Locus 4097

Sequence ID dm3.chr2R
Location 10,408,496 – 10,408,627
Length 131
Max. P 0.927735
window5620 window5621 window5622

overview

Window 0

Location 10,408,496 – 10,408,602
Length 106
Sequences 12
Columns 116
Reading direction reverse
Mean pairwise identity 72.21
Shannon entropy 0.59629
G+C content 0.54775
Mean single sequence MFE -26.07
Consensus MFE -20.90
Energy contribution -21.00
Covariance contribution 0.10
Combinations/Pair 1.13
Mean z-score -0.51
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.895668
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10408496 106 - 21146708
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAC--AUCUUCCCACACCCAAACCGAUUCCCGCAGCCCCGCAU--------
.......((((((((..((((...(((....)))..)))).))))))))......(((..(((((...--(((................)))....)))))...))).-------- ( -31.69, z-score =  -1.39, R)
>droAna3.scaffold_13266 10807678 115 - 19884421
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCUAUCGACCUUAU-CCCCCUAUCCCCAUCCCCAUCUCCAUCCCCUGCCAUGC
.....((((((((((..((((...(((....)))..)))).))))))..((..((.((.....)).))..)).....-...............................))))... ( -24.60, z-score =  -0.59, R)
>droEre2.scaffold_4845 7141927 92 + 22589142
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAC--AUCUUGCCACACCCAUUCCCGCAU----------------------
.....((((.(((((..((((...(((....)))..)))).)))))(((((((.....)))).)))..--.....))))...............---------------------- ( -25.70, z-score =  -0.13, R)
>droYak2.chr2R 10335004 92 - 21139217
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGAUGUAAAUUGCUUGCUGCCAC--AUCUUGCCACACCCAUCCUCGCAU----------------------
.....((((.(((((..((((...(((....)))..)))).)))))(((((.....((.....)).))--)))..))))...............---------------------- ( -25.40, z-score =  -0.64, R)
>droSec1.super_1 7919131 106 - 14215200
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAU--AUCUUCCCACACCCAUGCCCAUUCCCGCAGCCCCGCAG--------
.......((((((((..((((...(((....)))..)))).))))))))......(((..(((((...--..........................)))))...))).-------- ( -30.65, z-score =  -1.00, R)
>droSim1.chr2R 9163089 106 - 19596830
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAC--AUCUUCCCACACCCAUGCCCAUUCCCGCAGCCCCGCAG--------
.......((((((((..((((...(((....)))..)))).))))))))......(((..(((((...--..........................)))))...))).-------- ( -30.65, z-score =  -0.85, R)
>droWil1.scaffold_180701 968458 97 - 3904529
UCUUUUGGCCGCACAUUUGUGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUC-UACCCCACUACAAACGUCUCCGUCUCGUUCUCUUCU------------------
.......((((((((..((((...(((....)))..)))).))))))))............-............((((.........)))).......------------------ ( -21.30, z-score =  -0.44, R)
>droPer1.super_2 5236223 107 - 9036312
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUUCUAUCAACCUUCCACCACCUAGCCCUCCCCUCCCCCACAUAGU---------
......(((.(((((..((((...(((....)))..)))).)))))((((......(.(((.......))).)......))))..)))...................--------- ( -23.40, z-score =  -0.77, R)
>dp4.chr3 5036711 107 - 19779522
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUUCUAUCAACCUUCCACCACCUAGCCCUCCCCUCCCCCACAUAGU---------
......(((.(((((..((((...(((....)))..)))).)))))((((......(.(((.......))).)......))))..)))...................--------- ( -23.40, z-score =  -0.77, R)
>droVir3.scaffold_12875 10495288 98 + 20611582
UCCCGUAGCCGCACAUUUGCGGGCGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUG-UCCUAGUCA--UUGCACCACCCAACUGCAAUGUACUCAG---------------
.......((((((((..((((...(((....)))..)))).))))))))............-..(((((((--(((((.........))))))).))).))--------------- ( -30.90, z-score =  -1.07, R)
>droMoj3.scaffold_6496 16908414 86 - 26866924
UCCCGUAGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUACGGUGUAAAUUGCUUG-UCCUACUCA--UUGCAACAGGC-CCCGC--------------------------
..((((..(((((....)))))((((.((((....)))).))))))))........(((((-(..((....--.))..))))))-.....-------------------------- ( -22.80, z-score =   0.32, R)
>droGri2.scaffold_15245 15048896 95 + 18325388
UCCCGUAGCCAUACAUUUGCGGGCGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUG-CCCCACUCAACUUGCAACGACU-GCCACCACCGAC-------------------
..((((((........))))))(((..(((((....)))))..)))((((..(.(((.(((-(............))))))).)-..))))......------------------- ( -22.30, z-score =   1.17, R)
>consensus
UCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAC__AUCUUCCAACACCCAUCCCCACUCCCCC__________________
.......((((((((..((((...(((....)))..)))).))))))))................................................................... (-20.90 = -21.00 +   0.10)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,408,531 – 10,408,627
Length 96
Sequences 12
Columns 114
Reading direction forward
Mean pairwise identity 74.63
Shannon entropy 0.49105
G+C content 0.52151
Mean single sequence MFE -25.05
Consensus MFE -18.38
Energy contribution -18.33
Covariance contribution -0.05
Combinations/Pair 1.20
Mean z-score -1.04
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.876276
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10408531 96 + 21146708
-----GAU--GUGGCAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGAAAUAGAGGCAGCCAGG-----------
-----...--.((((.((...(.((((...(((((((.((((.((((....))))..))))..)))))))........(......))))).)..)).))))..----------- ( -26.80, z-score =  -1.41, R)
>droAna3.scaffold_13266 10807715 98 + 19884421
GAUAAGGUCGAUAGCAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGAAAUAGGG--AGCC--------------
......(((....((.....))........(((((((.((((.((((....))))..))))..)))))))......)))...............--....-------------- ( -24.60, z-score =  -1.38, R)
>droEre2.scaffold_4845 7141948 94 - 22589142
-----GAU--GUGGCAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGAAAUAGGG--AGCCCGG-----------
-----..(--.((((.(....).........((((((.((((.((((....))))..))))..)))))))))).)................((.--...))..----------- ( -25.30, z-score =  -0.62, R)
>droYak2.chr2R 10335025 92 + 21139217
-----GAU--GUGGCAGCAAGCAAUUUACAUCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGAAAUAGGG--AGCCU-------------
-----(((--(((((.....))....))))))(((((.((((.((((....))))..))))..)))))((((.....................)--.))).------------- ( -22.70, z-score =  -0.10, R)
>droSec1.super_1 7919166 96 + 14215200
-----GAU--AUGGCAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGAAAUAGAGGCAGCCAGG-----------
-----...--.((((.((...(.((((...(((((((.((((.((((....))))..))))..)))))))........(......))))).)..)).))))..----------- ( -26.90, z-score =  -2.09, R)
>droSim1.chr2R 9163124 96 + 19596830
-----GAU--GUGGCAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGAAAUAGAGGCAGCCAGG-----------
-----...--.((((.((...(.((((...(((((((.((((.((((....))))..))))..)))))))........(......))))).)..)).))))..----------- ( -26.80, z-score =  -1.41, R)
>droWil1.scaffold_180701 968490 85 + 3904529
------------GGUAG-AAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCACAAAUGUGCGGCCAAAAGACAAUGGCGUGCCUCAACCAG----------------
------------(((.(-(.(((........((((((.(..((.(((.......))).)).).))))))((((........)))).))).)).)))..---------------- ( -26.00, z-score =  -2.01, R)
>droPer1.super_2 5236257 109 + 9036312
-----GGUUGAUAGAAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGCCAGGCAGCCAGACACCCACCCAGAGAG
-----(((((......((((....))....(((((((.((((.((((....))))..))))..)))))))...............))....))))).................. ( -26.10, z-score =  -1.46, R)
>dp4.chr3 5036745 109 + 19779522
-----GGUUGAUAGAAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGCCAGGCAGCCAGACACCCACCCAGAGAG
-----(((((......((((....))....(((((((.((((.((((....))))..))))..)))))))...............))....))))).................. ( -26.10, z-score =  -1.46, R)
>droVir3.scaffold_12875 10495316 87 - 20611582
--------UGACUAGGACAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGCCCGCAAAUGUGCGGCUACGGGA-AGCC-C-AAAGACAAUGGG----------------
--------...(((................(((((((.((((.((((....))))..))))..)))))))....(((.-..))-)-........))).---------------- ( -23.10, z-score =  -0.49, R)
>droMoj3.scaffold_6496 16908430 89 + 26866924
--------UGAGUAGGACAAGCAAUUUACACCGUACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCUACGGGA-AGAGACCAAAGACAAUGGU----------------
--------...((((...((....))....(((((((.((((.((((....))))..))))..)))))))))))....-....((((.......))))---------------- ( -21.90, z-score =  -0.30, R)
>droGri2.scaffold_15245 15048919 89 - 18325388
------GUUGAGUGGGGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGCCCGCAAAUGUAUGGCUACGGGA-AGCC-CGAAAGACAAUGG-----------------
------(((...(.((((..........((.(((.....))).)).....(((.(((.((....))..))).)))...-.)))-).)..))).....----------------- ( -24.30, z-score =   0.21, R)
>consensus
_____GAU__AUGGCAGCAAGCAAUUUACACCGCACAAUGCGUUGACACACGUCGUCCGCAAAUGUGCGGCCAGAAGACAAUAGAGAAAUACAG_CAGCC______________
..............................(((((((.((((.((((....))))..))))..)))))))............................................ (-18.38 = -18.33 +  -0.05)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 10,408,531 – 10,408,627
Length 96
Sequences 12
Columns 114
Reading direction reverse
Mean pairwise identity 74.63
Shannon entropy 0.49105
G+C content 0.52151
Mean single sequence MFE -28.33
Consensus MFE -20.90
Energy contribution -21.00
Covariance contribution 0.10
Combinations/Pair 1.13
Mean z-score -1.19
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.927735
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10408531 96 - 21146708
-----------CCUGGCUGCCUCUAUUUCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAC--AUC-----
-----------..((((.((.......................((((((((..((((...(((....)))..)))).))))))))((.....))..)).)))).--...----- ( -29.40, z-score =  -1.87, R)
>droAna3.scaffold_13266 10807715 98 - 19884421
--------------GGCU--CCCUAUUUCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCUAUCGACCUUAUC
--------------....--...............(((.....((((((((..((((...(((....)))..)))).)))))))).......((.....))....)))...... ( -26.00, z-score =  -1.25, R)
>droEre2.scaffold_4845 7141948 94 + 22589142
-----------CCGGGCU--CCCUAUUUCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAC--AUC-----
-----------...(((.--.......................((((((((..((((...(((....)))..)))).))))))))((((.....)))).)))..--...----- ( -28.20, z-score =  -1.22, R)
>droYak2.chr2R 10335025 92 - 21139217
-------------AGGCU--CCCUAUUUCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGAUGUAAAUUGCUUGCUGCCAC--AUC-----
-------------.(((.--...............(((....)))((((((..((((...(((....)))..)))).))))))..((((.....)))).)))..--...----- ( -24.20, z-score =  -0.72, R)
>droSec1.super_1 7919166 96 - 14215200
-----------CCUGGCUGCCUCUAUUUCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAU--AUC-----
-----------..((((.((.......................((((((((..((((...(((....)))..)))).))))))))((.....))..)).)))).--...----- ( -29.50, z-score =  -2.14, R)
>droSim1.chr2R 9163124 96 - 19596830
-----------CCUGGCUGCCUCUAUUUCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAC--AUC-----
-----------..((((.((.......................((((((((..((((...(((....)))..)))).))))))))((.....))..)).)))).--...----- ( -29.40, z-score =  -1.87, R)
>droWil1.scaffold_180701 968490 85 - 3904529
----------------CUGGUUGAGGCACGCCAUUGUCUUUUGGCCGCACAUUUGUGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUU-CUACC------------
----------------..(((.((((((.((((........))))((((((..((((...(((....)))..)))).))))))........)))))-).)))------------ ( -32.00, z-score =  -2.40, R)
>droPer1.super_2 5236257 109 - 9036312
CUCUCUGGGUGGGUGUCUGGCUGCCUGGCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUUCUAUCAACC-----
.......((((((.((..(((.....(((......))).....((((((((..((((...(((....)))..)))).)))))))).......))).)).))))))....----- ( -34.40, z-score =  -1.10, R)
>dp4.chr3 5036745 109 - 19779522
CUCUCUGGGUGGGUGUCUGGCUGCCUGGCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUUCUAUCAACC-----
.......((((((.((..(((.....(((......))).....((((((((..((((...(((....)))..)))).)))))))).......))).)).))))))....----- ( -34.40, z-score =  -1.10, R)
>droVir3.scaffold_12875 10495316 87 + 20611582
----------------CCCAUUGUCUUU-G-GGCU-UCCCGUAGCCGCACAUUUGCGGGCGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGUCCUAGUCA--------
----------------.....((.((..-(-(((.-.......((((((((..((((...(((....)))..)))).))))))))...........)))).)).))-------- ( -28.41, z-score =  -1.04, R)
>droMoj3.scaffold_6496 16908430 89 - 26866924
----------------ACCAUUGUCUUUGGUCUCU-UCCCGUAGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUACGGUGUAAAUUGCUUGUCCUACUCA--------
----------------((((.......))))....-..((((..(((((....)))))((((.((((....)))).))))))))......................-------- ( -20.40, z-score =   0.12, R)
>droGri2.scaffold_15245 15048919 89 + 18325388
-----------------CCAUUGUCUUUCG-GGCU-UCCCGUAGCCAUACAUUUGCGGGCGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCCCCACUCAAC------
-----------------............(-(((.-..((((((........))))))((((.((((....)))).))))(((((....)))))..))))........------ ( -23.60, z-score =   0.36, R)
>consensus
______________GGCUG_CUCUAUUUCUCUAUUGUCUUCUGGCCGCACAUUUGCGGACGACGUGUGUCAACGCAUUGUGCGGUGUAAAUUGCUUGCUGCCAU__AUC_____
...........................................((((((((..((((...(((....)))..)))).))))))))............................. (-20.90 = -21.00 +   0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:22:47 2011