Locus 7807

Sequence ID 3R_DroMel_CAF1
Location 20,920,199 – 20,920,303
Length 104
Max. P 0.914181
window12589 window12590

overview

Window 9

Location 20,920,199 – 20,920,303
Length 104
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 84.80
Mean single sequence MFE -29.46
Consensus MFE -14.20
Energy contribution -14.60
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.90
Structure conservation index 0.48
SVM decision value 0.09
SVM RNA-class probability 0.576388
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20920199 104 + 27905053
AAAGCUUGCAAAUCAAGGGCUUUCCCC--UUGCA-AUUGUGCUUUUGCAGCACAUUUG-----------CACAUAUGUGAAUGCGAUUGUGCUGCUAUCUCGACGAAAAUUGAAAAUG
(((((..((((..((((((.....)))--)))..-.))))))))).((((((((.(((-----------((((....))..))))).))))))))....((((......))))..... ( -32.50)
>DroSec_CAF1 3498 104 + 1
AAAGCUUGCAAAUCAAGGGCUUUCCCC--UUGCA-AUUGUGCUUUUGCAGCACAUUUG-----------CACACAUGCGAAUGCGAUUGUGCUGCUAUCUCGCCGAAAAUUGAAAAUG
(((((..((((..((((((.....)))--)))..-.))))))))).((((((((.(((-----------((..(....)..))))).))))))))....................... ( -32.50)
>DroSim_CAF1 11908 104 + 1
AAAGCUUGCAAAUCAAGGGCUUUCCCC--UUGCA-AUUGUGCUUUUGCAGCACAUUUG-----------CACACAUGCGAAUGCGAUUGUGCUGCUAUCUCGCCGAAAAUUGAAAAUG
(((((..((((..((((((.....)))--)))..-.))))))))).((((((((.(((-----------((..(....)..))))).))))))))....................... ( -32.50)
>DroEre_CAF1 11905 102 + 1
AAAGCUUGCAAAUCAAGGGCUUUCCCCC-UAGCA-AUUGUGCUUUUGCAGCACAAUUC--------------ACAUUCACAUGUGAAUCACAUGCUAUCUCUCCGAAAAUUGAAAAUG
............(((((((......)))-(((((-.(((((((.....)))))))(((--------------((((....))))))).....)))))............))))..... ( -23.80)
>DroYak_CAF1 10096 118 + 1
AAAGCUUGCAAAUCAAGGGCUUUCCCCCAUAGCAAAUUGUGCUUUUGCAGCACAAUUCACAAUUCACAACUCACAUUCACAUGUGAAUCGCAUGCUAUCUCUUCGAAAAUUGAAAAUG
..(((.(((.......(((......)))...(..(((((((((.....)))))))))..)..........((((((....))))))...))).))).....(((((...))))).... ( -26.00)
>consensus
AAAGCUUGCAAAUCAAGGGCUUUCCCC__UUGCA_AUUGUGCUUUUGCAGCACAUUUG___________CACACAUGCGAAUGCGAUUGUGCUGCUAUCUCGCCGAAAAUUGAAAAUG
..(((.(((((.....(((....)))...)))))...((((((.....)))))).......................................)))...................... (-14.20 = -14.60 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,920,199 – 20,920,303
Length 104
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 84.80
Mean single sequence MFE -33.40
Consensus MFE -20.16
Energy contribution -20.72
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -3.01
Structure conservation index 0.60
SVM decision value 1.09
SVM RNA-class probability 0.914181
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20920199 104 - 27905053
CAUUUUCAAUUUUCGUCGAGAUAGCAGCACAAUCGCAUUCACAUAUGUG-----------CAAAUGUGCUGCAAAAGCACAAU-UGCAA--GGGGAAAGCCCUUGAUUUGCAAGCUUU
.......................((((((((...((((........)))-----------)...)))))))).(((((.(((.-..(((--(((.....))))))..)))...))))) ( -32.40)
>DroSec_CAF1 3498 104 - 1
CAUUUUCAAUUUUCGGCGAGAUAGCAGCACAAUCGCAUUCGCAUGUGUG-----------CAAAUGUGCUGCAAAAGCACAAU-UGCAA--GGGGAAAGCCCUUGAUUUGCAAGCUUU
..............(((......((((((((...((((........)))-----------)...))))))))....(((....-..(((--(((.....))))))...)))..))).. ( -32.80)
>DroSim_CAF1 11908 104 - 1
CAUUUUCAAUUUUCGGCGAGAUAGCAGCACAAUCGCAUUCGCAUGUGUG-----------CAAAUGUGCUGCAAAAGCACAAU-UGCAA--GGGGAAAGCCCUUGAUUUGCAAGCUUU
..............(((......((((((((...((((........)))-----------)...))))))))....(((....-..(((--(((.....))))))...)))..))).. ( -32.80)
>DroEre_CAF1 11905 102 - 1
CAUUUUCAAUUUUCGGAGAGAUAGCAUGUGAUUCACAUGUGAAUGU--------------GAAUUGUGCUGCAAAAGCACAAU-UGCUA-GGGGGAAAGCCCUUGAUUUGCAAGCUUU
..(((((........)))))..(((....(((((((((....))))--------------)))))(((((.....)))))..(-(((..-(((((....))))).....))))))).. ( -29.50)
>DroYak_CAF1 10096 118 - 1
CAUUUUCAAUUUUCGAAGAGAUAGCAUGCGAUUCACAUGUGAAUGUGAGUUGUGAAUUGUGAAUUGUGCUGCAAAAGCACAAUUUGCUAUGGGGGAAAGCCCUUGAUUUGCAAGCUUU
..(((((.......)))))...(((.((((((((((((....)))))))))..((((((..(((((((((.....)))))))))..)...(((((....))))))))))))).))).. ( -39.50)
>consensus
CAUUUUCAAUUUUCGGCGAGAUAGCAGCACAAUCGCAUUCGCAUGUGUG___________CAAAUGUGCUGCAAAAGCACAAU_UGCAA__GGGGAAAGCCCUUGAUUUGCAAGCUUU
......................(((........(((((....))))).................((((((.....))))))...(((((..((((....))))....))))).))).. (-20.16 = -20.72 +   0.56)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:12 2006