Locus 4519

Sequence ID dm3.chr2R
Location 13,722,467 – 13,722,636
Length 169
Max. P 0.986483
window6187 window6188

overview

Window 7

Location 13,722,467 – 13,722,568
Length 101
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 68.86
Shannon entropy 0.55627
G+C content 0.52469
Mean single sequence MFE -32.80
Consensus MFE -15.30
Energy contribution -15.50
Covariance contribution 0.20
Combinations/Pair 1.44
Mean z-score -1.38
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.735367
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13722467 101 - 21146708
GCAGGUGGCAG-----AGAAGAAAUCCCCUGCCUACGUUGCAUCAGCAUCAGUCUGACCGUUGUCAAGACGA-----CUGCUCUGAAUGCUGAUCGCUUUGUGAGGGGAGA--
((.....))..-----........((((((...((((..(((((((((((((...(.(.(((((....))))-----).)).))).)))))))).))..))))))))))..-- ( -35.60, z-score =  -1.24, R)
>droWil1.scaffold_180745 2164718 98 - 2843958
GGAAGCAACGACAACGACAACAACAUCGUCGUCCACAUCGUCGUCGUCGUGGUCU-UCUCUUCCUACGUUCA----UAUGUAUUUUAUAAUGAAAGAACCUUG----------
(((((....(((.(((((.........))))).(((..((....))..)))))).-...)))))....((((----((((.....))).))))).........---------- ( -19.80, z-score =  -0.48, R)
>droYak2.chr2R 5678480 96 + 21139217
GCAGGUGGC-------AGUAGAAAUCCCCUGCCUACGUUGCAUCAGCAUCAGUCUGACCGUUGUCAAGACGACUGCUCUGCUCUGAAUGCUGAUCGCUUUGGU----------
(((((((((-------((..(....)..))))).)).))))(((((((((((...(((.(((((....))))).).))....))).)))))))).........---------- ( -32.80, z-score =  -1.57, R)
>droEre2.scaffold_4845 7949769 97 - 22589142
GCAGGUGGCAGAAGGCAGUAGAAAUCCCCUGCCUACGUUGCAUCAGCAUCAGUCUGACCGUUGUCAAGACGA-----CUGCUCUGAAUGCUGAUCGCUUCGC-----------
(((((((((((.((((((..(....)..))))))...))))(((((((((((...(.(.(((((....))))-----).)).))).))))))))))))).))----------- ( -37.00, z-score =  -2.47, R)
>droSec1.super_1 11218669 103 - 14215200
GCAGGUGGCAG-----AGAAGAAAUCCCCUGCCUACGUUGCAUCAGCAUCAGUCUGACCGUUGUCAAGACGA-----CUGCUCUGAAUGUUGAACGCUUCGCGAGAGGGGAUG
(((((((((((-----.(.(....).).))))).)).)))).((((((((((...(.(.(((((....))))-----).)).))).))))))).(.((((....)))).)... ( -35.90, z-score =  -1.41, R)
>droSim1.chr2R 12462631 103 - 19596830
GCAGGUGGCAG-----CGAAGAAAUCCCCUGCCUACGUUGCAUCAGCAUCAGUCUGACCGUUGUCAAGACGA-----CUGCUCUGAAUGUUGAACGCUUCGCGAGAGGGGAUG
(((((((((((-----.(.(....).).))))).)).)))).((((((((((...(.(.(((((....))))-----).)).))).))))))).(.((((....)))).)... ( -35.70, z-score =  -1.14, R)
>consensus
GCAGGUGGCAG_____AGAAGAAAUCCCCUGCCUACGUUGCAUCAGCAUCAGUCUGACCGUUGUCAAGACGA_____CUGCUCUGAAUGCUGAACGCUUCGCG__________
(((((((((((.................))))).)).)))).((((((((((........((((....))))..........)))).)))))).................... (-15.30 = -15.50 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,722,534 – 13,722,636
Length 102
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 66.39
Shannon entropy 0.51771
G+C content 0.64571
Mean single sequence MFE -23.51
Consensus MFE -16.84
Energy contribution -16.91
Covariance contribution 0.06
Combinations/Pair 1.09
Mean z-score -1.65
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.24
SVM RNA-class probability 0.986483
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13722534 102 + 21146708
AACGUAGGCAGGGGAUUUCUUCU-----CUGCCACCUGCCUGCCCCCUCUCACCUGAGCUACACCCCCCUCCCCCCCCCACCGCGCUGCCCCUGCGCACCAGCAAUC
...(((((((((((.........-----...)).)))))))))...(((......)))........................((((.......)))).......... ( -27.40, z-score =  -2.38, R)
>droEre2.scaffold_4845 7949827 101 + 22589142
AACGUAGGCAGGGGAUUUCUACUGCCUUCUGCCACCUGCCUCUGCCCGCUCACCUGGGCCCCCUGCCCCCUGCCCCCUUUCCCACCUUCCCACUGGCAAUC------
...(..((((((((.........((.....))...........(((((......)))))))))))))..)((((....................))))...------ ( -28.25, z-score =  -1.18, R)
>droSec1.super_1 11218738 82 + 14215200
AACGUAGGCAGGGGAUUUCUUCU-----CUGCCACCUGCCUGCCCCCUCUCACCCGUGCCCCCC---CUCCCACUAACCAACCAGCAAUC-----------------
...(((((((((((.........-----...)).))))))))).....................---.......................----------------- ( -18.30, z-score =  -1.56, R)
>droSim1.chr2R 12462700 84 + 19596830
AACGUAGGCAGGGGAUUUCUUCG-----CUGCCACCUGCCUGCCCC-UCUCACCUGAGCCCCCCUCCCUCCCUCUACCCAACCAGCAAUC-----------------
...(((((((((((.........-----...)).)))))))))..(-((......)))................................----------------- ( -20.10, z-score =  -1.49, R)
>consensus
AACGUAGGCAGGGGAUUUCUUCU_____CUGCCACCUGCCUGCCCCCUCUCACCUGAGCCCCCC_CCCCCCCCCCACCCAACCAGCAACC_________________
...(((((((((((.................)).)))))))))................................................................ (-16.84 = -16.91 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:40 2011