Locus 1357

Sequence ID 2R_DroMel_CAF1
Location 5,233,425 – 5,233,526
Length 101
Max. P 0.969597
window2343 window2344

overview

Window 3

Location 5,233,425 – 5,233,526
Length 101
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 83.23
Mean single sequence MFE -28.73
Consensus MFE -21.36
Energy contribution -22.55
Covariance contribution 1.19
Combinations/Pair 1.08
Mean z-score -2.09
Structure conservation index 0.74
SVM decision value 1.06
SVM RNA-class probability 0.909379
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5233425 101 + 20766785
CAGAAUUGGAAUCGGAGGGAAUUAUGUU-CAGGCACUCGGACAAAUGUCAUCCGAGAUUUGCCUCAAGUGUCGACAACACAUC----------ACAAAA-AUCCUGCCGUUCC
.......((((.(((.((((.((.(((.-.(((((((((((.........))))))...)))))...((((.....))))...----------))).))-.)))).))))))) ( -30.90)
>DroSec_CAF1 108968 111 + 1
CAGAAUUGGAAUCGGAGGGAAUUAUGUU-CAGGCACUCGGACAAAUGUCAUCCGAGAUUUGUCUCAAGUGUCGACAACACAUCGCAACACAACACAAAA-AUCCUGCCGUUCC
.......((((.(((.((((.((.(((.-..((((((.((((((((.((....)).))))))).).))))))((.......))..........))).))-.)))).))))))) ( -32.10)
>DroEre_CAF1 109840 100 + 1
-------GGAAUCGGAGGGAAUUAUGUUCCAGGCACUCGGACAAAUGUCAUCCGAGAUUUGCCACAAGUGUCGAUAGCCC-----AAUACAUCACAAAA-AUCCUGCCGUUCC
-------((((.(((.((((.((.(((....((((((((((.........))))))...))))....((((.(......)-----.))))...))).))-.)))).))))))) ( -29.30)
>DroYak_CAF1 110615 100 + 1
-------GGAAUCGGAGAGAAUUAUGUU-CAGGCACUCGAACAAAUGUCAUCCGAGAUUUGCCUCAAGUGUCGAUACCAC-----AACACAUCACAAAAAACCCGGCCGUUCC
-------((((.(((...((((...)))-).((((((.((.(((((.((....)).)))))..)).))))))........-----.....................))))))) ( -22.60)
>consensus
_______GGAAUCGGAGGGAAUUAUGUU_CAGGCACUCGGACAAAUGUCAUCCGAGAUUUGCCUCAAGUGUCGACAACAC_____AACACAUCACAAAA_AUCCUGCCGUUCC
.......((((.(((.((((...........((((((((((.........))))))...))))....((((.....)))).....................)))).))))))) (-21.36 = -22.55 +   1.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,233,425 – 5,233,526
Length 101
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 83.23
Mean single sequence MFE -34.60
Consensus MFE -26.76
Energy contribution -27.20
Covariance contribution 0.44
Combinations/Pair 1.10
Mean z-score -2.38
Structure conservation index 0.77
SVM decision value 1.64
SVM RNA-class probability 0.969597
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5233425 101 - 20766785
GGAACGGCAGGAU-UUUUGU----------GAUGUGUUGUCGACACUUGAGGCAAAUCUCGGAUGACAUUUGUCCGAGUGCCUG-AACAUAAUUCCCUCCGAUUCCAAUUCUG
(((((((..(((.-..((((----------(..(((((...)))))((.(((((...((((((..(...)..))))))))))).-))))))).)))..))).))))....... ( -37.00)
>DroSec_CAF1 108968 111 - 1
GGAACGGCAGGAU-UUUUGUGUUGUGUUGCGAUGUGUUGUCGACACUUGAGACAAAUCUCGGAUGACAUUUGUCCGAGUGCCUG-AACAUAAUUCCCUCCGAUUCCAAUUCUG
(((((((..(((.-..(((((((......((((.....)))).((((((.(((((((.((....)).)))))))))))))....-))))))).)))..))).))))....... ( -36.70)
>DroEre_CAF1 109840 100 - 1
GGAACGGCAGGAU-UUUUGUGAUGUAUU-----GGGCUAUCGACACUUGUGGCAAAUCUCGGAUGACAUUUGUCCGAGUGCCUGGAACAUAAUUCCCUCCGAUUCC-------
(((((((..(((.-..(((((..((.((-----((....)))).))....((((...((((((..(...)..)))))))))).....))))).)))..))).))))------- ( -31.40)
>DroYak_CAF1 110615 100 - 1
GGAACGGCCGGGUUUUUUGUGAUGUGUU-----GUGGUAUCGACACUUGAGGCAAAUCUCGGAUGACAUUUGUUCGAGUGCCUG-AACAUAAUUCUCUCCGAUUCC-------
(((((((..(((....(((((..(((((-----(......))))))((.(((((...((((((..(...)..))))))))))).-)))))))..))).))).))))------- ( -33.30)
>consensus
GGAACGGCAGGAU_UUUUGUGAUGUGUU_____GUGUUAUCGACACUUGAGGCAAAUCUCGGAUGACAUUUGUCCGAGUGCCUG_AACAUAAUUCCCUCCGAUUCC_______
(((((((..(((....(((((............(((.......)))...(((((...((((((..(...)..)))))))))))....))))).)))..))).))))....... (-26.76 = -27.20 +   0.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:00 2006