Locus 2210

Sequence ID 3R_DroMel_CAF1
Location 6,310,781 – 6,310,971
Length 190
Max. P 0.980654
window3588 window3589

overview

Window 8

Location 6,310,781 – 6,310,881
Length 100
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 78.98
Mean single sequence MFE -21.78
Consensus MFE -13.64
Energy contribution -14.50
Covariance contribution 0.86
Combinations/Pair 1.08
Mean z-score -1.65
Structure conservation index 0.63
SVM decision value 0.44
SVM RNA-class probability 0.735927
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6310781 100 + 27905053
GUAAAAACACAA--CUCCGGCA---ACUUGACGACGGCAGCG--CAGACUGCGCCAAAAGUCAAAUUUUGUAGAUUGCAAUAAAUCAAAUAGCAAUUACACGAAAUU
............--....(...---.)(((((...(((.(((--.....))))))....)))))(((((((.((((((.............))))))..))))))). ( -19.42)
>DroPse_CAF1 73172 99 + 1
GCAAGUUGACGACUCUCUGGGA---CUUUGU---CGGCGGCA--CAGACUGCGCCAAAAGUCAAAUUUUGUAGAUUGCAAUAAAUCAAAUAGCAAUUACACGAAAUU
((..((((((((.((.....))---..))))---)))).)).--..((((........)))).((((((((.((((((.............))))))..)))))))) ( -22.72)
>DroEre_CAF1 83253 84 + 1
-----AA-------------CA---ACUUGACGACGGCGGCG--CAGACUGCGCCAAAAGUCAAAUUUUGUAGAUUGCAAUAAAUCAAAUAGCAAUUACACGAAAUU
-----..-------------..---.......(((...((((--(.....)))))....))).((((((((.((((((.............))))))..)))))))) ( -22.02)
>DroYak_CAF1 74821 89 + 1
GUAAAAA-------------CA---ACUUGACGACGGCAGCG--CAGACUGCGCCAAAAGUCAAAUUUUCUAGAUUGCAAUAAAUCAAAUAGCAAUUACACGAAAUU
((((...-------------..---..(((((...(((.(((--.....))))))....)))))........((((......)))).........))))........ ( -15.50)
>DroAna_CAF1 79060 103 + 1
--ACACAGGCCG--CUCCGGCAGGCAGUUGAUGGAGGCAGCGCCCAGACUGCGCCAAAAGUCAAAUUUUCCAGAUUGCAAUAAAUCAAAUGGCAAUUACACGAAAUU
--......((((--(....))..((((((..(((((((...)))..((((........))))......))))))))))............))).............. ( -23.90)
>DroPer_CAF1 78429 99 + 1
GCAAGUUGACGACUCUCUGGGA---CUUUGU---CGGCGGCA--CAGACUGCGCCAAAAGUCAAAUUUUGUAGAUUGCUAUAAAUCAAAUAGCAAUUACACGAAAUU
((..((((((((.((.....))---..))))---)))).)).--..((((........)))).((((((((.(((((((((.......)))))))))..)))))))) ( -27.10)
>consensus
G_AAAAAGAC_A__CUC_GGCA___ACUUGACGACGGCAGCG__CAGACUGCGCCAAAAGUCAAAUUUUGUAGAUUGCAAUAAAUCAAAUAGCAAUUACACGAAAUU
...........................(((((...(((.(((.......))))))....)))))(((((((.((((((.............))))))..))))))). (-13.64 = -14.50 +   0.86)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,310,881 – 6,310,971
Length 90
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 79.95
Mean single sequence MFE -25.03
Consensus MFE -10.34
Energy contribution -12.16
Covariance contribution 1.82
Combinations/Pair 1.13
Mean z-score -4.24
Structure conservation index 0.41
SVM decision value 1.87
SVM RNA-class probability 0.980654
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6310881 90 - 27905053
CCCACACACAUGCACACACACACACUAGCUCCUUUCAAUCCCCCGCUUAGCAAUGUGUGUG--UAUGUGUGCAAAAUUGAGAAAACAUGCCU
....((((((((((((((((......(((...............)))......))))))))--))))))))..................... ( -27.76)
>DroSec_CAF1 75751 82 - 1
CCCACACACA----CAUACACACACUAGCUCCUUUCAAUCCCCCGCUUUGCAAUGUGUG------UGUGUGCAAAAUUGAGAAAACAUGCCU
....((((((----((((((......(((...............)))......))))))------))))))..................... ( -19.16)
>DroSim_CAF1 81558 88 - 1
CCCACACACA----CGUACACACACUAGCUCCUUUCAAUCCCCCGCUUUGCCAUGUGUGUGUGUGUGUGUGCAAAAUUGAGAAAACAUGCCU
..((((((((----((((((((((...((....................))..))))))))))))))))))..................... ( -27.05)
>DroEre_CAF1 83337 82 - 1
CCCACACACA------CACACACACUAGCUCCUUUCAAUCCCCCGCCUAGCCA--UGUGUG--UGUGUGUGGAAAAUUGAGAAAACAUGCCU
.(((((((((------((((((..(((((...............).))))...--))))))--))))))))).................... ( -29.16)
>DroYak_CAF1 74910 84 - 1
CCCACACACA------UACACACACUAGCUCCUUUCAAUCCCCCGCCUAACAAAGUGUGUG--UGUGUGUGCAAAAUUGAGAAAACAUGCCU
....((((((------((((((((((...........................))))))))--))))))))..................... ( -24.13)
>DroAna_CAF1 79163 68 - 1
CCCACACACG-------------------UCCUCCCAG-CCACCCCCUGGCCG--GGGCUG--UGUGUGUGCGAAAUUGAGAAAACAUGCCU
.(((((((((-------------------...((((.(-(((.....)))).)--)))...--)))))))).)................... ( -22.90)
>consensus
CCCACACACA______UACACACACUAGCUCCUUUCAAUCCCCCGCCUAGCAAUGUGUGUG__UGUGUGUGCAAAAUUGAGAAAACAUGCCU
..((((((((......(((((((...............................)))))))..))))))))..................... (-10.34 = -12.16 +   1.82)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:55 2006