Locus 1425

Sequence ID 2R_DroMel_CAF1
Location 5,490,727 – 5,490,817
Length 90
Max. P 0.543770
window2435 window2436

overview

Window 5

Location 5,490,727 – 5,490,817
Length 90
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 80.78
Mean single sequence MFE -30.76
Consensus MFE -22.82
Energy contribution -22.93
Covariance contribution 0.11
Combinations/Pair 1.21
Mean z-score -1.15
Structure conservation index 0.74
SVM decision value 0.02
SVM RNA-class probability 0.543770
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5490727 90 + 20766785
C-CGCCCGUCCCGCUCGCUCCUGCGGAGCAAC-CGCCUGCGGGCGGGCGAGACAAAAGAUUCGCUCAUCCGCUAUGAAUAC--CAAAUCGGAA--------C
(-(((((((..((...(((((...)))))...-))...))))))))(((((.(....).)))))...((((...((.....--))...)))).--------. ( -33.60)
>DroVir_CAF1 12406 93 + 1
CACUCACGUCUCGUUCGCACCCGUGGCGCUGCCCGCUUGCGGACAAGCGAAACAAAAGAUUCGCUCAUACGCUAUGAAUAUAUGAAAUCGCAC---------
............(((((((..((.(((...)))))..)))))))..((((........((((((......))...))))........))))..--------- ( -23.59)
>DroSim_CAF1 11416 90 + 1
C-CGCCCGUCCCGCUCGCUCCUGCGGAGCAGC-CGCCUGCGGGCGGGCGAGACAAAAGAUUCGCUCAUCCGCUAUGAAUAC--CAAAUCGGAG--------C
(-(((((((.(.(((.(((((...))))))))-.)...))))))))(((((.(....).)))))...((((...((.....--))...)))).--------. ( -36.20)
>DroEre_CAF1 9400 98 + 1
C-CGCCCGUCCCGCUCGCUCCUGCGGAGCAGC-CGCCUGCGGGCGCGCGAGACAAAAGAUUCGCUCAUCCGCUAUGAAUAC--CAAAUCCAAGUCAGCGCGC
.-.((((((.(.(((.(((((...))))))))-.)...))))))((((..(((.........((......))..((.....--)).......))).)))).. ( -34.00)
>DroYak_CAF1 9558 93 + 1
--CGCCCGUCCCGCUCGCUCCUGCGGAGCAGC-CGCCUGCGGGCGGGCGAGACAAAAGAUUCGCUCAUCCGCUAUGAAUAC--CAAAUCCGAAU----GUGU
--((((((.(((((..((..((((...)))).-.))..))))))))))).......(.((((((......))..((.....--)).....))))----.).. ( -33.60)
>DroMoj_CAF1 18008 93 + 1
CACUCACGUCUCGUUCGCACCCGUGGCGCUGCCCGCUUGCGGACAAGCGAAACAAAAGAUUCGCUCAUACGCUAUGAAUAUAUGAAAUCGCAU---------
............(((((((..((.(((...)))))..)))))))..((((........((((((......))...))))........))))..--------- ( -23.59)
>consensus
C_CGCCCGUCCCGCUCGCUCCUGCGGAGCAGC_CGCCUGCGGGCGGGCGAGACAAAAGAUUCGCUCAUCCGCUAUGAAUAC__CAAAUCGGAA________C
.......(((.(((((((..((((((.((.....))))))))))))))).))).....((((((......))...))))....................... (-22.82 = -22.93 +   0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,490,727 – 5,490,817
Length 90
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.78
Mean single sequence MFE -37.72
Consensus MFE -25.92
Energy contribution -25.78
Covariance contribution -0.13
Combinations/Pair 1.20
Mean z-score -1.24
Structure conservation index 0.69
SVM decision value -0.02
SVM RNA-class probability 0.525210
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5490727 90 - 20766785
G--------UUCCGAUUUG--GUAUUCAUAGCGGAUGAGCGAAUCUUUUGUCUCGCCCGCCCGCAGGCG-GUUGCUCCGCAGGAGCGAGCGGGACGGGCG-G
(--------(((.((((((--.(((((.....)))))..))))))....((((((((((((....))))-)(((((((...)))))))))))))))))).-. ( -40.00)
>DroVir_CAF1 12406 93 - 1
---------GUGCGAUUUCAUAUAUUCAUAGCGUAUGAGCGAAUCUUUUGUUUCGCUUGUCCGCAAGCGGGCAGCGCCACGGGUGCGAACGAGACGUGAGUG
---------.............(((((((..(((..(((((((........)))))))(((((....))))).(((((...)))))..)))....))))))) ( -29.60)
>DroSim_CAF1 11416 90 - 1
G--------CUCCGAUUUG--GUAUUCAUAGCGGAUGAGCGAAUCUUUUGUCUCGCCCGCCCGCAGGCG-GCUGCUCCGCAGGAGCGAGCGGGACGGGCG-G
(--------(.((((((((--.(((((.....)))))..))))))....((((((((((((....))))-).((((((...)))))).))))))))))).-. ( -41.00)
>DroEre_CAF1 9400 98 - 1
GCGCGCUGACUUGGAUUUG--GUAUUCAUAGCGGAUGAGCGAAUCUUUUGUCUCGCGCGCCCGCAGGCG-GCUGCUCCGCAGGAGCGAGCGGGACGGGCG-G
(((((..(((..(((((((--.(((((.....)))))..)))))))...))).)))))(((((....(.-((((((((...))))).))).)..))))).-. ( -45.30)
>DroYak_CAF1 9558 93 - 1
ACAC----AUUCGGAUUUG--GUAUUCAUAGCGGAUGAGCGAAUCUUUUGUCUCGCCCGCCCGCAGGCG-GCUGCUCCGCAGGAGCGAGCGGGACGGGCG--
..((----(...(((((((--.(((((.....)))))..)))))))..)))..(((((((((((..((.-.((((...))))..))..))))).))))))-- ( -40.80)
>DroMoj_CAF1 18008 93 - 1
---------AUGCGAUUUCAUAUAUUCAUAGCGUAUGAGCGAAUCUUUUGUUUCGCUUGUCCGCAAGCGGGCAGCGCCACGGGUGCGAACGAGACGUGAGUG
---------.............(((((((..(((..(((((((........)))))))(((((....))))).(((((...)))))..)))....))))))) ( -29.60)
>consensus
G________CUCCGAUUUG__GUAUUCAUAGCGGAUGAGCGAAUCUUUUGUCUCGCCCGCCCGCAGGCG_GCUGCUCCGCAGGAGCGAGCGGGACGGGCG_G
.............((((((...(((((.....)))))..)))))).((((((((((.((((....)))).)).(((((...)))))....)))))))).... (-25.92 = -25.78 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:30 2006