Locus 4370

Sequence ID 3R_DroMel_CAF1
Location 11,527,667 – 11,527,809
Length 142
Max. P 0.613096
window7143 window7144

overview

Window 3

Location 11,527,667 – 11,527,772
Length 105
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 75.00
Mean single sequence MFE -17.70
Consensus MFE -9.76
Energy contribution -12.60
Covariance contribution 2.84
Combinations/Pair 1.11
Mean z-score -1.81
Structure conservation index 0.55
SVM decision value 0.01
SVM RNA-class probability 0.536521
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11527667 105 + 27905053
AAUACAUAGAUACUGAUAAACAAAAAAAAACAGUGUAAUAAAUAAAAUAAAAAU-----UCACCUUAAUUAGAAAUAACUUGAGGU-----GCAUACCUUUGCGGAAAUGCACUG
..............................(((((((.................-----..((((((((((....))).)))))))-----(((......))).....))))))) ( -19.70)
>DroSec_CAF1 61221 103 + 1
AAUACACAGAUACCGAUAAA------AAGGAUGUGUAAAAA-AAAAAUAAAAAU-----GCACCAUAAUUAGAAAUAACUUGAGGCCAGUGGCAUACCUUUGCGGAAAUGCACUU
..((((((....((......------..)).))))))....-............-----((..((...(((....)))..))..)).((((.(((.((.....))..))))))). ( -16.50)
>DroYak_CAF1 60030 100 + 1
AAUAUAUAGAUACUGAUAAA------AA-GUGGAGUAAUAA-------AAAUAUUUCCCGUACCUUAAUUAGUAAUAACUUGAGGCCAGU-GCAUACCUUUGCGGAAAUGCACUC
....................------..-(.((((......-------......)))))...(((((((((....))).))))))..(((-((((.((.....))..))))))). ( -16.90)
>consensus
AAUACAUAGAUACUGAUAAA______AA_GAAGUGUAAUAA__AAAAUAAAAAU_____GCACCUUAAUUAGAAAUAACUUGAGGCCAGU_GCAUACCUUUGCGGAAAUGCACUC
..............................(((((((.........................(((((((((....))).))))))......(((......))).....))))))) ( -9.76 = -12.60 +   2.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,527,704 – 11,527,809
Length 105
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 84.02
Mean single sequence MFE -21.13
Consensus MFE -16.30
Energy contribution -17.97
Covariance contribution 1.67
Combinations/Pair 1.08
Mean z-score -1.75
Structure conservation index 0.77
SVM decision value 0.16
SVM RNA-class probability 0.613096
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11527704 105 + 27905053
AUAAAUAAAAUAAAAAU-----UCACCUUAAUUAGAAAUAACUUGAGGU-----GCAUACCUUUGCGGAAAUGCACUGUGGGCUUAUAAAUUUCAUUAGGGAAAAGCGAAAACAU
.................-----...(((((((.(((.((((((((.(((-----((((.((.....))..))))))).)))).))))...))).))))))).............. ( -18.20)
>DroSec_CAF1 61252 109 + 1
AAAA-AAAAAUAAAAAU-----GCACCAUAAUUAGAAAUAACUUGAGGCCAGUGGCAUACCUUUGCGGAAAUGCACUUUGGGCUUAUAAAUUUCAUUAGGGAAAAGCGAAAACAU
....-...........(-----((.((.((((..(((((....((((.((((..((((.((.....))..))))...)))).))))...))))))))).))....)))....... ( -20.00)
>DroYak_CAF1 60060 107 + 1
AUAA-------AAAUAUUUCCCGUACCUUAAUUAGUAAUAACUUGAGGCCAGU-GCAUACCUUUGCGGAAAUGCACUCUGGGCUUAUAAAAUUCAUUAGGGAAAAGCGAAAACAU
....-------.....((((((....((((((((....))).)))))((((((-((((.((.....))..)))))))...)))...............))))))........... ( -25.20)
>consensus
AUAA__AAAAUAAAAAU_____GCACCUUAAUUAGAAAUAACUUGAGGCCAGU_GCAUACCUUUGCGGAAAUGCACUCUGGGCUUAUAAAUUUCAUUAGGGAAAAGCGAAAACAU
.........................(((((((..(((((....((((.((((..((((.((.....))..))))...)))).))))...)))))))))))).............. (-16.30 = -17.97 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:28 2006