Locus 1060

Sequence ID 2L_DroMel_CAF1
Location 2,941,142 – 2,941,252
Length 110
Max. P 0.998429
window1712 window1713

overview

Window 2

Location 2,941,142 – 2,941,252
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.59
Mean single sequence MFE -34.64
Consensus MFE -19.65
Energy contribution -21.71
Covariance contribution 2.06
Combinations/Pair 1.13
Mean z-score -2.81
Structure conservation index 0.57
SVM decision value 3.10
SVM RNA-class probability 0.998429
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2941142 110 + 22407834
GUACAGACAGACAGACGAAAGUGUGUACUGUGCACGCUGCCAUCCGA-AGGAUGUUUGUUGUGGGAAAUGGCGGGAAAUGGUGGAAAGUGG--U-GGUGGCAGCAGGCGAGGUG------
((((((....(((.((....)).))).))))))..((((((((((..-..)..((((.((((.(....).)))).))))............--.-)))))))))..........------ ( -36.70)
>DroSim_CAF1 58126 100 + 1
GCACGGACAGACAGACGAAAG----UACUGUGCGCGCUGCCAUCCGA-AGGAUGUUUGUUGUGGGAAAUGGCGGGAAA---------GUGGGCUGGCUGGCAGCAGGACACACG------
((.((.((((....((....)----).)))).)).))((((((((..-(.(((....))).).)))..))))).....---------(((.((((.....))))....)))...------ ( -31.30)
>DroEre_CAF1 58531 84 + 1
GUAC----AGACAGACGAAAG----UACUGUGCGCGCUGCCAUCCAA-AGGAUGUUUGUUGUGGGAA----------AUGGUGGAAAAUGG----GGUGGCGGCAGG-------------
((((----((....((....)----).))))))..((((((((((..-......((..(..(.....----------)..)..)).....)----)))))))))...------------- ( -33.72)
>DroYak_CAF1 58535 108 + 1
GUAC----AGACAGACGAAAG----UACUGUGCGCGCUGCCAUCCAAAAGGAUGUUUGUUGUGGGAAAUGGCGGGAAAUGGUGGAAAAUGG----GGUGGCAGCAGGACACACGGCGAGG
((((----((....((....)----).))))))((((((((((((.......(((((.((((.(....).)))).)))))..........)----))))))))).(......).)).... ( -36.83)
>consensus
GUAC____AGACAGACGAAAG____UACUGUGCGCGCUGCCAUCCAA_AGGAUGUUUGUUGUGGGAAAUGGCGGGAAAUGGUGGAAAAUGG____GGUGGCAGCAGGACACACG______
((((((.........(....)......))))))..((((((((((....)))).(((((..(.....)..))))).......................))))))................ (-19.65 = -21.71 +   2.06)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 2,941,142 – 2,941,252
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.59
Mean single sequence MFE -21.57
Consensus MFE -12.40
Energy contribution -12.89
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.57
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2941142 110 - 22407834
------CACCUCGCCUGCUGCCACC-A--CCACUUUCCACCAUUUCCCGCCAUUUCCCACAACAAACAUCCU-UCGGAUGGCAGCGUGCACAGUACACACUUUCGUCUGUCUGUCUGUAC
------......((.((((((((((-.--...........................................-..)).)))))))).))((((.(((.((........)).))))))).. ( -23.85)
>DroSim_CAF1 58126 100 - 1
------CGUGUGUCCUGCUGCCAGCCAGCCCAC---------UUUCCCGCCAUUUCCCACAACAAACAUCCU-UCGGAUGGCAGCGCGCACAGUA----CUUUCGUCUGUCUGUCCGUGC
------...(((..((((.....).)))..)))---------......(((((((.................-..))))))).(((((.((((.(----(........)))))).))))) ( -24.41)
>DroEre_CAF1 58531 84 - 1
-------------CCUGCCGCCACC----CCAUUUUCCACCAU----------UUCCCACAACAAACAUCCU-UUGGAUGGCAGCGCGCACAGUA----CUUUCGUCUGUCU----GUAC
-------------...((.((((..----(((...........----------...................-.))).)))).))(((.((((.(----(....)))))).)----)).. ( -15.48)
>DroYak_CAF1 58535 108 - 1
CCUCGCCGUGUGUCCUGCUGCCACC----CCAUUUUCCACCAUUUCCCGCCAUUUCCCACAACAAACAUCCUUUUGGAUGGCAGCGCGCACAGUA----CUUUCGUCUGUCU----GUAC
.......((((((...(((((((..----(((..........................................))).))))))))))))).(((----(............----)))) ( -22.55)
>consensus
______CGUGUGUCCUGCUGCCACC____CCACUUUCCACCAUUUCCCGCCAUUUCCCACAACAAACAUCCU_UCGGAUGGCAGCGCGCACAGUA____CUUUCGUCUGUCU____GUAC
................((((((..........................(........).........((((....))))))))))..(.((((.............)))))......... (-12.40 = -12.89 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:26 2006