Locus 812

Sequence ID 3R_DroMel_CAF1
Location 2,770,977 – 2,771,073
Length 96
Max. P 0.896079
window1294 window1295

overview

Window 4

Location 2,770,977 – 2,771,073
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.99
Mean single sequence MFE -24.37
Consensus MFE -12.52
Energy contribution -12.55
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -2.17
Structure conservation index 0.51
SVM decision value 0.95
SVM RNA-class probability 0.888019
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2770977 96 + 27905053
------UGC-GGC-A-AAUGGCGAAAUGAUUGC-UUUUUAUGACCUCAUAAAAUUAGAUACAAAUCGCUUUGUCGACGUUUAUCUUU-UGCUC-------------GGUAUCUCCAUCUC
------..(-(((-(-(..(((((..(((((..-.(((((((....)))))))...))).))..)))))))))))............-.....-------------((.....))..... ( -20.80)
>DroPse_CAF1 76856 105 + 1
------GGC-GGC-AUUAUGGCAAAAUGAUUGCCUUUUUAUGACCUCAUAAAAUUAGAUACAAAUCGCUUUGUCGACGUUUAUCUUUUUGGUC-------GUCUGCCAUUGCUCCAUCUC
------((.-(((-(..((((((....(((.((..(((((((....)))))))...(((....)))))...)))((((.(((......))).)-------)))))))))))))))..... ( -26.60)
>DroGri_CAF1 89588 96 + 1
UGAGUCUGGGGCC-A-AAUGGCAAAAUGAUUGC-UUUUUAUGACCUCAUAAAAUUAGAUACAAAUCGCUCUGUCGACAUUUAUCUU---------------------UUCUCUCUCUAUC
.(((...((((((-.-...)))....((((.((-.(((((((....)))))))...(((....)))))...))))...........---------------------..))).))).... ( -17.80)
>DroWil_CAF1 62382 105 + 1
------UGC-GGCCA-AAUGGCAAAAUGAUUGC-UUUUUAUGACCUCAUAAAAUUAGAUACAAAUCGUUUUGUCGACAUUUAUCUAU-CGCUAUGUUGUGG-----AGUGUCUUUAGCUU
------.((-.....-...((((((((((((.(-((((((((....)))))))..)).....))))))))))))(((((...(((((-.((...)).))))-----))))))....)).. ( -26.50)
>DroMoj_CAF1 96007 97 + 1
UGAGACUGGGGCC-A-AAUGGCAAAAUGAUUGC-UUUUUAUGACCUCAUAAAAUUAGAUACAAAUCGCUUUGUCGACGUUUAUCUC--------------------AGUCUCUCCCUCUC
.((((((((((..-(-(.(((((((.(((((.(-((((((((....)))))))..)).....))))).)))))))...))..))))--------------------))))))........ ( -27.90)
>DroPer_CAF1 76389 105 + 1
------GGC-GGC-AUUAUGGCAAAAUGAUUGCCUUUUUAUGACCUCAUAAAAUUAGAUACAAAUCGCUUUGUCGACGUUUAUCUUUUUGGUC-------GUCUGCCAUUGCUCCAUCUC
------((.-(((-(..((((((....(((.((..(((((((....)))))))...(((....)))))...)))((((.(((......))).)-------)))))))))))))))..... ( -26.60)
>consensus
______UGC_GGC_A_AAUGGCAAAAUGAUUGC_UUUUUAUGACCUCAUAAAAUUAGAUACAAAUCGCUUUGUCGACGUUUAUCUUU_UG_UC_____________AGUCUCUCCAUCUC
..................(((((((.(((((.(..(((((((....)))))))...).....))))).)))))))............................................. (-12.52 = -12.55 +   0.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,770,977 – 2,771,073
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.99
Mean single sequence MFE -24.05
Consensus MFE -13.73
Energy contribution -13.90
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.57
SVM decision value 0.99
SVM RNA-class probability 0.896079
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2770977 96 - 27905053
GAGAUGGAGAUACC-------------GAGCA-AAAGAUAAACGUCGACAAAGCGAUUUGUAUCUAAUUUUAUGAGGUCAUAAAAA-GCAAUCAUUUCGCCAUU-U-GCC-GCA------
.((((((.((....-------------..((.-..(((((...((((......))))...)))))..(((((((....))))))).-)).......)).)))))-)-...-...------ ( -20.42)
>DroPse_CAF1 76856 105 - 1
GAGAUGGAGCAAUGGCAGAC-------GACCAAAAAGAUAAACGUCGACAAAGCGAUUUGUAUCUAAUUUUAUGAGGUCAUAAAAAGGCAAUCAUUUUGCCAUAAU-GCC-GCC------
.............((((...-------((((....(((((...((((......))))...)))))..((....)))))).......(((((.....)))))....)-)))-...------ ( -25.10)
>DroGri_CAF1 89588 96 - 1
GAUAGAGAGAGAA---------------------AAGAUAAAUGUCGACAGAGCGAUUUGUAUCUAAUUUUAUGAGGUCAUAAAAA-GCAAUCAUUUUGCCAUU-U-GGCCCCAGACUCA
....(((.((((.---------------------.(((((...((((......))))...)))))..)))).((.(((((......-((((.....))))....-)-)))).))..))). ( -21.90)
>DroWil_CAF1 62382 105 - 1
AAGCUAAAGACACU-----CCACAACAUAGCG-AUAGAUAAAUGUCGACAAAACGAUUUGUAUCUAAUUUUAUGAGGUCAUAAAAA-GCAAUCAUUUUGCCAUU-UGGCC-GCA------
..((..........-----......(((((.(-.((((((...((((......))))...)))))).).))))).(((((......-((((.....))))....-)))))-)).------ ( -23.70)
>DroMoj_CAF1 96007 97 - 1
GAGAGGGAGAGACU--------------------GAGAUAAACGUCGACAAAGCGAUUUGUAUCUAAUUUUAUGAGGUCAUAAAAA-GCAAUCAUUUUGCCAUU-U-GGCCCCAGUCUCA
........((((((--------------------((((((...((((......))))...)))))..........(((((......-((((.....))))....-)-)))).))))))). ( -28.10)
>DroPer_CAF1 76389 105 - 1
GAGAUGGAGCAAUGGCAGAC-------GACCAAAAAGAUAAACGUCGACAAAGCGAUUUGUAUCUAAUUUUAUGAGGUCAUAAAAAGGCAAUCAUUUUGCCAUAAU-GCC-GCC------
.............((((...-------((((....(((((...((((......))))...)))))..((....)))))).......(((((.....)))))....)-)))-...------ ( -25.10)
>consensus
GAGAUGGAGAAACG_____________GA_CA_AAAGAUAAACGUCGACAAAGCGAUUUGUAUCUAAUUUUAUGAGGUCAUAAAAA_GCAAUCAUUUUGCCAUU_U_GCC_GCA______
...................................(((((...((((......))))...)))))..(((((((....)))))))..((((.....)))).................... (-13.73 = -13.90 +   0.17)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:47 2006