Locus 3658

Sequence ID 3R_DroMel_CAF1
Location 9,904,664 – 9,904,757
Length 93
Max. P 0.599658
window5876 window5877

overview

Window 6

Location 9,904,664 – 9,904,757
Length 93
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 82.63
Mean single sequence MFE -26.53
Consensus MFE -19.77
Energy contribution -21.58
Covariance contribution 1.81
Combinations/Pair 1.14
Mean z-score -1.54
Structure conservation index 0.75
SVM decision value 0.13
SVM RNA-class probability 0.599658
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9904664 93 + 27905053
---UUGUGUAGACG---AUGUCGAUUCGCUGUCAUUACGCUGCUUACACGCGGUUAUUUAUGACAAUUGUUGGAAAAUAUGAAUUGACAG-CGACGACGG-------
---((((....)))---)(((((..(((((((((....(((((......)))))(((((.((((....))))..))))).....))))))-)))))))).------- ( -27.30)
>DroPse_CAF1 128588 98 + 1
UGUUGGUGUAGUCG--AAUGUCGAUUUGCUGUCAUUACGCUGCUUACACGCGGUUAUUUAUGACAAUUGCUGGAAAAUAUGAAUUGACAGGCGACGACGA-------
......(((.((((--..(((((((((((((((((...(((((......))))).....))))))...))(....)....)))))))))..)))).))).------- ( -28.90)
>DroWil_CAF1 136028 97 + 1
---GAAAAUAGAAUGGCUUGUCGAUUUGCUGUCAUUACGUUGCUUA--CGCGUUUAUUUAUGACUAUUGUUAUAAAAUAUGAAUUGACAG-CUUAAACAGCGA----
---............(((.((..(...(((((((...(((.((...--.)).....((((((((....))))))))..)))...))))))-).)..)))))..---- ( -21.30)
>DroYak_CAF1 111754 100 + 1
---UUGUGUAGACG---AUGUCGAUUCGCUGUCAUUACGCUGCUUACACGCGGUUAUUUAUGACAAUUGUUGGAAAAUAUGAAUUGACAG-CGACGAUGGCGAUGGC
---.........((---..((((..(((((((((....(((((......)))))(((((.((((....))))..))))).....))))))-)))))))..))..... ( -27.40)
>DroAna_CAF1 108095 94 + 1
---CUGUGUAGUCG---AUGUCGAUUUGCUGUCAUUACGUUGCUUACACGCGGUUAUUUAUGACAAUUGUUGGAAAAUAUGAAUUGACAGUCGACGGGGA-------
---.......((((---((((((((((..((((((....((((......))))......))))))..((((....)))).))))))))).))))).....------- ( -25.40)
>DroPer_CAF1 130251 98 + 1
UGUUGGUGUAGUCG--AAUGUCGAUUUGCUGUCAUUACGCUGCUUACACGCGGUUAUUUAUGACAAUUGCUGGAAAAUAUGAAUUGACAGGCGACGACGA-------
......(((.((((--..(((((((((((((((((...(((((......))))).....))))))...))(....)....)))))))))..)))).))).------- ( -28.90)
>consensus
___UUGUGUAGACG___AUGUCGAUUUGCUGUCAUUACGCUGCUUACACGCGGUUAUUUAUGACAAUUGUUGGAAAAUAUGAAUUGACAG_CGACGACGA_______
..........((((....(((((((((..((((((...(((((......))))).....))))))..((((....)))).)))))))))..))))............ (-19.77 = -21.58 +   1.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,904,664 – 9,904,757
Length 93
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 82.63
Mean single sequence MFE -19.72
Consensus MFE -12.80
Energy contribution -13.17
Covariance contribution 0.36
Combinations/Pair 1.14
Mean z-score -1.69
Structure conservation index 0.65
SVM decision value -0.04
SVM RNA-class probability 0.511180
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9904664 93 - 27905053
-------CCGUCGUCG-CUGUCAAUUCAUAUUUUCCAACAAUUGUCAUAAAUAACCGCGUGUAAGCAGCGUAAUGACAGCGAAUCGACAU---CGUCUACACAA---
-------..(((((((-((((((.....(((((....((....))...)))))..(((.((....)))))...)))))))))..))))..---...........--- ( -24.30)
>DroPse_CAF1 128588 98 - 1
-------UCGUCGUCGCCUGUCAAUUCAUAUUUUCCAGCAAUUGUCAUAAAUAACCGCGUGUAAGCAGCGUAAUGACAGCAAAUCGACAUU--CGACUACACCAACA
-------..((.((((..(((((((....))).....((...((((((.......(((.((....)))))..)))))))).....))))..--)))).))....... ( -18.40)
>DroWil_CAF1 136028 97 - 1
----UCGCUGUUUAAG-CUGUCAAUUCAUAUUUUAUAACAAUAGUCAUAAAUAAACGCG--UAAGCAACGUAAUGACAGCAAAUCGACAAGCCAUUCUAUUUUC---
----..((((((...(-((((((........(((((.((....)).))))).....((.--...)).......))))))).....))).)))............--- ( -19.60)
>DroYak_CAF1 111754 100 - 1
GCCAUCGCCAUCGUCG-CUGUCAAUUCAUAUUUUCCAACAAUUGUCAUAAAUAACCGCGUGUAAGCAGCGUAAUGACAGCGAAUCGACAU---CGUCUACACAA---
.....((...((((((-((((((.....(((((....((....))...)))))..(((.((....)))))...)))))))))..)))...---)).........--- ( -20.50)
>DroAna_CAF1 108095 94 - 1
-------UCCCCGUCGACUGUCAAUUCAUAUUUUCCAACAAUUGUCAUAAAUAACCGCGUGUAAGCAACGUAAUGACAGCAAAUCGACAU---CGACUACACAG---
-------.....(((((((((((.....(((((....((....))...)))))...((((.......))))..))))))....)))))..---...........--- ( -17.10)
>DroPer_CAF1 130251 98 - 1
-------UCGUCGUCGCCUGUCAAUUCAUAUUUUCCAGCAAUUGUCAUAAAUAACCGCGUGUAAGCAGCGUAAUGACAGCAAAUCGACAUU--CGACUACACCAACA
-------..((.((((..(((((((....))).....((...((((((.......(((.((....)))))..)))))))).....))))..--)))).))....... ( -18.40)
>consensus
_______CCGUCGUCG_CUGUCAAUUCAUAUUUUCCAACAAUUGUCAUAAAUAACCGCGUGUAAGCAGCGUAAUGACAGCAAAUCGACAU___CGACUACACAA___
.........((((....((((((.....(((((....((....))...)))))...((((.......))))..)))))).....))))................... (-12.80 = -13.17 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:44 2006