Locus 2503

Sequence ID 2R_DroMel_CAF1
Location 8,919,721 – 8,919,820
Length 99
Max. P 0.994030
window4132 window4133

overview

Window 2

Location 8,919,721 – 8,919,820
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.51
Mean single sequence MFE -35.32
Consensus MFE -24.64
Energy contribution -25.60
Covariance contribution 0.96
Combinations/Pair 1.11
Mean z-score -2.60
Structure conservation index 0.70
SVM decision value 2.44
SVM RNA-class probability 0.994030
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8919721 99 + 20766785
GCCAAGUAUGCAACAGUUUUCGAUUGCCAGCGUCCA----U-GCAGGCGACUGCAAAGUGUUGCAUACUUCUUGGCU---------GAAACCACUUUGUA-------UCCGGAAUCCGGA
(((((((((((((((.(((.((.(((((.(((....----)-)).))))).)).))).)))))))))))...)))).---------..............-------(((((...))))) ( -39.40)
>DroSec_CAF1 164710 92 + 1
GCCAAGUAUGCAACAGUUUUCGAUUGCUAGCGUCCA----U-GCAGGCGACUGCAAAGAGUUGCAUACUUCUUGGCU---------GAAACCAAUUUGUA-------UCC-------GGA
(((((((((((((((((........)))....((..----(-((((....)))))..))))))))))))...)))).---------..............-------...-------... ( -29.80)
>DroSim_CAF1 165334 92 + 1
GCCAAGUAUGCAACAGUUUUCGAUUGCCAGCGUCCA----U-GCAGGCGACUGCAAAUAGUUGCAUACUUCUAGGCU---------GAAACCAAUUUGUA-------UCC-------GGA
((((((((((((((.((((.((.(((((.(((....----)-)).))))).)).)))).)))))))))))...))).---------..............-------...-------... ( -31.00)
>DroEre_CAF1 168876 105 + 1
GCCAAGUAUGCAACAGUUUUCGAUUGCAAUUG-CCAGCGCUGGCAGGCGACUGCAAAGUGUUGCAUACUUCUGGGCGGAGCGAGCCGAAACGACUUUGGA-------CCC-------GGA
...((((((((((((.(((.((.((((...((-(((....))))).)))).)).))).))))))))))))((((((((((((........)).)))))..-------)))-------)). ( -42.70)
>DroYak_CAF1 171257 108 + 1
GCCAAGUAUGCAACAGUUUUCGAUUGCCAGCG-CCA----UGGAUGCUGACUGCCAAGUGUUGCAUACUUCUGGGCUGGGUAAGCCGAAAUGACUUGGGAUACGGAAUCC-------GGA
.(((((((((((((.............(((((-(..----..).)))))(((....))))))))))))))...((((.....))))...........((((.....))))-------)). ( -33.70)
>consensus
GCCAAGUAUGCAACAGUUUUCGAUUGCCAGCGUCCA____U_GCAGGCGACUGCAAAGUGUUGCAUACUUCUGGGCU_________GAAACCACUUUGUA_______UCC_______GGA
(((((((((((((((.(((.((.(((((.((...........)).))))).)).))).))))))))))))...)))............................................ (-24.64 = -25.60 +   0.96)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,919,721 – 8,919,820
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.51
Mean single sequence MFE -32.52
Consensus MFE -19.72
Energy contribution -20.60
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -2.22
Structure conservation index 0.61
SVM decision value 1.38
SVM RNA-class probability 0.948267
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8919721 99 - 20766785
UCCGGAUUCCGGA-------UACAAAGUGGUUUC---------AGCCAAGAAGUAUGCAACACUUUGCAGUCGCCUGC-A----UGGACGCUGGCAAUCGAAAACUGUUGCAUACUUGGC
(((((...)))))-------.......((((...---------.))))..((((((((((((.(((.(.((.(((.((-.----.....)).))).)).).))).))))))))))))... ( -34.20)
>DroSec_CAF1 164710 92 - 1
UCC-------GGA-------UACAAAUUGGUUUC---------AGCCAAGAAGUAUGCAACUCUUUGCAGUCGCCUGC-A----UGGACGCUAGCAAUCGAAAACUGUUGCAUACUUGGC
.((-------...-------......(((((...---------.))))).(((((((((((((.((((((.((((...-.----.)).)))).))))..)).....))))))))))))). ( -27.70)
>DroSim_CAF1 165334 92 - 1
UCC-------GGA-------UACAAAUUGGUUUC---------AGCCUAGAAGUAUGCAACUAUUUGCAGUCGCCUGC-A----UGGACGCUGGCAAUCGAAAACUGUUGCAUACUUGGC
...-------.((-------.((......)).))---------.(((...(((((((((((..(((.(.((.(((.((-.----.....)).))).)).).)))..)))))))))))))) ( -27.10)
>DroEre_CAF1 168876 105 - 1
UCC-------GGG-------UCCAAAGUCGUUUCGGCUCGCUCCGCCCAGAAGUAUGCAACACUUUGCAGUCGCCUGCCAGCGCUGG-CAAUUGCAAUCGAAAACUGUUGCAUACUUGGC
.((-------(((-------(....(((((...)))))......))))..((((((((((((..(((((((.(((.((....)).))-).)))))))........)))))))))))))). ( -39.10)
>DroYak_CAF1 171257 108 - 1
UCC-------GGAUUCCGUAUCCCAAGUCAUUUCGGCUUACCCAGCCCAGAAGUAUGCAACACUUGGCAGUCAGCAUCCA----UGG-CGCUGGCAAUCGAAAACUGUUGCAUACUUGGC
...-------((((.....)))).(((((.....))))).....(((...((((((((((((.((((..((((((.....----...-.))))))..))))....))))))))))))))) ( -34.50)
>consensus
UCC_______GGA_______UACAAAGUGGUUUC_________AGCCAAGAAGUAUGCAACACUUUGCAGUCGCCUGC_A____UGGACGCUGGCAAUCGAAAACUGUUGCAUACUUGGC
((((.....))))...............................(((...((((((((((((..(((((((..((..........))..))).))))........))))))))))))))) (-19.72 = -20.60 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:43 2006