Locus 12273

Sequence ID dm3.chr3R
Location 27,013,787 – 27,013,877
Length 90
Max. P 0.995359
window16876 window16877

overview

Window 6

Location 27,013,787 – 27,013,877
Length 90
Sequences 10
Columns 106
Reading direction forward
Mean pairwise identity 67.83
Shannon entropy 0.63530
G+C content 0.52973
Mean single sequence MFE -21.86
Consensus MFE -12.31
Energy contribution -12.45
Covariance contribution 0.14
Combinations/Pair 1.14
Mean z-score -1.83
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.79
SVM RNA-class probability 0.995359
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27013787 90 + 27905053
----------UUCCCCUGCUCACUAUUUCCCCCGUUUUGCCAUCGCAGGCCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCU------
----------.......((((................(((....)))((((((((....))))).)))..((((((......)))))).....))))...------ ( -21.00, z-score =  -1.60, R)
>droSim1.chr3R 26654922 90 + 27517382
----------GGCCCCUGCCCACUUCUUCCCCCGUUUUCCCAUCGCAGGCCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCACACAUUCGGGCGCU------
----------.......((((..........................((((((((....))))).)))....((((......)))).......))))...------ ( -20.80, z-score =  -1.01, R)
>droSec1.super_4 5832011 90 + 6179234
----------GGCCCCUGCCCACAACUUCCUCCGUUUUCCCAUCGCAGGCCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCU------
----------.......((((..........................((((((((....))))).)))..((((((......)))))).....))))...------ ( -23.10, z-score =  -1.81, R)
>droYak2.chr3R 27949746 90 + 28832112
----------GCCCCCCGCCCACUAUUUCCCCCGUUUUCCCAUCGCAGGCCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCU------
----------......(((((..........................((((((((....))))).)))..((((((......)))))).....)))))..------ ( -24.50, z-score =  -3.44, R)
>droEre2.scaffold_4820 9501622 89 - 10470090
----------AACCCACGCCCACUAUUUCC-CCGUUUUCCCAUCGCAGGCCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCU------
----------......(((((.........-................((((((((....))))).)))..((((((......)))))).....)))))..------ ( -24.70, z-score =  -3.70, R)
>dp4.chr2 30676035 97 - 30794189
UUCAACACCCCCCUC---UAUCACUCCGCCAGGCCCCCCUUUAUCCCAGGCAGUUCUUGAACUACGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCU------
...............---..............((((............(((((((....))))..)))..((((((......)))))).....))))...------ ( -17.30, z-score =  -0.87, R)
>droPer1.super_7 1535281 100 - 4445127
UUCAACACCCCCCCCCCCUAUCACUCCGCCAGGCCCCCCUUUAUCCCAGGCAGUUCUUGAACUACGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCU------
................................((((............(((((((....))))..)))..((((((......)))))).....))))...------ ( -17.30, z-score =  -0.96, R)
>droWil1.scaffold_181108 680219 72 + 4707319
------------------------------CCUCUCUGCAUUUGCUCGGCCAGUUCUUGAACUGUGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGUUCU----
------------------------------.............((((((((((((....))))).)))..((((((......)))))).....)))).....---- ( -20.20, z-score =  -3.00, R)
>droVir3.scaffold_12855 8896617 83 - 10161210
-----------------------GCCCCCUGCCACUGGCAUUUGGCGUGCCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCCGCCGCC
-----------------------((....((((...))))...((((.(((((((....))))).(((...(((((..........)))))...))))))))))). ( -25.90, z-score =  -0.83, R)
>droMoj3.scaffold_6540 7136169 83 - 34148556
------------------AGCAGCACCGCCUCGCGCCUCCUCUGCUC--GCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCAUACAUUUGGGCGCCGCC---
------------------.........((...((((((........(--((((((....)))))))....((((((......)))))).....)))))).)).--- ( -23.80, z-score =  -1.05, R)
>consensus
____________CCCC_GCCCACUACUUCCCCCGUUUUCCCAUCGCAGGCCAGUUCUUGAACUGCGCCAUUAUGUACUUUAUUGCAUACAUUCGGGCGCU______
...................................................((((....))))(((((...(((((..........)))))...)))))....... (-12.31 = -12.45 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 27,013,787 – 27,013,877
Length 90
Sequences 10
Columns 106
Reading direction reverse
Mean pairwise identity 67.83
Shannon entropy 0.63530
G+C content 0.52973
Mean single sequence MFE -26.86
Consensus MFE -14.69
Energy contribution -14.66
Covariance contribution -0.03
Combinations/Pair 1.13
Mean z-score -1.21
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.62
SVM RNA-class probability 0.955355
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 27013787 90 - 27905053
------AGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGGCCUGCGAUGGCAAAACGGGGGAAAUAGUGAGCAGGGGAA----------
------.(((((...((((((........))))))...))))).((((....((((.(((.((.........)).)))...)))))))).......---------- ( -25.90, z-score =  -1.26, R)
>droSim1.chr3R 26654922 90 - 27517382
------AGCGCCCGAAUGUGUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGGCCUGCGAUGGGAAAACGGGGGAAGAAGUGGGCAGGGGCC----------
------...((((...(((((((......)))))))...((.((.(((.....(((.(((.....)))....))).....))).)).))..)))).---------- ( -29.20, z-score =  -1.56, R)
>droSec1.super_4 5832011 90 - 6179234
------AGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGGCCUGCGAUGGGAAAACGGAGGAAGUUGUGGGCAGGGGCC----------
------.(((((...((((((........))))))...))))).(((((..((((..(((.((.........)).))).)))).))))).......---------- ( -28.70, z-score =  -1.50, R)
>droYak2.chr3R 27949746 90 - 28832112
------AGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGGCCUGCGAUGGGAAAACGGGGGAAAUAGUGGGCGGGGGGC----------
------.(((((...((((((........))))))...))))).((((..(.((((.(((.((.........)).)))...))))...)...))))---------- ( -26.00, z-score =  -1.10, R)
>droEre2.scaffold_4820 9501622 89 + 10470090
------AGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGGCCUGCGAUGGGAAAACGG-GGAAAUAGUGGGCGUGGGUU----------
------.(((((((.((((((........))))))...(((.(((((....))))))))................-........))))))).....---------- ( -26.80, z-score =  -1.31, R)
>dp4.chr2 30676035 97 + 30794189
------AGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGUAGUUCAAGAACUGCCUGGGAUAAAGGGGGGCCUGGCGGAGUGAUA---GAGGGGGGUGUUGAA
------(((((((..((((((........)))))).((.((...((...((..((.(((.......))).))..)).))...)).)).---.....)))))))... ( -25.80, z-score =  -0.26, R)
>droPer1.super_7 1535281 100 + 4445127
------AGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGUAGUUCAAGAACUGCCUGGGAUAAAGGGGGGCCUGGCGGAGUGAUAGGGGGGGGGGGUGUUGAA
------(((((((..((((((........)))))).((.((...((...((..((.(((.......))).))..)).))...)).)).........)))))))... ( -25.80, z-score =   0.14, R)
>droWil1.scaffold_181108 680219 72 - 4707319
----AGAACGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCACAGUUCAAGAACUGGCCGAGCAAAUGCAGAGAGG------------------------------
----.....((.(..((((((........))))))...(((.(((((....))))))))).)).............------------------------------ ( -17.10, z-score =  -1.88, R)
>droVir3.scaffold_12855 8896617 83 + 10161210
GGCGGCGGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGGCACGCCAAAUGCCAGUGGCAGGGGGC-----------------------
((((((.(((((...((((((........))))))...)))))((((....)))).)).))))...((((...))))......----------------------- ( -30.60, z-score =  -1.19, R)
>droMoj3.scaffold_6540 7136169 83 + 34148556
---GGCGGCGCCCAAAUGUAUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGC--GAGCAGAGGAGGCGCGAGGCGGUGCUGCU------------------
---(((((((((...((((((........))))))..((.(((((((....))))))--)..)).....(.(....).))))))))))------------------ ( -32.70, z-score =  -2.13, R)
>consensus
______AGCGCCCGAAUGUAUGCAAUAAAGUACAUAAUGGCGCAGUUCAAGAACUGGCCUGCGAUAGGAAAACGGGGGAAGUAGUGGGC_GGGG____________
.......(((((...((((((........))))))...)))))((((....))))................................................... (-14.69 = -14.66 +  -0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:59:03 2011