Locus 6421

Sequence ID dm3.chr3L
Location 6,574,781 – 6,574,938
Length 157
Max. P 0.997315
window8839 window8840 window8841

overview

Window 9

Location 6,574,781 – 6,574,901
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 56.60
Shannon entropy 0.72388
G+C content 0.32911
Mean single sequence MFE -27.40
Consensus MFE -6.34
Energy contribution -11.90
Covariance contribution 5.56
Combinations/Pair 1.09
Mean z-score -2.45
Structure conservation index 0.23
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.915498
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6574781 120 + 24543557
UUAUUUCAAACUUACAAAGUGAGAGAUUUCAAUAAAAAAAGUUGAAACUAACAGUGAAAUCUCUGAGGUGUUAAGCAACUUUUACGAAAGGGCCUUAACACCCUUGGGAUUUCUUUGUUA
..........(((((...)))))((.(((((((.......)))))))))(((((.((((((((...(((((((((...((((....))))...)))))))))...)))))))).))))). ( -34.80, z-score =  -3.86, R)
>droEre2.scaffold_4784 9248758 93 + 25762168
-UAGUUUUAGUUCACAGAA--AAAGGUAAACAUAGGAAGA-UUCAGGAUAACACUGAAAACUGUAGGAUGUUGAGAAACUAAAACACCUCGUUGUUA-----------------------
-..((((((((((((....--....)).(((((....((.-(((((.......)))))..)).....)))))..).)))))))))............----------------------- ( -15.30, z-score =   0.05, R)
>droSec1.super_2 6511418 117 + 7591821
-UAGUUUCAAAUAACAGAAAGAG-AAUUUCAAUGAAAAUA-UUCAUAUGAACUCUAAAAUCUGUGGGGUGUUAAGAUACUUCCACCAAAGGGUCUUAACACCCUUGGGAUUUCUUUGUUA
-..........(((((((.((((-...(((((((((....-))))).)))))))).((((((..((((((((((((..(((......)))..))))))))))))..)))))).))))))) ( -37.20, z-score =  -4.57, R)
>droSim1.chr3L 6046467 96 + 22553184
-----------------------UAGUUUCAAUAAAAAGA-UUCAGAUUAACACUAAAAUCUGGUGGGUGUUAAGAUACUCUUACCAAAGGGCCUUAACAACCUAGGGAUUUCUUUGUUA
-----------------------.......((((((.(((-((((((((........)))))..(((((((((((...(((((....))))).)))))).))))).)))))).)))))). ( -22.30, z-score =  -1.41, R)
>consensus
_UAGUUU_AA_U_ACAGAA__AGAAAUUUCAAUAAAAAGA_UUCAGAUUAACACUAAAAUCUGUGGGGUGUUAAGAAACUUUUACCAAAGGGCCUUAACACCCUUGGGAUUUCUUUGUUA
........................................................((((((..(((((((((((((.(((......))).)))))))))))))..))))))........ ( -6.34 = -11.90 +   5.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,574,781 – 6,574,901
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 56.60
Shannon entropy 0.72388
G+C content 0.32911
Mean single sequence MFE -24.70
Consensus MFE -10.00
Energy contribution -12.12
Covariance contribution 2.12
Combinations/Pair 1.43
Mean z-score -2.36
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.08
SVM RNA-class probability 0.997315
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6574781 120 - 24543557
UAACAAAGAAAUCCCAAGGGUGUUAAGGCCCUUUCGUAAAAGUUGCUUAACACCUCAGAGAUUUCACUGUUAGUUUCAACUUUUUUUAUUGAAAUCUCUCACUUUGUAAGUUUGAAAUAA
(((((..((((((.(..((((((((((...((((....))))...))))))))))..).))))))..)))))((((((((((.......(((......)))......))).))))))).. ( -30.42, z-score =  -3.26, R)
>droEre2.scaffold_4784 9248758 93 - 25762168
-----------------------UAACAACGAGGUGUUUUAGUUUCUCAACAUCCUACAGUUUUCAGUGUUAUCCUGAA-UCUUCCUAUGUUUACCUUU--UUCUGUGAACUAAAACUA-
-----------------------............((((((((((..((((((.....((..(((((.(....))))))-.))....))))........--...)).))))))))))..- ( -12.00, z-score =   0.15, R)
>droSec1.super_2 6511418 117 - 7591821
UAACAAAGAAAUCCCAAGGGUGUUAAGACCCUUUGGUGGAAGUAUCUUAACACCCCACAGAUUUUAGAGUUCAUAUGAA-UAUUUUCAUUGAAAUU-CUCUUUCUGUUAUUUGAAACUA-
...((((..........(((((((((((..((((....))))..))))))))))).(((((....((((((((.(((((-....)))))))))...-)))).)))))..))))......- ( -34.40, z-score =  -4.24, R)
>droSim1.chr3L 6046467 96 - 22553184
UAACAAAGAAAUCCCUAGGUUGUUAAGGCCCUUUGGUAAGAGUAUCUUAACACCCACCAGAUUUUAGUGUUAAUCUGAA-UCUUUUUAUUGAAACUA-----------------------
(((((..((((((....((.((((((((..((((....))))..)))))))).))....))))))..))))).......-.................----------------------- ( -22.00, z-score =  -2.09, R)
>consensus
UAACAAAGAAAUCCCAAGGGUGUUAAGACCCUUUGGUAAAAGUAUCUUAACACCCCACAGAUUUCAGUGUUAAUCUGAA_UCUUUUUAUUGAAACCUCU__UUCUGU_A_UU_AAACUA_
.................(((((((((((..((((....))))..)))))))))))..((((((........))))))........................................... (-10.00 = -12.12 +   2.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,574,821 – 6,574,938
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 73.53
Shannon entropy 0.43757
G+C content 0.35033
Mean single sequence MFE -25.20
Consensus MFE -16.31
Energy contribution -19.38
Covariance contribution 3.06
Combinations/Pair 1.31
Mean z-score -1.32
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.63
SVM RNA-class probability 0.767484
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 6574821 117 - 24543557
AUCUUGUAAACAACUACUAAAUAGAACUUGAAAGAGGUAACAAAGAAAUCCCAAGGGUGUUAAGGCCCUUUCGUAAAAGUUGCUUAACACCUCAGAGAUUUCACUGUUAGUUUCAAC
...(((.((((...............(((....))).(((((..((((((.(..((((((((((...((((....))))...))))))))))..).))))))..)))))))))))). ( -29.90, z-score =  -2.60, R)
>droEre2.scaffold_4784 9248795 93 - 25762168
AUCUUUUAAACAACUUCAGAAUGGAUCAUGAAAAGGGUAACAACGA---------GGUGU--------UUU------AGUUUCUCAACAUCCUACAGUUUUCAGUGUUAUCCUGAA-
..............((((((.....)).)))).(((((((((((.(---------(((((--------(..------........)))).)))...))......)))))))))...- ( -14.70, z-score =   0.70, R)
>droSec1.super_2 6511456 116 - 7591821
AUCUUGUAAACAACUUCUAAAUAGAACUUGAAAAGGGUAACAAAGAAAUCCCAAGGGUGUUAAGACCCUUUGGUGGAAGUAUCUUAACACCCCACAGAUUUUAGAGUUCAUAUGAA-
.......................((((((.(((((((............)))..(((((((((((..((((....))))..)))))))))))......)))).)))))).......- ( -31.20, z-score =  -2.41, R)
>droSim1.chr3L 6046484 116 - 22553184
AUAUUGUAAACCACUUCUAAAAAGAACUUGAAAAGGGUAACAAAGAAAUCCCUAGGUUGUUAAGGCCCUUUGGUAAGAGUAUCUUAACACCCACCAGAUUUUAGUGUUAAUCUGAA-
......................(((.(((....))).(((((..((((((....((.((((((((..((((....))))..)))))))).))....))))))..))))).)))...- ( -25.00, z-score =  -0.96, R)
>consensus
AUCUUGUAAACAACUUCUAAAUAGAACUUGAAAAGGGUAACAAAGAAAUCCCAAGGGUGUUAAGGCCCUUUGGUAAAAGUAUCUUAACACCCCACAGAUUUCAGUGUUAAUCUGAA_
.................................(((.(((((..((((((....(((((((((((..((((....))))..)))))))))))....))))))..))))).))).... (-16.31 = -19.38 +   3.06)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:07:28 2011