUAAUAAUAAUAUUAUUUGGUUGAUGUCACCAGCUGACUGGUGCUGUAGCCCUGUGUAUUGCAGGUGGGCAGGGCAAAUGGAUU
.....((((((((...(-----------((((.....(((((....)))))...)))))..)))(((((....)))))))))).(((((((.(((.....))).)))))))......... ( -34.40)
>DroWil_CAF1 22355 115 + 1
---GAGCCC--UCCAAUUUAUUUCUUUUUUUUUCGUUUAAUAAUAGUAUUAUUUGGUUGAGGUCACCAACUGGCUGGUGCUAUAGCCCUGGGUAUUACAGGUGGGCAGGGCGAAGGGAUU
---...(((--(.(............................(((((((((.(..((((.(....)))))..).))))))))).((((((..(((.....)))..))))))).))))... ( -33.40)
>DroMoj_CAF1 5308 107 + 1
UC-CAGCCA-GGACAUC-----------CGACUAACUUAAUAAUAAUAUUAUUUACUGGAUGUCACCAGCUGACUGGUGCUAUAGCCCUGUGUGUUGCAGGUGGGCAGGGCAAAUGGAUU
((-((((..-.((((((-----------((..(((..(((((....))))).))).))))))))(((((....))))))))...(((((((.(.........).)))))))....))).. ( -35.70)
>DroAna_CAF1 7502 107 + 1
UGGUGGCCU--GCCAAU-----------AGCCUCAUUUAGUAGUAAUAUUAUUUGGUUGACGUCACCAGCUGACUGGUGCUAUAGCCCUGGGUAUUGCAGGUGGGCAGGGCGAAGGGAUU
...((.(((--(((...-----------.((((.........((((((((....(((((..(.((((((....)))))))..)))))...)))))))))))).)))))).))........ ( -37.00)
>consensus
UCGGAGCCU__GCCAAU___________AGCCUCAUUUAAUAAUAAUAUUAUUUGGUUGAUGUCACCAGCUGACUGGUGCUAUAGCCCUGUGUAUUGCAGGUGGGCAGGGCGAAGGGAUU
......(((...................((((.....(((((....)))))...))))...(.((((((....)))))))....(((((((.(((.....))).)))))))...)))... (-21.67 = -22.65 +   0.98)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,288,746 – 10,288,850
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.70
Mean single sequence MFE -28.10
Consensus MFE -18.04
Energy contribution -18.77
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -2.36
Structure conservation index 0.64
SVM decision value 1.20
SVM RNA-class probability 0.930234
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10288746 104 - 20766785
AAUCCCUUCGCCCUGCCCACCUGCAAUACACAGGGCUAUAGCACC---CAACUGGUGACGUCAACCAAAUAAUAUUACUACUAAAUGAGGCU-----------AUUGGC--AGGCCCCAA
...........((((((..((((.......))))...(((((...---....((((.......)))).............((.....)))))-----------)).)))--)))...... ( -22.80)
>DroVir_CAF1 8903 109 - 1
AACCCAUUCGCCCUGCCCACCUGCAACACACAGGGCUAUAGCACCAGUCAGCUGGUGACAUCAACCAAAUAAUAUUAUUAUUAAGGGAAGCU-----------GUUGGCCCAGGCUCCGA
.........(((.(((......))).......(((((((((((((((....)))))........((...(((((....)))))..))..)))-----------).)))))).)))..... ( -32.20)
>DroGri_CAF1 4912 109 - 1
AAUCCAUUUGCCCUGCCCACCUGCAAUACACAGGGCUACAGCACCAGUCAGCUGGUGACAUCAACCAAAUAAUAUUAUUAUUAAAUGAGGCU-----------AUUGGCCACUGCUCUUG
....(((((((((((...............))))))....(((((((....)))))).).......................))))).(((.-----------....))).......... ( -26.46)
>DroWil_CAF1 22355 115 - 1
AAUCCCUUCGCCCUGCCCACCUGUAAUACCCAGGGCUAUAGCACCAGCCAGUUGGUGACCUCAACCAAAUAAUACUAUUAUUAAACGAAAAAAAAAGAAAUAAAUUGGA--GGGCUC---
...((((((((((((...............)))))).....((((((....)))))).................................................)))--)))...--- ( -26.06)
>DroMoj_CAF1 5308 107 - 1
AAUCCAUUUGCCCUGCCCACCUGCAACACACAGGGCUAUAGCACCAGUCAGCUGGUGACAUCCAGUAAAUAAUAUUAUUAUUAAGUUAGUCG-----------GAUGUCC-UGGCUG-GA
.........((((((...............))))))...........(((((..(.((((((((.(((.(((((....)))))..))).).)-----------)))))))-..))))-). ( -34.26)
>DroAna_CAF1 7502 107 - 1
AAUCCCUUCGCCCUGCCCACCUGCAAUACCCAGGGCUAUAGCACCAGUCAGCUGGUGACGUCAACCAAAUAAUAUUACUACUAAAUGAGGCU-----------AUUGGC--AGGCCACCA
.........(.((((((..((((.......))))(((...(((((((....)))))).).............((((.......)))).))).-----------...)))--))).).... ( -26.80)
>consensus
AAUCCAUUCGCCCUGCCCACCUGCAAUACACAGGGCUAUAGCACCAGUCAGCUGGUGACAUCAACCAAAUAAUAUUAUUAUUAAAUGAGGCU___________AUUGGC__AGGCUCCGA
.........(((..(((..((((.......))))......(((((((....)))))).)...............................................)))...)))..... (-18.04 = -18.77 +   0.72)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,288,773 – 10,288,887
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.83
Mean single sequence MFE -27.12
Consensus MFE -22.69
Energy contribution -21.94
Covariance contribution -0.75
Combinations/Pair 1.24
Mean z-score -1.39
Structure conservation index 0.84
SVM decision value -0.03
SVM RNA-class probability 0.515804
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10288773 114 - 20766785
-UGUUUAACUA--UUUGCAGGGGUCAGCAGCCUGAGCUUCAAUCCCUUCGCCCUGCCCACCUGCAAUACACAGGGCUAUAGCACC---CAACUGGUGACGUCAACCAAAUAAUAUUACUA
-(((((.....--.(((((((((...((((..((((..........))))..)))))).)))))))......((.......((((---.....)))).......)))))))......... ( -25.64)
>DroVir_CAF1 8932 118 - 1
UUUUUUUUUUA--CUUGCAGGAGUCAGCAGCUUGAGUUUCAACCCAUUCGCCCUGCCCACCUGCAACACACAGGGCUAUAGCACCAGUCAGCUGGUGACAUCAACCAAAUAAUAUUAUUA
...........--.(((((((.(...((((..(((((........)))))..)))).).)))))))......((.......((((((....)))))).......)).............. ( -30.14)
>DroGri_CAF1 4941 120 - 1
UUUCAAUCUUAUCGUUUCAGGGGUCAGCAGCUUGAGCUUCAAUCCAUUUGCCCUGCCCACCUGCAAUACACAGGGCUACAGCACCAGUCAGCUGGUGACAUCAACCAAAUAAUAUUAUUA
....(((..(((..(((..((.((((.(((((.((.((...........((((((...............)))))).........))))))))).)))).....)))))..)))..))). ( -26.31)
>DroWil_CAF1 22390 113 - 1
-UCUU----UC--GUUCCAGGAGUUAGCAGUUUAAGCUUCAAUCCCUUCGCCCUGCCCACCUGUAAUACCCAGGGCUAUAGCACCAGCCAGUUGGUGACCUCAACCAAAUAAUACUAUUA
-....----..--......(((...(((.......)))....)))....((((((...............)))))).....((((((....))))))....................... ( -22.46)
>DroMoj_CAF1 5335 118 - 1
GGUUUCUCUUA--CUUUCAGGAGUCAGCAGCUUGAGCUUCAAUCCAUUUGCCCUGCCCACCUGCAACACACAGGGCUAUAGCACCAGUCAGCUGGUGACAUCCAGUAAAUAAUAUUAUUA
........(((--((....(((((((.(((((.((.((...........((((((...............)))))).........))))))))).)))).))))))))............ ( -29.51)
>DroAna_CAF1 7529 113 - 1
-UUUUUG------AUUUCAGGGGUCAGCAGCCUGAGUUUCAAUCCCUUCGCCCUGCCCACCUGCAAUACCCAGGGCUAUAGCACCAGUCAGCUGGUGACGUCAACCAAAUAAUAUUACUA
-...(((------(.((((((.(....)..))))))..)))).......((((((...............))))))....(((((((....)))))).)..................... ( -28.66)
>consensus
_UUUUUU_UUA__CUUUCAGGAGUCAGCAGCUUGAGCUUCAAUCCAUUCGCCCUGCCCACCUGCAAUACACAGGGCUAUAGCACCAGUCAGCUGGUGACAUCAACCAAAUAAUAUUAUUA
...................((((((((....)))).)))).........((((((...............))))))....(((((((....)))))).)..................... (-22.69 = -21.94 +  -0.75)

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 10:44:36 2006