Locus 1275

Sequence ID 2R_DroMel_CAF1
Location 5,007,624 – 5,007,743
Length 119
Max. P 0.805037
window2209 window2210

overview

Window 9

Location 5,007,624 – 5,007,714
Length 90
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 81.55
Mean single sequence MFE -28.25
Consensus MFE -19.00
Energy contribution -19.67
Covariance contribution 0.67
Combinations/Pair 1.05
Mean z-score -2.13
Structure conservation index 0.67
SVM decision value 0.63
SVM RNA-class probability 0.805037
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5007624 90 + 20766785
UGUC--UCUGUGUGUGUGCUUCAACUGCUAUCUAAUUGCCUUGAUGCAGUUGCAGUUGCAAUAAGUUGAGUGUAUCUCAAAGAUACGCGAUG-
.(((--.((...((((.(((.(((((((.(((..........)))))))))).)))))))...))....(((((((.....)))))))))).- ( -26.20)
>DroPse_CAF1 63027 93 + 1
CGUCCGUAUCUGUGGCUGUUUCGACUGCUAUCUAAUUGCCCCGAUGCAGUUGCAGUUGCAAUGAGUGGAGUGUAUCUUUAAGAUACGCGGCCC
.....(((.(((..(((((.(((...((.........))..))).)))))..))).))).......((.(((((((.....)))))))..)). ( -32.30)
>DroSim_CAF1 64143 90 + 1
UGUC--UCUGUGUGUGUGCUUCAACUGCUAUCUAAUUGCCUUGAUGCAGUUGCAGUUGCAAUAAGUUGAGUGUAUCUCAAAGAUACGCGGCG-
.(((--.((...((((.(((.(((((((.(((..........)))))))))).)))))))...))....(((((((.....)))))))))).- ( -27.70)
>DroYak_CAF1 66831 90 + 1
GCUC--UGUGUGUGUGUGUUUCAACUGCUAUCUAAUUGCCUUGAUGCAGUUGCAGUUGCAAUAAGUUGAGUGUAUCUCAAAGAUACGCGCUG-
....--.((((((((.((((.(((((((.....((((((......))))))))))))).))))..(((((.....)))))..))))))))..- ( -28.30)
>DroAna_CAF1 62642 77 + 1
GCCA--GGUCUG-------------CGCUAUCUAAUUGCCUUGAUGCAGUUGCAGUUGCAAUAAGUUGAGUGUAUCUUUAAGAUACGCGACU-
....--((((.(-------------((.(((((((.(((((..((...(((((....)))))..))..)).)))...)).))))))))))))- ( -22.70)
>DroPer_CAF1 63217 93 + 1
CGUCCGUAUCUGUGGCUGUUUCGACUGCUAUCUAAUUGCCCCGAUGCAGUUGCAGUUGCAAUGAGUGGAGUGUAUCUUUAAGAUACGCGGCCC
.....(((.(((..(((((.(((...((.........))..))).)))))..))).))).......((.(((((((.....)))))))..)). ( -32.30)
>consensus
CGUC__UAUCUGUGUGUGUUUCAACUGCUAUCUAAUUGCCUUGAUGCAGUUGCAGUUGCAAUAAGUUGAGUGUAUCUCAAAGAUACGCGGCG_
.....................(((((((.....((((((......)))))))))))))...........(((((((.....)))))))..... (-19.00 = -19.67 +   0.67)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,007,647 – 5,007,743
Length 96
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.15
Mean single sequence MFE -23.35
Consensus MFE -16.02
Energy contribution -16.02
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.69
SVM decision value 0.24
SVM RNA-class probability 0.649195
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5007647 96 - 20766785
AUAAAACACAGAAAUUGGUU---GGGGGAACA------CAUCGCGUAUCUUUGAGAUACACUCAACUUAUUGCAACUGCAACUGCAUCAAGGCAAUUAGAUAGCA
................((((---(((.((...------..))..(((((.....))))).))))))).(((((...(((....))).....)))))......... ( -17.90)
>DroSec_CAF1 61813 96 - 1
AUAAAACACAGAAAGUGGUG---GGGGGAGCA------CACCGCGUAUCUUUGAGAUACACUCAACUUAUUGCAACUGCAACUGCAUCAAGGCAAUUAGAUAGCA
..........((..((((((---..(....).------))))))(((((.....)))))..))..((.(((((...(((....))).....))))).))...... ( -23.70)
>DroSim_CAF1 64166 96 - 1
AUAAGACACAGAAAGUGGUG---GGGGGAACA------CGCCGCGUAUCUUUGAGAUACACUCAACUUAUUGCAACUGCAACUGCAUCAAGGCAAUUAGAUAGCA
..........((..((((((---..(....).------))))))(((((.....)))))..))..((.(((((...(((....))).....))))).))...... ( -24.30)
>DroYak_CAF1 66854 96 - 1
AUAAAACACAGAAAGUGGUG---AGGGGAACA------CAGCGCGUAUCUUUGAGAUACACUCAACUUAUUGCAACUGCAACUGCAUCAAGGCAAUUAGAUAGCA
......(((.....)))((.---..(....).------..))(((((((.....)))))......((.(((((...(((....))).....))))).))...)). ( -20.00)
>DroAna_CAF1 62652 88 - 1
-----AGGCAGAAAACGGCC---AACUAA---------AGUCGCGUAUCUUAAAGAUACACUCAACUUAUUGCAACUGCAACUGCAUCAAGGCAAUUAGAUAGCG
-----.(((........)))---......---------...((((((((.....)))))......((.(((((...(((....))).....))))).))...))) ( -20.90)
>DroPer_CAF1 63242 96 - 1
---------AGAGAGUGGGGGAGAGAGGAACCGAGUGGGGCCGCGUAUCUUAAAGAUACACUCCACUCAUUGCAACUGCAACUGCAUCGGGGCAAUUAGAUAGCA
---------...((((((((....(.((..((....))..)).)(((((.....))))).))))))))(((((..((((....)))..)..)))))......... ( -33.30)
>consensus
AUAAAACACAGAAAGUGGUG___AGGGGAACA______CACCGCGUAUCUUUGAGAUACACUCAACUUAUUGCAACUGCAACUGCAUCAAGGCAAUUAGAUAGCA
..........................................(((((((.....)))))......((.(((((...(((....))).....))))).))...)). (-16.02 = -16.02 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:43 2006