Locus 4801

Sequence ID dm3.chr2R
Location 15,682,336 – 15,682,451
Length 115
Max. P 0.914421
window6596 window6597

overview

Window 6

Location 15,682,336 – 15,682,432
Length 96
Sequences 9
Columns 97
Reading direction reverse
Mean pairwise identity 72.36
Shannon entropy 0.58082
G+C content 0.45819
Mean single sequence MFE -16.11
Consensus MFE -9.22
Energy contribution -8.80
Covariance contribution -0.42
Combinations/Pair 1.22
Mean z-score -1.19
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.914421
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15682336 96 - 21146708
CAAAGCACUGGGUACCCCAACUCUCCCUCUCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCAAAAACUGGA-GUCGUCUUUCCUAUUUGCA
....(((.((((((.............................((((((.......))))))))))))......(((-(......))))....))). ( -18.85, z-score =  -1.55, R)
>droSim1.chr2R 14340284 93 - 19596830
---CAAAGCCCUGGGUACCCCAACUCUCCUCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCAAAAACUGGA-GUCGUCUUUCCUAUUUGCA
---....((..((((((..........................((((((.......)))))))))))).(((..(((-(......))))..))))). ( -17.66, z-score =  -1.16, R)
>droSec1.super_1 13172431 93 - 14215200
---CAAAGCCCUGAGUACCCCAACUCUCCUCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCAAAAACUGGA-GUCGUCUUUCCUAUUUGCA
---....((...((((......)))).................((((((.......)))))).......(((..(((-(......))))..))))). ( -14.90, z-score =  -1.03, R)
>droYak2.chr2R 7614036 89 + 21139217
-------CCAAGCCUUGCAUACCCCAAACUCGCCCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCAAAAACUGGA-GUCGUCUUUCCUAUUUGCA
-------........((((........................((((((.......))))))............(((-(......))))....)))) ( -13.60, z-score =  -0.37, R)
>droEre2.scaffold_4845 9844226 86 - 22589142
---------CAAAGCCGGGUACCCCCACUCCCC-CAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCGAAAACUGGA-GUCGUCUUUCCUAUUUGCA
---------....((((((((............-.........((((((.......)))))))))))).(((..(((-(......))))..))))). ( -19.19, z-score =  -1.61, R)
>droAna3.scaffold_13266 10238444 77 + 19884421
-------------------CGCAGCCACCUCACUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCGAAAAGCGGA-GCCGUCUUUGCUAUUUGCA
-------------------.((((...................((((((.......)))))).........((((((-(....)))))))..)))). ( -17.30, z-score =  -0.59, R)
>dp4.chr3 12807140 80 - 19779522
---------------CACCACCCACUGUUCCUCUCAUUAUAUUUGUGCACUGACUUUGCACAUGCCCG-AAACUGGA-GUCGUCUUUCCUAUUUGCA
---------------............................((((((.......))))))(((...-(((..(((-(......))))..)))))) ( -11.00, z-score =  -0.18, R)
>droPer1.super_2 218916 80 + 9036312
---------------CACCACCCACUGUUCCUCUCAUUAUAUUUGUGCACUGACUUUGCACAUGCCCG-AAACUGGA-GUCGUCUUUCCUAUUUGCA
---------------............................((((((.......))))))(((...-(((..(((-(......))))..)))))) ( -11.00, z-score =  -0.18, R)
>droGri2.scaffold_15112 2217398 75 - 5172618
---------------CUCUCUGUGGACUCUCACUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCGAAAAACGGGCAUCGUCUUUACA-------
---------------......((((((................((((((.......))))))((((((.....))))))..))))..)).------- ( -21.50, z-score =  -4.00, R)
>consensus
_______________CACCCCCCCCCACCUCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCGAAAACUGGA_GUCGUCUUUCCUAUUUGCA
...........................................((((((.......))))))...(((.....)))..................... ( -9.22 =  -8.80 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,682,355 – 15,682,451
Length 96
Sequences 9
Columns 111
Reading direction reverse
Mean pairwise identity 64.04
Shannon entropy 0.63657
G+C content 0.48961
Mean single sequence MFE -14.85
Consensus MFE -7.20
Energy contribution -7.20
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.71
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr2R 15682355 96 - 21146708
-------------CUGCCAAAGUCCAAAAUCGCAAAGCACUGGGUACCCCAACUCUCCCUCUCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCC-AAAAACUGGA-
-------------.........((((.....((...))..((((((.............................((((((.......)))))))))))-).....))))- ( -15.65, z-score =  -0.17, R)
>droSim1.chr2R 14340303 93 - 19596830
-------------CUGCCACAGUCCAAAAUCGCAAAGCCCUGGGUACCCCAACUCUCC---UCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCC-AAAAACUGGA-
-------------......((((........(((......((((...)))).......---..............((((((.......)))))))))..-....))))..- ( -15.94, z-score =  -0.22, R)
>droSec1.super_1 13172450 93 - 14215200
-------------CUGCCAAAGUCCAAAAUCGCAAAGCCCUGAGUACCCCAACUCUCC---UCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCC-AAAAACUGGA-
-------------.(((.((((((...(((((((((....((((..............---...)))).....)))))).)))))))))))).....((-(.....))).- ( -16.63, z-score =  -1.71, R)
>droEre2.scaffold_4845 9844245 99 - 22589142
UGCCCCCUGCCCCCUGCCAUAAUCCAAAAUCUCAAAGCC--GGGUACCCCCAC--------UCCCCCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCC-GAAAACUGGA-
.....((.((.....)).....................(--(((((.......--------..............((((((.......)))))))))))-)......)).- ( -14.99, z-score =  -0.00, R)
>droAna3.scaffold_13266 10238463 74 + 19884421
----------------------------CUGCCACCACCCCCAUCGCAGCCAC---C----UCACUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCC-GAAAAGCGGA-
----------------------------((((.............))))....---.----..............((((((.......))))))...((-(.....))).- ( -12.32, z-score =  -0.52, R)
>dp4.chr3 12807159 76 - 19779522
----------------------------UUUCUAGCUCCCCCACACCACCCACUGUU----CCUCUCAUUAUAUUUGUGCACUGACUUUGCACAUGCCC-G-AAACUGGA-
----------------------------..(((((.......(((........))).----..............((((((.......)))))).....-.-...)))))- (  -8.90, z-score =  -0.64, R)
>droPer1.super_2 218935 76 + 9036312
----------------------------UUUCUAGCUCCCCCACACCACCCACUGUU----CCUCUCAUUAUAUUUGUGCACUGACUUUGCACAUGCCC-G-AAACUGGA-
----------------------------..(((((.......(((........))).----..............((((((.......)))))).....-.-...)))))- (  -8.90, z-score =  -0.64, R)
>droVir3.scaffold_12875 16633259 76 + 20611582
----------------------UUCUGGA---GUGCGUACU---CCUCCCUGCUC------UCACUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCC-GAAAAACUGGC
----------------------.....((---(((.(..(.---.......)..)------.)))))........((((((.......)))))).(((.-(.....).))) ( -15.90, z-score =  -1.30, R)
>droMoj3.scaffold_6496 21069958 84 - 26866924
---------------------UCGCUGGAUAUCUGCGUACCCAGCACCCCUGCUC------GCACUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCCUGUAAGGCAGGC
---------------------..(((((.(((....))).)))))...((((((.------((((...........)))).......(((((.......))))))))))). ( -24.40, z-score =  -1.19, R)
>consensus
______________________UCCAAAAUCCCAACGCCCCCAGUACCCCCACUCUC____UCUCUCAUUAUAUUUGUGCAUUGACUUUGCACAUGCCC_GAAAACUGGA_
...........................................................................((((((.......))))))................. ( -7.20 =  -7.20 +   0.00)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:36:15 2011