Locus 2126

Sequence ID X_DroMel_CAF1
Location 5,766,404 – 5,766,551
Length 147
Max. P 0.999974
window3454 window3455 window3456

overview

Window 4

Location 5,766,404 – 5,766,514
Length 110
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 74.50
Mean single sequence MFE -25.38
Consensus MFE -17.66
Energy contribution -17.60
Covariance contribution -0.06
Combinations/Pair 1.20
Mean z-score -2.88
Structure conservation index 0.70
SVM decision value 4.24
SVM RNA-class probability 0.999846
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5766404 110 + 22224390
ACCAAAGGAAAAAAAAUCUGAACUAAUAAAUAAGUUACCCGGGCAACAAUGCGUAUGAGUGAUAUGCAGAAAAUGCAUGUCCAUAUGCAUAUGCAUAUGCUUUCGCACAU
.((...(((.......))).((((........))))....))(((...(((((((((...((((((((.....))))))))))))))))).)))...(((....)))... ( -27.00)
>DroSec_CAF1 39261 109 + 1
ACCAAAGGAAUGAGUA-CAAAACGAAUAAAUAAGUUACCCGGGCAACACUGCGUAUGAGUGAUAUGCAGAAAAUGCAUGUCCAUAUGCAUAUGCACAUGCUUUCGCAUAU
.((...((..((....-)).(((..........))).)).))(((....((((((((...((((((((.....))))))))))))))))..)))..((((....)))).. ( -24.50)
>DroEre_CAF1 40100 96 + 1
GCCAAAGGGAAACCUAGCAAAACCAAUAAAUAAUUUAUGGAGGCAACACUGCGUAUGUGUGAUAUGCAGAAAGUGCAA------------UUGCACAUGCUA--AAAUAA
(((..(((....))).......(((.(((.....)))))).)))........(((((((..((.((((.....)))))------------)..)))))))..--...... ( -29.40)
>DroYak_CAF1 41870 97 + 1
AGCAGAGGAAGAAAUA-CAAAACCAAUAAAUGAUUUAGCGAGGCAACACUGCGUAUGAGUGAUAUGCAGAAAGUGCAU------------AUGCAUAUGUUUUUGCACAU
.(((((((........-.....)).............(((..(((...((((((((.....))))))))....)))..------------.))).......))))).... ( -20.62)
>consensus
ACCAAAGGAAAAAAUA_CAAAACCAAUAAAUAAGUUACCCAGGCAACACUGCGUAUGAGUGAUAUGCAGAAAAUGCAU____________AUGCACAUGCUUUCGCACAU
.........................................((((...((((((((.....))))))))...((((((((........)))))))).))))......... (-17.66 = -17.60 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,766,434 – 5,766,551
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 74.22
Mean single sequence MFE -28.50
Consensus MFE -20.89
Energy contribution -21.40
Covariance contribution 0.51
Combinations/Pair 1.17
Mean z-score -2.96
Structure conservation index 0.73
SVM decision value 5.11
SVM RNA-class probability 0.999974
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5766434 117 + 22224390
UAAGUUACCCGGGCAACAAUGCGUAUGAGUGAUAUGCAGAAAAUGCAUGUCCAUAUGCAUAUGCAUAUGCUUUCGCACAUACUGAAAUAAAUGCAUAUGUGUAAUUUUUUCAAAG---AU
.(((((((...(....).(((((((((...((((((((.....)))))))))))))))))..(((((((((((((.......))))).....)))))))))))))))........---.. ( -33.50)
>DroSec_CAF1 39290 113 + 1
UAAGUUACCCGGGCAACACUGCGUAUGAGUGAUAUGCAGAAAAUGCAUGUCCAUAUGCAUAUGCACAUGCUUUCGCAUAUACUAAAAUAAA----UAAGUGUAAUUUUUUCAAAG---AU
.(((((((.(..(((....((((((((...((((((((.....))))))))))))))))..)))..((((....)))).............----...).)))))))........---.. ( -28.20)
>DroYak_CAF1 41899 93 + 1
UGAUUUAGCGAGGCAACACUGCGUAUGAGUGAUAUGCAGAAAGUGCAU------------AUGCAUAUGUUUUUGCACAUACUGAA---------------UACUUUAUUUAAAGUGUAU
....((((...(....).((((((((.....))))))))...(((((.------------..((....))...)))))...))))(---------------((((((....))))))).. ( -23.80)
>consensus
UAAGUUACCCGGGCAACACUGCGUAUGAGUGAUAUGCAGAAAAUGCAUGUCCAUAUGCAUAUGCAUAUGCUUUCGCACAUACUGAAAUAAA____UA_GUGUAAUUUUUUCAAAG___AU
.(((((((....(((....)))(((((.((((...(((....((((((((........)))))))).)))..)))).)))))..................)))))))............. (-20.89 = -21.40 +   0.51)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,766,434 – 5,766,551
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.22
Mean single sequence MFE -27.20
Consensus MFE -17.37
Energy contribution -17.60
Covariance contribution 0.23
Combinations/Pair 1.11
Mean z-score -3.37
Structure conservation index 0.64
SVM decision value 5.11
SVM RNA-class probability 0.999974
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5766434 117 - 22224390
AU---CUUUGAAAAAAUUACACAUAUGCAUUUAUUUCAGUAUGUGCGAAAGCAUAUGCAUAUGCAUAUGGACAUGCAUUUUCUGCAUAUCACUCAUACGCAUUGUUGCCCGGGUAACUUA
..---...(((..........(((((((((........((((((((....))))))))..)))))))))((.(((((.....))))).))..)))........(((((....)))))... ( -34.20)
>DroSec_CAF1 39290 113 - 1
AU---CUUUGAAAAAAUUACACUUA----UUUAUUUUAGUAUAUGCGAAAGCAUGUGCAUAUGCAUAUGGACAUGCAUUUUCUGCAUAUCACUCAUACGCAGUGUUGCCCGGGUAACUUA
..---....................----.........((((((((....))))))))...(((.((((((.(((((.....))))).))...)))).)))..(((((....)))))... ( -29.50)
>DroYak_CAF1 41899 93 - 1
AUACACUUUAAAUAAAGUA---------------UUCAGUAUGUGCAAAAACAUAUGCAU------------AUGCACUUUCUGCAUAUCACUCAUACGCAGUGUUGCCUCGCUAAAUCA
....(((((....))))).---------------....(((((((((........)))))------------)))).......(((...(((((....).)))).)))............ ( -17.90)
>consensus
AU___CUUUGAAAAAAUUACAC_UA____UUUAUUUCAGUAUGUGCGAAAGCAUAUGCAUAUGCAUAUGGACAUGCAUUUUCUGCAUAUCACUCAUACGCAGUGUUGCCCGGGUAACUUA
......................................((((((((....))))))))................(((....((((.(((.....))).))))...)))............ (-17.37 = -17.60 +   0.23)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:53 2006