Locus 4858

Sequence ID 3R_DroMel_CAF1
Location 12,744,792 – 12,744,912
Length 120
Max. P 0.947738
window7956 window7957 window7958

overview

Window 6

Location 12,744,792 – 12,744,889
Length 97
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 78.32
Mean single sequence MFE -24.28
Consensus MFE -14.44
Energy contribution -14.25
Covariance contribution -0.19
Combinations/Pair 1.12
Mean z-score -1.46
Structure conservation index 0.59
SVM decision value -0.03
SVM RNA-class probability 0.517422
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12744792 97 + 27905053
GCCAACCA------GCACAAACACAUUCGAAUAAGACUCACUCACACAGUGGCAAGCUGUGCAAGGCAUUUGUGUUGGUGAGCAAGCGAAGAGUUCCAUUCUC
((..((((------(((((((.....((......))....((..((((((.....))))))..))...)))))))))))..))....(((........))).. ( -27.20)
>DroPse_CAF1 124204 89 + 1
GGCAACCA------ACACAAGCACAUAUAAAUUACACUCACUCAUACAGCUGCCAAUUGGAGUUUGUGGGUGUGUUGGUGAGCA----CAGAGUC----UCUC
.((.((((------((((.......((.....)).....(((((((.((((.((....)))))))))))))))))))))..)).----.......----.... ( -23.70)
>DroSim_CAF1 121593 103 + 1
GCCAACCAGCACCAGCACAAACACAUUCAAAUAAGACUCACUCACACAGCGGCAAGUGGUGAAAGGCAUUUGUGUUGGUGAGCAAGCGAAGAGUUCCAUUCUC
((.......((((((((((((.....((......)).((((.(((..........)))))))......)))))))))))).....))(((........))).. ( -24.10)
>DroEre_CAF1 126671 97 + 1
GCCAACCA------GCACAAACACAUUCAAAUCAGACUCACUCACACAGCGGCAAGCUGUAAAAGGCAUUUGUGUUGGUGAGCAGGCGAAGAGUUUCAUGCUC
(((.((((------(((((((.............((.....))..(((((.....)))))........))))))))))).....)))...((((.....)))) ( -27.60)
>DroYak_CAF1 116625 97 + 1
GCCAACCA------GCACAAACACAUUCAAAUCAGACUCACUCACACAGCGGCAAGCUGUAAAAGGCACUUGUGUUGGUGAGCAAGCAAAGAGAUCCAAUCUC
((..((((------((((((..............((.....))..(((((.....))))).........))))))))))..)).......(((((...))))) ( -25.80)
>DroAna_CAF1 106604 96 + 1
GCCAGCCA------GCACAAACACUUUCAAAUCAGACUCACCAAUACAACCGCAAACUCUA-GAUGCAAGUGUGUUAGUGAGCAAGCGAAGAGUAUGAUUCUC
((......------)).............((((((.(((((.((((((...(((.......-..)))...)))))).))))))..((.....)).)))))... ( -17.30)
>consensus
GCCAACCA______GCACAAACACAUUCAAAUCAGACUCACUCACACAGCGGCAAGCUGUAAAAGGCAUUUGUGUUGGUGAGCAAGCGAAGAGUUCCAUUCUC
....................................((((((.(((((...((............))...))))).))))))........(((.......))) (-14.44 = -14.25 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,744,821 – 12,744,912
Length 91
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 79.21
Mean single sequence MFE -28.37
Consensus MFE -19.34
Energy contribution -19.82
Covariance contribution 0.47
Combinations/Pair 1.23
Mean z-score -2.28
Structure conservation index 0.68
SVM decision value 1.35
SVM RNA-class probability 0.944743
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12744821 91 + 27905053
ACUCACUCACACAGUGGCAAGCUGUGCAAGGCAUUUGUGUUGGUGAGCAAGCGAAGAGUUCCAUUCUCUGCUUCG-AAGUACGAAGAGAGAA---------
.((((((.((((((((.(..((...))..).)).)))))).))))))................((((((.(((((-.....)))))))))))--------- ( -29.10)
>DroSec_CAF1 120029 91 + 1
ACUCACUCACACAGCGGCAAGCGGUGAAAGGCAUUUGUGUUGGUGAGCAAGCGAAGAGUUCCAUUCUCU-CUUCGUAAGUAAGAAGAGGGAA---------
.((((((.(((((((.....))(.(....).)...))))).))))))................((((((-((((........))))))))))--------- ( -29.90)
>DroSim_CAF1 121628 92 + 1
ACUCACUCACACAGCGGCAAGUGGUGAAAGGCAUUUGUGUUGGUGAGCAAGCGAAGAGUUCCAUUCUCUGCUUCGUAAGUAGGAAGAGAGAA---------
((((.(((((.(((((.((((((.(....).))))))))))))))))(....)..))))....((((((.((((........))))))))))--------- ( -30.30)
>DroEre_CAF1 126700 91 + 1
ACUCACUCACACAGCGGCAAGCUGUAAAAGGCAUUUGUGUUGGUGAGCAGGCGAAGAGUUUCAUGCUCUGCCUU-UCAGUGAGAAGAGAGAA---------
.(((.(((((.(((((.((((.(((.....)))))))))))).((((.((((..(((((.....))))))))))-))))))))..)))....--------- ( -30.70)
>DroYak_CAF1 116654 91 + 1
ACUCACUCACACAGCGGCAAGCUGUAAAAGGCACUUGUGUUGGUGAGCAAGCAAAGAGAUCCAAUCUCUGUUUU-UAGGUGAGAAGAGAGAA---------
.(((.((((((((((.....))))).((((((.(((((........)))))...((((((...)))))))))))-)..)))))..)))....--------- ( -27.70)
>DroAna_CAF1 106633 100 + 1
ACUCACCAAUACAACCGCAAACUCUA-GAUGCAAGUGUGUUAGUGAGCAAGCGAAGAGUAUGAUUCUCCGAAUAUUCAGAUAGGAAAGAGAAUUCGAGAAG
.(((((.((((((...(((.......-..)))...)))))).)))))((.((.....)).)).(((((.((((.(((..........))).))))))))). ( -22.50)
>consensus
ACUCACUCACACAGCGGCAAGCUGUAAAAGGCAUUUGUGUUGGUGAGCAAGCGAAGAGUUCCAUUCUCUGCUUCGUAAGUAAGAAGAGAGAA_________
.((((((.(((((...((............))...))))).)))))).................(((((.((((........))))))))).......... (-19.34 = -19.82 +   0.47)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,744,821 – 12,744,912
Length 91
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 79.21
Mean single sequence MFE -25.50
Consensus MFE -15.66
Energy contribution -16.13
Covariance contribution 0.47
Combinations/Pair 1.10
Mean z-score -2.49
Structure conservation index 0.61
SVM decision value 1.37
SVM RNA-class probability 0.947738
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12744821 91 - 27905053
---------UUCUCUCUUCGUACUU-CGAAGCAGAGAAUGGAACUCUUCGCUUGCUCACCAACACAAAUGCCUUGCACAGCUUGCCACUGUGUGAGUGAGU
---------(((((((((((.....-))))).))))))...............((((((..(((((...((...((...))..))...)))))..)))))) ( -27.80)
>DroSec_CAF1 120029 91 - 1
---------UUCCCUCUUCUUACUUACGAAG-AGAGAAUGGAACUCUUCGCUUGCUCACCAACACAAAUGCCUUUCACCGCUUGCCGCUGUGUGAGUGAGU
---------(((.((((((........))))-)).)))...........(((..(((((((.(.(((..((........)))))..).)).)))))..))) ( -23.10)
>DroSim_CAF1 121628 92 - 1
---------UUCUCUCUUCCUACUUACGAAGCAGAGAAUGGAACUCUUCGCUUGCUCACCAACACAAAUGCCUUUCACCACUUGCCGCUGUGUGAGUGAGU
---------((((((((((........)))).))))))...........(((..(((((((.(.(((.((........)).)))..).)).)))))..))) ( -23.70)
>DroEre_CAF1 126700 91 - 1
---------UUCUCUCUUCUCACUGA-AAGGCAGAGCAUGAAACUCUUCGCCUGCUCACCAACACAAAUGCCUUUUACAGCUUGCCGCUGUGUGAGUGAGU
---------....(((..(((((.((-(((((((((((((((....))))..)))))...........))))))))(((((.....)))))))))).))). ( -30.10)
>DroYak_CAF1 116654 91 - 1
---------UUCUCUCUUCUCACCUA-AAAACAGAGAUUGGAUCUCUUUGCUUGCUCACCAACACAAGUGCCUUUUACAGCUUGCCGCUGUGUGAGUGAGU
---------...(((..((((.....-......))))..))).......(((..(((((...((....))......(((((.....))))))))))..))) ( -23.20)
>DroAna_CAF1 106633 100 - 1
CUUCUCGAAUUCUCUUUCCUAUCUGAAUAUUCGGAGAAUCAUACUCUUCGCUUGCUCACUAACACACUUGCAUC-UAGAGUUUGCGGUUGUAUUGGUGAGU
.(((((((((..((..........))..)))).)))))...............(((((((((.(((.(((((..-.......))))).))).))))))))) ( -25.10)
>consensus
_________UUCUCUCUUCUUACUUACGAAGCAGAGAAUGGAACUCUUCGCUUGCUCACCAACACAAAUGCCUUUCACAGCUUGCCGCUGUGUGAGUGAGU
............................((((((((.......))))..))))((((((..(((((...((............))...)))))..)))))) (-15.66 = -16.13 +   0.47)

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 11:40:33 2006