Locus 7900

Sequence ID 3L_DroMel_CAF1
Location 21,044,644 – 21,044,829
Length 185
Max. P 0.979082
window12865 window12866 window12867 window12868

overview

Window 5

Location 21,044,644 – 21,044,749
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -30.10
Consensus MFE -24.01
Energy contribution -25.57
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -1.40
Structure conservation index 0.80
SVM decision value 0.01
SVM RNA-class probability 0.536835
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044644 105 + 23771897
UUUGCAUUGCAAAAGGAAAGUGACAAAAAGGCGAGAGGAAAAU--AUAAGGAGACAGUGGCACUGGCAGUGGC-------------GAUCUGCGAUCACUGAUCACAAGUCGGCGAUACG
.(((((((((...((....((.((.......(....)......--....(....).)).)).)).)))))..(-------------((..((.((((...)))).))..))))))).... ( -23.20)
>DroSec_CAF1 99880 120 + 1
UUUGCAUUGCAAAAGGAAAGUGACAAAAAGGCGAGAGGAAAAUGUAUAAGGAGACAGUGGCAGUGGCAGUGGCAGUGCCACAUGGGGAACUGCGAUCACUGAUCACAAGUCGCCGAUACG
((((((((..........)))).))))..(((((...............(....).(((((((((...((.(((((.((......)).))))).))))))).))))...)))))...... ( -35.40)
>DroSim_CAF1 6128 120 + 1
UUUGCAUUGCAAAAGGAAAGUGACAAAAAGGCGAGAGGAAAAUAUACAAGGAGACAGUGGCAGUGGCAGUGGCAGUGCCACAUGGCGAUCUGCGAUCACUGAUCACAAGUCGCCGAUACG
((((((((..........)))).))))..(((((...............(....).((((((((((..(..(...((((....))))..)..)..)))))).))))...)))))...... ( -36.20)
>DroEre_CAF1 22076 111 + 1
UUUGCAUUGCAAAAGGAAAGUGACAAAAAGGCGACAGAAAAAUG--UAAGGAGACAGUGGCAGUGGCAGUGGCAGUGU-------UGAUCAGCGAUCACUGAUCACAACUCGUCGAUACG
.(((((((((.......................(((......))--)..(....)....))))).))))(((((((..-------(((((((......)))))))..))).))))..... ( -25.60)
>consensus
UUUGCAUUGCAAAAGGAAAGUGACAAAAAGGCGAGAGGAAAAUG_AUAAGGAGACAGUGGCAGUGGCAGUGGCAGUGC________GAUCUGCGAUCACUGAUCACAAGUCGCCGAUACG
((((((((..........)))).))))..(((((...............(....).((((((((((..((((...((((....))))..))))..)))))).))))...)))))...... (-24.01 = -25.57 +   1.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,044,684 – 21,044,789
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -38.73
Consensus MFE -29.13
Energy contribution -29.69
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.51
Structure conservation index 0.75
SVM decision value 0.12
SVM RNA-class probability 0.593681
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044684 105 + 23771897
AAU--AUAAGGAGACAGUGGCACUGGCAGUGGC-------------GAUCUGCGAUCACUGAUCACAAGUCGGCGAUACGGCAAGGAUGCCAUAAUUGCGUGUGAGUUUGGCCACUCGUU
...--....(....)(((((((((.(((....(-------------((..((.((((...)))).))..)))(((((..((((....))))...))))).))).)))...)))))).... ( -34.40)
>DroSec_CAF1 99920 120 + 1
AAUGUAUAAGGAGACAGUGGCAGUGGCAGUGGCAGUGCCACAUGGGGAACUGCGAUCACUGAUCACAAGUCGCCGAUACGGCAAGGAUGCCAUAAUUGCGUGUGAGUUUGGCCACUCGUU
.........(....)((((((.((((((((((((((.((......)).)))))...))))).))))((.((((((.((.((((....)))).))....)).)))).))..)))))).... ( -41.70)
>DroSim_CAF1 6168 120 + 1
AAUAUACAAGGAGACAGUGGCAGUGGCAGUGGCAGUGCCACAUGGCGAUCUGCGAUCACUGAUCACAAGUCGCCGAUACGGCAAGGAUGCCAUAAUUGCGUGUGAGUUUGGCCACUCGUU
...((((..(....)....(((((....((((((.((((...((((((..((.((((...)))).))..))))))....))))....)))))).)))))))))((((......))))... ( -43.40)
>DroEre_CAF1 22116 111 + 1
AAUG--UAAGGAGACAGUGGCAGUGGCAGUGGCAGUGU-------UGAUCAGCGAUCACUGAUCACAACUCGUCGAUACGGCAAGGAUGCCAUAAUUGCGUGUGAGUUUGGCCAUUCGCU
.(((--((((....).((((((((((((((((...(((-------(....)))).)))))).))))..((.((((...)))).))..))))))..))))))((((((......)))))). ( -35.40)
>consensus
AAUG_AUAAGGAGACAGUGGCAGUGGCAGUGGCAGUGC________GAUCUGCGAUCACUGAUCACAAGUCGCCGAUACGGCAAGGAUGCCAUAAUUGCGUGUGAGUUUGGCCACUCGUU
.........(....)((((((.....(((((((((..............))))...))))).(((((...((.((((..((((....))))...))))))))))).....)))))).... (-29.13 = -29.69 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,044,684 – 21,044,789
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Mean single sequence MFE -37.48
Consensus MFE -28.75
Energy contribution -30.07
Covariance contribution 1.31
Combinations/Pair 1.03
Mean z-score -3.01
Structure conservation index 0.77
SVM decision value 1.83
SVM RNA-class probability 0.979082
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044684 105 - 23771897
AACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGCCGACUUGUGAUCAGUGAUCGCAGAUC-------------GCCACUGCCAGUGCCACUGUCUCCUUAU--AUU
....(((((((..........((...(((((((....)))))))..))(((.((((((((...)))))))).))-------------).........).))))))..........--... ( -31.70)
>DroSec_CAF1 99920 120 - 1
AACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGGCGACUUGUGAUCAGUGAUCGCAGUUCCCCAUGUGGCACUGCCACUGCCACUGCCACUGUCUCCUUAUACAUU
....((((((.....((((((((...(((((((....)))))))...)))...))))).(((((...(((((.((......)).)))))))))).....))))))............... ( -41.70)
>DroSim_CAF1 6168 120 - 1
AACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGGCGACUUGUGAUCAGUGAUCGCAGAUCGCCAUGUGGCACUGCCACUGCCACUGCCACUGUCUCCUUGUAUAUU
....((((((................(((((((....)))))))..(((((.((((((((...)))))))).)))))..((((((.......)))))).))))))............... ( -45.40)
>DroEre_CAF1 22116 111 - 1
AGCGAAUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGACGAGUUGUGAUCAGUGAUCGCUGAUCA-------ACACUGCCACUGCCACUGCCACUGUCUCCUUA--CAUU
.(((..((((..(((((...((....(((((((....))))))).))..))))).((((((((....))))))))-------.....)))).)))...................--.... ( -31.10)
>consensus
AACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGGCGACUUGUGAUCAGUGAUCGCAGAUC________GCACUGCCACUGCCACUGCCACUGUCUCCUUAU_CAUU
.((.((((((.....((((((((...(((((((....)))))))...)))...))))).(((((...((((..............))))))))).....))))))))............. (-28.75 = -30.07 +   1.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,044,715 – 21,044,829
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.19
Mean single sequence MFE -34.45
Consensus MFE -26.60
Energy contribution -27.10
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.77
SVM decision value 0.32
SVM RNA-class probability 0.685141
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21044715 114 - 23771897
UCGUUGGUGCUAGCCUACAUACAUAACAAUUAGGCAACAAAACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGCCGACUUGUGAUCAGUGAUCGCAGAUC------
..((((((((..(((((.............)))))........((((......))))....))...(((((((....)))))))..))))))((((((((...))))))))...------ ( -36.12)
>DroSec_CAF1 99960 120 - 1
UCGCUGGUGCUAGCCUACAUACAUAACAAUUAGCCAACAAAACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGGCGACUUGUGAUCAGUGAUCGCAGUUCCCCAUG
((((((((((.................................((((......))))............((((....)))))))))))))).((((((((...))))))))......... ( -32.70)
>DroSim_CAF1 6208 120 - 1
UCGGCGGUGCUAGCCUACAUACAUAACAAUUAGCCAACAAAACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGGCGACUUGUGAUCAGUGAUCGCAGAUCGCCAUG
...((((((((((................))))).........((((......)))))).)))...(((((((....)))))))..(((((.((((((((...)))))))).)))))... ( -38.39)
>DroEre_CAF1 22152 115 - 1
UCGGUGGUGCUAGCCUACAUACAUAACAAUUAGCCAACGGAGCGAAUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGACGAGUUGUGAUCAGUGAUCGCUGAUCA-----
...((((.(....))))).......((((((.((((..........))))..........((....(((((((....)))))))....))))))))(((((((....))))))).----- ( -30.60)
>consensus
UCGGUGGUGCUAGCCUACAUACAUAACAAUUAGCCAACAAAACGAGUGGCCAAACUCACACGCAAUUAUGGCAUCCUUGCCGUAUCGGCGACUUGUGAUCAGUGAUCGCAGAUC______
.....(((....))).................(((........((((......)))).........(((((((....)))))))..)))((.((((((((...)))))))).))...... (-26.60 = -27.10 +   0.50)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:02 2006