Locus 2278

Sequence ID X_DroMel_CAF1
Location 6,164,081 – 6,164,187
Length 106
Max. P 0.994457
window3691 window3692

overview

Window 1

Location 6,164,081 – 6,164,187
Length 106
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 82.25
Mean single sequence MFE -27.30
Consensus MFE -19.56
Energy contribution -19.60
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.72
SVM decision value 0.49
SVM RNA-class probability 0.757221
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6164081 106 + 22224390
UAUAUACAAUAUCCUCGUCUGCAUCUGCAGCGCUCUUUAGCAACGUACUCACUUCCACAGUUUGCGUGUGAAAGGAUUUCUCCUUGAGCGCAUUUAAUGCGAG--UGC
.............(((((.(((....)))((((((....(((.((((...(((.....))).)))))))..(((((....))))))))))).......)))))--... ( -27.80)
>DroSec_CAF1 2728 103 + 1
UGUAUAUAUUAUCG-----UGCAUCUGCAGCGCUCUUUAGCAUCGUACUCACUUCCACAGUUUGCGUGUGAAAGGAUUUCUCCUUGAGCGCAUUUAAUGCGAGUGUGC
.............(-----..((..((((((((((....(((.((((...(((.....))).)))))))..(((((....)))))))))))......))))..))..) ( -27.40)
>DroSim_CAF1 5074 103 + 1
UGUAUAUAUUAUCG-----UGCAUCUGCAGCGCUCUUUAGCACCGUACUCACUUCCACAGUUUGCGUGUGAAAGGAUUUCUCCUUGAGCGCAUUUAAUGCGAGUGUGC
.............(-----..((..((((((((((.....(((((((...(((.....))).)))).))).(((((....)))))))))))......))))..))..) ( -29.00)
>DroEre_CAF1 2681 82 + 1
UG--UAUGUCCUCA-----UGCAUCUGCAGCGCUCU-----------------UCCACAUUUUGCGUGUGAAAGGAUUUCACCUUGAGCGCUUUUAAUGCGAG--UGC
..--...(..(((.-----.((((..(.(((((((.-----------------..(((((.....))))).((((......))))))))))).)..)))))))--..) ( -25.60)
>DroYak_CAF1 8453 99 + 1
UG--UAUAUCCUCU-----UGCAUCUGCAUUGCUCUUUAGCACCGCACUCACUUUCACAGUUUGCGUGUGAAAGGAUUUCACCUUGAGCGCUUUUAAUGCGAG--UGC
..--..........-----.(((..(((((((((....)))...((.(((((((((((((....).))))))))(....)....)))).))....))))))..--))) ( -26.70)
>consensus
UGUAUAUAUUAUCG_____UGCAUCUGCAGCGCUCUUUAGCACCGUACUCACUUCCACAGUUUGCGUGUGAAAGGAUUUCUCCUUGAGCGCAUUUAAUGCGAG__UGC
...................(((((.....((((((....................((((.......)))).((((......)))))))))).....)))))....... (-19.56 = -19.60 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,164,081 – 6,164,187
Length 106
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 82.25
Mean single sequence MFE -30.14
Consensus MFE -23.26
Energy contribution -23.90
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -2.88
Structure conservation index 0.77
SVM decision value 2.48
SVM RNA-class probability 0.994457
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6164081 106 - 22224390
GCA--CUCGCAUUAAAUGCGCUCAAGGAGAAAUCCUUUCACACGCAAACUGUGGAAGUGAGUACGUUGCUAAAGAGCGCUGCAGAUGCAGACGAGGAUAUUGUAUAUA
...--(((((.......(((((((((((....)))))((((.(((.....)))...)))).............))))))(((....)))).))))............. ( -31.70)
>DroSec_CAF1 2728 103 - 1
GCACACUCGCAUUAAAUGCGCUCAAGGAGAAAUCCUUUCACACGCAAACUGUGGAAGUGAGUACGAUGCUAAAGAGCGCUGCAGAUGCA-----CGAUAAUAUAUACA
........(((((....(((((((((((....)))))((((.(((.....)))...)))).............))))))....))))).-----.............. ( -30.40)
>DroSim_CAF1 5074 103 - 1
GCACACUCGCAUUAAAUGCGCUCAAGGAGAAAUCCUUUCACACGCAAACUGUGGAAGUGAGUACGGUGCUAAAGAGCGCUGCAGAUGCA-----CGAUAAUAUAUACA
........(((((....(((((((((((....)))))((((.(((.....)))...)))).............))))))....))))).-----.............. ( -30.40)
>DroEre_CAF1 2681 82 - 1
GCA--CUCGCAUUAAAAGCGCUCAAGGUGAAAUCCUUUCACACGCAAAAUGUGGA-----------------AGAGCGCUGCAGAUGCA-----UGAGGACAUA--CA
(..--((((((((...(((((((...(((((.....))))).(((.....)))..-----------------.)))))))...))))).-----.)))..)...--.. ( -28.80)
>DroYak_CAF1 8453 99 - 1
GCA--CUCGCAUUAAAAGCGCUCAAGGUGAAAUCCUUUCACACGCAAACUGUGAAAGUGAGUGCGGUGCUAAAGAGCAAUGCAGAUGCA-----AGAGGAUAUA--CA
(((--((.(((((....(((((((.((......))(((((((.......))))))).)))))))...(((....)))))))))).))).-----..........--.. ( -29.40)
>consensus
GCA__CUCGCAUUAAAUGCGCUCAAGGAGAAAUCCUUUCACACGCAAACUGUGGAAGUGAGUACGGUGCUAAAGAGCGCUGCAGAUGCA_____CGAUAAUAUAUACA
........(((((....((((((.((((....))))((((((.......))))))..................))))))....))))).................... (-23.26 = -23.90 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:28 2006