Locus 2230

Sequence ID 3R_DroMel_CAF1
Location 6,349,175 – 6,349,274
Length 99
Max. P 0.930305
window3622 window3623

overview

Window 2

Location 6,349,175 – 6,349,274
Length 99
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 83.73
Mean single sequence MFE -33.05
Consensus MFE -20.61
Energy contribution -21.17
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.96
Structure conservation index 0.62
SVM decision value 0.33
SVM RNA-class probability 0.692500
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6349175 99 + 27905053
CUCGCUUAUUAUUGUUAUAAUAACGAUGUGCAAAAGCACUUGUGCCACUUGAAAGGGCACUCGUGUUGCAC--AAGGA-AAGUG--GGGCCAGA--AAGGGGCAAA
(((((((...(((((((...)))))))(((((...((((..(((((.((....)))))))..)))))))))--.....-)))))--))(((...--....)))... ( -34.90)
>DroSec_CAF1 113858 98 + 1
CUCGCUUAUUAUUGUUAUAAUAACGAUGUGCAAAAGCACUUGUGCCACUUGAAAGGGCACUCGUGUUGCAC--AAGGA-AAGUG--GGGCCAGU---AGGGGCAAA
(((((((...(((((((...)))))))(((((...((((..(((((.((....)))))))..)))))))))--.....-)))))--))(((...---...)))... ( -35.40)
>DroSim_CAF1 127503 98 + 1
CUCGCUUAUUAUUGUUAUAAUAACGAUGUGCAAAAGCACUUGUGCCACUUGAAAGGGCACUCGUGUUGCAC--AAGGA-AAGUG--GGGCCAGU---AGGGGCAAA
(((((((...(((((((...)))))))(((((...((((..(((((.((....)))))))..)))))))))--.....-)))))--))(((...---...)))... ( -35.40)
>DroEre_CAF1 125099 97 + 1
CUCGCUUAUUAUUGUUAUAAUAACGAUGUGCAAAAGCACUUGUGCCACUUGAAAGGGCACUCGUGUUGCAC--AAGGCGAAAGG--GGGGC----AAAGGAGC-GG
..(((((....(((((..........((((((...((((..(((((.((....)))))))..)))))))))--)...(....).--..)))----))..))))-). ( -32.30)
>DroYak_CAF1 114927 100 + 1
CUCGCUUAUUAUUGUUAUAAUAACGAUGUGCAAAAGCACUUGUGCCACUUGAAAGGGCACUCGUGUUGCAC--AUGGA-AAAGG--GGAUCUUUAAGGGGGUC-AG
(((..(((((((....)))))))(.(((((((...((((..(((((.((....)))))))..)))))))))--)).).-...))--)((((((....))))))-.. ( -33.70)
>DroAna_CAF1 115824 95 + 1
CCCGCUUAUUAUUGUUAUAAUAACGAUGUGCAAAAGCACUUGUGCCACUCGAAAGGGCACUCGAGGUUUUUGGGGGGG-AAAUGAUUGGGGAGU---GG-------
(((.((...((((((((...))))))))..(((((((.((((((((...(....))))))..)))))))))))).)))-...............---..------- ( -26.60)
>consensus
CUCGCUUAUUAUUGUUAUAAUAACGAUGUGCAAAAGCACUUGUGCCACUUGAAAGGGCACUCGUGUUGCAC__AAGGA_AAAUG__GGGCCAGU___AGGGGC_AA
.(((.(((((((....)))))))))).(((((...((((..(((((.((....)))))))..)))))))))................................... (-20.61 = -21.17 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,349,175 – 6,349,274
Length 99
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 83.73
Mean single sequence MFE -27.40
Consensus MFE -21.45
Energy contribution -22.32
Covariance contribution 0.86
Combinations/Pair 1.04
Mean z-score -3.23
Structure conservation index 0.78
SVM decision value 1.20
SVM RNA-class probability 0.930305
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6349175 99 - 27905053
UUUGCCCCUU--UCUGGCCC--CACUU-UCCUU--GUGCAACACGAGUGCCCUUUCAAGUGGCACAAGUGCUUUUGCACAUCGUUAUUAUAACAAUAAUAAGCGAG
...(((....--...)))..--.....-....(--(((((((((..(((((((....)).)))))..)))...)))))))((((((((((....))))).))))). ( -28.40)
>DroSec_CAF1 113858 98 - 1
UUUGCCCCU---ACUGGCCC--CACUU-UCCUU--GUGCAACACGAGUGCCCUUUCAAGUGGCACAAGUGCUUUUGCACAUCGUUAUUAUAACAAUAAUAAGCGAG
...(((...---...)))..--.....-....(--(((((((((..(((((((....)).)))))..)))...)))))))((((((((((....))))).))))). ( -28.90)
>DroSim_CAF1 127503 98 - 1
UUUGCCCCU---ACUGGCCC--CACUU-UCCUU--GUGCAACACGAGUGCCCUUUCAAGUGGCACAAGUGCUUUUGCACAUCGUUAUUAUAACAAUAAUAAGCGAG
...(((...---...)))..--.....-....(--(((((((((..(((((((....)).)))))..)))...)))))))((((((((((....))))).))))). ( -28.90)
>DroEre_CAF1 125099 97 - 1
CC-GCUCCUUU----GCCCC--CCUUUCGCCUU--GUGCAACACGAGUGCCCUUUCAAGUGGCACAAGUGCUUUUGCACAUCGUUAUUAUAACAAUAAUAAGCGAG
..-((......----))...--....((((..(--(((((((((..(((((((....)).)))))..)))...)))))))...(((((((....))))))))))). ( -28.90)
>DroYak_CAF1 114927 100 - 1
CU-GACCCCCUUAAAGAUCC--CCUUU-UCCAU--GUGCAACACGAGUGCCCUUUCAAGUGGCACAAGUGCUUUUGCACAUCGUUAUUAUAACAAUAAUAAGCGAG
..-.................--.....-....(--(((((((((..(((((((....)).)))))..)))...)))))))((((((((((....))))).))))). ( -26.10)
>DroAna_CAF1 115824 95 - 1
-------CC---ACUCCCCAAUCAUUU-CCCCCCCAAAAACCUCGAGUGCCCUUUCGAGUGGCACAAGUGCUUUUGCACAUCGUUAUUAUAACAAUAAUAAGCGGG
-------..---...............-....(((........((((((((((....)).)))))..((((....)))).)))(((((((....)))))))..))) ( -23.20)
>consensus
UU_GCCCCU___ACUGGCCC__CACUU_UCCUU__GUGCAACACGAGUGCCCUUUCAAGUGGCACAAGUGCUUUUGCACAUCGUUAUUAUAACAAUAAUAAGCGAG
...................................(((((((((..(((((((....)).)))))..)))...)))))).((((((((((....))))).))))). (-21.45 = -22.32 +   0.86)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:27 2006