Locus 253

Sequence ID	dm3.chr2L
Location	1,831,670 – 1,831,778
Length	108
Max. P	0.995560

overview

Window 3

Location	1,831,670 – 1,831,778
Length	108
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	66.34
Shannon entropy	0.61341
G+C content	0.32389
Mean single sequence MFE	-22.51
Consensus MFE	-8.62
Energy contribution	-9.27
Covariance contribution	0.64
Combinations/Pair	1.33
Mean z-score	-1.79
Structure conservation index	0.38
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.95
SVM RNA-class probability	0.860979
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1831670 108 + 23011544
-AAACGCAUUUUUAGUCCGUGGUUGCACUGAAUA-UCCCCUUCAGUUAGCUUGG-----AAGUAAAUUACUAGUUUCUGUGAAUAAUAU-UUUAUUGCCAAGCUAAGAAAACGGGA
-..............(((((..((..((((((..-.....))))))((((((((-----.((((((((((........)))).......-)))))).)))))))).))..))))). ( -25.61, z-score =  -1.63, R)
>droWil1.scaffold_180708 721781 113 - 12563649
-AAAACGAGUUUAUAAUGUUAAUUG--AUUAAUUGUUUCCUUUUAUUAACUAAUGUACCAAAAAAGUAAUUAAAUACAACGGACCCUUCAUUCCUCGUUAAACUAACGCAACUAAA
-..((((((........(((..(((--.(((((((....(((((....((....)).....))))))))))))...)))..))).........))))))................. (  -9.63, z-score =   0.73, R)
>droEre2.scaffold_4929 1878584 94 + 26641161
--------------AAAUGCAUUUGCAGUGAAUA-UCCCCUUUAGUUGGCUUGG-----AAUUAAAUUACUAGUU-CGAUGAAUAAUAU-UUUAUUGCCAAGCUAAGAAAAUGGGA
--------------...(((....))).......-((((.(((..(((((((((-----(((((......)))))-(((((((......-))))))))))))))))..))).)))) ( -24.70, z-score =  -2.82, R)
>droYak2.chr2L 1804987 96 + 22324452
--------------AAACCCAUUUGUUGUAGAAUAUCCACUUCAGUUAGCUUGG-----AAGUAAAUUACUAGUUUCAAUCAACAAUAU-UUUAUUGCCAAGCUAACAAAAUGGGA
--------------...(((((((......(((.......))).((((((((((-----.((((((.((...(((......)))..)).-)))))).)))))))))).))))))). ( -27.80, z-score =  -4.70, R)
>droSec1.super_14 1778365 109 + 2068291
AAAAAGCAUUUUUAGUCCGUGGUUGCACUGAAUA-UCCCCUUCAGUUAGCUUGG-----AAGUAAGUUACUAGUUUCUGUGAAUAAUAU-UUUAUUGCCAAGCAAAGAAAACGGGA
...............(((((..((..((((((..-.....))))))..((((((-----.((((((((((........)))).......-)))))).))))))...))..))))). ( -23.31, z-score =  -0.79, R)
>droSim1.chr2L 1818710 110 + 22036055
AAAAAGCAUUUUUAGUCCGAUGUUGCACUGAAUAAUUCCCUUCAGUUAGCUUGG-----AAGUAAAUUACUAGUUUCUGUGAAUAAUAU-UUUAUUGCCAAGCUAAGAAAACGGGA
...............((((.......((((((........))))))((((((((-----.((((((((((........)))).......-)))))).))))))))......)))). ( -24.01, z-score =  -1.51, R)
>consensus
_AAAAGCAUUUUUAAACCGUAGUUGCACUGAAUA_UCCCCUUCAGUUAGCUUGG_____AAGUAAAUUACUAGUUUCUAUGAAUAAUAU_UUUAUUGCCAAGCUAAGAAAACGGGA
...................................((((......(((((((((......(((.....)))..........(((((.....))))).)))))))))......)))) ( -8.62 =  -9.27 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	1,831,670 – 1,831,778
Length	108
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	66.34
Shannon entropy	0.61341
G+C content	0.32389
Mean single sequence MFE	-22.38
Consensus MFE	-11.66
Energy contribution	-11.87
Covariance contribution	0.20
Combinations/Pair	1.41
Mean z-score	-2.10
Structure conservation index	0.52
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.82
SVM RNA-class probability	0.995560
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1831670 108 - 23011544
UCCCGUUUUCUUAGCUUGGCAAUAAA-AUAUUAUUCACAGAAACUAGUAAUUUACUU-----CCAAGCUAACUGAAGGGGA-UAUUCAGUGCAACCACGGACUAAAAAUGCGUUU-
((((.(((..(((((((((...((((-.((((((((...)))..))))).))))...-----)))))))))..))).))))-.....(((.(......).)))............- ( -25.80, z-score =  -2.58, R)
>droWil1.scaffold_180708 721781 113 + 12563649
UUUAGUUGCGUUAGUUUAACGAGGAAUGAAGGGUCCGUUGUAUUUAAUUACUUUUUUGGUACAUUAGUUAAUAAAAGGAAACAAUUAAU--CAAUUAACAUUAUAAACUCGUUUU-
.(((((((.(((((((((((..(((........)))..(((((..((.......))..)))))...))))......(....))))))))--))))))).................- ( -15.60, z-score =   0.45, R)
>droEre2.scaffold_4929 1878584 94 - 26641161
UCCCAUUUUCUUAGCUUGGCAAUAAA-AUAUUAUUCAUCG-AACUAGUAAUUUAAUU-----CCAAGCCAACUAAAGGGGA-UAUUCACUGCAAAUGCAUUU--------------
((((.(((..((.((((((...((((-.((((((((...)-)).))))).))))...-----)))))).))..))).))))-.......(((....)))...-------------- ( -19.90, z-score =  -2.69, R)
>droYak2.chr2L 1804987 96 - 22324452
UCCCAUUUUGUUAGCUUGGCAAUAAA-AUAUUGUUGAUUGAAACUAGUAAUUUACUU-----CCAAGCUAACUGAAGUGGAUAUUCUACAACAAAUGGGUUU--------------
.(((((((.((((((((((...((((-.(((((((......))).)))).))))...-----))))))))))....((((.....))))...)))))))...-------------- ( -30.20, z-score =  -4.97, R)
>droSec1.super_14 1778365 109 - 2068291
UCCCGUUUUCUUUGCUUGGCAAUAAA-AUAUUAUUCACAGAAACUAGUAACUUACUU-----CCAAGCUAACUGAAGGGGA-UAUUCAGUGCAACCACGGACUAAAAAUGCUUUUU
((((.(((..((.((((((...(((.-.((((((((...)))..)))))..)))...-----)))))).))..))).))))-.....(((.(......).)))............. ( -19.50, z-score =  -0.59, R)
>droSim1.chr2L 1818710 110 - 22036055
UCCCGUUUUCUUAGCUUGGCAAUAAA-AUAUUAUUCACAGAAACUAGUAAUUUACUU-----CCAAGCUAACUGAAGGGAAUUAUUCAGUGCAACAUCGGACUAAAAAUGCUUUUU
((((.(((..(((((((((...((((-.((((((((...)))..))))).))))...-----)))))))))..))))))).......(((.(......).)))............. ( -23.30, z-score =  -2.25, R)
>consensus
UCCCGUUUUCUUAGCUUGGCAAUAAA_AUAUUAUUCACAGAAACUAGUAAUUUACUU_____CCAAGCUAACUGAAGGGGA_UAUUCAGUGCAACUACGGACUAAAAAUGCUUUU_
((((.(((..(((((((((..........((((((..........))))))...........)))))))))..))).))))................................... (-11.66 = -11.87 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:09:26 2011