Locus 4928

Sequence ID X_DroMel_CAF1
Location 12,836,761 – 12,836,853
Length 92
Max. P 0.951855
window8040 window8041

overview

Window 0

Location 12,836,761 – 12,836,853
Length 92
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 66.60
Mean single sequence MFE -22.12
Consensus MFE -9.52
Energy contribution -9.47
Covariance contribution -0.05
Combinations/Pair 1.06
Mean z-score -2.05
Structure conservation index 0.43
SVM decision value 1.42
SVM RNA-class probability 0.951855
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12836761 92 + 22224390
AUUUUAUGUUUUUUGCUUUUUU-----U---UUUUUUUUGAA-GAGGCCUCAAA----GAGCGCUUUGAUUUUCUCACGCCGAUAAAAUCAAAGGCUCGAAAGAC
.......(((((((((((((((-----.---........)))-)))))......----((((.((((((((((.((.....)).))))))))))))))))))))) ( -26.60)
>DroPse_CAF1 56372 91 + 1
CGCGUC---GUUCUGUUGUCAC--------UCUUCCAUUGAACGUGUCUUCAAAGUGUGAGGGCUUUGAUUUUCUUACGACGAUAAAAUCAAAGU---AAAAGAC
..((((---((......(((((--------(((..(((((((......))))..)))..))))...))))......)))))).............---....... ( -18.90)
>DroSim_CAF1 44760 91 + 1
AUUUUAUGUAUUUUGUUUUUUC---------UUUUUUUUGAA-GAGGCCUCAAA----GAGCGCUUUGAUUUUCUCACGCCGAUAAAAUCAAAGGCUCGACAGAC
......(((.....((((((((---------........)))-)))))......----((((.((((((((((.((.....)).)))))))))))))).)))... ( -25.00)
>DroWil_CAF1 40024 90 + 1
AUUGAG--------GUUGUCACUUUGACGUUGCAUGUUUGAG-GGCGCUUCAAA----GUUAACUUUGAUUUUUUCACGCCGAUAAAAUCAAAGCC--CAAAGAC
.(((((--------((.(((.(((.(((((...))))).)))-)))))))))).----.....((((((((((.((.....)).))))))))))..--....... ( -24.00)
>DroYak_CAF1 43500 77 + 1
AUUUA----AU-------------------UUUUUUCUUGAA-GAGGCCUCAAA----GAGCGCUUUGAUUUUCACACGCCGAUAAAAUCAAAGGCUCGCAAGAC
.....----..-------------------.....(((((..-((....))...----((((.((((((((((..(.....)..)))))))))))))).))))). ( -19.30)
>DroPer_CAF1 53804 91 + 1
CGCGUC---GUUCUGUUGUCAC--------UCUUCCAUUGAACGUGUCUUCAAAGUGUGAGGGCUUUGAUUUUCUUACGACGAUAAAAUCAAAGU---AAAAGAC
..((((---((......(((((--------(((..(((((((......))))..)))..))))...))))......)))))).............---....... ( -18.90)
>consensus
AUUGUA___AUU_UGUUGUCAC________UUUUUUUUUGAA_GAGGCCUCAAA____GAGCGCUUUGAUUUUCUCACGCCGAUAAAAUCAAAGGC__GAAAGAC
.....................................((((........))))..........((((((((((.((.....)).))))))))))........... ( -9.52 =  -9.47 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,836,761 – 12,836,853
Length 92
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 66.60
Mean single sequence MFE -19.53
Consensus MFE -8.22
Energy contribution -8.72
Covariance contribution 0.50
Combinations/Pair 1.06
Mean z-score -1.67
Structure conservation index 0.42
SVM decision value 0.36
SVM RNA-class probability 0.702382
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12836761 92 - 22224390
GUCUUUCGAGCCUUUGAUUUUAUCGGCGUGAGAAAAUCAAAGCGCUC----UUUGAGGCCUC-UUCAAAAAAAA---A-----AAAAAAGCAAAAAACAUAAAAU
(((((..((((((((((((((.((.....)).)))))))))).))))----...)))))...-...........---.-----...................... ( -21.70)
>DroPse_CAF1 56372 91 - 1
GUCUUUU---ACUUUGAUUUUAUCGUCGUAAGAAAAUCAAAGCCCUCACACUUUGAAGACACGUUCAAUGGAAGA--------GUGACAACAGAAC---GACGCG
((((((.---.(((((((((.....((....)))))))))))............)))))).(((((..((.....--------....))...))))---)..... ( -16.64)
>DroSim_CAF1 44760 91 - 1
GUCUGUCGAGCCUUUGAUUUUAUCGGCGUGAGAAAAUCAAAGCGCUC----UUUGAGGCCUC-UUCAAAAAAAA---------GAAAAAACAAAAUACAUAAAAU
.(((...((((((((((((((.((.....)).)))))))))).))))----(((((((...)-))))))....)---------)).................... ( -21.90)
>DroWil_CAF1 40024 90 - 1
GUCUUUG--GGCUUUGAUUUUAUCGGCGUGAAAAAAUCAAAGUUAAC----UUUGAAGCGCC-CUCAAACAUGCAACGUCAAAGUGACAAC--------CUCAAU
(((....--((((((((((((.((.....)).)))))))))))).((----(((((.(((..-........)))....))))))))))...--------...... ( -21.50)
>DroYak_CAF1 43500 77 - 1
GUCUUGCGAGCCUUUGAUUUUAUCGGCGUGUGAAAAUCAAAGCGCUC----UUUGAGGCCUC-UUCAAGAAAAAA-------------------AU----UAAAU
(((((..((((((((((((((...........)))))))))).))))----...)))))...-............-------------------..----..... ( -18.80)
>DroPer_CAF1 53804 91 - 1
GUCUUUU---ACUUUGAUUUUAUCGUCGUAAGAAAAUCAAAGCCCUCACACUUUGAAGACACGUUCAAUGGAAGA--------GUGACAACAGAAC---GACGCG
((((((.---.(((((((((.....((....)))))))))))............)))))).(((((..((.....--------....))...))))---)..... ( -16.64)
>consensus
GUCUUUC__GCCUUUGAUUUUAUCGGCGUGAGAAAAUCAAAGCGCUC____UUUGAAGCCUC_UUCAAAAAAAAA________GUGACAACA_AAC___GAAAAU
...........((((((((((.((.....)).))))))))))..........(((((......)))))..................................... ( -8.22 =  -8.72 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:19 2006