Locus 4524

Sequence ID dm3.chr2R
Location 13,767,086 – 13,767,259
Length 173
Max. P 0.762194
window6194 window6195 window6196

overview

Window 4

Location 13,767,086 – 13,767,179
Length 93
Sequences 9
Columns 111
Reading direction forward
Mean pairwise identity 48.00
Shannon entropy 1.09343
G+C content 0.44371
Mean single sequence MFE -27.51
Consensus MFE -5.31
Energy contribution -6.58
Covariance contribution 1.27
Combinations/Pair 2.07
Mean z-score -1.47
Structure conservation index 0.19
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.711529
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13767086 93 + 21146708
---------UUGGUUUUCAUUGAAGGACAUCUUUAAGUCCAAUGA---------AAGUUUAGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCG
---------........(((((((((((........))))...((---------(.(((.((....(((((((......))))))).....))))).)))..))))))).. ( -25.30, z-score =  -2.61, R)
>droEre2.scaffold_4845 7994789 102 + 22589142
---------UUGUUGCCCAUUGCGGGGCAGCUUUGGGGCCACAGUCAGUUGAGUAAGUUGGGUAAUUGGCUCCUUAUUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCG
---------..(((((((......))))))).....(((....))).((((((((.((((((....(((((((......)))))))....))))))....))))))))... ( -35.80, z-score =  -1.61, R)
>droYak2.chr2R 5723710 93 - 21139217
---------UUGUUGUCCAUUGUGGGGCAACUUUAAGUCCACAGU---------AAGUUGAGUAGUUGGCUCUUUGCUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCG
---------..(((((((......))))))).....(((.((((.---------..(((((((.((.((((((......)))))))).)))).)))...))))..)))... ( -31.40, z-score =  -2.77, R)
>droSec1.super_1 11262660 93 + 14215200
---------UUGGGUUUCGUUGAAGGACAACUUUAAGUCCACUGG---------AAGUUUGGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCG
---------........(((((((((((........))))...((---------(((((.((....(((((((......)))))))....)).))).)))).))))))).. ( -26.30, z-score =  -1.72, R)
>droSim1.chr2R 12508966 93 + 19596830
---------UUGGUUUUCGUUAAAGGACAUCUUUAAGUCCACUGG---------AAGUUUAGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCG
---------...((..(((.....((((........))))...((---------((..((((....(((((((......))))))).....))))..))))...))).)). ( -23.40, z-score =  -1.71, R)
>droWil1.scaffold_180745 2230479 81 + 2843958
---------------------------UUCCUGAAAGAACGUUGAUGCU---GCGGAUGAUGCUUUUCUUUUAUGGAAUGGAAUGACAUGGUCAAUGUUUUGCCAAAUGCC
---------------------------((((((((((((.((....)).---(((.....)))..)))))))).))))(((...(((((.....)))))...)))...... ( -18.20, z-score =  -0.96, R)
>droVir3.scaffold_12875 5200638 107 - 20611582
----AAAAUUUCAUUGGCAGUACGCCUUUUACGGGGCAGCAGAAAUUUCCAAAAGGAUUCUGUUCUUUUAUCUUCAAUAUUUUUCAAAAACUCGGCAUUCUGUUCGAUUCG
----........((((((((...((((......))))(((((((...(((....))))))))))...................................))).)))))... ( -18.10, z-score =  -0.59, R)
>droMoj3.scaffold_6496 8382322 111 + 26866924
AACUAUUUGCUCGCCCUUCGUCUGCUGCUUGCUCUGGCUGACGUACUUGAGAAGGGAUGCUGCACGUUUCUCCUCGAUGCUGCCAUCGAUGUUCGCUUUCUGGUCGACAAU
.......(((.(((((((((((.((.....))...)))...((....)).)))))).))..))).........((((((....))))))((((.(((....))).)))).. ( -26.10, z-score =   0.68, R)
>droGri2.scaffold_15245 6109255 111 - 18325388
UUCAGUUGUUUCAGGGGAGGAAGGCUGCCUGUUGUGGGUCAAGAGGUUGAGGAACGAGGCAGCCUUCUUAUCCUUGAUCUGUUGCACAAAGUCAGCAUGCUGCUCGAUGCG
..(((.....(((((((((((((((((((((((.(...((((....))))).))).))))))))))))).))))))).)))..(((...((.(((....)))))...))). ( -43.00, z-score =  -1.99, R)
>consensus
_________UUGGUUUUCAUUGAGGGGCAUCUUUAAGUCCACUGA_________AAGUUCAGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCG
........................((((........))))..........................((((((........))))))........(((((......))))). ( -5.31 =  -6.58 +   1.27)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,767,112 – 13,767,219
Length 107
Sequences 10
Columns 116
Reading direction forward
Mean pairwise identity 57.58
Shannon entropy 0.89014
G+C content 0.49909
Mean single sequence MFE -33.10
Consensus MFE -10.88
Energy contribution -9.97
Covariance contribution -0.91
Combinations/Pair 2.09
Mean z-score -1.04
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.61
SVM RNA-class probability 0.762194
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13767112 107 + 21146708
-------AGUCCAAUGA--AAGUUUAGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCA
-------..........--............(((((((......))))))).....((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).. ( -34.60, z-score =  -2.69, R)
>droAna3.scaffold_13337 4134837 100 + 23293914
-------AGUCUGCGGA---------GUCAUUGGGUUGCCCUUUGAAGCCAAGAGUCUAGCGUGUUGCUGGACUGUAUUGCGAAUGUUCGUCUGUCGCUCCCGGCAAUCGUUGGCA
-------.(((.((((.---------.(((..(((...)))..))).(((.(.((((((((.....)))))))).)...((((..(.....)..))))....)))..)))).))). ( -34.20, z-score =  -1.12, R)
>droEre2.scaffold_4845 7994815 116 + 22589142
GGGCCACAGUCAGUUGAGUAAGUUGGGUAAUUGGCUCCUUAUUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGCCCGUCAGUCGCUCCUGACAGCCGUUAGCA
(((((.(((.(.((((((((.((((((....(((((((......)))))))....))))))....))))))))..).))).)...))))(((((......))))).((.....)). ( -40.20, z-score =  -1.56, R)
>droYak2.chr2R 5723736 107 - 21139217
-------AGUCCACAGU--AAGUUGAGUAGUUGGCUCUUUGCUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGCCCGUCAGUCGCUCCUGACAGCCGUUAGCA
-------.(((.((((.--..(((((((.((.((((((......)))))))).)))).)))...))))..)))(((.(((((......)).))).)))..(((((....))))).. ( -33.80, z-score =  -1.07, R)
>droSec1.super_1 11262686 107 + 14215200
-------AGUCCACUGG--AAGUUUGGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCA
-------.....((..(--....)..))...(((((((......))))))).....((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).. ( -35.50, z-score =  -1.81, R)
>droSim1.chr2R 12508992 107 + 19596830
-------AGUCCACUGG--AAGUUUAGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCAGUCAGUCGCUCUUGACAGCCGCUAGCA
-------.....(((((--....)))))...(((((((......))))))).....((((((..(((((.((.(((.((((........).))).)))))..))))).)))))).. ( -32.80, z-score =  -1.25, R)
>droWil1.scaffold_180745 2230496 104 + 2843958
-------AUGCUGCGGA-----UGAUGCUUUUCUUUUAUGGAAUGGAAUGACAUGGUCAAUGUUUUGCCAAAUGCCUUCACGUAUAUUACGCAAACGCGUUUUGCAAUCACUGGCA
-------.((((...((-----(((.((..((((.....))))(((...(((((.....)))))...)))...))..))..(((....((((....))))..))).)))...)))) ( -22.10, z-score =   0.85, R)
>droVir3.scaffold_12875 5200676 109 - 20611582
-------AAAUUUCCAAAAGGAUUCUGUUCUUUUAUCUUCAAUAUUUUUCAAAAACUCGGCAUUCUGUUCGAUUCGUUGGAGUAUGUCCUGUUGUUGCCUCUUGUAGAUGUCGGCC
-------......((((((((((...))))))))((((.(((.......(((.(((..(((((....(((((....)))))..)))))..))).)))....))).))))...)).. ( -15.40, z-score =   0.85, R)
>droMoj3.scaffold_6496 8382362 111 + 26866924
-----ACGUACUUGAGAAGGGAUGCUGCACGUUUCUCCUCGAUGCUGCCAUCGAUGUUCGCUUUCUGGUCGACAAUCUGGCGCAGCACGUGCUGGCGCUUCUUGUUGUCGCUGGCG
-----..(((.(((((.((..(((.....)))..)).)))))))).((((.(((.....(((....)))((((((...((((((((....))).)))))..))))))))).)))). ( -38.80, z-score =  -0.58, R)
>droGri2.scaffold_15245 6109295 111 - 18325388
-----AAGAGGUUGAGGAACGAGGCAGCCUUCUUAUCCUUGAUCUGUUGCACAAAGUCAGCAUGCUGCUCGAUGCGACGACGUAUGUCCAGUUGCCGCUUCUUGCAGCCGCUGGCA
-----((.((((..((((..((((....))))...))))..)))).)).......((((((..(((((..((.(((.((((.........)))).))).))..))))).)))))). ( -43.60, z-score =  -2.02, R)
>consensus
_______AGUCUACUGA__AAGUUCAGUAAUUGGCUCUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCA
...............................((((((........)))))).....((((((..((((...........((((.((.....)).)))).....)))).)))))).. (-10.88 =  -9.97 +  -0.91)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,767,139 – 13,767,259
Length 120
Sequences 10
Columns 120
Reading direction forward
Mean pairwise identity 64.87
Shannon entropy 0.76906
G+C content 0.50743
Mean single sequence MFE -37.03
Consensus MFE -7.62
Energy contribution -6.39
Covariance contribution -1.23
Combinations/Pair 2.00
Mean z-score -2.06
Structure conservation index 0.21
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.719379
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13767139 120 + 21146708
CUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCAUAGUAGCUCCAAGUGGCACGGAAAACCGAAUCCCUAUUUG
.......((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).))))))((.((..(((....)))...))))..... ( -41.20, z-score =  -3.52, R)
>droAna3.scaffold_13337 4134857 120 + 23293914
UGCCCUUUGAAGCCAAGAGUCUAGCGUGUUGCUGGACUGUAUUGCGAAUGUUCGUCUGUCGCUCCCGGCAAUCGUUGGCAUAGUAGCUCCAGGAGGCCCGGAACAGGCCCUCCAUGUUGG
((((...(((.(((.(.((((((((.....)))))))).)...((((..(.....)..))))....)))..)))..))))...((((....(((((.((......)).)))))..)))). ( -39.60, z-score =  -0.31, R)
>droEre2.scaffold_4845 7994851 120 + 22589142
CCUUAUUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGCCCGUCAGUCGCUCCUGACAGCCGUUAGCAUAGUAGCUCCAUGUGGCCCGGAACAGCGAAUCCCUACUUG
.......((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).)))))).((((...(((........)))))))... ( -38.00, z-score =  -2.11, R)
>droYak2.chr2R 5723763 120 - 21139217
CUUUGCUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGCCCGUCAGUCGCUCCUGACAGCCGUUAGCAUAGUAGCUCCAAGUGGCCCGGAACACCGAGUCCCUGUUUG
....(((((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).)))))))))(((.(((....))).)))........ ( -45.60, z-score =  -3.82, R)
>droSec1.super_1 11262713 120 + 14215200
CUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCAUAGUAGCUCCAAGUGGCCCGGAAAACCGAAUCCCUAUUUG
.......((((((.((.((.((((((..(((((.(..(((.(((((......)).))).)))..).))))).)))))).)).)).))))))((.((..(((....)))...))))..... ( -41.20, z-score =  -3.77, R)
>droSim1.chr2R 12509019 120 + 19596830
CUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCAGUCAGUCGCUCUUGACAGCCGCUAGCAUAGUAGCUCCAAGUGGCCCGGAAAACCGAAUCCCUAUUGG
.......((((((.((.((.((((((..(((((.((.(((.((((........).))).)))))..))))).)))))).)).)).))))))((.((..(((....)))...))))..... ( -38.40, z-score =  -2.19, R)
>droWil1.scaffold_180745 2230520 113 + 2843958
UAUGGAAUGGAAUGACAUGGUCAAUGUUUUGCCAAAUGCCUUCACGUAUAUUACGCAAACGCGUUUUGCAAUCACUGGCAUAGUAACUCCAUGAGUCACGAAAGAAAGCAUCC-------
...((((((((...((...((((.((..((((.((((((.((..((((...))))..)).)))))).)))).)).))))...))...)))))......(....)......)))------- ( -27.20, z-score =  -0.87, R)
>droVir3.scaffold_12875 5200705 120 - 20611582
CUUCAAUAUUUUUCAAAAACUCGGCAUUCUGUUCGAUUCGUUGGAGUAUGUCCUGUUGUUGCCUCUUGUAGAUGUCGGCCAAGUAGCUCCAAUAGGCACAAAAUACUUCAUUAUUAUUUC
....................(((((.....).)))).....(((((((((((((((((..((..((((..(....)...))))..))..))))))).)))...))))))).......... ( -25.60, z-score =  -1.70, R)
>droMoj3.scaffold_6496 8382393 120 + 26866924
CCUCGAUGCUGCCAUCGAUGUUCGCUUUCUGGUCGACAAUCUGGCGCAGCACGUGCUGGCGCUUCUUGUUGUCGCUGGCGAAAUAGUUCCAAUACUCACAGAAAUCCUUGUUCAAAUUAU
..((((((....))))))..((((((....((.(((((((..((((((((....))).)))))....)))))))))))))))...................................... ( -33.50, z-score =  -0.92, R)
>droGri2.scaffold_15245 6109326 120 - 18325388
CCUUGAUCUGUUGCACAAAGUCAGCAUGCUGCUCGAUGCGACGACGUAUGUCCAGUUGCCGCUUCUUGCAGCCGCUGGCAAAGUAACUCCAAUAGGCCCGGAACAGUGAGUCCGUGUCAU
.........(((((.....((((((..(((((..((.(((.((((.........)))).))).))..))))).))))))...))))).......(((.((((........)))).))).. ( -40.00, z-score =  -1.35, R)
>consensus
CUUUAAUUGGAGCCACAAUUCUAGCGUUCUGUUCGAUGCGCCUGCGAAUGUCCGUCAGUCGCUCCUGACAGCCGCUAGCAUAGUAGCUCCAAGAGGCCCGGAAAACCGAAUCCCUAUUUG
....................((((((..((((...........((((.((.....)).)))).....)))).)))))).......................................... ( -7.62 =  -6.39 +  -1.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:46 2011