Locus 5024

Sequence ID dm3.chr2R
Location 17,163,425 – 17,163,523
Length 98
Max. P 0.998391
window6899 window6900

overview

Window 9

Location 17,163,425 – 17,163,523
Length 98
Sequences 11
Columns 119
Reading direction forward
Mean pairwise identity 63.64
Shannon entropy 0.70365
G+C content 0.59425
Mean single sequence MFE -50.20
Consensus MFE -8.60
Energy contribution -8.67
Covariance contribution 0.08
Combinations/Pair 1.50
Mean z-score -4.31
Structure conservation index 0.17
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.34
SVM RNA-class probability 0.998391
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17163425 98 + 21146708
--------GCCCUUGCGGCAGGAAGCUGUAAUUUCUGC-CGCGGCUACGUGGCGUAUGCGCAACGAGUCGCGAAGU-CAGCGCACGUUGCACAUACGCCGCGUAUGAC-----------
--------(((...((((((((((.......)))))))-))))))(((((((((((((.((((((.(.(((.....-..)))).)))))).)))))))))))))....----------- ( -58.80, z-score =  -6.36, R)
>droPer1.super_2 3820013 109 + 9036312
--------GCCCUUGUGGCAGGAAGCUGUAAUUUCUGC-CUGGGCAACGUGGCGUAUGCGCAACGUGGCAUUGGCU-UUGCACGCGUUGCACAUACGCCCUGUCGUGCGCGACUCCAGC
--------((((....((((((((.......)))))))-).))))...(.((((((((.(((((((((((......-.))).)))))))).))))))))).((((....))))...... ( -56.70, z-score =  -4.06, R)
>dp4.chr3 3629765 109 + 19779522
--------GCCCUUGUGGCAGGAAGCUGUAAUUUCUGC-CUGGGCAACGUGUCGUAUGCGCAACGUGGCAUUGGCU-UUGCACGCGUUGCACAUACGCCCUGUCGUGCGCGACUCCGGC
--------((((....((((((((.......)))))))-).))))........(((((.(((((((((((......-.))).)))))))).)))))(((..((((....))))...))) ( -52.80, z-score =  -3.20, R)
>droAna3.scaffold_13266 4961980 84 + 19884421
--------GCCCUUGCGGCAGGAAACUGUAAUUCCUGC-CGGCGCUACGUGGCGUAUGCGCAACGUUGCACAUACG-CCCCGUGUGCCAGUGGC-------------------------
--------(((((...((((((((.......)))))))-)(((((.(((.((((((((.(((....))).))))))-)).)))))))))).)))------------------------- ( -48.90, z-score =  -5.26, R)
>droEre2.scaffold_4845 11307512 98 + 22589142
--------GGCCUUGCGGCAGGAAGCUGUAAUUUCUGC-CGCGGCUACGUGGCGUAUGCGCAACGAGUCGUAAAGC-CAGCGCACGUUGCACAUACGCCGCGUAUGAC-----------
--------((((..((((((((((.......)))))))-)))))))((((((((((((.((((((.(.(((.....-..)))).)))))).)))))))))))).....----------- ( -56.60, z-score =  -5.79, R)
>droYak2.chr2R 9114291 98 - 21139217
--------GCCCUUGCGGCCAGAAGCUGUAAUUUCUGC-CGCGGCUACGUGGCGUAUGCGCAACGAGUCGCAAAGU-CAGCGCACGUUGCACAUACGCCGCGUAUGAC-----------
--------(((...(((((.(((((......)))))))-))))))(((((((((((((.((((((.(.(((.....-..)))).)))))).)))))))))))))....----------- ( -54.00, z-score =  -5.55, R)
>droSec1.super_9 493389 98 + 3197100
--------GCCCUUGCGGCAGGAAGCUGUAAUUUCUGC-CGCGGCUACGUGGCGUAUGCGCAACGAGUCGCGAAGU-CAGCGCACGUUGCACAUACGCCGCGUAUGAC-----------
--------(((...((((((((((.......)))))))-))))))(((((((((((((.((((((.(.(((.....-..)))).)))))).)))))))))))))....----------- ( -58.80, z-score =  -6.36, R)
>droSim1.chr2R 15814922 98 + 19596830
--------GCCCUUGCGGCAGGAAGCUGUAAUUUCUGC-CGCGGCUACGUGGCGUAUGCGCAACGAGUCGCGAAGU-CAGCGCACGUUGCACAUACGCCGCGUAUGAC-----------
--------(((...((((((((((.......)))))))-))))))(((((((((((((.((((((.(.(((.....-..)))).)))))).)))))))))))))....----------- ( -58.80, z-score =  -6.36, R)
>droVir3.scaffold_12875 14347912 99 + 20611582
AGAGUCUGCUGCCUCCGGCAGGCAAACGUAAUUUUAGCCAGGCUCAACGCGGCGUAUGAGUAACACAUGCCGUCUCGUUGCGCAUACGCCGCAUAGGCC--------------------
.((((((((((((...)))))(((((......))).)))))))))...((((((((((.(((((............))))).)))))))))).......-------------------- ( -41.60, z-score =  -2.97, R)
>droMoj3.scaffold_6496 9809200 90 + 26866924
---------GGCCUGCGGCUGGCAACUGUAAUUUUAGCUCGGCUCAACGUGGCGUAUGAGCAACAUAUGGC---------CGCACGUUGCGCAUACGCCGCAUCUGCC-----------
---------(((.((.(((((((.............)).)))))))..((((((((((.(((((.......---------.....))))).))))))))))....)))----------- ( -34.92, z-score =  -0.82, R)
>droGri2.scaffold_15245 14331355 94 + 18325388
GCAUUUUGCUGCCUACGGCUGCCAACAGCAAUUUUCGCCAUGCACAACAUGGCGUAUGAGCAACACAUGGUGAAUGAUUGCGCAUACAUUGCGU-------------------------
.......((.(((...))).)).....(((((....((((((.....))))))(((((.((((..(((.....))).)))).))))))))))..------------------------- ( -30.30, z-score =  -0.70, R)
>consensus
________GCCCUUGCGGCAGGAAGCUGUAAUUUCUGC_CGGGGCUACGUGGCGUAUGCGCAACGAGUCGCGAAGU_CAGCGCACGUUGCACAUACGCCGCGUAUGAC___________
.............((((((((....))))...................((.((......)).))................))))................................... ( -8.60 =  -8.67 +   0.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,163,425 – 17,163,523
Length 98
Sequences 11
Columns 119
Reading direction reverse
Mean pairwise identity 63.64
Shannon entropy 0.70365
G+C content 0.59425
Mean single sequence MFE -47.83
Consensus MFE -8.70
Energy contribution -9.68
Covariance contribution 0.98
Combinations/Pair 1.68
Mean z-score -3.86
Structure conservation index 0.18
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.87
SVM RNA-class probability 0.995994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17163425 98 - 21146708
-----------GUCAUACGCGGCGUAUGUGCAACGUGCGCUG-ACUUCGCGACUCGUUGCGCAUACGCCACGUAGCCGCG-GCAGAAAUUACAGCUUCCUGCCGCAAGGGC--------
-----------....((((.(((((((((((((((.((((..-.....))).).))))))))))))))).))))((((((-((((.............)))))))...)))-------- ( -53.92, z-score =  -5.33, R)
>droPer1.super_2 3820013 109 - 9036312
GCUGGAGUCGCGCACGACAGGGCGUAUGUGCAACGCGUGCAA-AGCCAAUGCCACGUUGCGCAUACGCCACGUUGCCCAG-GCAGAAAUUACAGCUUCCUGCCACAAGGGC--------
((((..((((....))))..(((((((((((((((.(.(((.-......)))).)))))))))))))))...((((....-))))......)))).((((......)))).-------- ( -49.20, z-score =  -2.81, R)
>dp4.chr3 3629765 109 - 19779522
GCCGGAGUCGCGCACGACAGGGCGUAUGUGCAACGCGUGCAA-AGCCAAUGCCACGUUGCGCAUACGACACGUUGCCCAG-GCAGAAAUUACAGCUUCCUGCCACAAGGGC--------
(((...((((....)))).((((((((((((((((.(.(((.-......)))).))))))))))))((....)))))).(-((((.............))))).....)))-------- ( -45.42, z-score =  -2.15, R)
>droAna3.scaffold_13266 4961980 84 - 19884421
-------------------------GCCACUGGCACACGGGG-CGUAUGUGCAACGUUGCGCAUACGCCACGUAGCGCCG-GCAGGAAUUACAGUUUCCUGCCGCAAGGGC--------
-------------------------(((.(((((.((((.((-((((((((((....)))))))))))).))).).)))(-(((((((.......))))))))...)))))-------- ( -50.10, z-score =  -5.89, R)
>droEre2.scaffold_4845 11307512 98 - 22589142
-----------GUCAUACGCGGCGUAUGUGCAACGUGCGCUG-GCUUUACGACUCGUUGCGCAUACGCCACGUAGCCGCG-GCAGAAAUUACAGCUUCCUGCCGCAAGGCC--------
-----------....((((.(((((((((((((((.(((...-......)).).))))))))))))))).))))((((((-((((.............)))))))..))).-------- ( -50.92, z-score =  -4.75, R)
>droYak2.chr2R 9114291 98 + 21139217
-----------GUCAUACGCGGCGUAUGUGCAACGUGCGCUG-ACUUUGCGACUCGUUGCGCAUACGCCACGUAGCCGCG-GCAGAAAUUACAGCUUCUGGCCGCAAGGGC--------
-----------....((((.(((((((((((((((.((((..-.....))).).))))))))))))))).))))((((((-((((((........)))).)))))...)))-------- ( -54.20, z-score =  -5.29, R)
>droSec1.super_9 493389 98 - 3197100
-----------GUCAUACGCGGCGUAUGUGCAACGUGCGCUG-ACUUCGCGACUCGUUGCGCAUACGCCACGUAGCCGCG-GCAGAAAUUACAGCUUCCUGCCGCAAGGGC--------
-----------....((((.(((((((((((((((.((((..-.....))).).))))))))))))))).))))((((((-((((.............)))))))...)))-------- ( -53.92, z-score =  -5.33, R)
>droSim1.chr2R 15814922 98 - 19596830
-----------GUCAUACGCGGCGUAUGUGCAACGUGCGCUG-ACUUCGCGACUCGUUGCGCAUACGCCACGUAGCCGCG-GCAGAAAUUACAGCUUCCUGCCGCAAGGGC--------
-----------....((((.(((((((((((((((.((((..-.....))).).))))))))))))))).))))((((((-((((.............)))))))...)))-------- ( -53.92, z-score =  -5.33, R)
>droVir3.scaffold_12875 14347912 99 - 20611582
--------------------GGCCUAUGCGGCGUAUGCGCAACGAGACGGCAUGUGUUACUCAUACGCCGCGUUGAGCCUGGCUAAAAUUACGUUUGCCUGCCGGAGGCAGCAGACUCU
--------------------((((.((((((((((((.(.((((..........)))).).)))))))))))).).))).............((((((.((((...))))))))))... ( -40.40, z-score =  -1.90, R)
>droMoj3.scaffold_6496 9809200 90 - 26866924
-----------GGCAGAUGCGGCGUAUGCGCAACGUGCG---------GCCAUAUGUUGCUCAUACGCCACGUUGAGCCGAGCUAAAAUUACAGUUGCCAGCCGCAGGCC---------
-----------(((...(((((((((((.((((((((..---------....)))))))).))))))))..((((.((..((((........)))))))))).))).)))--------- ( -39.10, z-score =  -2.33, R)
>droGri2.scaffold_15245 14331355 94 - 18325388
-------------------------ACGCAAUGUAUGCGCAAUCAUUCACCAUGUGUUGCUCAUACGCCAUGUUGUGCAUGGCGAAAAUUGCUGUUGGCAGCCGUAGGCAGCAAAAUGC
-------------------------..(((..(((((.((((((((.....))).))))).)))))((((((.....)))))).....(((((((..((....))..)))))))..))) ( -35.00, z-score =  -1.33, R)
>consensus
___________GUCAUACGCGGCGUAUGUGCAACGUGCGCUG_ACUUCGCGACUCGUUGCGCAUACGCCACGUAGCCCCG_GCAGAAAUUACAGCUUCCUGCCGCAAGGGC________
....................(((.((((.((((((((((........))))...)))))).)))).........((.....)).................)))................ ( -8.70 =  -9.68 +   0.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:40:27 2011