Locus 294

Sequence ID 3L_DroMel_CAF1
Location 834,164 – 834,299
Length 135
Max. P 0.628715
window442 window443 window444

overview

Window 2

Location 834,164 – 834,272
Length 108
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 84.26
Mean single sequence MFE -43.99
Consensus MFE -29.33
Energy contribution -30.92
Covariance contribution 1.59
Combinations/Pair 1.28
Mean z-score -2.56
Structure conservation index 0.67
SVM decision value 0.11
SVM RNA-class probability 0.589194
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 834164 108 + 23771897
GACUC------CACGCCUGCAGAGGCGGCACGUCUGCAGCAGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGCUCUGCAGCAGGAGUUGCAGAAGCGAACCACCAAGUGCAGC
.....------..(((((....)))))((((.((((((((..(.((.(((((((.((((((......))))))))))))))).)..))))))))...(......)..))))... ( -46.00)
>DroSec_CAF1 1246 105 + 1
GACUC------CACGCCUGCAGAGGCGACACGUCUGCAGCAGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGCUCUGCAGCAGGAGCUGCAAAAGCGAAC---CAAGUGCAGC
...((------(..(((((((((.(.....).)))))))..)).((.(((((((.((((((......))))))))))))))).)))((((((.........---....)))))) ( -44.92)
>DroSim_CAF1 1443 105 + 1
GACUC------CACGCCUGCAGAGGCGGCACGUCUGCAGCAGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGGCCUGCAGCAGGAGCUGCAAAAGCGAAC---CAAGUGCAGC
.....------..(((((....)))))((((.((((((((....)).))))))((((((((......))))))((.((((((....))))))...))...)---)..))))... ( -42.70)
>DroEre_CAF1 1245 105 + 1
GACUC------CACUCCUGCAGAGGCGGCACGUCUGCAGCAGCAGCAUGCAGAGGCGCUGGACAAAAUAAGAGCUCUGCAGCAGGAGCUGCAGAAGCGGAC---CAAGUGCAGC
.....------.....(((((..((((((.(.((((((((....)).)))))).).))))............((((((((((....))))))).)))...)---)...))))). ( -43.60)
>DroYak_CAF1 1146 105 + 1
GACUC------CGCACCUCCAGAGGCGACACGCCUGCAGCAGCAGCAUGCCGAGGCGCUGGAGAAGAUUAGCGCUUUGCAGCAGGAGCUGCAAAAGCGGAC---GAAGUGCAGC
.....------.((((((((((.(....).((((((((((....)).)))..)))))))))))........(((((((((((....))))).))))))...---...))))... ( -44.70)
>DroPer_CAF1 1262 111 + 1
GACUCUUCGGCCACACCUUCAGACGUGGCCCAGUGGCAACAGCAGCAUGCGGAGUCUAUGCAGAAGAUUUCUGGUCUGCAGCAAGAGCUCCAGAAGCGGAG---CAAGUGCAGC
((((((.(((((((..........))))))..((.((....)).))..).))))))..((((((((....))..))))))(((...(((((......))))---)...)))... ( -42.00)
>consensus
GACUC______CACGCCUGCAGAGGCGGCACGUCUGCAGCAGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGCUCUGCAGCAGGAGCUGCAAAAGCGAAC___CAAGUGCAGC
.............(((((....)))))((((.(((((.((....)).((((((.(((((((......)))))))))))))))))).(((.....)))..........))))... (-29.33 = -30.92 +   1.59) 

alignment

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secondary structure

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dotplot

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Window 3

Location 834,164 – 834,272
Length 108
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 84.26
Mean single sequence MFE -45.68
Consensus MFE -30.31
Energy contribution -30.98
Covariance contribution 0.67
Combinations/Pair 1.23
Mean z-score -2.74
Structure conservation index 0.66
SVM decision value 0.20
SVM RNA-class probability 0.628715
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 834164 108 - 23771897
GCUGCACUUGGUGGUUCGCUUCUGCAACUCCUGCUGCAGAGCACUGAUUUUCUCCAGCGCCUCUGCAUGCUGCUGCUGCAGACGUGCCGCCUCUGCAGGCGUG------GAGUC
.(((((...((((((.((..((((((.(..(.((((((((((.(((........))).).))))))).)).)..).)))))))).))))))..))))).....------..... ( -46.20)
>DroSec_CAF1 1246 105 - 1
GCUGCACUUG---GUUCGCUUUUGCAGCUCCUGCUGCAGAGCACUGAUUUUCUCCAGCGCCUCUGCAUGCUGCUGCUGCAGACGUGUCGCCUCUGCAGGCGUG------GAGUC
(((.(((...---...(((.((((((((..(.((((((((((.(((........))).).))))))).)).)..)))))))).)))..((((....)))))))------.))). ( -45.50)
>DroSim_CAF1 1443 105 - 1
GCUGCACUUG---GUUCGCUUUUGCAGCUCCUGCUGCAGGCCACUGAUUUUCUCCAGCGCCUCUGCAUGCUGCUGCUGCAGACGUGCCGCCUCUGCAGGCGUG------GAGUC
.......(..---((..(((..((((((....))))))))).))..)....(((((((((.((((((.((....)))))))).))))(((((....)))))))------))).. ( -44.90)
>DroEre_CAF1 1245 105 - 1
GCUGCACUUG---GUCCGCUUCUGCAGCUCCUGCUGCAGAGCUCUUAUUUUGUCCAGCGCCUCUGCAUGCUGCUGCUGCAGACGUGCCGCCUCUGCAGGAGUG------GAGUC
(((.(((...---....(((.(((((((....))))))))))..........(((.((((.((((((.((....)))))))).)))).((....)).))))))------.))). ( -45.00)
>DroYak_CAF1 1146 105 - 1
GCUGCACUUC---GUCCGCUUUUGCAGCUCCUGCUGCAAAGCGCUAAUCUUCUCCAGCGCCUCGGCAUGCUGCUGCUGCAGGCGUGUCGCCUCUGGAGGUGCG------GAGUC
.((((((...---...((((((.(((((....)))))))))))........((((((.(...(((((((((((....))).)))))))).).)))))))))))------).... ( -50.80)
>DroPer_CAF1 1262 111 - 1
GCUGCACUUG---CUCCGCUUCUGGAGCUCUUGCUGCAGACCAGAAAUCUUCUGCAUAGACUCCGCAUGCUGCUGUUGCCACUGGGCCACGUCUGAAGGUGUGGCCGAAGAGUC
...(((...(---(((((....))))))...)))((((((..(....)..))))))..(((((.(((.((....))))).....((((((..(....)..))))))...))))) ( -41.70)
>consensus
GCUGCACUUG___GUCCGCUUCUGCAGCUCCUGCUGCAGAGCACUGAUUUUCUCCAGCGCCUCUGCAUGCUGCUGCUGCAGACGUGCCGCCUCUGCAGGCGUG______GAGUC
((((.............(((.(((((((....))))))))))............))))..(((.(((((((((....)))).)))))(((((....)))))........))).. (-30.31 = -30.98 +   0.67) 

alignment

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secondary structure

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dotplot

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Window 4

Location 834,198 – 834,299
Length 101
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 87.14
Mean single sequence MFE -34.98
Consensus MFE -26.81
Energy contribution -26.46
Covariance contribution -0.36
Combinations/Pair 1.35
Mean z-score -2.47
Structure conservation index 0.77
SVM decision value 0.14
SVM RNA-class probability 0.603156
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 834198 101 + 23771897
AGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGCUCUGCAGCAGGAGUUGCAGAAGCGAACCACCAAGUGCAGCCAAUGCGGGGGACGCAGCAAGGUAGGU
.(((((.(((((((.((((((......))))))))))))))).((..((((....)))).))......))).(((..((((.....))))....))).... ( -37.90)
>DroSec_CAF1 1280 98 + 1
AGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGCUCUGCAGCAGGAGCUGCAAAAGCGAAC---CAAGUGCAGCCAAUGCGGGGGACGCAGUAAGGUAGGU
.(((((.(((((((.((((((......)))))))))))))......)))))....(((..(---(...((((.....)))).))..)))............ ( -38.00)
>DroSim_CAF1 1477 98 + 1
AGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGGCCUGCAGCAGGAGCUGCAAAAGCGAAC---CAAGUGCAGCCAAUGCGGGGGACGCAGUAAGGUAGGU
.(((((.(((((.(.((((((......)))))).))))))......)))))....(((..(---(...((((.....)))).))..)))............ ( -35.50)
>DroEre_CAF1 1279 98 + 1
AGCAGCAUGCAGAGGCGCUGGACAAAAUAAGAGCUCUGCAGCAGGAGCUGCAGAAGCGGAC---CAAGUGCAGCCAAUGCGGUGGACGCAGCAAGGUGGGU
..((.(.(((....(.((((.((.........((((((((((....))))))).)))....---...)).)))))..((((.....))))))).).))... ( -35.89)
>DroYak_CAF1 1180 98 + 1
AGCAGCAUGCCGAGGCGCUGGAGAAGAUUAGCGCUUUGCAGCAGGAGCUGCAAAAGCGGAC---GAAGUGCAGCCAGUGCGGUGGACGCAGUAAGGUAGGU
.(((((.((((((((((((((......)))))))))))..)))...)))))....(((..(---(..(..(.....)..)..))..)))............ ( -38.60)
>DroAna_CAF1 1297 98 + 1
AACAACAUGCAGAGGCGCUGGCGAAGAUUAACGCUCUGCAACAAGAGCUCCAAAAGCGAAC---CAAGUGCAGUCAAUGUAGUGGGCGCAGUAAGGUGAGA
.....(((......(((((.((..(.(((.(((((((......))))).......(((...---....))).)).))).).)).)))))......)))... ( -24.00)
>consensus
AGCAGCAUGCAGAGGCGCUGGAGAAAAUCAGUGCUCUGCAGCAGGAGCUGCAAAAGCGAAC___CAAGUGCAGCCAAUGCGGGGGACGCAGUAAGGUAGGU
.((.((.(((((.((((((((......)))))))))))))(((...((((((................))))))...))).......)).))......... (-26.81 = -26.46 +  -0.36) 

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 09:38:35 2006