Locus 2803

Sequence ID dm3.chr2L
Location 22,471,201 – 22,471,323
Length 122
Max. P 0.996860
window3865 window3866

overview

Window 5

Location 22,471,201 – 22,471,323
Length 122
Sequences 5
Columns 130
Reading direction forward
Mean pairwise identity 71.72
Shannon entropy 0.49452
G+C content 0.35196
Mean single sequence MFE -31.94
Consensus MFE -12.69
Energy contribution -12.97
Covariance contribution 0.28
Combinations/Pair 1.26
Mean z-score -3.14
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.57
SVM RNA-class probability 0.992900
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22471201 122 + 23011544
UGGUGAUGGGUAAA---ACAGA-AAAAUCUAACAUCGAUGUCCGAAAAUUUCGAUGUUUCCGAUUUUUUUUUAAAUAUCUAUGUAGCGC----UAUCUCCGAUGUUUCUUCCAGCUCUAUUUUGUAGUUU
.....(((((((..---..(((-((((((.((((((((.((......)).))))))))...))))))))).....)))))))((((.((----(......((....))....))).)))).......... ( -22.80, z-score =  -0.64, R)
>droSim1.chr2h_random 3518 125 - 3178526
UAGCGAUGGGUAAA---ACAGA-AACAUCGAAUAUCGAUGCUUGAAAAUUUUGAUGUUUCCGAUUU-AUUAAAAACAUCGAUGUAUCGCGAUACAUCGCCGAUGUUUCUUUCAACUCUUUCUUUUACUUU
....((.((((..(---(.(((-(((((((......(((((((((...((((((((.........)-)))))))...)))).)))))((((....))))))))))))))))..))))..))......... ( -31.50, z-score =  -3.02, R)
>droSec1.super_42 81997 125 + 298440
UAGCGAUGGGUAAA---ACAGA-AACAUCGAUUAUCGAUGCUUGAAAAUUUUGAUGUUUCCGAUUU-AUUAAAAACAUGGAUGUAUCGCGAUACAUCGCCGAUGUUUCUUUCAACUCUUUCUUUUACUUU
....((.((((..(---(.(((-(((((((......(((((((.(...((((((((.........)-)))))))...).)).)))))((((....))))))))))))))))..))))..))......... ( -28.10, z-score =  -1.83, R)
>droYak2.chr2h_random 646676 113 - 3774259
AAGUGUUGGGUAAA---GCGGA-AACAUCGAACAUCGAUGUUUAAAAAUCUCGAUGUUUCCGAUG--AUUUGAAACAUCGAUGUAUCG----------CCGAUGUUUUUUCCAGCUCUACUUUUAAUAU-
..((((((((((.(---(((((-(((((((.((((((((((((..((((((((.......))).)--)))).))))))))))))....----------.))))))...)))).))).))))..))))))- ( -38.20, z-score =  -5.06, R)
>droMoj3.scaffold_6473 17351 126 - 16943266
UAGUGGUGGGAACAUUUAUACACAACAUCGAUCAUCGAAAAACAAACAU--CGAUGUUUCUCAUUUUAUUUCAAACAUCGAUGUAUCG--AUAUUACAUCGAUGUUGCGCCCAGCACUACUGGACAGCCU
(((((.((((..........(.((((((((((.(((((.......((((--((((((((.............)))))))))))).)))--)).....)))))))))).))))).)))))..((....)). ( -39.12, z-score =  -5.16, R)
>consensus
UAGUGAUGGGUAAA___ACAGA_AACAUCGAACAUCGAUGCUUGAAAAUUUCGAUGUUUCCGAUUU_AUUUAAAACAUCGAUGUAUCGC_AUACAUCGCCGAUGUUUCUUCCAGCUCUAUUUUUUACUUU
.((.(.((((................((((((((((((............))))))))..))))........((((((((...................))))))))..)))).).))............ (-12.69 = -12.97 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 22,471,201 – 22,471,323
Length 122
Sequences 5
Columns 130
Reading direction reverse
Mean pairwise identity 71.72
Shannon entropy 0.49452
G+C content 0.35196
Mean single sequence MFE -34.26
Consensus MFE -11.22
Energy contribution -11.38
Covariance contribution 0.16
Combinations/Pair 1.40
Mean z-score -3.85
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.00
SVM RNA-class probability 0.996860
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22471201 122 - 23011544
AAACUACAAAAUAGAGCUGGAAGAAACAUCGGAGAUA----GCGCUACAUAGAUAUUUAAAAAAAAAUCGGAAACAUCGAAAUUUUCGGACAUCGAUGUUAGAUUUU-UCUGU---UUUACCCAUCACCA
.......((((((((((((...((....)).....))----))....................((((((...((((((((..((....))..)))))))).))))))-)))))---)))........... ( -20.80, z-score =  -0.79, R)
>droSim1.chr2h_random 3518 125 + 3178526
AAAGUAAAAGAAAGAGUUGAAAGAAACAUCGGCGAUGUAUCGCGAUACAUCGAUGUUUUUAAU-AAAUCGGAAACAUCAAAAUUUUCAAGCAUCGAUAUUCGAUGUU-UCUGU---UUUACCCAUCGCUA
...(((((((((((..((((.(((((((((...(((((((....))))))))))))))))...-.....(....).))))..)))))((((((((.....)))))))-)...)---)))))......... ( -34.50, z-score =  -3.65, R)
>droSec1.super_42 81997 125 - 298440
AAAGUAAAAGAAAGAGUUGAAAGAAACAUCGGCGAUGUAUCGCGAUACAUCCAUGUUUUUAAU-AAAUCGGAAACAUCAAAAUUUUCAAGCAUCGAUAAUCGAUGUU-UCUGU---UUUACCCAUCGCUA
...(((((((((((..((((.((((((((..(.(((((((....))))))))))))))))...-.....(....).))))..)))))((((((((.....)))))))-)...)---)))))......... ( -31.50, z-score =  -3.28, R)
>droYak2.chr2h_random 646676 113 + 3774259
-AUAUUAAAAGUAGAGCUGGAAAAAACAUCGG----------CGAUACAUCGAUGUUUCAAAU--CAUCGGAAACAUCGAGAUUUUUAAACAUCGAUGUUCGAUGUU-UCCGC---UUUACCCAACACUU
-.........(((((((.((((...(((((((----------....((((((((((((.((((--(.((((.....)))))))))..))))))))))))))))))))-)))))---)))))......... ( -40.20, z-score =  -6.76, R)
>droMoj3.scaffold_6473 17351 126 + 16943266
AGGCUGUCCAGUAGUGCUGGGCGCAACAUCGAUGUAAUAU--CGAUACAUCGAUGUUUGAAAUAAAAUGAGAAACAUCG--AUGUUUGUUUUUCGAUGAUCGAUGUUGUGUAUAAAUGUUCCCACCACUA
.((.((.((((.....))))(((((((((((((....(((--(((.((((((((((((.............))))))))--)))).......)))))))))))))))))))...........)))).... ( -44.32, z-score =  -4.78, R)
>consensus
AAACUAAAAAAUAGAGCUGGAAGAAACAUCGGCGAUAUAU_GCGAUACAUCGAUGUUUUAAAU_AAAUCGGAAACAUCGAAAUUUUCAAACAUCGAUGUUCGAUGUU_UCUGU___UUUACCCAUCACUA
.................((((((....((((...........)))).....((((((((...........))))))))....))))))(((((((.....)))))))....................... (-11.22 = -11.38 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:21 2011