Locus 4569

Sequence ID dm3.chr2R
Location 14,142,586 – 14,142,710
Length 124
Max. P 0.999398
window6261 window6262 window6263

overview

Window 1

Location 14,142,586 – 14,142,687
Length 101
Sequences 11
Columns 116
Reading direction forward
Mean pairwise identity 68.89
Shannon entropy 0.63820
G+C content 0.55709
Mean single sequence MFE -39.10
Consensus MFE -18.61
Energy contribution -20.24
Covariance contribution 1.62
Combinations/Pair 1.10
Mean z-score -2.83
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.85
SVM RNA-class probability 0.999398
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14142586 101 + 21146708
-------GGUUUAGCUGCUGCAUGAG---AGCUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCACUUGACGGCCAUUACUCAGCGCGGCGAUGCUGCUGAAGU-----
-------..((((((....((((...---.(((((.(((.(.((((((((((....))))))))))..(((........)))....).))).))))).)))).))))))..----- ( -40.30, z-score =  -2.54, R)
>droSim1.chr2R 12879299 101 + 19596830
-------GGUUUAGCUGCUGCAUGAG---AGCUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCACUUGACGGCCAUUACUCAGCGCGGCGAUGCUGCUGAAGU-----
-------..((((((....((((...---.(((((.(((.(.((((((((((....))))))))))..(((........)))....).))).))))).)))).))))))..----- ( -40.30, z-score =  -2.54, R)
>droSec1.super_1 11632689 101 + 14215200
-------GGUUUAGCUGCUGCAUGAG---AGCUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCACUUGACGGCCAUUACUCAGCGCGGCGAUGCUGCUGAAGU-----
-------..((((((....((((...---.(((((.(((.(.((((((((((....))))))))))..(((........)))....).))).))))).)))).))))))..----- ( -40.30, z-score =  -2.54, R)
>droYak2.chr2R 6099613 103 - 21139217
-------AGUUUAGCUGCCGCAUGAGUUGAGUUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCACUUGACGGCCAUUACUCAGU-CGACGAUGCUGCUGAAGU-----
-------..((((((....((((..((..(((.((((...((.(((((((((....))))))))))))))))))..))(((.........))-)....)))).))))))..----- ( -38.70, z-score =  -3.08, R)
>droEre2.scaffold_4845 8363639 100 + 22589142
-------AGUUUAGCUGCAGCAGGAG---AGCUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCUCUUGACGGCCAUUACUCAGC-CGACGAUGCUGCUGAAGU-----
-------......(((.(((((((((---((((......(((.(((((((((....)))))))))))))))))))..((((.........))-))......)))))).)))----- ( -39.80, z-score =  -2.78, R)
>droAna3.scaffold_13266 15502618 112 - 19884421
CGUGGUGGAUGGAGCGAUGGAAGGAA---CACUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCGGUUGACGGCCAUUACUCAGA-UUCUGCUGCCACUGCCACAGAGC
.((((..(.(((((..((((..(..(---.(((((((.((...(((((((((....)))))))))))))))))))..)..))))..))(((.-.....)))))))..))))..... ( -48.00, z-score =  -3.99, R)
>dp4.chr3 11417770 82 + 19779522
---------------------GGGAGCUGGCCUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCAUUUGACUGCCAUUACUCAG----GCGCUGCCGCUG---------
---------------------...(((.(((..((((((.(..(((((((((....)))))))))...((((......))))....).)))----).)).)))))).--------- ( -36.90, z-score =  -3.39, R)
>droPer1.super_4 6821556 82 + 7162766
---------------------GGGAGCUGGCCUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCAUUUGACUGCCAUUACUCAG----GCGCUGCCGCUG---------
---------------------...(((.(((..((((((.(..(((((((((....)))))))))...((((......))))....).)))----).)).)))))).--------- ( -36.90, z-score =  -3.39, R)
>droWil1.scaffold_181141 1629602 98 - 5303230
----GAAGUUGCUGCUGUGGCUGUGGC--UGUUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCCCAGGCCAUCGGCGGCCAUUACUCAGUCGCAUCGUGGGC------------
----...(.(((.((((.(...(((((--(((((.((((.(..(((((((((....))))))))))))))....))))))))))..).)))).))).)......------------ ( -41.90, z-score =  -2.44, R)
>droVir3.scaffold_12875 463264 84 - 20611582
--------UGGUCGCGGUCGCGGUCGC--UGUUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCGCUUGCUGGCCAUUACUCAGUCG----------------------
--------(((((((((..(((.((((--..(..(...)..).(((((((((....))))))))))))).))))))).)))))...........---------------------- ( -33.50, z-score =  -1.44, R)
>droGri2.scaffold_15245 11391396 84 + 18325388
------CAGCUGAGUGCCGCGAAGAA----GCUGCCCUCUGAAGGACAUUAUGGAAAUGAUGUCCGCGAGCGCUUGCUGGCCAUUACUCAGUCG----------------------
------((((.(((((((((..(((.----.......)))...(((((((((....)))))))))))).))))))))))...............---------------------- ( -33.50, z-score =  -2.99, R)
>consensus
_______GGUUUAGCUGCGGCAGGAG___AGCUGCCCUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCACUUGACGGCCAUUACUCAGC_CGGCGAUGCUGCUG_________
..............................((((....((((.(((((((((....)))))))))...(((........))).)))).))))........................ (-18.61 = -20.24 +   1.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 14,142,586 – 14,142,687
Length 101
Sequences 11
Columns 116
Reading direction reverse
Mean pairwise identity 68.89
Shannon entropy 0.63820
G+C content 0.55709
Mean single sequence MFE -29.81
Consensus MFE -13.32
Energy contribution -13.15
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -1.44
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.22
SVM RNA-class probability 0.911889
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14142586 101 - 21146708
-----ACUUCAGCAGCAUCGCCGCGCUGAGUAAUGGCCGUCAAGUGCCCGAGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGCU---CUCAUGCAGCAGCUAAACC-------
-----..((((((.((......))))))))...((((.((....(((((((((((((.((....)).))))))))....)))))((.---.....)).)).))))....------- ( -32.20, z-score =  -1.90, R)
>droSim1.chr2R 12879299 101 - 19596830
-----ACUUCAGCAGCAUCGCCGCGCUGAGUAAUGGCCGUCAAGUGCCCGAGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGCU---CUCAUGCAGCAGCUAAACC-------
-----..((((((.((......))))))))...((((.((....(((((((((((((.((....)).))))))))....)))))((.---.....)).)).))))....------- ( -32.20, z-score =  -1.90, R)
>droSec1.super_1 11632689 101 - 14215200
-----ACUUCAGCAGCAUCGCCGCGCUGAGUAAUGGCCGUCAAGUGCCCGAGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGCU---CUCAUGCAGCAGCUAAACC-------
-----..((((((.((......))))))))...((((.((....(((((((((((((.((....)).))))))))....)))))((.---.....)).)).))))....------- ( -32.20, z-score =  -1.90, R)
>droYak2.chr2R 6099613 103 + 21139217
-----ACUUCAGCAGCAUCGUCG-ACUGAGUAAUGGCCGUCAAGUGCCCGAGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAACUCAACUCAUGCGGCAGCUAAACU-------
-----........(((...((((-..(((((..((.....))..(((((((((((((.((....)).))))))))....))))).....)))))..)))).))).....------- ( -28.20, z-score =  -1.38, R)
>droEre2.scaffold_4845 8363639 100 - 22589142
-----ACUUCAGCAGCAUCGUCG-GCUGAGUAAUGGCCGUCAAGAGCCCGAGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGCU---CUCCUGCUGCAGCUAAACU-------
-----......((((((..(.((-(((.......))))).)....((((((((((((.((....)).))))))))....))))....---....)))))).........------- ( -35.50, z-score =  -2.67, R)
>droAna3.scaffold_13266 15502618 112 + 19884421
GCUCUGUGGCAGUGGCAGCAGAA-UCUGAGUAAUGGCCGUCAACCGCCCGCGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGUG---UUCCUUCCAUCGCUCCAUCCACCACG
..(((((.((....)).))))).-...(((..((((......((.((((..((((((.((....)).))))))......)))).)).---......))))..)))........... ( -31.62, z-score =  -0.83, R)
>dp4.chr3 11417770 82 - 19779522
---------CAGCGGCAGCGC----CUGAGUAAUGGCAGUCAAAUGCCCGCGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGGCCAGCUCCC---------------------
---------.((((((.((.(----(((.((...((((......)))).))((((((.((....)).))))))....))))))..))).)))...--------------------- ( -28.50, z-score =  -1.64, R)
>droPer1.super_4 6821556 82 - 7162766
---------CAGCGGCAGCGC----CUGAGUAAUGGCAGUCAAAUGCCCGCGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGGCCAGCUCCC---------------------
---------.((((((.((.(----(((.((...((((......)))).))((((((.((....)).))))))....))))))..))).)))...--------------------- ( -28.50, z-score =  -1.64, R)
>droWil1.scaffold_181141 1629602 98 + 5303230
------------GCCCACGAUGCGACUGAGUAAUGGCCGCCGAUGGCCUGGGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAACA--GCCACAGCCACAGCAGCAACUUC----
------------........(((..(((.....((((.((.(.((.(((((((((((.((....)).)))))))...)))).)).).--))....)))))))..))).....---- ( -28.70, z-score =  -0.43, R)
>droVir3.scaffold_12875 463264 84 + 20611582
----------------------CGACUGAGUAAUGGCCAGCAAGCGCCCGCGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAACA--GCGACCGCGACCGCGACCA--------
----------------------((.(((.......((......))((((..((((((.((....)).))))))......))))..))--)))..(((....)))....-------- ( -22.40, z-score =  -0.21, R)
>droGri2.scaffold_15245 11391396 84 - 18325388
----------------------CGACUGAGUAAUGGCCAGCAAGCGCUCGCGGACAUCAUUUCCAUAAUGUCCUUCAGAGGGCAGC----UUCUUCGCGGCACUCAGCUG------
----------------------.(.((((((....(((.....((.(((..((((((.((....)).))))))....))).)).((----......))))))))))))..------ ( -27.90, z-score =  -1.37, R)
>consensus
_________CAGCAGCAUCGCCG_ACUGAGUAAUGGCCGUCAAGUGCCCGAGGACAUCAUUUCCAUAAUGUCCUUCACAGGGCAGCU___CUCCUGCAGCAGCUAAACC_______
.............................................((((..((((((.((....)).))))))......))))................................. (-13.32 = -13.15 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,142,612 – 14,142,710
Length 98
Sequences 7
Columns 114
Reading direction forward
Mean pairwise identity 70.57
Shannon entropy 0.53334
G+C content 0.55843
Mean single sequence MFE -37.30
Consensus MFE -18.14
Energy contribution -19.64
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.57
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.71
SVM RNA-class probability 0.994534
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14142612 98 + 21146708
CUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCACUUGACGGCCAUUACUCAGCGCGGCGAUGCUGCUGAAGUA-ACCCUCUCUCU--GCCCCGCCAUC-------------
..(((.((((((((((....)))))))))).(((((...((.((...((((((((((((....))).)))).))))-))).))....)--)))))))....------------- ( -38.10, z-score =  -3.53, R)
>droSim1.chr2R 12879325 100 + 19596830
CUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCACUUGACGGCCAUUACUCAGCGCGGCGAUGCUGCUGAAGUA-ACCCUCUCUCUCUGCCCCGCCAUC-------------
..(((.((((((((((....)))))))))).(((((...((.((...((((((((((((....))).)))).))))-)....)).))..))))))))....------------- ( -37.00, z-score =  -3.09, R)
>droSec1.super_1 11632715 100 + 14215200
CUGUGAAGGACAUUAUGGAAAUGAUGUCCUCGGGCACUUGACGGCCAUUACUCAGCGCGGCGAUGCUGCUGAAGUA-ACCCUCUCUCCCUGCCCCGCCAUC-------------
..(((.((((((((((....)))))))))).(((((...((.((...((((((((((((....))).)))).))))-)..)).))....))))))))....------------- ( -37.00, z-score =  -3.08, R)
>droAna3.scaffold_13266 15502651 113 - 19884421
CUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCGGUUGACGGCCAUUACUCAG-AUUCUGCUGCCACUGCCACAGAGCAAGGCUCUCGACUCAGCCACACAGUCUCUGCCUC
(((((..(((((((((....)))))))))...(((((((((.((((......(((-......)))....(((......))).)))).))))))..))).))))).......... ( -40.80, z-score =  -1.82, R)
>dp4.chr3 11417785 95 + 19779522
CUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCAUUUGACUGCCAUUACUCAG-GCGCUGCCGCUGUUCCUGC----CACAGUCACCGGCGGAGCUUU--------------
..((((.(((((((((....)))))))))...((((......)))).))))..((-((.((((((.((...(((.----..))).)).)))))).)))).-------------- ( -37.00, z-score =  -2.21, R)
>droPer1.super_4 6821571 95 + 7162766
CUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCAUUUGACUGCCAUUACUCAG-GCGCUGCCGCUGUUCCUGC----CACAGUCACCGGCGCAGCUUU--------------
(((.(..(((((((((....)))))))))...((((......))))....).)))-((((((..(((((......----.)))))...))))))......-------------- ( -36.40, z-score =  -1.98, R)
>droWil1.scaffold_181141 1629632 90 - 5303230
CUGUGAAGGACAUUAUGGAAAUGAUGUCCCCAGGCCAUCGGCGGCCAUUACUCAG-UCGC-AUCGUGGGCAACGC---CCCGAUUGAUCAAUGCU-------------------
..((((.(((((((((....)))))))))...((((......)))).))))...(-(((.-((((.((((...))---)))))))))).......------------------- ( -34.80, z-score =  -2.27, R)
>consensus
CUGUGAAGGACAUUAUGGAAAUGAUGUCCGCGGGCACUUGACGGCCAUUACUCAG_GCGCCGAUGCUGCUGAAGCA_ACCCUAUCUCUCGGCCCAGCCAU______________
..((((.(((((((((....)))))))))...(((........))).))))............................................................... (-18.14 = -19.64 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:31:42 2011