Locus 2713

Sequence ID	dm3.chr2L
Location	21,467,135 – 21,467,276
Length	141
Max. P	0.883039

overview

Window 1

Location	21,467,135 – 21,467,276
Length	141
Sequences	11
Columns	147
Reading direction	forward
Mean pairwise identity	62.04
Shannon entropy	0.82995
G+C content	0.29934
Mean single sequence MFE	-28.90
Consensus MFE	-4.82
Energy contribution	-5.36
Covariance contribution	0.55
Combinations/Pair	1.33
Mean z-score	-2.41
Structure conservation index	0.17
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.06
SVM RNA-class probability	0.883039
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21467135 141 + 23011544
CAAAAAGUAAAUUGUGAA-AAAGUGCAGUAUU-UGGUACAUGUUCGCAAUUAAAAUUUUAGAUUUAUGUUUUAUAGAUCUGAAAUUUGUUUA---AACAAGUCCUUUUCAGGGCUACAACGUUCCGUU-GCAAGAGAAAAAAACUUU
.........(((((((((-...((((......-..))))...))))))))).((((((((((((((((...))))))))))))))))((((.---....((((((....)))))).(((((...))))-)..........))))... ( -35.20, z-score =  -3.55, R)
>droSim1.chrU 1893125 141 - 15797150
CAAAAAGUAAAUUGUGAA-AAAGUACAGUAUU-UGGUACAUGUUCGCAAUCAAAAAUUUAGAUUUAUGAUUUAUAGAUCUGAAAUUUGUUUA---UACAAGUCCUUUUCAGGGCUACAACGUUCUUUU-GCAAGAGAAAAAAACUUU
......(((.((((((((-...((((......-..))))...))))))))((((..((((((((((((...)))))))))))).))))....---))).((((((....))))))......((((((.-...))))))......... ( -30.10, z-score =  -2.36, R)
>droSec1.super_91 82787 141 + 125313
CAAAAAGUAAAUUGUGAA-AAAGUACAGUAUU-UGGUACAUGUUCGCAAUCAAAACUUUAGAUUUAUGAUUUAUAGAUCUGAAAUUUGUUUA---UACAAGUCCUUUUCAGGGCUACAACGUUCUGUU-GCAAGAGAAAAAAACUUU
...(((((..((((((((-...((((......-..))))...))))))))......((((((((((((...))))))))))))((((((...---.)))))).(((((((((((......))))))..-..)))))......))))) ( -29.60, z-score =  -1.83, R)
>droYak2.chr2R_random 60105 133 - 67238
CAAGAAGUAAAUUGUGAA-AAAGUACAGUAGU-UAGUACAUGUUCGCAAUCAAAAUUUUAGAUU-------UCAACAUCUGAAAUUUGUUUA---AACAAGCCCUUUUCAGGGCUACAACGAUUCGUU-GCAAGAGAAAAAACUUU-
...(((((...(((((((-...((((......-..))))...)))))))((.(((((((((((.-------.....))))))))))).....---....((((((....)))))).(((((...))))-)...))......)))))- ( -32.50, z-score =  -3.43, R)
>droEre2.scaffold_4845 19565555 123 - 22589142
CAAGAAGUAAAUUGCGAA-AAAGUACAGUAGU-UGGUACAUGUUCGCAAUCAAAA----------------UAUAUAUCUGAAAUUUGUUUA---AACAAGCCCUUUUCAGGGCUACAACAUUCACUU-GCAAGAGAAAAAAAAU--
((((......((((((((-...((((......-..))))...)))))))).....----------------........((((..((((...---....((((((....))))))))))..)))))))-)...............-- ( -26.21, z-score =  -2.56, R)
>droAna3.scaffold_12943 4888478 135 - 5039921
GAAAAAAUAAAUUGUGAU-AAUGUGCAUUAAAAUUGCACACGUUUGCAAUCGAAAUUUUAGAUU-------UCGAAAUCUAAAAUUAAAUUA---AACAAGCCCUUUUCAGGACUACAAGA-UAUGUUUUAAAGAGAAAGAAAUUAU
..........((((..(.-..((((((.......))))))...)..))))...(((((((((((-------....)))))))))))......---........(((((.(((((.......-...))))).)))))........... ( -24.70, z-score =  -2.39, R)
>dp4.Unknown_singleton_1517 15533 135 + 24252
CAAAAAGUAAAGUGUGAA-ACAGUACACGUUG-GUGUACAAGGUCGCAUUCGAAAUUUUAGAUG-------UAUCCGUCUGAAAUUGAUUUA---AACAAGCCCUUUUCAGGGCUACAAAACUAUAUUCAAAAGAGAUACAAAUUAU
......(((.(((((((.-...((((((....-))))))....))))))).(((((((((((((-------....)))))))))))......---....((((((....))))))............))........)))....... ( -34.60, z-score =  -3.74, R)
>droPer1.super_0 3274818 135 + 11822988
CAAAAAGUAAAGUGUGAA-ACUGUACACGUUG-GUGUACAAGGUCGCAUUCGAAAUUUUAGAUG-------UAUCCGUCUGAAAUUGAUUUA---AACAAGCCCUUUUCAGGGCUACAAAACUAUAUUCAAAAGAGAUACAAAUUAU
......(((.(((((((.-..(((((((....-)))))))...))))))).(((((((((((((-------....)))))))))))......---....((((((....))))))............))........)))....... ( -36.30, z-score =  -4.06, R)
>droWil1.scaffold_181036 31085 135 + 110856
CAAGAAGUGAAUAAUUAAUACUUUAUUGCAAU----CGUAAUAUUGAA---AAAAUUUUAGAUAUCGAAUACGAAAAUCUAAAAUUUUACUU--AAACACAGCCAGGUCGGCGCGUUAAGUUUCAGCG-UUAAGCGUUAAGUUUU--
.((((..(((....(((((....((((((...----.))))))(((((---((((((((((((.(((....)))..))))))))))))((((--((.....(((.....)))...))))))))))).)-))))...)))..))))-- ( -26.60, z-score =  -1.36, R)
>droVir3.scaffold_13047 1628447 122 + 19223366
----GAAGAAAUAAUUUA-AAAUUGC--UAAC----UGCUUGUCAGCAUAUGCAAAUU-------------UCUAAUAAUGAAAUUUGUUUUCCUACAAAGCCCUUUUAAGGGCUACAAAUACGAUUUUCUAAGAGAAAGAAUUUU-
----...((((.......-....(((--(.((----.....)).))))...(((((((-------------((.......)))))))))))))......((((((....))))))..........(((((.....)))))......- ( -24.20, z-score =  -1.87, R)
>apiMel3.Group1 12264768 133 - 25854376
-AAUAUAUAAAAUAUUAG-AAAUUAAAGUAUU---UAGCGAAUUUACAUCAUUGAUCGUGACAUCGAAUGUUCCUCAUAUGAACUGCGCAAG---UCAAAGCACUGCAAAACACCGCGGAAAACAAUU----AGAAAAAUGAUUU--
-........(((((((..-.......))))))---)...........((((((..((.((((..((...((((.......))))..))...)---))).....((((........)))).........----.))..))))))..-- ( -17.90, z-score =   0.60, R)
>consensus
CAAAAAGUAAAUUGUGAA_AAAGUACAGUAUU_UGGUACAUGUUCGCAAUCAAAAUUUUAGAUU_______UAUACAUCUGAAAUUUGUUUA___AACAAGCCCUUUUCAGGGCUACAACAUUCUGUU_GCAAGAGAAAAAAAUUUU
...................................................................................................((((((....))))))................................ ( -4.82 =  -5.36 +   0.55)

alignment

secondary structure

dotplot

Window 2

Location	21,467,135 – 21,467,276
Length	141
Sequences	11
Columns	147
Reading direction	reverse
Mean pairwise identity	62.04
Shannon entropy	0.82995
G+C content	0.29934
Mean single sequence MFE	-27.77
Consensus MFE	-2.65
Energy contribution	-2.28
Covariance contribution	-0.37
Combinations/Pair	2.00
Mean z-score	-2.57
Structure conservation index	0.10
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.44
SVM RNA-class probability	0.695276
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21467135 141 - 23011544
AAAGUUUUUUUCUCUUGC-AACGGAACGUUGUAGCCCUGAAAAGGACUUGUU---UAAACAAAUUUCAGAUCUAUAAAACAUAAAUCUAAAAUUUUAAUUGCGAACAUGUACCA-AAUACUGCACUUU-UUCACAAUUUACUUUUUG
.(((((((((((..((((-((((...))))))))....)))))))))))...---.....((((((.((((.(((.....))).)))).)))))).(((((.(((..((((...-.....))))....-))).)))))......... ( -24.40, z-score =  -1.88, R)
>droSim1.chrU 1893125 141 + 15797150
AAAGUUUUUUUCUCUUGC-AAAAGAACGUUGUAGCCCUGAAAAGGACUUGUA---UAAACAAAUUUCAGAUCUAUAAAUCAUAAAUCUAAAUUUUUGAUUGCGAACAUGUACCA-AAUACUGUACUUU-UUCACAAUUUACUUUUUG
.(((((((((((..((((-((.......))))))....)))))))))))(((---.....((((((.((((.(((.....))).))))))))))..(((((.(((...((((..-......))))...-))).))))))))...... ( -23.00, z-score =  -1.34, R)
>droSec1.super_91 82787 141 - 125313
AAAGUUUUUUUCUCUUGC-AACAGAACGUUGUAGCCCUGAAAAGGACUUGUA---UAAACAAAUUUCAGAUCUAUAAAUCAUAAAUCUAAAGUUUUGAUUGCGAACAUGUACCA-AAUACUGUACUUU-UUCACAAUUUACUUUUUG
.(((((((((((..((((-(((.....)))))))....)))))))))))...---............((((.(((.....))).))))(((((...(((((.(((...((((..-......))))...-))).))))).)))))... ( -28.10, z-score =  -2.59, R)
>droYak2.chr2R_random 60105 133 + 67238
-AAAGUUUUUUCUCUUGC-AACGAAUCGUUGUAGCCCUGAAAAGGGCUUGUU---UAAACAAAUUUCAGAUGUUGA-------AAUCUAAAAUUUUGAUUGCGAACAUGUACUA-ACUACUGUACUUU-UUCACAAUUUACUUCUUG
-...((((...(...(((-((((...)))))))(((((....)))))..)..---.))))((((((.((((.....-------.)))).)))))).(((((.(((...((((..-......))))...-))).)))))......... ( -31.40, z-score =  -3.51, R)
>droEre2.scaffold_4845 19565555 123 + 22589142
--AUUUUUUUUCUCUUGC-AAGUGAAUGUUGUAGCCCUGAAAAGGGCUUGUU---UAAACAAAUUUCAGAUAUAUA----------------UUUUGAUUGCGAACAUGUACCA-ACUACUGUACUUU-UUCGCAAUUUACUUCUUG
--................-(((((((((((..((((((....))))))....---..))))....(((((......----------------.)))))(((((((...((((..-......))))...-)))))))))))))).... ( -30.40, z-score =  -3.92, R)
>droAna3.scaffold_12943 4888478 135 + 5039921
AUAAUUUCUUUCUCUUUAAAACAUA-UCUUGUAGUCCUGAAAAGGGCUUGUU---UAAUUUAAUUUUAGAUUUCGA-------AAUCUAAAAUUUCGAUUGCAAACGUGUGCAAUUUUAAUGCACAUU-AUCACAAUUUAUUUUUUC
.................((((.(((-..((((.(((((....)))))((((.---......(((((((((((....-------)))))))))))......))))..(((((((.......))))))).-...))))..))).)))). ( -28.02, z-score =  -3.79, R)
>dp4.Unknown_singleton_1517 15533 135 - 24252
AUAAUUUGUAUCUCUUUUGAAUAUAGUUUUGUAGCCCUGAAAAGGGCUUGUU---UAAAUCAAUUUCAGACGGAUA-------CAUCUAAAAUUUCGAAUGCGACCUUGUACAC-CAACGUGUACUGU-UUCACACUUUACUUUUUG
......(((((((..((((((....((((...((((((....))))))....---.))))....)))))).)))))-------))..............((.((....((((((-....))))))...-.)).))............ ( -31.70, z-score =  -3.24, R)
>droPer1.super_0 3274818 135 - 11822988
AUAAUUUGUAUCUCUUUUGAAUAUAGUUUUGUAGCCCUGAAAAGGGCUUGUU---UAAAUCAAUUUCAGACGGAUA-------CAUCUAAAAUUUCGAAUGCGACCUUGUACAC-CAACGUGUACAGU-UUCACACUUUACUUUUUG
......(((((((..((((((....((((...((((((....))))))....---.))))....)))))).)))))-------))..............((.((..((((((((-....)))))))).-.)).))............ ( -34.50, z-score =  -4.02, R)
>droWil1.scaffold_181036 31085 135 - 110856
--AAAACUUAACGCUUAA-CGCUGAAACUUAACGCGCCGACCUGGCUGUGUUU--AAGUAAAAUUUUAGAUUUUCGUAUUCGAUAUCUAAAAUUUU---UUCAAUAUUACG----AUUGCAAUAAAGUAUUAAUUAUUCACUUCUUG
--.....((((..(((..-.((....((((((((((((.....))).))).))--))))((((((((((((..(((....))).))))))))))))---............----...))....)))..)))).............. ( -26.40, z-score =  -2.35, R)
>droVir3.scaffold_13047 1628447 122 - 19223366
-AAAAUUCUUUCUCUUAGAAAAUCGUAUUUGUAGCCCUUAAAAGGGCUUUGUAGGAAAACAAAUUUCAUUAUUAGA-------------AAUUUGCAUAUGCUGACAAGCA----GUUA--GCAAUUU-UAAAUUAUUUCUUC----
-...............(((((.((.(((....((((((....))))))..))).))...((((((((.......))-------------))))))....(((((((.....----))))--)))....-.......)))))..---- ( -28.60, z-score =  -2.95, R)
>apiMel3.Group1 12264768 133 + 25854376
--AAAUCAUUUUUCU----AAUUGUUUUCCGCGGUGUUUUGCAGUGCUUUGA---CUUGCGCAGUUCAUAUGAGGAACAUUCGAUGUCACGAUCAAUGAUGUAAAUUCGCUA---AAUACUUUAAUUU-CUAAUAUUUUAUAUAUU-
--.............----...(((((...((((...((((((((((.....---...))))...((((.((((..((((...))))..)..))))))))))))).)))).)---)))).........-.................- ( -19.00, z-score =   1.27, R)
>consensus
AAAAUUUUUUUCUCUUGC_AACAGAAUGUUGUAGCCCUGAAAAGGGCUUGUU___UAAACAAAUUUCAGAUGUAUA_______AAUCUAAAAUUUUGAUUGCGAACAUGUACCA_AAUACUGUACUUU_UUCACAAUUUACUUUUUG
................................((.(((....))).))................................................................................................... ( -2.65 =  -2.28 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:24 2011