Locus 1213

Sequence ID 3R_DroMel_CAF1
Location 3,654,192 – 3,654,294
Length 102
Max. P 0.988892
window1981 window1982

overview

Window 1

Location 3,654,192 – 3,654,294
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 90.49
Mean single sequence MFE -29.00
Consensus MFE -25.60
Energy contribution -25.93
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.88
SVM decision value 0.50
SVM RNA-class probability 0.761020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3654192 102 + 27905053
AGGCGUAAAUAAAUAAAUAAUCAUAUUUCUCAUUUUCCGAGUGGACAGCGUGGGCCUUACACCUGUGCUAGUGCCCACCGGAAAUGGAAAAUGUUUUAGUUG
......................((((((..(((((.(((.((((((((((..((.......))..)))).))..))))))))))))..))))))........ ( -28.40)
>DroSec_CAF1 12943 97 + 1
AGGU-UGUGU----AAAUAAUCAAAUUUCUCAUUUUCCGAGUGGAAAGCGUGGGCCUUGCACCUGUGUUAGUGCCCACCGGAAAUGGAAAAUGUUUUAGAUG
.(((-(((..----..))))))..((((..(((((.(((.((.....))((((((((.(((....))).)).))))))))))))))..)))).......... ( -29.90)
>DroSim_CAF1 15161 101 + 1
AGGC-UGUGUCAAUAAAUAAUCAUAUUUCUCAUUUUCCGAGUGGAAAGCGUGGGCCUUGCACCUGUGUUAGUGCCCACCGGAAAUGGAAAAUGUUUUAGAUG
.(..-(((........)))..)((((((..(((((.(((.((.....))((((((((.(((....))).)).))))))))))))))..))))))........ ( -28.70)
>consensus
AGGC_UGUGU_AAUAAAUAAUCAUAUUUCUCAUUUUCCGAGUGGAAAGCGUGGGCCUUGCACCUGUGUUAGUGCCCACCGGAAAUGGAAAAUGUUUUAGAUG
......................((((((..(((((.(((.((.....))((((((((..((....))..)).))))))))))))))..))))))........ (-25.60 = -25.93 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 3,654,192 – 3,654,294
Length 102
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 90.49
Mean single sequence MFE -26.87
Consensus MFE -25.29
Energy contribution -25.73
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -2.98
Structure conservation index 0.94
SVM decision value 2.14
SVM RNA-class probability 0.988892
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3654192 102 - 27905053
CAACUAAAACAUUUUCCAUUUCCGGUGGGCACUAGCACAGGUGUAAGGCCCACGCUGUCCACUCGGAAAAUGAGAAAUAUGAUUAUUUAUUUAUUUACGCCU
.........((((((((((((((((((((((...((...(((.....)))...))))))))).))).))))).)))).)))..................... ( -26.30)
>DroSec_CAF1 12943 97 - 1
CAUCUAAAACAUUUUCCAUUUCCGGUGGGCACUAACACAGGUGCAAGGCCCACGCUUUCCACUCGGAAAAUGAGAAAUUUGAUUAUUU----ACACA-ACCU
.........((.(((((((((((((((((((((......)))))(((((....))))))))).))).))))).))))..)).......----.....-.... ( -26.70)
>DroSim_CAF1 15161 101 - 1
CAUCUAAAACAUUUUCCAUUUCCGGUGGGCACUAACACAGGUGCAAGGCCCACGCUUUCCACUCGGAAAAUGAGAAAUAUGAUUAUUUAUUGACACA-GCCU
.........((((((((((((((((((((((((......)))))(((((....))))))))).))).))))).)))).)))................-.... ( -27.60)
>consensus
CAUCUAAAACAUUUUCCAUUUCCGGUGGGCACUAACACAGGUGCAAGGCCCACGCUUUCCACUCGGAAAAUGAGAAAUAUGAUUAUUUAUU_ACACA_GCCU
.........((((((((((((((((((((((((......)))))(((((....))))))))).))).))))).)))).)))..................... (-25.29 = -25.73 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:45 2006