Locus 9227

Sequence ID	dm3.chr3R
Location	5,014,246 – 5,014,390
Length	144
Max. P	0.954479

overview

Window 5

Location	5,014,246 – 5,014,390
Length	144
Sequences	8
Columns	163
Reading direction	forward
Mean pairwise identity	60.50
Shannon entropy	0.78227
G+C content	0.36093
Mean single sequence MFE	-34.93
Consensus MFE	-9.68
Energy contribution	-9.58
Covariance contribution	-0.11
Combinations/Pair	1.38
Mean z-score	-2.10
Structure conservation index	0.28
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.61
SVM RNA-class probability	0.954479
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5014246 144 + 27905053
------AGUUGCAGCU-GUAUAAAGCCAGACACUUUAUGAUGUCGAUAAAUCAGCUGCAGGUAAUACCACGAUUCC-ACAAAGG-AAAAGUGUG----GGAACUUAUAAAAGACAUAAUUUUACU----GUCAUUCAAUCAAAUUGUAAUAAUUGUCAAAU--
------(.((((((((-(..........(((((.....).)))).......))))))))).)....(((((.((((-.....))-))...))))----)............((((.....((((.----................))))....))))....-- ( -32.56, z-score =  -1.96, R)
>droSim1.chr3R 11219686 145 - 27517382
------AGUUGCAGCU-GGAUAAAGCCAGACACUUUAUGAUGUCGAUAAAUCAGCUGCAGGUAAUACCACGAUUCC-ACAAAGGGAAAAGUGUG----GGAAAUUAUCAUAGACAUACAUUUAUU----UUCAUUCAAUCAAAUUGAAAUAAUUGUCAAAU--
------...(((((((-((.........(((((.....).))))......)))))))))((((((.(((((.((((-......))))...))))----)...))))))...((((.....(((((----((.(((......))).))))))).))))....-- ( -37.26, z-score =  -3.23, R)
>droSec1.super_0 4252801 145 - 21120651
------AGUUGCAGCU-GGAUAAAGCCAGACACUUUAUGAUGUCGAUAAAUCAGCUGCAGGUAAUACCACGAUUUC-ACAAAGGGAAAAGUGUG----GGAAAUUAUCAGAGACACACAUUUAUU----UUCAUUCAAUCAAAUUGAAAUAAUUGUCAAAU--
------...(((((((-((.........(((((.....).))))......)))))))))((((((.(((((.((((-......))))...))))----)...))))))...((((.....(((((----((.(((......))).))))))).))))....-- ( -33.66, z-score =  -2.10, R)
>droYak2.chr3R 9063382 125 + 28832112
------AGUUGCAGCA-GGUUAAAGCCAGACACUUUAUGAUGUCGAUAAAUCAGCUGCAGGUAAUACU--GAUUCC-ACAAAGGGAGAGG----------------------ACAUACAGCAAUU----UUCAUUUAAUCAAUGCAACAUAAUUGUCAUAU--
------.((((((...-(((((((....(((((.....).)))).........(((((((......))--).((((-......))))...----------------------.....))))....----....)))))))..)))))).............-- ( -28.20, z-score =  -1.71, R)
>droEre2.scaffold_4770 1159364 146 - 17746568
------AGUUGCAGCA-GGAUAAAGCCAGACAUUUUAUGAUGUCGAUAAAUCAGCUGCAGGUAAUACC--GAAUCC-ACAAAGGAAAAAGUAAGUGCUAGAAAUUAUCA-AGACAUACAUUUAUU----UUCAUUCAAUCAGUUUGAAAUAAUUGUCGAAU--
------...((((((.-((......)).((((((....)))))).........))))))((((((...--...(((-.....)))...(((....)))....)))))).-.((((.....(((((----(.((..(.....)..)))))))).))))....-- ( -30.70, z-score =  -2.04, R)
>droAna3.scaffold_13340 9172340 145 - 23697760
-------AGUGCAGCA-GUAUUAAGCCAGACACUUUAUGAUAUCGGUAUAUCAGCUUUGGGCAGCAAAACAAACAG-CCACCCUGUAUACCCGUUC---ACGUUUAAAUAAUUUCCAAAUUUAAU----AUUACAAAAAUUCACUUCAAAGUGUAUCAUAU--
-------(((((.((.-.......))..).)))).(((((((..((((((.(((.....(((.............)-))...))))))))).....---..........................----............((((....))))))))))).-- ( -22.02, z-score =  -0.21, R)
>dp4.chr2 6488040 160 - 30794189
UGUGGGGGAUGCAGGAUACAGGAUGCCAGACAUUUUACGAUGUCGAUAAAUCCUGUGCAUUAUCGAUUUUGAAUCCUGUAUCGAUGCAAGCGGCCCAGAAAACUCCUAAUAGAAAAUUACUUACU--UAGCCCUUGCGAGCAA-GUAAAAAUCCACCUUGAAA
.(((((.(((((((((((((((((....((((((....)))))).....)))))))......(((....)))))))))))))..((((((.(((..((.........................))--..))))))))).....-.......)))))....... ( -46.91, z-score =  -2.99, R)
>droPer1.super_3 299867 163 - 7375914
UGUGGGGGUUGCAGGAUGCAGGAUGCCAGACAUUUUACGAUGUCGAUAAAUCCUGUGCAUUAUCGAUUUUGAUUCCUGUAUCGAUGCAAGCGGCCCAUAAAACUCCUAAUAGAAAAUUACUUAAUGGCGGCUAUCGAGAAUAAUGUGAAAAAACCCCUAGAAA
(.((((((((((((((.(((((((....((((((....)))))).....))))))).....((((....)))))))))).(((((...(((.(((..............................))).))))))))..............)))))))).).. ( -48.11, z-score =  -2.60, R)
>consensus
______AGUUGCAGCA_GGAUAAAGCCAGACACUUUAUGAUGUCGAUAAAUCAGCUGCAGGUAAUACCACGAUUCC_ACAAAGGGAAAAGUGGG____AGAAAUUAUAAUAGACAUACAUUUAUU____UUCAUUCAAUCAAAUUGAAAUAAUUGUCAAAU__
........(((((((.............((((........))))((....)).)))))))....................................................................................................... ( -9.68 =  -9.58 +  -0.11)

alignment

secondary structure

dotplot

Window 6

Location	5,014,246 – 5,014,390
Length	144
Sequences	8
Columns	163
Reading direction	reverse
Mean pairwise identity	60.50
Shannon entropy	0.78227
G+C content	0.36093
Mean single sequence MFE	-34.06
Consensus MFE	-9.19
Energy contribution	-9.85
Covariance contribution	0.66
Combinations/Pair	1.15
Mean z-score	-1.69
Structure conservation index	0.27
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.64
SVM RNA-class probability	0.769874
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5014246 144 - 27905053
--AUUUGACAAUUAUUACAAUUUGAUUGAAUGAC----AGUAAAAUUAUGUCUUUUAUAAGUUCC----CACACUUUU-CCUUUGU-GGAAUCGUGGUAUUACCUGCAGCUGAUUUAUCGACAUCAUAAAGUGUCUGGCUUUAUAC-AGCUGCAACU------
--......((((((........))))))...(((----(.........))))............(----(((....((-((.....-))))..)))).......((((((((.......(....)(((((((.....))))))).)-)))))))...------ ( -31.80, z-score =  -1.72, R)
>droSim1.chr3R 11219686 145 + 27517382
--AUUUGACAAUUAUUUCAAUUUGAUUGAAUGAA----AAUAAAUGUAUGUCUAUGAUAAUUUCC----CACACUUUUCCCUUUGU-GGAAUCGUGGUAUUACCUGCAGCUGAUUUAUCGACAUCAUAAAGUGUCUGGCUUUAUCC-AGCUGCAACU------
--......((((((........))))))......----.......(((...(((((((......(----((((..........)))-)).)))))))...))).((((((((((...(((((((......))))).))....)).)-)))))))...------ ( -30.90, z-score =  -1.52, R)
>droSec1.super_0 4252801 145 + 21120651
--AUUUGACAAUUAUUUCAAUUUGAUUGAAUGAA----AAUAAAUGUGUGUCUCUGAUAAUUUCC----CACACUUUUCCCUUUGU-GAAAUCGUGGUAUUACCUGCAGCUGAUUUAUCGACAUCAUAAAGUGUCUGGCUUUAUCC-AGCUGCAACU------
--((((.((((((((((..((((....))))..)----)))))..(((((...............----)))))........))))-.))))...((.....))((((((((((...(((((((......))))).))....)).)-)))))))...------ ( -28.26, z-score =  -0.97, R)
>droYak2.chr3R 9063382 125 - 28832112
--AUAUGACAAUUAUGUUGCAUUGAUUAAAUGAA----AAUUGCUGUAUGU----------------------CCUCUCCCUUUGU-GGAAUC--AGUAUUACCUGCAGCUGAUUUAUCGACAUCAUAAAGUGUCUGGCUUUAACC-UGCUGCAACU------
--....((((....)))).((((.....))))..----...(((((....(----------------------((.(.......).-)))..)--)))).....((((((.........(((((......))))).((......))-.))))))...------ ( -24.80, z-score =  -0.74, R)
>droEre2.scaffold_4770 1159364 146 + 17746568
--AUUCGACAAUUAUUUCAAACUGAUUGAAUGAA----AAUAAAUGUAUGUCU-UGAUAAUUUCUAGCACUUACUUUUUCCUUUGU-GGAUUC--GGUAUUACCUGCAGCUGAUUUAUCGACAUCAUAAAAUGUCUGGCUUUAUCC-UGCUGCAACU------
--..((.((((....(((((.....))))).(((----((.....(((.((((-.((.....)).)).)).))).)))))..))))-.))...--((.....))((((((.(((...(((((((......))))).))....))).-.))))))...------ ( -26.70, z-score =  -1.14, R)
>droAna3.scaffold_13340 9172340 145 + 23697760
--AUAUGAUACACUUUGAAGUGAAUUUUUGUAAU----AUUAAAUUUGGAAAUUAUUUAAACGU---GAACGGGUAUACAGGGUGG-CUGUUUGUUUUGCUGCCCAAAGCUGAUAUACCGAUAUCAUAAAGUGUCUGGCUUAAUAC-UGCUGCACU-------
--.((((((((((((((((...(((((..(....----........)..))))).)))))).))---)....(((((((((((..(-(..........))..))).....)).))))))..))))))).(((((..(((.......-.))))))))------- ( -36.30, z-score =  -1.99, R)
>dp4.chr2 6488040 160 + 30794189
UUUCAAGGUGGAUUUUUAC-UUGCUCGCAAGGGCUA--AGUAAGUAAUUUUCUAUUAGGAGUUUUCUGGGCCGCUUGCAUCGAUACAGGAUUCAAAAUCGAUAAUGCACAGGAUUUAUCGACAUCGUAAAAUGUCUGGCAUCCUGUAUCCUGCAUCCCCCACA
.(((..((((((..(((((-((((((....)))).)--))))))......))))))..))).....((((.....((((..(((((((((((((.....(((((..........)))))(((((......)))))))).)))))))))).))))...)))).. ( -50.00, z-score =  -3.19, R)
>droPer1.super_3 299867 163 + 7375914
UUUCUAGGGGUUUUUUCACAUUAUUCUCGAUAGCCGCCAUUAAGUAAUUUUCUAUUAGGAGUUUUAUGGGCCGCUUGCAUCGAUACAGGAAUCAAAAUCGAUAAUGCACAGGAUUUAUCGACAUCGUAAAAUGUCUGGCAUCCUGCAUCCUGCAACCCCCACA
......((((((..............((((((((.(((.....((((..((((....))))..)))).))).)))...)))))..((((((((......)))......((((((.(...(((((......)))))..).))))))..))))).)))))).... ( -43.70, z-score =  -2.24, R)
>consensus
__AUUUGACAAUUAUUUCAAUUUGAUUGAAUGAA____AAUAAAUGUAUGUCUAUUAUAAGUUCC____CACACUUUUCCCUUUGU_GGAAUCGUGGUAUUACCUGCAGCUGAUUUAUCGACAUCAUAAAGUGUCUGGCUUUAUCC_UGCUGCAACU______
........................................................................................................((((((.((....))(((((......))))).............))))))......... ( -9.19 =  -9.85 +   0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:00:16 2011