Locus 4351

Sequence ID 2L_DroMel_CAF1
Location 12,462,906 – 12,463,026
Length 120
Max. P 0.952983
window6853 window6854

overview

Window 3

Location 12,462,906 – 12,463,026
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.96
Mean single sequence MFE -26.42
Consensus MFE -18.57
Energy contribution -20.37
Covariance contribution 1.80
Combinations/Pair 1.07
Mean z-score -2.11
Structure conservation index 0.70
SVM decision value 1.43
SVM RNA-class probability 0.952983
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12462906 120 + 22407834
AACUUUAAGAUAAGCAGCUCUAGCUUAUCAUUGUUAUCAUUGAAUGCGAUAGAUAACUCAAUGUAAAGACGAGGAAGUCGCCAAGAAAAAACGUCUCUCAUUGCAAAACAUUCGGAAAAU
........(((((((.......)))))))...((((((((((....)))).)))))).(((((...(((((......((.....)).....)))))..)))))................. ( -25.40)
>DroSec_CAF1 35905 107 + 1
AACUUUAAGAUAAGCAGCUCUAGCUUAUCAUUGUUAUCAUUGAAUGCGAUAGAUAACUCAAUGUAAAGACGAGGAAGUC-------------GUCUCUCUUUGCAGCCCGUUCGGAAAAU
........(((((((.......)))))))...((((((((((....)))).))))))....((((((((.((((.....-------------.))))))))))))..((....))..... ( -28.40)
>DroSim_CAF1 37034 107 + 1
AACUUUAAGAUAAGCAGCUCUAGCUUAUCAUUGUUAUCAUUGAAUGCGAUAGAUAACUCAAUGUAAAGACGAGGAAGUC-------------GUCUCUCUUUGCAGCCCGUUCGGAAAAU
........(((((((.......)))))))...((((((((((....)))).))))))....((((((((.((((.....-------------.))))))))))))..((....))..... ( -28.40)
>DroEre_CAF1 33004 111 + 1
AACUUUAAGAUAAGCAGGUGUUGCUUA---------UCAUUGAAUGCGAUAGAUUACUCGAUGCAAAGACGAGGAAGUCGGCAAGAAGAAUCACCUAUAUUUGCAAACCAUUUACAAAUU
...((((((((((((((...)))))))---------)).)))))(((((..((((..((..(((...(((......))).))).))..))))........)))))............... ( -23.40)
>DroYak_CAF1 35613 106 + 1
AACUUUAAGAUAAGCAGGACUUGCUUAUCAAUGUUAUCAUUGAAUGCGAUAGAUAACUCGAUGCAAAGACGAGG--------------AAUCGUCUAUCUUCGCAAAGCAUUUGGAAAAU
........(((((((((...)))))))))...((((((((((....)))).))))))..(((((...(.(((((--------------(........)))))))...)))))........ ( -26.50)
>consensus
AACUUUAAGAUAAGCAGCUCUAGCUUAUCAUUGUUAUCAUUGAAUGCGAUAGAUAACUCAAUGUAAAGACGAGGAAGUC_________AA_CGUCUCUCUUUGCAAACCAUUCGGAAAAU
........(((((((.......)))))))...((((((((((....)))).))))))....((((((((.((((...................))))))))))))............... (-18.57 = -20.37 +   1.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,462,906 – 12,463,026
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.96
Mean single sequence MFE -25.44
Consensus MFE -13.27
Energy contribution -14.55
Covariance contribution 1.28
Combinations/Pair 1.09
Mean z-score -1.85
Structure conservation index 0.52
SVM decision value 0.02
SVM RNA-class probability 0.544951
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12462906 120 - 22407834
AUUUUCCGAAUGUUUUGCAAUGAGAGACGUUUUUUCUUGGCGACUUCCUCGUCUUUACAUUGAGUUAUCUAUCGCAUUCAAUGAUAACAAUGAUAAGCUAGAGCUGCUUAUCUUAAAGUU
.................((((((((((((.....((.....))......))))))).))))).((((((.............))))))...(((((((.......)))))))........ ( -25.72)
>DroSec_CAF1 35905 107 - 1
AUUUUCCGAACGGGCUGCAAAGAGAGAC-------------GACUUCCUCGUCUUUACAUUGAGUUAUCUAUCGCAUUCAAUGAUAACAAUGAUAAGCUAGAGCUGCUUAUCUUAAAGUU
....(((....)))...(((.(((((((-------------((.....)))))))).).))).((((((.............))))))...(((((((.......)))))))........ ( -24.72)
>DroSim_CAF1 37034 107 - 1
AUUUUCCGAACGGGCUGCAAAGAGAGAC-------------GACUUCCUCGUCUUUACAUUGAGUUAUCUAUCGCAUUCAAUGAUAACAAUGAUAAGCUAGAGCUGCUUAUCUUAAAGUU
....(((....)))...(((.(((((((-------------((.....)))))))).).))).((((((.............))))))...(((((((.......)))))))........ ( -24.72)
>DroEre_CAF1 33004 111 - 1
AAUUUGUAAAUGGUUUGCAAAUAUAGGUGAUUCUUCUUGCCGACUUCCUCGUCUUUGCAUCGAGUAAUCUAUCGCAUUCAAUGA---------UAAGCAACACCUGCUUAUCUUAAAGUU
.((((((((.....))))))))...((((((((((..(((.(((......)))...)))..))).)))).))).........((---------((((((.....))))))))........ ( -25.20)
>DroYak_CAF1 35613 106 - 1
AUUUUCCAAAUGCUUUGCGAAGAUAGACGAUU--------------CCUCGUCUUUGCAUCGAGUUAUCUAUCGCAUUCAAUGAUAACAUUGAUAAGCAAGUCCUGCUUAUCUUAAAGUU
...........(((((((((.(..((((((..--------------..))))))...).))).((((((.............))))))...((((((((.....)))))))).)))))). ( -26.82)
>consensus
AUUUUCCGAAUGGUUUGCAAAGAGAGACG_UU_________GACUUCCUCGUCUUUACAUUGAGUUAUCUAUCGCAUUCAAUGAUAACAAUGAUAAGCUAGAGCUGCUUAUCUUAAAGUU
......................(((((((....................))))))).((((((((..........))))))))........(((((((.......)))))))........ (-13.27 = -14.55 +   1.28)

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 11:15:42 2006