Locus 5549

Sequence ID 2L_DroMel_CAF1
Location 15,814,189 – 15,814,279
Length 90
Max. P 0.989408
window8803 window8804

overview

Window 3

Location 15,814,189 – 15,814,279
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.27
Mean single sequence MFE -25.34
Consensus MFE -13.69
Energy contribution -15.92
Covariance contribution 2.22
Combinations/Pair 1.05
Mean z-score -2.33
Structure conservation index 0.54
SVM decision value 1.11
SVM RNA-class probability 0.916562
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15814189 90 + 22407834
UUGGCUUGCAGUUUACUUGACUCGAGCAAGUCAAGUUGAUGGCG---ACACUACGU---------------------------CCCUGCUACAGGAAUUUAUUUCGCCUUACUUAUUUUC
..(((((((((((.....))))...)))))))((((....((((---(...((.((---------------------------.((((...)))).)).))..)))))..))))...... ( -24.20)
>DroSec_CAF1 8862 90 + 1
UUGGCUUGCAGUUUACUUGACUCGAGCAAGUCAAGUUGAUGGCG---ACACUACGU---------------------------CCCUGCUACAGGAAUUUAUUUCGCCUUACUUAUUUUC
..(((((((((((.....))))...)))))))((((....((((---(...((.((---------------------------.((((...)))).)).))..)))))..))))...... ( -24.20)
>DroSim_CAF1 8883 90 + 1
UUGGCUUGCAGUUUACUUGACUCGAGCAAGUCAAGUUGAUGGCG---ACACUACGU---------------------------CCCUGCUACAGGAAUUUAUUUCGCCUUACUUAUUUUC
..(((((((((((.....))))...)))))))((((....((((---(...((.((---------------------------.((((...)))).)).))..)))))..))))...... ( -24.20)
>DroPer_CAF1 16661 120 + 1
UUUACUUGCAGUUUACUUGACUCGAGGAAGUCAAGUCGAUGGCAGAGCCCCUGCGCCUGCCACGGCUGCCACGGCUGCCUCUGCCUUGCUGCACGAAUUUAUUUCUUCUUACUUAUUUUC
....(.((((((..((((((((......))))))))....((((((((((.((.((..((....)).)))).))..).)))))))..)))))).)......................... ( -36.50)
>DroEre_CAF1 8946 90 + 1
UUGGCUUGCAGUUUACUUGACUCAAGCAAGUCAAGUUGAUGGCG---ACACUACGU---------------------------CCCUGCUGCAGGAAUUUAUUUCGCCUUACUUAUUUUC
..((((((((((..((((((((......))))))))....((.(---((.....))---------------------------))).)))))))(((.....))))))............ ( -26.80)
>DroYak_CAF1 34533 72 + 1
UUGGCUUGC------------------AAGUCAAGUUGAUGGCG---ACACUACGU---------------------------CCCUACUACAGGAAAUUAUUUCGCCUUACUUAUUUUC
(..(((((.------------------....)))))..).((((---(.......(---------------------------((........))).......)))))............ ( -16.14)
>consensus
UUGGCUUGCAGUUUACUUGACUCGAGCAAGUCAAGUUGAUGGCG___ACACUACGU___________________________CCCUGCUACAGGAAUUUAUUUCGCCUUACUUAUUUUC
..(((..((.(((.((((((((......)))))))).))).)).........................................((((...))))..........)))............ (-13.69 = -15.92 +   2.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,814,189 – 15,814,279
Length 90
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.27
Mean single sequence MFE -29.07
Consensus MFE -14.61
Energy contribution -16.20
Covariance contribution 1.59
Combinations/Pair 1.11
Mean z-score -3.28
Structure conservation index 0.50
SVM decision value 2.16
SVM RNA-class probability 0.989408
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15814189 90 - 22407834
GAAAAUAAGUAAGGCGAAAUAAAUUCCUGUAGCAGGG---------------------------ACGUAGUGU---CGCCAUCAACUUGACUUGCUCGAGUCAAGUAAACUGCAAGCCAA
........(((.(((((..((..((((((...)))))---------------------------)..))...)---))))....(((((((((....)))))))))....)))....... ( -29.10)
>DroSec_CAF1 8862 90 - 1
GAAAAUAAGUAAGGCGAAAUAAAUUCCUGUAGCAGGG---------------------------ACGUAGUGU---CGCCAUCAACUUGACUUGCUCGAGUCAAGUAAACUGCAAGCCAA
........(((.(((((..((..((((((...)))))---------------------------)..))...)---))))....(((((((((....)))))))))....)))....... ( -29.10)
>DroSim_CAF1 8883 90 - 1
GAAAAUAAGUAAGGCGAAAUAAAUUCCUGUAGCAGGG---------------------------ACGUAGUGU---CGCCAUCAACUUGACUUGCUCGAGUCAAGUAAACUGCAAGCCAA
........(((.(((((..((..((((((...)))))---------------------------)..))...)---))))....(((((((((....)))))))))....)))....... ( -29.10)
>DroPer_CAF1 16661 120 - 1
GAAAAUAAGUAAGAAGAAAUAAAUUCGUGCAGCAAGGCAGAGGCAGCCGUGGCAGCCGUGGCAGGCGCAGGGGCUCUGCCAUCGACUUGACUUCCUCGAGUCAAGUAAACUGCAAGUAAA
............(((........))).(((((...(((((((.(..((...((.(((......))))).))).)))))))....(((((((((....)))))))))...)))))...... ( -42.50)
>DroEre_CAF1 8946 90 - 1
GAAAAUAAGUAAGGCGAAAUAAAUUCCUGCAGCAGGG---------------------------ACGUAGUGU---CGCCAUCAACUUGACUUGCUUGAGUCAAGUAAACUGCAAGCCAA
........(((.(((((..((..((((((...)))))---------------------------)..))...)---))))....(((((((((....)))))))))....)))....... ( -28.60)
>DroYak_CAF1 34533 72 - 1
GAAAAUAAGUAAGGCGAAAUAAUUUCCUGUAGUAGGG---------------------------ACGUAGUGU---CGCCAUCAACUUGACUU------------------GCAAGCCAA
............(((((.((.((.((((......)))---------------------------).)).)).)---)))).....((((....------------------.)))).... ( -16.00)
>consensus
GAAAAUAAGUAAGGCGAAAUAAAUUCCUGUAGCAGGG___________________________ACGUAGUGU___CGCCAUCAACUUGACUUGCUCGAGUCAAGUAAACUGCAAGCCAA
............(((..........((((...)))).........................................((.....(((((((((....))))))))).....))..))).. (-14.61 = -16.20 +   1.59)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:54 2006