Locus 4845

Sequence ID dm3.chr2R
Location 15,934,308 – 15,934,410
Length 102
Max. P 0.958490
window6655 window6656

overview

Window 5

Location 15,934,308 – 15,934,410
Length 102
Sequences 11
Columns 120
Reading direction forward
Mean pairwise identity 83.05
Shannon entropy 0.33827
G+C content 0.49237
Mean single sequence MFE -26.82
Consensus MFE -16.40
Energy contribution -16.58
Covariance contribution 0.18
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947912
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15934308 102 + 21146708
--------CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CCCG----UCUGUCCUGCUCCCAA-----
--------...................((..(((((((((((.((((........)))))))))))))...)).))(((.(((..(((((-....----.)))))..))))))..----- ( -29.00, z-score =  -3.14, R)
>droSim1.chr2R 14582789 102 + 19596830
--------CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CCCG----UCUGUCCUGCUCCCAA-----
--------...................((..(((((((((((.((((........)))))))))))))...)).))(((.(((..(((((-....----.)))))..))))))..----- ( -29.00, z-score =  -3.14, R)
>droSec1.super_1 13412177 102 + 14215200
--------CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CCCG----UCUGUCCUGCUCCCAA-----
--------...................((..(((((((((((.((((........)))))))))))))...)).))(((.(((..(((((-....----.)))))..))))))..----- ( -29.00, z-score =  -3.14, R)
>droYak2.chr2R 7863199 111 - 21139217
--------CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CCCGCCCGUCUGUCCCGCUCCCAACCCAA
--------...................((.(..(((((((((.((((........))))))))))))).).)).(((((....(((((..-.......))))).)))))........... ( -29.60, z-score =  -3.43, R)
>droEre2.scaffold_4845 10085330 102 + 22589142
--------CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CCCG----UCUGUGCUGCUCCCAA-----
--------...................((..(((((((((((.((((........)))))))))))))...)).))((((((((((((..-...)----)))).)))))))....----- ( -30.30, z-score =  -2.85, R)
>droAna3.scaffold_13266 10480902 101 - 19884421
--------CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CCCA---GUCGGUCC--CCCCUAA-----
--------............((((...((..(((((((((((.((((........)))))))))))))...)).))((((.(.....).)-))).---...)))).--.......----- ( -25.20, z-score =  -2.53, R)
>dp4.chr3 13061875 102 + 19779522
--------CUAUCUUAACACGAUCAAAGCCAUCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAGGCACCAGGCACCGCGUACCA----------
--------........((.((............(((((((((.((((........)))))))))))))...(((...(((.(((.....)))))).)))..)).))....---------- ( -27.30, z-score =  -2.49, R)
>droWil1.scaffold_180701 2268277 88 + 3904529
--------CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGCCAGACAG-GCCCAA-----------------------
--------...................(((.(((((((((((.((((........)))))))))))))......)).))).(((.....)-))....----------------------- ( -20.30, z-score =  -1.47, R)
>droVir3.scaffold_12875 16985084 103 - 20611582
UCUGCCUGCUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CACCGGAUCCCAG----------------
.((((((((.(((.......)))....((.(..(((((((((.((((........))))))))))))).).)).))))))))........-.............---------------- ( -25.90, z-score =  -1.57, R)
>droMoj3.scaffold_6496 21484346 102 + 26866924
UCUGCCAGCUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CACCGGAUCCAG-----------------
((((...(((.(((....((.(((...((..(((((((((((.((((........)))))))))))))...)).)).))).)).))).))-)..)))).....----------------- ( -24.00, z-score =  -1.24, R)
>droGri2.scaffold_15112 2543361 99 + 5172618
----UGUGCUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG-CACCGGAUCCCAG----------------
----.(((((.(((....((.(((...((..(((((((((((.((((........)))))))))))))...)).)).))).)).))).))-)))..........---------------- ( -25.40, z-score =  -1.83, R)
>consensus
________CUAUCUUAACACGAUCAAAGCCAGCCACAACAACAGAAGCAAUCAAUUUUCGUUGUUGUGAUAGCCGCGGGUAGUCAGACAG_CCCC____UCUGUCC__CUCC_AA_____
....................(((....(((.(((((((((((.((((........)))))))))))))......)).))).))).................................... (-16.40 = -16.58 +   0.18)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 15,934,308 – 15,934,410
Length 102
Sequences 11
Columns 120
Reading direction reverse
Mean pairwise identity 83.05
Shannon entropy 0.33827
G+C content 0.49237
Mean single sequence MFE -32.86
Consensus MFE -25.67
Energy contribution -25.59
Covariance contribution -0.08
Combinations/Pair 1.03
Mean z-score -1.96
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.65
SVM RNA-class probability 0.958490
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15934308 102 - 21146708
-----UUGGGAGCAGGACAGA----CGGG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG--------
-----..(((((..((((((.----....-))))))..)).)))..((((((((((((((((((..........))).)))))))))).)))))...(((.......)))..-------- ( -33.40, z-score =  -2.06, R)
>droSim1.chr2R 14582789 102 - 19596830
-----UUGGGAGCAGGACAGA----CGGG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG--------
-----..(((((..((((((.----....-))))))..)).)))..((((((((((((((((((..........))).)))))))))).)))))...(((.......)))..-------- ( -33.40, z-score =  -2.06, R)
>droSec1.super_1 13412177 102 - 14215200
-----UUGGGAGCAGGACAGA----CGGG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG--------
-----..(((((..((((((.----....-))))))..)).)))..((((((((((((((((((..........))).)))))))))).)))))...(((.......)))..-------- ( -33.40, z-score =  -2.06, R)
>droYak2.chr2R 7863199 111 + 21139217
UUGGGUUGGGAGCGGGACAGACGGGCGGG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG--------
...(((..(..(((((.(((((((.....-)))))))....)))))((((((((((((((((((..........))).)))))))))).))))))..)))............-------- ( -40.70, z-score =  -2.76, R)
>droEre2.scaffold_4845 10085330 102 - 22589142
-----UUGGGAGCAGCACAGA----CGGG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG--------
-----..((((((((.((((.----....-))))))).)).)))..((((((((((((((((((..........))).)))))))))).)))))...(((.......)))..-------- ( -32.10, z-score =  -1.48, R)
>droAna3.scaffold_13266 10480902 101 + 19884421
-----UUAGGGG--GGACCGAC---UGGG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG--------
-----....((.--...))...---....-(((((((((.((.((.((((((((((((((((((..........))).)))))))))).))))).))...))))).))))))-------- ( -30.50, z-score =  -1.39, R)
>dp4.chr3 13061875 102 - 19779522
----------UGGUACGCGGUGCCUGGUGCCUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGAUGGCUUUGAUCGUGUUAAGAUAG--------
----------.(((((.(((...))))))))((((((((.((.((.((((((((((((((((((..........))).)))))))).))))))).))...))))).))))).-------- ( -31.90, z-score =  -1.84, R)
>droWil1.scaffold_180701 2268277 88 - 3904529
-----------------------UUGGGC-CUGUCUGGCUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG--------
-----------------------...(((-(.....))))...((.((((((((((((((((((..........))).)))))))))).))))).))(((.......)))..-------- ( -25.60, z-score =  -1.48, R)
>droVir3.scaffold_12875 16985084 103 + 20611582
----------------CUGGGAUCCGGUG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAGCAGGCAGA
----------------((((...))))((-(((((((((.((.((.((((((((((((((((((..........))).)))))))))).))))).))...))))).))))))))...... ( -33.20, z-score =  -1.48, R)
>droMoj3.scaffold_6496 21484346 102 - 26866924
-----------------CUGGAUCCGGUG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAGCUGGCAGA
-----------------(((...(((..(-(((((((((.((.((.((((((((((((((((((..........))).)))))))))).))))).))...))))).))))))))))))). ( -32.40, z-score =  -1.83, R)
>droGri2.scaffold_15112 2543361 99 - 5172618
----------------CUGGGAUCCGGUG-CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAGCACA----
----------------..........(((-(((((((((.((.((.((((((((((((((((((..........))).)))))))))).))))).))...))))).))))))))).---- ( -34.90, z-score =  -3.16, R)
>consensus
_____UU_GGAG__GGACAGA____CGGG_CUGUCUGACUACCCGCGGCUAUCACAACAACGAAAAUUGAUUGCUUCUGUUGUUGUGGCUGGCUUUGAUCGUGUUAAGAUAG________
..............................(((((((((.((.((.((((((((((((((((((..........))).)))))))))).))))).))...))))).))))))........ (-25.67 = -25.59 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:37:05 2011