Locus 475

Sequence ID dm3.chr2L
Location 3,302,098 – 3,302,242
Length 144
Max. P 0.757158
window640 window641

overview

Window 0

Location 3,302,098 – 3,302,242
Length 144
Sequences 4
Columns 159
Reading direction forward
Mean pairwise identity 77.61
Shannon entropy 0.35379
G+C content 0.41429
Mean single sequence MFE -40.84
Consensus MFE -19.93
Energy contribution -21.81
Covariance contribution 1.88
Combinations/Pair 1.21
Mean z-score -2.24
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.682573
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3302098 144 + 23011544
ACAGGGGCGGACUU-AAAACCUAUUCAAGGGGGUUGGAGUUAAAUUUUGAAAUUAUUUGU----GUAUCUGAAGACAUGCGGGCAUAGUAAACACA----UACG----ACAAAUUACAGUAUCUACAUUUUCUC--AAAACCCCCUUUCUACGCCACUG
.(((.(((((....-....)).....(((((((((.(((..((((...((.(((((((((----((((.((...(((((....))).))...)).)----))).----))))))...))).))...)))).)))--..))))))))).....))).))) ( -36.70, z-score =  -2.08, R)
>droYak2.chr2L 3286446 159 + 22324452
ACAGGGGCGUGCUCCAAAGCAAAUGCAAUGGGGUUGAAGUUGAAUUCCCAAGUUCUGUAUUCCGGUAUAGGAAGACAUGCUGGCAUACUAAGCACAUACAUACAUAUAACAAAUAACAGUCUGUGGUUUGCCCCCAAAAAUCCCCUCUCUGCGCCCCUG
.((((((((((((....)))........(((((..(((.(((......))).))).((((.(((((((.(.....)))))))).))))...(((..((((.((...............)).))))...))))))))..............))))))))) ( -48.46, z-score =  -1.95, R)
>droSec1.super_5 1444535 147 + 5866729
ACAGGGGCGGAUUU-AAAAAAGAUUCAAGGGGGUUGAAGUUACAUGUUUAAGUUAUUUGU----GCAUCUGAAGACAAGCAGGCAUACUAAGCACAUAGAUACA----AUAAAUUACAGUAUCUGCGUUUCCUC--AAA-CCCCCUUUCUACGCCACUG
.(((.(((((((((-.....))))))(((((((((((.(..((.((((((.((.....((----((..(((........)))))))))))))))..(((((((.----..........))))))).))..).))--.))-))))))).....))).))) ( -41.70, z-score =  -2.91, R)
>droSim1.chr2L 3239653 147 + 22036055
ACAGGGGCGGACUU-AAAACAGAUUCAAGGGGGUUUAAGUUACAUGUUUAAGUUAUUUGU----GUAUCUAAAGACAAGCGGGCAUAAUAAACACAUAGAUACA----AUAAAUUACAGUAUCUGCGCUACCUC--AAA-CCCCCUUUCUACGCCACUG
.(((.((((((.((-......)).))((((((((((.((............(((..((((----((..((.......))...))))))..)))...(((((((.----..........)))))))......)).--)))-)))))))....)))).))) ( -36.50, z-score =  -2.01, R)
>consensus
ACAGGGGCGGACUU_AAAACAGAUUCAAGGGGGUUGAAGUUAAAUGUUUAAGUUAUUUGU____GUAUCUGAAGACAAGCGGGCAUACUAAACACAUAGAUACA____ACAAAUUACAGUAUCUGCGUUUCCUC__AAA_CCCCCUUUCUACGCCACUG
.(((.((((.................(((((((((................(((..((((....((((........))))....))))..)))...(((((((...............))))))).............)))))))))....)))).))) (-19.93 = -21.81 +   1.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 3,302,098 – 3,302,242
Length 144
Sequences 4
Columns 159
Reading direction reverse
Mean pairwise identity 77.61
Shannon entropy 0.35379
G+C content 0.41429
Mean single sequence MFE -43.69
Consensus MFE -20.37
Energy contribution -21.81
Covariance contribution 1.44
Combinations/Pair 1.22
Mean z-score -2.42
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.757158
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3302098 144 - 23011544
CAGUGGCGUAGAAAGGGGGUUUU--GAGAAAAUGUAGAUACUGUAAUUUGU----CGUA----UGUGUUUACUAUGCCCGCAUGUCUUCAGAUAC----ACAAAUAAUUUCAAAAUUUAACUCCAACCCCCUUGAAUAGGUUUU-AAGUCCGCCCCUGU
(((.(((.....(((((((((..--(((.((((...((....((.((((((----.(((----(.((...((.(((....)))))...)).))))----)))))).)).))...))))..))).))))))))).....((....-....))))).))). ( -38.80, z-score =  -2.54, R)
>droYak2.chr2L 3286446 159 - 22324452
CAGGGGCGCAGAGAGGGGAUUUUUGGGGGCAAACCACAGACUGUUAUUUGUUAUAUGUAUGUAUGUGCUUAGUAUGCCAGCAUGUCUUCCUAUACCGGAAUACAGAACUUGGGAAUUCAACUUCAACCCCAUUGCAUUUGCUUUGGAGCACGCCCCUGU
((((((((....(((((((((((..((((((.((((((.((...(((.......)))...)).))))....)).))))....(((.((((......)))).)))...))..)))))))..))))....(((..((....))..)))....)))))))). ( -51.90, z-score =  -1.43, R)
>droSec1.super_5 1444535 147 - 5866729
CAGUGGCGUAGAAAGGGGG-UUU--GAGGAAACGCAGAUACUGUAAUUUAU----UGUAUCUAUGUGCUUAGUAUGCCUGCUUGUCUUCAGAUGC----ACAAAUAACUUAAACAUGUAACUUCAACCCCCUUGAAUCUUUUUU-AAAUCCGCCCCUGU
(((.((((....(((((((-((.--((((..(((.((((((..........----.)))))).(((((..((((....)))).(((....)))))----))).............)))..)))))))))))))(((.....)))-.....)))).))). ( -40.60, z-score =  -2.53, R)
>droSim1.chr2L 3239653 147 - 22036055
CAGUGGCGUAGAAAGGGGG-UUU--GAGGUAGCGCAGAUACUGUAAUUUAU----UGUAUCUAUGUGUUUAUUAUGCCCGCUUGUCUUUAGAUAC----ACAAAUAACUUAAACAUGUAACUUAAACCCCCUUGAAUCUGUUUU-AAGUCCGCCCCUGU
(((.(((((((((((((((-(((--(((........(((((..........----.)))))((((((((((...........((((....)))).----..........)))))))))).)))))))))))))...))))....-.....)))).))). ( -43.45, z-score =  -3.20, R)
>consensus
CAGUGGCGUAGAAAGGGGG_UUU__GAGGAAACGCAGAUACUGUAAUUUAU____UGUAUCUAUGUGCUUAGUAUGCCCGCAUGUCUUCAGAUAC____ACAAAUAACUUAAAAAUGUAACUUCAACCCCCUUGAAUCUGUUUU_AAGUCCGCCCCUGU
(((.((((....(((((((((....(((...(((.((((((...............)))))).)))................((((....))))..........................))).))))))))).................)))).))). (-20.37 = -21.81 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:13:34 2011