Locus 6523

Sequence ID 3R_DroMel_CAF1
Location 17,200,439 – 17,200,530
Length 91
Max. P 0.988065
window10613 window10614

overview

Window 3

Location 17,200,439 – 17,200,530
Length 91
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 79.52
Mean single sequence MFE -29.13
Consensus MFE -14.44
Energy contribution -14.72
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -2.90
Structure conservation index 0.50
SVM decision value 1.28
SVM RNA-class probability 0.940057
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17200439 91 + 27905053
CGCGAUCUCC-GUC-CAGCAU--UUAACAAAUA------------UGCAUCGGACAGCA--GAUCUGCCUAGUGCUCUUUGUCGAUUCGAAAUAGAACACAGGCCCG-UA
.((((((((.-(((-(.((((--.........)------------)))...)))).).)--)))).((((.(((.(((...(((...)))...))).)))))))..)-). ( -27.40)
>DroSec_CAF1 22075 91 + 1
CGUGAUCUGC-GUC-CAGCAU--UUAACAAAUA------------UGCAGCGGACAGCA--GAUCUGCCUAGUGCUCUUUGUCGCUUCGAAAUAGAACACAGGCCCG-UA
...(((((((-(((-(.((((--.........)------------)))...)))).)))--)))).((((.(((.(((...(((...)))...))).)))))))...-.. ( -32.60)
>DroSim_CAF1 22954 91 + 1
CGUGAUCUGC-GUC-CAGCAU--UUAACAAAUA------------UGCAUCGGACAGCA--GAUCUGCCUAGUGCUCUUUGUCGCUUCGAAAUAGAACACAGGCCCG-UA
...(((((((-(((-(.((((--.........)------------)))...)))).)))--)))).((((.(((.(((...(((...)))...))).)))))))...-.. ( -32.60)
>DroEre_CAF1 24127 88 + 1
CGCGAUCUGC-GUC-CAGCAU--UUAGUAAAUA------------UGCA---GACAGCA--GAUCUGCCUAGUGCUCUUUAUCGAUUUCAAAUAGAACACAGGCUUG-UU
...(((((((-(((-..((((--.........)------------))).---))).)))--)))).((((.(((.(((...............))).)))))))...-.. ( -26.96)
>DroYak_CAF1 23813 93 + 1
CGCGAUCUGC-GUC-CAGCAU--UUAGCAAAUA------------UGCAUCGGACAGCAAAAAUCUGCCUAGUGCUCUUUAUCGAUUUCAAAUAGAACACAGGCUGG-UA
.......(((-(((-(.((((--.........)------------)))...)))).)))...(((.((((.(((.(((...............))).))))))).))-). ( -22.36)
>DroAna_CAF1 25117 107 + 1
CGAGACCGGUUGUCUUAGCUUUCUUAACUAAUAUUUUGAUUUAAAUGCUUGAGACAACC--GAUCGGCCAGAUGUUCUUUAGCG-UUUAAAAUAGAACACAGGCUGGCUU
...((.(((((((((((((...........................)).))))))))))--).))((((((.((((((......-........))))))....)))))). ( -32.87)
>consensus
CGCGAUCUGC_GUC_CAGCAU__UUAACAAAUA____________UGCAUCGGACAGCA__GAUCUGCCUAGUGCUCUUUAUCGAUUCGAAAUAGAACACAGGCCCG_UA
...(((((((.(((...((...........................))....))).)))..)))).((((.(((.(((...............))).)))))))...... (-14.44 = -14.72 +   0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,200,439 – 17,200,530
Length 91
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 79.52
Mean single sequence MFE -35.01
Consensus MFE -21.85
Energy contribution -21.07
Covariance contribution -0.77
Combinations/Pair 1.26
Mean z-score -4.15
Structure conservation index 0.62
SVM decision value 2.10
SVM RNA-class probability 0.988065
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17200439 91 - 27905053
UA-CGGGCCUGUGUUCUAUUUCGAAUCGACAAAGAGCACUAGGCAGAUC--UGCUGUCCGAUGCA------------UAUUUGUUAA--AUGCUG-GAC-GGAGAUCGCG
..-...(((((((((((.(.(((...))).).))))))).)))).((((--(.(((((((..(((------------(.........--))))))-)))-)))))))... ( -35.10)
>DroSec_CAF1 22075 91 - 1
UA-CGGGCCUGUGUUCUAUUUCGAAGCGACAAAGAGCACUAGGCAGAUC--UGCUGUCCGCUGCA------------UAUUUGUUAA--AUGCUG-GAC-GCAGAUCACG
..-((.(((((((((((.(.(((...))).).))))))).)))).((((--(((.(((((..(((------------(.........--))))))-)))-))))))).)) ( -37.20)
>DroSim_CAF1 22954 91 - 1
UA-CGGGCCUGUGUUCUAUUUCGAAGCGACAAAGAGCACUAGGCAGAUC--UGCUGUCCGAUGCA------------UAUUUGUUAA--AUGCUG-GAC-GCAGAUCACG
..-((.(((((((((((.(.(((...))).).))))))).)))).((((--(((.(((((..(((------------(.........--))))))-)))-))))))).)) ( -37.20)
>DroEre_CAF1 24127 88 - 1
AA-CAAGCCUGUGUUCUAUUUGAAAUCGAUAAAGAGCACUAGGCAGAUC--UGCUGUC---UGCA------------UAUUUACUAA--AUGCUG-GAC-GCAGAUCGCG
..-...(((((((((((..(((....)))...))))))).)))).((((--(((.(((---((((------------(.........--)))).)-)))-)))))))... ( -36.10)
>DroYak_CAF1 23813 93 - 1
UA-CCAGCCUGUGUUCUAUUUGAAAUCGAUAAAGAGCACUAGGCAGAUUUUUGCUGUCCGAUGCA------------UAUUUGCUAA--AUGCUG-GAC-GCAGAUCGCG
..-...(((((((((((..(((....)))...))))))).)))).((((..(((.(((((..(((------------(.........--))))))-)))-)))))))... ( -30.80)
>DroAna_CAF1 25117 107 - 1
AAGCCAGCCUGUGUUCUAUUUUAAA-CGCUAAAGAACAUCUGGCCGAUC--GGUUGUCUCAAGCAUUUAAAUCAAAAUAUUAGUUAAGAAAGCUAAGACAACCGGUCUCG
..(((((...(((((((........-......)))))))))))).((((--((((((((..(((.(((...................))).))).))))))))))))... ( -33.65)
>consensus
UA_CGAGCCUGUGUUCUAUUUCAAAUCGACAAAGAGCACUAGGCAGAUC__UGCUGUCCGAUGCA____________UAUUUGUUAA__AUGCUG_GAC_GCAGAUCGCG
......(((((((((((...............))))))).)))).((((..(((.(((....((...........................))...))).)))))))... (-21.85 = -21.07 +  -0.77)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:28 2006