Locus 5646

Sequence ID 2R_DroMel_CAF1
Location 17,947,943 – 17,948,165
Length 222
Max. P 0.728977
window9051 window9052

overview

Window 1

Location 17,947,943 – 17,948,063
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.93
Mean single sequence MFE -37.36
Consensus MFE -27.57
Energy contribution -28.38
Covariance contribution 0.81
Combinations/Pair 1.06
Mean z-score -1.85
Structure conservation index 0.74
SVM decision value 0.42
SVM RNA-class probability 0.728977
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17947943 120 - 20766785
AGCGGUGUUAACUUUGCCACAUUCCCCGAAGAUUUGGGCCGGGAUCCUCCCCCCAUCCCCGAAUCACCCAGUUUGCUUCUGGCUAGCUGUGGCAGACAAACUAUUGUCAGUGCAAAUAAA
.(((.(........(((((((.........((((((((..(((........)))...))))))))..((((.......)))).....)))))))(((((....)))))).)))....... ( -38.10)
>DroSec_CAF1 5267 120 - 1
AGCGGUGUUAACUUUGCCACGUUCCCCGAAGAUUUGGGCCGGGCUCCUCGCCCAAUCCCCGAAUCACCCAGCUUGCUUCUGGCUAGCUGUGGCAGACAAACUAUUGUCAGUGCAAAUAAA
.(((.(........((((((..........((((((((..((((.....))))....))))))))....((((.((.....)).))))))))))(((((....)))))).)))....... ( -42.90)
>DroSim_CAF1 1003 120 - 1
AGCGGUGUUAACUUUGCCACGUUCCCCGAAGAUUUGGGCCGGGCUCCUCCCCGAAUCCCCGCAUCGCCCAGCUUGCUUCUGGCUAGAUGUGGCAGACAAACUAUUGUCAGUGCAAAUAAA
.(((.(........(((((((((.((.((((..((((((((((.((......))...))))....))))))....)))).))...)))))))))(((((....)))))).)))....... ( -39.80)
>DroEre_CAF1 10049 114 - 1
AGCGGUGUUAACUUUGCCACGUUCCCCGAAGAUUUGGCCCGGGUUUCUGCC------CCCCAAUCCGCCAGUUUGCUUCUGGCUAGCUGUGGCAGACAAACUAUUGUCAGUGCAAAUAAA
.(((.(........((((((..........(..((((...((((....)))------).))))..)(((((.......))))).....))))))(((((....)))))).)))....... ( -35.00)
>DroYak_CAF1 10048 102 - 1
AGCGGUGUUAACUUUGCCACGUUCCCCAAAGAUUUGGGCC------------------ACGAAUCCCCCAGUUUGCUUCUGGCUAGCGGGGGCAGACAAACUAUUGUCAGUGCAAAUAAA
.((((((.......)))).(((..(((((....)))))..------------------)))...(((((.(((.((.....)).))))))))..(((((....)))))...))....... ( -31.00)
>consensus
AGCGGUGUUAACUUUGCCACGUUCCCCGAAGAUUUGGGCCGGGCUCCUCCCC__AUCCCCGAAUCACCCAGUUUGCUUCUGGCUAGCUGUGGCAGACAAACUAUUGUCAGUGCAAAUAAA
.(((.(........(((((((...((.((((..(((((.((((..............)))).....)))))....)))).)).....)))))))(((((....)))))).)))....... (-27.57 = -28.38 +   0.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,948,063 – 17,948,165
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.30
Mean single sequence MFE -32.32
Consensus MFE -21.76
Energy contribution -25.36
Covariance contribution 3.60
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.67
SVM decision value 0.14
SVM RNA-class probability 0.604698
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17948063 102 - 20766785
------------------CUUCAGUAUUGGCCUGCCAAAAAAUCGAUGGCAACACAAAGUAAACGGACUGCAAACGGGGGGCUUCGUUUCCAGCUCCUCGCAGCAUGUUUAUUGGCCUGC
------------------..........(((((((((.........)))))......((((((((..((((....((((((((........))))))))))))..))))))))))))... ( -36.10)
>DroSec_CAF1 5387 101 - 1
------------------CUCCAGUAUUGGCCUGCCAAAAAAUCGAUGGCAACACAAAGUAAACGGACUGCA-ACGGGAGGCUUCGCUUCCAGCUCCUCGCAGCAUGUUUAUUGGCCUGC
------------------..........(((((((((.........)))))......((((((((..((((.-..(((((.((........))))))).))))..))))))))))))... ( -31.90)
>DroSim_CAF1 1123 101 - 1
------------------CUCCAGUAUUGGCCUGCCAA-AAAUCGAUGGCAACACAAAGUAAACGGACUGCAAACGGGGGGCUUCGCUUCCAGCUCCUCGCAGCAUGUUUAUUGGCCUGC
------------------..........(((((((((.-.......)))))......((((((((..((((....((((((((........))))))))))))..))))))))))))... ( -36.90)
>DroEre_CAF1 10163 100 - 1
------------------CUGCAGUAUUGGCCGCCCAAAAAAUCGAUGCCAACACAAAGUAAACGGACUGCAAAAA--GCCCCCCGUUUCCAGCUCCUCGCAGCAUGUUUAUUGGCCUGC
------------------..((((..((((....)))).........(((((.(((..(.((((((...((.....--))...)))))).).(((......))).)))...))))))))) ( -22.50)
>DroYak_CAF1 10150 118 - 1
ACUAUGGCAUCCAGUGUGAUGCAGUAUUGGGCUGCCAAAAAAUCGAUGGCAACACAAAGUAAACGGACUGCAAAAA--GCCCCCCGUUUGCAGCCACUCGCAGCUUGUUUAUUGGCCUGC
..(((.(((((......))))).)))...((((((((.........))))........((((((((...((.....--))...))))))))))))....((((((........)).)))) ( -34.20)
>consensus
__________________CUCCAGUAUUGGCCUGCCAAAAAAUCGAUGGCAACACAAAGUAAACGGACUGCAAACGGGGGGCUUCGUUUCCAGCUCCUCGCAGCAUGUUUAUUGGCCUGC
............................(((((((((.........)))))......((((((((..((((....((((((((........))))))))))))..))))))))))))... (-21.76 = -25.36 +   3.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:55 2006