Locus 5502

Sequence ID dm3.chr2R
Location 20,899,003 – 20,899,130
Length 127
Max. P 0.870343
window7551 window7552

overview

Window 1

Location 20,899,003 – 20,899,130
Length 127
Sequences 5
Columns 131
Reading direction forward
Mean pairwise identity 73.51
Shannon entropy 0.46216
G+C content 0.46188
Mean single sequence MFE -35.54
Consensus MFE -18.20
Energy contribution -18.76
Covariance contribution 0.56
Combinations/Pair 1.13
Mean z-score -1.49
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.574883
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20899003 127 + 21146708
GAUGGUAAUCGAUGCCUUCCGAUUCCAUUCGGACAUAUCGAUGCAUCGAUAUGUCGUAGUUCACACGACGGCCGCGGCAGCGCUUUCUGA----AAACACAUACAUCGAUAUGUCAACACUGAUUAAAAUU
(((((.(((((........))))))))))..((((((((((((.........(((((.(....))))))(((.((....)))))......----.........))))))))))))................ ( -36.80, z-score =  -1.98, R)
>droEre2.scaffold_4845 22274376 129 + 22589142
GAUGGUAAUCGAUGCCUUCCGAUUUCUUCCACA--UAUCGAUGCAUCGAUACGAUUUAGUUCGUCACGCGGCCGCAGCAGCGCUUUGUGCUUAUCGACACAUCCAUACAUAUUUUACCAAAGAUAGAGAUU
..(((((((((((((....((((..........--.))))..)))))))).((((..(((.((...(((.((....)).)))...)).))).))))..................)))))............ ( -29.80, z-score =  -0.80, R)
>droYak2.chr2R 20863975 128 + 21139217
GAUGGUAAUCGAUGCCUUCCGAUUACCUUCGCAC-UAUCGAUGCAUCGAUUCUAUUUAGUUCAUCACGCGGCCGCAGCAGCGCUUUGUGCUUACCGAGUUGUUAAGACACACAU--CCAAAGACAGAGGUU
((.((((((((........)))))))).))((((-....((((.((..(......)..)).)))).(((.((....)).)))....))))..(((...(((((...........--.....))))).))). ( -31.29, z-score =  -0.33, R)
>droSec1.super_23 756271 121 + 989336
GAUGGUAAUCGAUGCCUUCCGAUUCCGUUCGGACAUAUCGAUGCAUCGAUAUGUUUUAGUACACAAGGCGGCCACGGCAGCGCUUU--------GAGCUCAUCGAAU--UGUGAAGUCACUGAUUAAGGUU
(((..((((((.((.((((((((((.((..(((((((((((....)))))))))))....)).(((((((((....))..))))))--------)........))))--)).)))).)).))))))..))) ( -39.90, z-score =  -2.16, R)
>droSim1.chr2R 19350907 121 + 19596830
GAUGGUAAUCGAUGCCUUCCGAUUCCGUUCGGACAUAUCGAUGCAUCGAUAUGUUUUAGUACACAAGGCGGCCACGGCAGCGCUUU--------GAGCUCAUCGAAU--UGUGAAGUCACUGAUUAAGGUU
(((..((((((.((.((((((((((.((..(((((((((((....)))))))))))....)).(((((((((....))..))))))--------)........))))--)).)))).)).))))))..))) ( -39.90, z-score =  -2.16, R)
>consensus
GAUGGUAAUCGAUGCCUUCCGAUUCCGUUCGGACAUAUCGAUGCAUCGAUAUGUUUUAGUUCACAAGGCGGCCGCGGCAGCGCUUU_UG_____CAACUCAUCCAAA_AUAUGUAACCACUGAUUAAGGUU
((((...((((((((....(((((((....)))...))))..)))))))).................((.((....)).))..................))))............................ (-18.20 = -18.76 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,899,003 – 20,899,130
Length 127
Sequences 5
Columns 131
Reading direction reverse
Mean pairwise identity 73.51
Shannon entropy 0.46216
G+C content 0.46188
Mean single sequence MFE -37.30
Consensus MFE -20.80
Energy contribution -20.44
Covariance contribution -0.36
Combinations/Pair 1.15
Mean z-score -1.70
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.870343
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20899003 127 - 21146708
AAUUUUAAUCAGUGUUGACAUAUCGAUGUAUGUGUUU----UCAGAAAGCGCUGCCGCGGCCGUCGUGUGAACUACGACAUAUCGAUGCAUCGAUAUGUCCGAAUGGAAUCGGAAGGCAUCGAUUACCAUC
.....(((((.(((((..(((((((((((((((((((----.....)))))).((....)).((((((....).)))))......)))))))))))))(((((......))))).))))).)))))..... ( -43.00, z-score =  -2.48, R)
>droEre2.scaffold_4845 22274376 129 - 22589142
AAUCUCUAUCUUUGGUAAAAUAUGUAUGGAUGUGUCGAUAAGCACAAAGCGCUGCUGCGGCCGCGUGACGAACUAAAUCGUAUCGAUGCAUCGAUA--UGUGGAAGAAAUCGGAAGGCAUCGAUUACCAUC
............((((((..(((((((.(((((((((((.........((((.((....)).)))).((((......))))))))))))))).)))--))))...((..((....))..))..)))))).. ( -40.30, z-score =  -2.25, R)
>droYak2.chr2R 20863975 128 - 21139217
AACCUCUGUCUUUGG--AUGUGUGUCUUAACAACUCGGUAAGCACAAAGCGCUGCUGCGGCCGCGUGAUGAACUAAAUAGAAUCGAUGCAUCGAUA-GUGCGAAGGUAAUCGGAAGGCAUCGAUUACCAUC
....(((((..((((--...((((.((((.(.....).))))))))..((((.((....)).))))......)))))))))((((((((.(((((.-.(((....))))))))...))))))))....... ( -36.20, z-score =  -0.62, R)
>droSec1.super_23 756271 121 - 989336
AACCUUAAUCAGUGACUUCACA--AUUCGAUGAGCUC--------AAAGCGCUGCCGUGGCCGCCUUGUGUACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGAUUACCAUC
.....(((((.(((....))).--....((((.((.(--------((.(((..((....))))).))).)).((....((((((((....))))))))(((((......))))))).)))))))))..... ( -33.50, z-score =  -1.58, R)
>droSim1.chr2R 19350907 121 - 19596830
AACCUUAAUCAGUGACUUCACA--AUUCGAUGAGCUC--------AAAGCGCUGCCGUGGCCGCCUUGUGUACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGAUUACCAUC
.....(((((.(((....))).--....((((.((.(--------((.(((..((....))))).))).)).((....((((((((....))))))))(((((......))))))).)))))))))..... ( -33.50, z-score =  -1.58, R)
>consensus
AACCUUAAUCAGUGACUACAUAU_AAUCGAUGAGUUC_____CA_AAAGCGCUGCCGCGGCCGCCUUGUGAACUAAAACAUAUCGAUGCAUCGAUAUGUCCGAACGGAAUCGGAAGGCAUCGAUUACCAUC
..................................................((.((....)).)).................((((((((.(((((...(((....))))))))...))))))))....... (-20.80 = -20.44 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:49:39 2011