Locus 6237

Sequence ID dm3.chr3L
Location 4,878,266 – 4,878,376
Length 110
Max. P 0.962049
window8568 window8569

overview

Window 8

Location 4,878,266 – 4,878,376
Length 110
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 66.11
Shannon entropy 0.60458
G+C content 0.36063
Mean single sequence MFE -24.48
Consensus MFE -8.48
Energy contribution -10.16
Covariance contribution 1.68
Combinations/Pair 1.26
Mean z-score -2.39
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.70
SVM RNA-class probability 0.962049
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4878266 110 + 24543557
AAAACUGCUAGAGAACAUUUGUUGCUAUUGCAAUAAUUGAAAACCCAAAGGAUACAAAAAAAUCAGUUCGUUAGAACUCCUCAUAUUUGCAGCAACAG------UUCUACGUAAAG
.....(((...(((((...(((((((...((((....(((...((....)).............(((((....)))))..)))...))))))))))))------))))..)))... ( -23.40, z-score =  -2.70, R)
>droAna3.scaffold_13337 2971376 105 + 23293914
AUGAUUCCCAA------AUAAUUGCUCAUG---UAAAUAAAAACUUGAAUAAUUCAGUUUGCAACUUUCGUUGGAUGGCAGCCCUCUUGU-GCAUCUG-AAUAGUUUCAAACAAAG
...........------..(((((.(((.(---(........)).))).)))))..(((((.((((....(..((((((((.....))))-.))))..-)..)))).))))).... ( -18.60, z-score =  -0.66, R)
>droYak2.chr3L 5463399 96 + 24197627
GAAGCUAUAGG--AACCUUUCUUGCUGUUGCAAUAAUUGAAAACAUAAGGGAUACCAACAAAUCAGUUCGUUAGAGCUCCUCAUAUUUGCAGCAAAAG------------------
..(((...(((--(....)))).)))(((((((....(((........((....))........(((((....)))))..)))...))))))).....------------------ ( -20.60, z-score =  -1.33, R)
>droSec1.super_2 4865365 113 + 7591821
AAAACUGCUGA---ACAUUUGUUGCCGUUGCAAUAAUUGAAAACCUAAAGGAUACCGAAAAAUCAGUUCGUUAGAACUCCUCAUAUUUGCAGCGACAGCAACAGUUCUACGUAAAG
.....(((.((---((..((((((.((((((((....(((...((....)).............(((((....)))))..)))...)))))))).))))))..))))...)))... ( -29.60, z-score =  -3.62, R)
>droSim1.chr3L 4417416 114 + 22553184
AAAACUGCUGG--AACAUUUGUUGCUGUUGCAAUAAUUGAAACCCUAAAGGAUACCGAAAAAUCAGUUCGUUAGAAAUCCUCAUAUUUGCAGCAACAGCAACAGUUCUACGUAAAG
.....((((((--(((...((((((((((((.................(((((...((....))..(((....))))))))((....))..)))))))))))))))))).)))... ( -30.20, z-score =  -3.64, R)
>consensus
AAAACUGCUGG__AACAUUUGUUGCUGUUGCAAUAAUUGAAAACCUAAAGGAUACCGAAAAAUCAGUUCGUUAGAACUCCUCAUAUUUGCAGCAACAG_AA_AGUUCUACGUAAAG
..................(((((((...(((((....(((..........(((........)))(((((....)))))..)))...)))))))))))).................. ( -8.48 = -10.16 +   1.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 4,878,266 – 4,878,376
Length 110
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 66.11
Shannon entropy 0.60458
G+C content 0.36063
Mean single sequence MFE -25.98
Consensus MFE -9.92
Energy contribution -9.96
Covariance contribution 0.04
Combinations/Pair 1.53
Mean z-score -1.67
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.63
SVM RNA-class probability 0.769345
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4878266 110 - 24543557
CUUUACGUAGAA------CUGUUGCUGCAAAUAUGAGGAGUUCUAACGAACUGAUUUUUUUGUAUCCUUUGGGUUUUCAAUUAUUGCAAUAGCAACAAAUGUUCUCUAGCAGUUUU
........((((------((((((.((((((...((..(((((....)))))..))..))))))......(((....((.((.((((....)))).)).))..))))))))))))) ( -24.70, z-score =  -1.39, R)
>droAna3.scaffold_13337 2971376 105 - 23293914
CUUUGUUUGAAACUAUU-CAGAUGC-ACAAGAGGGCUGCCAUCCAACGAAAGUUGCAAACUGAAUUAUUCAAGUUUUUAUUUA---CAUGAGCAAUUAU------UUGGGAAUCAU
.....((((((...(((-(((.(((-......(((......)))(((....))))))..))))))..))))))......((((---.((((....))))------.))))...... ( -18.10, z-score =   0.34, R)
>droYak2.chr3L 5463399 96 - 24197627
------------------CUUUUGCUGCAAAUAUGAGGAGCUCUAACGAACUGAUUUGUUGGUAUCCCUUAUGUUUUCAAUUAUUGCAACAGCAAGAAAGGUU--CCUAUAGCUUC
------------------(((((..((.((((((((((....((((((((....))))))))....)))))))))).))....((((....)))))))))...--........... ( -22.40, z-score =  -1.31, R)
>droSec1.super_2 4865365 113 - 7591821
CUUUACGUAGAACUGUUGCUGUCGCUGCAAAUAUGAGGAGUUCUAACGAACUGAUUUUUCGGUAUCCUUUAGGUUUUCAAUUAUUGCAACGGCAACAAAUGU---UCAGCAGUUUU
......((.(((((((((((((.((((.((((..(((((..((....))(((((....))))).)))))...)))).))......)).)))))))))...))---)).))...... ( -31.20, z-score =  -2.54, R)
>droSim1.chr3L 4417416 114 - 22553184
CUUUACGUAGAACUGUUGCUGUUGCUGCAAAUAUGAGGAUUUCUAACGAACUGAUUUUUCGGUAUCCUUUAGGGUUUCAAUUAUUGCAACAGCAACAAAUGUU--CCAGCAGUUUU
......((.((((((((((((((((((.((((..((((((.((....))(((((....)))))))))))....))))))......))))))))))))...)))--)..))...... ( -33.50, z-score =  -3.45, R)
>consensus
CUUUACGUAGAACU_UU_CUGUUGCUGCAAAUAUGAGGAGUUCUAACGAACUGAUUUUUCGGUAUCCUUUAGGUUUUCAAUUAUUGCAACAGCAACAAAUGUU__CCAGCAGUUUU
...................((((((((.......((..(((((....)))))..)).........((....))................))))))))................... ( -9.92 =  -9.96 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:03:44 2011