Locus 4791

Sequence ID 3R_DroMel_CAF1
Location 12,524,035 – 12,524,126
Length 91
Max. P 0.951529
window7862 window7863

overview

Window 2

Location 12,524,035 – 12,524,126
Length 91
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 80.35
Mean single sequence MFE -32.26
Consensus MFE -22.70
Energy contribution -22.95
Covariance contribution 0.25
Combinations/Pair 1.19
Mean z-score -2.78
Structure conservation index 0.70
SVM decision value 1.41
SVM RNA-class probability 0.951529
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12524035 91 + 27905053
---------C-GCUGCAGUUG------CUGCUGCGUUAAUGGCCUGGGUAAUUGCUUUUAAUUGCCAUUGUAAAGUUUUUCGCAUCGCAACCAAAAAUGGCAGCGGC------------
---------(-(((((.((((------(.(.((((..(((.((...((((((((....))))))))...))...)))...)))).))))))((....))))))))..------------ ( -30.90)
>DroPse_CAF1 12169 98 + 1
---------CUGCUGCCUGUGCCGCCGCUGCUGCGUUAAUGACUUUGGUAAUUACUUUUAAUUGCCAUUGUAAAGCUUUUCGCAUCGCCACCAAAAAUGGUAGCGGC------------
---------..((.......)).((((((((((((......((..(((((((((....)))))))))..)).........))))..)).((((....))))))))))------------ ( -29.06)
>DroYak_CAF1 9899 91 + 1
---------C-GCUGCGGUUG------CCGCUGCGUUAAUGGCCUGGGUAAUUGCUUUUAAUUGCCAUUGUAAAGUUUUUCGCAUCGCAACCGAAAAUGGCAGCGGC------------
---------(-((((((((((------(.(.((((..(((.((...((((((((....))))))))...))...)))...)))).))))))).......))))))..------------ ( -33.11)
>DroMoj_CAF1 4986 110 + 1
UUUUGUUGUC-GCUGCUGCUG------CUGCUGCGUUAAUGGCUGUGGUAAUUACUUUUAAUUGCCAUUGUAAAGUU-UUCGCAUCGC-ACCAAAAAUGGCAGCGCCUCAGCAUCUUGG
...(((((.(-(((((((.((------.(((((((..(((.((.((((((((((....)))))))))).))...)))-..))))..))-).))....))))))))...)))))...... ( -37.80)
>DroAna_CAF1 13351 98 + 1
--UGACUGCC-ACUGCUGCUG------CUGCUGCGUUAAUGGCUUUGGUAAUUACUUUUAAUUGCCAUUGUAAAGUUUUUCGCAUCGCAACCGAAAAUGGCAGCAGC------------
--........-...(((((((------((..((((..(((.((..(((((((((....)))))))))..))...)))...))))(((....)))....)))))))))------------ ( -34.00)
>DroPer_CAF1 16061 92 + 1
---------CUGCUGCCUGUG------CUGCUGCGUUAAUGACUCUGGUAAUUACUUUUAAUUGCCAUUGUAAAGCUUUUCGCAUCGCCACCAAAAAUGGUAGCGGC------------
---------((((((((.(((------.((.((((......((..(((((((((....)))))))))..)).........)))).)).))).......)))))))).------------ ( -28.66)
>consensus
_________C_GCUGCCGCUG______CUGCUGCGUUAAUGGCUUUGGUAAUUACUUUUAAUUGCCAUUGUAAAGUUUUUCGCAUCGCAACCAAAAAUGGCAGCGGC____________
...........((((((...........((.((((..(((.((..(((((((((....)))))))))..))...)))...)))).))...........))))))............... (-22.70 = -22.95 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,524,035 – 12,524,126
Length 91
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 80.35
Mean single sequence MFE -27.72
Consensus MFE -15.86
Energy contribution -15.45
Covariance contribution -0.41
Combinations/Pair 1.14
Mean z-score -2.08
Structure conservation index 0.57
SVM decision value 0.42
SVM RNA-class probability 0.729323
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12524035 91 - 27905053
------------GCCGCUGCCAUUUUUGGUUGCGAUGCGAAAAACUUUACAAUGGCAAUUAAAAGCAAUUACCCAGGCCAUUAACGCAGCAG------CAACUGCAGC-G---------
------------..((((((.......((((((..((((((.....))..((((((......((....))......))))))..))))...)------))))))))))-)--------- ( -26.51)
>DroPse_CAF1 12169 98 - 1
------------GCCGCUACCAUUUUUGGUGGCGAUGCGAAAAGCUUUACAAUGGCAAUUAAAAGUAAUUACCAAAGUCAUUAACGCAGCAGCGGCGGCACAGGCAGCAG---------
------------((((((((((....)))))))(((((.....)).......(((.(((((....))))).)))..)))......((.((....)).))...))).....--------- ( -27.80)
>DroYak_CAF1 9899 91 - 1
------------GCCGCUGCCAUUUUCGGUUGCGAUGCGAAAAACUUUACAAUGGCAAUUAAAAGCAAUUACCCAGGCCAUUAACGCAGCGG------CAACCGCAGC-G---------
------------((((((((..((((((.........)))))).......((((((......((....))......))))))...)))))))------).........-.--------- ( -28.30)
>DroMoj_CAF1 4986 110 - 1
CCAAGAUGCUGAGGCGCUGCCAUUUUUGGU-GCGAUGCGAA-AACUUUACAAUGGCAAUUAAAAGUAAUUACCACAGCCAUUAACGCAGCAG------CAGCAGCAGC-GACAACAAAA
....(.(((((..(((((((..((..((((-((...))...-..........(((.(((((....))))).)))..))))..)).))))).)------)..))))).)-.......... ( -28.00)
>DroAna_CAF1 13351 98 - 1
------------GCUGCUGCCAUUUUCGGUUGCGAUGCGAAAAACUUUACAAUGGCAAUUAAAAGUAAUUACCAAAGCCAUUAACGCAGCAG------CAGCAGCAGU-GGCAGUCA--
------------...(((((((((....(((((..((((((.....))..((((((......((....))......))))))..))))...)------))))...)))-))))))..-- ( -29.70)
>DroPer_CAF1 16061 92 - 1
------------GCCGCUACCAUUUUUGGUGGCGAUGCGAAAAGCUUUACAAUGGCAAUUAAAAGUAAUUACCAGAGUCAUUAACGCAGCAG------CACAGGCAGCAG---------
------------((((((((((....)))))))(.((((....((((.....(((.(((((....))))).)))))))......)))).)..------....))).....--------- ( -26.00)
>consensus
____________GCCGCUGCCAUUUUUGGUUGCGAUGCGAAAAACUUUACAAUGGCAAUUAAAAGUAAUUACCAAAGCCAUUAACGCAGCAG______CAACAGCAGC_G_________
............(((((.(((......))).))).((((((.....))..((((((......((....))......))))))..))))))............................. (-15.86 = -15.45 +  -0.41)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:02 2006