Locus 2967

Sequence ID 2R_DroMel_CAF1
Location 10,229,665 – 10,229,793
Length 128
Max. P 0.979862
window4907 window4908

overview

Window 7

Location 10,229,665 – 10,229,759
Length 94
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 77.21
Mean single sequence MFE -25.09
Consensus MFE -18.35
Energy contribution -20.02
Covariance contribution 1.67
Combinations/Pair 1.04
Mean z-score -2.34
Structure conservation index 0.73
SVM decision value 1.85
SVM RNA-class probability 0.979862
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10229665 94 + 20766785
--------CGGCAUUCUUUCAGAACUCCACUUGAACUCACUGCCGGUAAUUGCCAUUGACAUGUGCUCCCGGUGGCAAUUAUACCACCCCCACCCCCCCUGG
--------(((((....(((((........))))).....)))))(((((((((((((...........))))))))))))).................... ( -24.40)
>DroSec_CAF1 58714 84 + 1
--------CGGCAUUCUUUCAGAACUCCACUUGAACUCAGUGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC----------CCCCCUGG
--------(((((((..(((((........)))))...)))))))(((((((((((((...........)))))))))))))..----------........ ( -28.90)
>DroSim_CAF1 58995 84 + 1
--------CGGCAUUCUUUCAGAACUCCACUUGAACUCAGUGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC----------CCCCCUGG
--------(((((((..(((((........)))))...)))))))(((((((((((((...........)))))))))))))..----------........ ( -28.90)
>DroEre_CAF1 63435 92 + 1
GUCCGGUCCGGCAUUCUUUCAGAACUCCACUUGAACUCACUUCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUAUAC----------CCCCCCGC
...(((.((((......(((((........))))).......))))((((((((((((...........))))))))))))...----------....))). ( -22.92)
>DroYak_CAF1 58835 92 + 1
CUUCGCUUCGACAUUCUUUCAGAACUCCACUUGAACUCAGUGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC----------CCCCUCCC
........((.((((..(((((........)))))...)))).))(((((((((((((...........)))))))))))))..----------........ ( -21.90)
>DroPer_CAF1 41500 72 + 1
--------GGGGAGUUGAUCGGAACUUCAGUGGAAAAC-------UUAAUUGCCACUGGCAUGUGCCCCCGAUGGCAAUUAC---------------CCGGG
--------(((.((((((((((......(((((.((..-------....)).)))))(((....))).)))))..))))).)---------------))... ( -23.50)
>consensus
________CGGCAUUCUUUCAGAACUCCACUUGAACUCAGUGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC__________CCCCCUGG
........(((((....(((((........))))).....)))))(((((((((((((...........))))))))))))).................... (-18.35 = -20.02 +   1.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,229,697 – 10,229,793
Length 96
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 70.66
Mean single sequence MFE -25.95
Consensus MFE -17.58
Energy contribution -17.75
Covariance contribution 0.17
Combinations/Pair 1.22
Mean z-score -1.28
Structure conservation index 0.68
SVM decision value 0.96
SVM RNA-class probability 0.891119
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10229697 96 + 20766785
UGCCGGUAAUUGCCAUUGACAUGUGCUCCCGGUGGCAAUUAUACCACCCCCACCCCCCCUGGAUCCAUUGUCCCAUCCCU----CGGGGA--AGCGCAGUCU
....(((....)))...(((.((((((...(((((........))))).....((((...((((..........))))..----.)))).--))))))))). ( -30.80)
>DroPse_CAF1 42443 77 + 1
-----CUAAUUGCCACUGACAUGUGCCCCCGAUGGCAAUUAC---------------CCGGGGCCCAUACACC-ACCUCA----CAGGACUCGAUCCACGGU
-----......(((......(((.(((((....((......)---------------).))))).))).....-......----..(((.....)))..))) ( -17.20)
>DroSec_CAF1 58746 90 + 1
UGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC----------CCCCCUGGAUCCAUUGACCCAUUCCAUUGACGGGGA--AGUGCAGUCU
((((.(((((((((((((...........))))))))))))).(----------(((..((((.............)))).....)))).--.).))).... ( -29.02)
>DroSim_CAF1 59027 86 + 1
UGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC----------CCCCCUGGAUCCAUUGACCCAUCCCA----CGGGGA--AGAGCAGUCU
((((.(((((((((((((...........)))))))))))))..----------((((.(((...............)))----.)))).--.).))).... ( -29.96)
>DroEre_CAF1 63475 86 + 1
UUCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUAUAC----------CCCCCCGCAUUGAUGGACCCAACCCA----CGAGGA--AGAGCAGUCU
((((.(((((((((((((...........)))))))))))))..----------.........(((.(((.......)))----))))))--)......... ( -22.20)
>DroYak_CAF1 58875 75 + 1
UGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC----------CCCCUCCC-----------CCGGUGA----GGAGCA--GGAGCAGUCU
(((..(((((((((((((...........))))))))))))).(----------(..((((.-----------.......----))))..--)).))).... ( -26.50)
>consensus
UGCCGGUAAUUGCCAUUGACAUGUGCCCCCGGUGGCAAUUACAC__________CCCCCUGGAUCCAUUGACCCAUCCCA____CGGGGA__AGAGCAGUCU
.....(((((((((((((...........)))))))))))))..............(((((.......................)))))............. (-17.58 = -17.75 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:13 2006