Locus 7611

Sequence ID 3R_DroMel_CAF1
Location 20,410,132 – 20,410,272
Length 140
Max. P 0.783799
window12281 window12282

overview

Window 1

Location 20,410,132 – 20,410,249
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.41
Mean single sequence MFE -45.20
Consensus MFE -23.68
Energy contribution -24.93
Covariance contribution 1.26
Combinations/Pair 1.35
Mean z-score -1.91
Structure conservation index 0.52
SVM decision value 0.57
SVM RNA-class probability 0.783799
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20410132 117 + 27905053
UUCUGACUGGCGAUUGAUUGCCAUUCCUGGCCUUUCGGGGUGGACUCUGAUCGGAAUCCCUGUGCUUUUGGCGUGGCGGAGACUGAUCGCCAUCUCGCCCUCGUCUGGUGGGACUCU
....((.((((((....)))))).))((.(((...(((((((((...(((((((..((((..(((.....)))..).)))..)))))))...)).))))).))...))).))..... ( -46.90)
>DroVir_CAF1 41058 114 + 1
UCCUGGGCGGCGACUGAUCCGCAUCUCUUCUUCUCCUGGGCGGCGACUGAUCCACAUCACGACC---CCGCCUGGGCGGGCUUUGAUCUGCCCCACGCCGUCGUCUGACUGGACUAU
.....(((((((......................((..(((((.(.(((((....)))).).).---)))))..)).((((........))))..)))))))((((....))))... ( -42.50)
>DroSec_CAF1 32517 117 + 1
UUCCGGCUGGCGAUGGUUUGUCAUUCCUGGCCUUUCUGGGCGGACUCUGAUCGGAAUCUCUCCGCUUUCUGCGAGACGGAGACUGAUCGCCAUCUCGCCCUCGUCUAGGAGGACUCU
(((((((..(.(((((....))))).)..))).....(((((((...(((((((..(((.(((((.....))).)).)))..)))))))...)).))))).......))))...... ( -44.90)
>DroSim_CAF1 35822 117 + 1
UCCUUGCUGGCGAAUGUUUGUCAUUCCUGGCCUUUCUGGGCGGACUCUGAUCGGAAUCUCUCCGCUUUCUGCGAGGCGGAGACUGAUCGCCAUCUCGCCCUCGUCUAGGAGGACUCU
(((((((..(.(((((.....))))))..))......(((((((...(((((((....((((((((((....)))))))))))))))))...)).)))))........))))).... ( -48.70)
>DroEre_CAF1 32124 117 + 1
UCCUGGCUGGCGACUGAUUGCCAUUCCUGGCUUUUCUGGGUGGACUCUGAUCGGAAUCUCUGCGCUUUCGGCGAGGCGGCGAUUGAUCGCCAACUCUUUCUCGCCUUGGAGGACUCU
(((.(((((((((..(((((((...(((.(((.....(.(..((.(((....)))...))..).)....))).))).)))))))..))))))..........)))..)))....... ( -41.30)
>DroYak_CAF1 36449 117 + 1
UCCUAGCUGGCGAUUGAUCGCCAUUUUUGGCUUUUCUGGGUGGACUCUGAUCGGAAUCUCUGCGCUUUCGGCCAGGCGGCGAUUGAUCGCCAUCUCUUCCCCGUCUGGGCGGACUCU
....((.(((((((..((((((...(((((((.....(.(..((.(((....)))...))..).)....))))))).))))))..))))))).)).....((((....))))..... ( -46.90)
>consensus
UCCUGGCUGGCGAUUGAUUGCCAUUCCUGGCCUUUCUGGGCGGACUCUGAUCGGAAUCUCUGCGCUUUCGGCGAGGCGGAGACUGAUCGCCAUCUCGCCCUCGUCUGGGAGGACUCU
(((.....(((((......((((....))))......(((((((...(((((((..(((((.(((.....))).)).)))..)))))))...)).)))))))))).....))).... (-23.68 = -24.93 +   1.26)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,410,172 – 20,410,272
Length 100
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 73.88
Mean single sequence MFE -37.81
Consensus MFE -15.58
Energy contribution -17.13
Covariance contribution 1.56
Combinations/Pair 1.05
Mean z-score -1.92
Structure conservation index 0.41
SVM decision value 0.12
SVM RNA-class probability 0.595492
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20410172 100 - 27905053
-----------------AAGAAGGGCGGGAAGCUCAGAUCAGAGUCCCACCAGACGAGGGCGAGAUGGCGAUCAGUCUCCGCCACGCCAAAAGCACAGGGAUUCCGAUCAGAGUCCA
-----------------.....(((((((...))).((((.(((((((..........((((.((.(((.....)))))))))..((.....))...))))))).))))...)))). ( -36.90)
>DroVir_CAF1 41098 112 - 1
CAAUCAAAGCCCUCACAGACAACGCCGCG--ACUCAGAUCAUAGUCCAGUCAGACGACGGCGUGGGGCAGAUCAAAGCCCGCCCAGGCGG---GGUCGUGAUGUGGAUCAGUCGCCG
........(((((........((((((.(--(((........))))).(((....))))))))))))).........(((((....))))---)...(((((........))))).. ( -37.20)
>DroSec_CAF1 32557 100 - 1
-----------------AAGAAGGGCGGCAAGCUCAGAUCAGAGUCCUCCUAGACGAGGGCGAGAUGGCGAUCAGUCUCCGUCUCGCAGAAAGCGGAGAGAUUCCGAUCAGAGUCCG
-----------------........(((...((((.((((.(((((((((.........(((((((((.((....)).))))))))).......)))).))))).)))).))))))) ( -40.99)
>DroSim_CAF1 35862 100 - 1
-----------------AAGAAGGGCGGCAAGCUCAGAUCAGAGUCCUCCUAGACGAGGGCGAGAUGGCGAUCAGUCUCCGCCUCGCAGAAAGCGGAGAGAUUCCGAUCAGAGUCCG
-----------------........(((...((((.((((.(((((((((.....((((.((.((.(((.....)))))))))))((.....)))))).))))).)))).))))))) ( -38.50)
>DroEre_CAF1 32164 100 - 1
-----------------AAGAAGGGCGGAAAGCUCAGAUCAGAGUCCUCCAAGGCGAGAAAGAGUUGGCGAUCAAUCGCCGCCUCGCCGAAAGCGCAGAGAUUCCGAUCAGAGUCCA
-----------------.....(((((((..((((......))))..)))..((((.(((.(((.((((((....)))))).)))(((....).)).....))))).))...)))). ( -35.80)
>DroYak_CAF1 36489 100 - 1
-----------------AAGAAGGGCGGAAAGCUCGGAUCAGAGUCCGCCCAGACGGGGAAGAGAUGGCGAUCAAUCGCCGCCUGGCCGAAAGCGCAGAGAUUCCGAUCAGAGUCCA
-----------------.....((((((...((((......)))))))))).(((((((...((.((((((....)))))).)).(((....).)).....))))).))........ ( -37.50)
>consensus
_________________AAGAAGGGCGGAAAGCUCAGAUCAGAGUCCUCCCAGACGAGGGCGAGAUGGCGAUCAAUCUCCGCCUCGCCGAAAGCGCAGAGAUUCCGAUCAGAGUCCA
..........................((...((((.((((.((((((...................((((.........))))..((.....))...).))))).)))).)))))). (-15.58 = -17.13 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:09 2006