Locus 1313

Sequence ID dm3.chr2L
Location 10,109,327 – 10,109,476
Length 149
Max. P 0.998390
window1793 window1794 window1795 window1796

overview

Window 3

Location 10,109,327 – 10,109,417
Length 90
Sequences 9
Columns 97
Reading direction forward
Mean pairwise identity 74.77
Shannon entropy 0.49686
G+C content 0.42064
Mean single sequence MFE -22.82
Consensus MFE -15.61
Energy contribution -15.47
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -1.92
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989567
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10109327 90 + 23011544
-AGAGACUGGAUUCAGGAUUCAGGAAUCCAGGUGUCUUG--CCGGCUGU-UGACACCUGCGUCGU---GUACUUCAAUUAAAUUUUAAUUGAAAUGA
-...(((.((((((.........))))))(((((((..(--(.....))-.)))))))..)))..---....((((((((.....)))))))).... ( -25.40, z-score =  -1.56, R)
>droSim1.chr2L 9900501 82 + 22036055
---------GAGACUGGAUUCAGGAUUCCAGGUGUCUUG--CCGGCUGU-UGACACCUGCGUCGU---GUACUUCAAUUAAAUUUUAAUUGAAAUGA
---------...........((.(((..((((((((..(--(.....))-.)))))))).))).)---)...((((((((.....)))))))).... ( -21.70, z-score =  -1.40, R)
>droSec1.super_3 5547139 82 + 7220098
---------GAGACUGGAUUCAGGAUUCCAGGUGUCUUG--CCGGCUGU-UGACACCUGCGUCGU---GUACUUCAAUUAAAUUUUAAUUGAAAUGA
---------...........((.(((..((((((((..(--(.....))-.)))))))).))).)---)...((((((((.....)))))))).... ( -21.70, z-score =  -1.40, R)
>droYak2.chr2L 12793282 91 + 22324452
AGGAGGCAGGAUUCAGGAUUCAGAAUUCCAGGUGUCUUG--CCGACUGU-UGACACCUGCGUCGU---GUACUUCAAUUAAAUUUUAAUUGAAAUGA
((..((((((((.(.(((........)))..).))))))--))..))..-.(((......)))..---....((((((((.....)))))))).... ( -24.90, z-score =  -1.34, R)
>droEre2.scaffold_4929 10724585 91 + 26641161
GAGACCGGGGAUUCAGGAUUCAGGAUUCCAGGUGUCUUG--CCGGCUGU-UGACACCUGCGUCGU---GUACUUCAAUUAAAUUUUAAUUGAAAUGA
..((((.(((((((........)))))))(((((((..(--(.....))-.)))))))).)))..---....((((((((.....)))))))).... ( -25.90, z-score =  -1.06, R)
>droAna3.scaffold_12916 13942510 68 + 16180835
-----------------------GUUUCCAGGUGUCUUG--CCGGCUGU-UGACAUCUGCGUCGU---GUACUUCAAUUAAAUUUUAAUUGAAAUGA
-----------------------.....((((((((..(--(.....))-.))))))))......---....((((((((.....)))))))).... ( -14.90, z-score =  -1.44, R)
>dp4.chr4_group3 11609438 75 - 11692001
----------GCCAUGUACACCCGUGGCCAGGUGUCUUG--C-GGCUGU-UGACAUCUGC--------GUACUUCAAUUAAAAUUUAAUUGAAAUAC
----------((((((......))))))((((((((..(--(-....))-.)))))))).--------(((.((((((((.....)))))))).))) ( -24.90, z-score =  -3.57, R)
>droPer1.super_1 8726356 75 - 10282868
----------GCCAUGUACACCCGUGGCCAGGUGUCUUG--C-GGCUGU-UGACAUCUGC--------GUACUUCAAUUAAAAUUUAAUUGAAAUAC
----------((((((......))))))((((((((..(--(-....))-.)))))))).--------(((.((((((((.....)))))))).))) ( -24.90, z-score =  -3.57, R)
>droWil1.scaffold_181132 86985 85 + 1035393
----------GUCACACAUACUGAGA--CAGGUGUCUUUGCCUAGUUGUAUGACAUCUGCAUCGUCAUGUACCUCAAUUAAAUUUUAAUUGAAAUGA
----------.....((((..(((..--((((((((..(((......))).))))))))..)))..))))...(((((((.....)))))))..... ( -21.10, z-score =  -1.92, R)
>consensus
_________GAUCCUGGAUUCAGGAUUCCAGGUGUCUUG__CCGGCUGU_UGACACCUGCGUCGU___GUACUUCAAUUAAAUUUUAAUUGAAAUGA
............................((((((((...............)))))))).............((((((((.....)))))))).... (-15.61 = -15.47 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,109,327 – 10,109,417
Length 90
Sequences 9
Columns 97
Reading direction reverse
Mean pairwise identity 74.77
Shannon entropy 0.49686
G+C content 0.42064
Mean single sequence MFE -22.59
Consensus MFE -12.55
Energy contribution -12.45
Covariance contribution -0.10
Combinations/Pair 1.06
Mean z-score -2.91
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.34
SVM RNA-class probability 0.998390
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10109327 90 - 23011544
UCAUUUCAAUUAAAAUUUAAUUGAAGUAC---ACGACGCAGGUGUCA-ACAGCCGG--CAAGACACCUGGAUUCCUGAAUCCUGAAUCCAGUCUCU-
..((((((((((.....))))))))))..---..(((..(((((((.-........--...)))))))((((((..(....).)))))).)))...- ( -26.20, z-score =  -3.55, R)
>droSim1.chr2L 9900501 82 - 22036055
UCAUUUCAAUUAAAAUUUAAUUGAAGUAC---ACGACGCAGGUGUCA-ACAGCCGG--CAAGACACCUGGAAUCCUGAAUCCAGUCUC---------
..((((((((((.....))))))))))..---..(((..(((((((.-........--...)))))))(((........))).)))..--------- ( -21.90, z-score =  -2.99, R)
>droSec1.super_3 5547139 82 - 7220098
UCAUUUCAAUUAAAAUUUAAUUGAAGUAC---ACGACGCAGGUGUCA-ACAGCCGG--CAAGACACCUGGAAUCCUGAAUCCAGUCUC---------
..((((((((((.....))))))))))..---..(((..(((((((.-........--...)))))))(((........))).)))..--------- ( -21.90, z-score =  -2.99, R)
>droYak2.chr2L 12793282 91 - 22324452
UCAUUUCAAUUAAAAUUUAAUUGAAGUAC---ACGACGCAGGUGUCA-ACAGUCGG--CAAGACACCUGGAAUUCUGAAUCCUGAAUCCUGCCUCCU
..((((((((((.....))))))))))..---..((.(((((..(((-...(((..--...)))....(((........))))))..))))).)).. ( -23.40, z-score =  -2.57, R)
>droEre2.scaffold_4929 10724585 91 - 26641161
UCAUUUCAAUUAAAAUUUAAUUGAAGUAC---ACGACGCAGGUGUCA-ACAGCCGG--CAAGACACCUGGAAUCCUGAAUCCUGAAUCCCCGGUCUC
..((((((((((.....))))))))))..---..(((..(((((((.-........--...)))))))(((.((..(....).)).)))...))).. ( -21.40, z-score =  -1.46, R)
>droAna3.scaffold_12916 13942510 68 - 16180835
UCAUUUCAAUUAAAAUUUAAUUGAAGUAC---ACGACGCAGAUGUCA-ACAGCCGG--CAAGACACCUGGAAAC-----------------------
..((((((((((.....))))))))))..---......(((.((((.-........--...)))).))).....----------------------- ( -12.90, z-score =  -1.94, R)
>dp4.chr4_group3 11609438 75 + 11692001
GUAUUUCAAUUAAAUUUUAAUUGAAGUAC--------GCAGAUGUCA-ACAGCC-G--CAAGACACCUGGCCACGGGUGUACAUGGC----------
((((((((((((.....))))))))))))--------..........-...(((-(--....(((((((....)))))))...))))---------- ( -26.90, z-score =  -4.34, R)
>droPer1.super_1 8726356 75 + 10282868
GUAUUUCAAUUAAAUUUUAAUUGAAGUAC--------GCAGAUGUCA-ACAGCC-G--CAAGACACCUGGCCACGGGUGUACAUGGC----------
((((((((((((.....))))))))))))--------..........-...(((-(--....(((((((....)))))))...))))---------- ( -26.90, z-score =  -4.34, R)
>droWil1.scaffold_181132 86985 85 - 1035393
UCAUUUCAAUUAAAAUUUAAUUGAGGUACAUGACGAUGCAGAUGUCAUACAACUAGGCAAAGACACCUG--UCUCAGUAUGUGUGAC----------
..((((((((((.....))))))))))................((((((((((((((((........))--))).))).))))))))---------- ( -21.80, z-score =  -2.07, R)
>consensus
UCAUUUCAAUUAAAAUUUAAUUGAAGUAC___ACGACGCAGGUGUCA_ACAGCCGG__CAAGACACCUGGAAUCCUGAAUCCAGAAUC_________
..((((((((((.....))))))))))...........(((.((((...............)))).)))............................ (-12.55 = -12.45 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,109,380 – 10,109,476
Length 96
Sequences 8
Columns 106
Reading direction forward
Mean pairwise identity 75.12
Shannon entropy 0.45644
G+C content 0.34993
Mean single sequence MFE -19.34
Consensus MFE -8.12
Energy contribution -7.78
Covariance contribution -0.34
Combinations/Pair 1.31
Mean z-score -2.66
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.60
SVM RNA-class probability 0.953854
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10109380 96 + 23011544
UGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUAU---AUUCGUGUGCG-------AACACAUGCUAGUGUGCAUCUUUUUUGUCGCCUCCUUUCUUUGU
.((((((..(((((((((((.....))))))))..(((...---.))))))..))-------).(((((....)))))............)))............. ( -19.90, z-score =  -1.91, R)
>droSim1.chr2L 9900546 96 + 22036055
UGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUAU---AUUCGUGUGCG-------AACACAUGCUAGUGUGCAUCUUUUUUGUCGCCUCCUUCCUUUGU
.((((((..(((((((((((.....))))))))..(((...---.))))))..))-------).(((((....)))))............)))............. ( -19.90, z-score =  -2.08, R)
>droSec1.super_3 5547184 96 + 7220098
UGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAAAU---AUUCGUGUGCG-------AACACAUGCUAGUGUGCAUCUUUUUUGUCGCCUCCUUCCUUUGU
.((((((..(((((((((((.....))))))))..(((...---.))))))..))-------).(((((....)))))............)))............. ( -19.90, z-score =  -2.11, R)
>droYak2.chr2L 12793336 96 + 22324452
UGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUAU---AUUCGUGUGCG-------CACACAUGCUAGUGUGCAUCUUUUUUGUCGCCUCCAUCCUUUGU
.(((.((.((((((((((((.....))))))))(((((...---.)))))))))(-------(((((......))))))........)).)))............. ( -24.50, z-score =  -3.23, R)
>droEre2.scaffold_4929 10724639 96 + 26641161
UGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUAU---AUUCGUGUGCG-------AACACAUGCUAGUGUGCAUCUUUUUUGUCGCCUCCUUCCUUUGU
.((((((..(((((((((((.....))))))))..(((...---.))))))..))-------).(((((....)))))............)))............. ( -19.90, z-score =  -2.08, R)
>droAna3.scaffold_12916 13942541 104 + 16180835
UGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUACGACAUACACACAUGCCACUAUACUAUGUAUGUAUGUGCAUCUUUUUUGUGGCCUUCCUUUUGU--
...(((((((.(((((((((.....))))))))..).)))))))..........(((((......((((((....)))))).......)))))...........-- ( -25.22, z-score =  -3.00, R)
>dp4.chr4_group3 11609481 75 - 11692001
-----UGCGUACUUCAAUUAAAAUUUAAUUGAAAUACAUAC------------------------AUAUGUCUGUGUACAUCCUUUUUGCCGCCUUCCUUUCAU--
-----.(((((.((((((((.....)))))))).))).(((------------------------(((....)))))).............))...........-- ( -12.70, z-score =  -3.45, R)
>droPer1.super_1 8726399 75 - 10282868
-----UGCGUACUUCAAUUAAAAUUUAAUUGAAAUACAUAC------------------------AUAUGUCUGUGUACAUCCUUUUUGCCGCCUUCCUUUCAU--
-----.(((((.((((((((.....)))))))).))).(((------------------------(((....)))))).............))...........-- ( -12.70, z-score =  -3.45, R)
>consensus
UGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUAU___AUUCGUGUGCG_______AACACAUGCUAGUGUGCAUCUUUUUUGUCGCCUCCUUCCUUUGU
......(((...((((((((.....))))))))...............................(((((....)))))............)))............. ( -8.12 =  -7.78 +  -0.34)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,109,380 – 10,109,476
Length 96
Sequences 8
Columns 106
Reading direction reverse
Mean pairwise identity 75.12
Shannon entropy 0.45644
G+C content 0.34993
Mean single sequence MFE -19.90
Consensus MFE -8.70
Energy contribution -8.53
Covariance contribution -0.17
Combinations/Pair 1.14
Mean z-score -2.62
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.71
SVM RNA-class probability 0.962288
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10109380 96 - 23011544
ACAAAGAAAGGAGGCGACAAAAAAGAUGCACACUAGCAUGUGUU-------CGCACACGAAU---AUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCA
.............(((........(((((......)))((((((-------((....)))))---))).))((((((((((.....))))))))))......))). ( -19.70, z-score =  -2.49, R)
>droSim1.chr2L 9900546 96 - 22036055
ACAAAGGAAGGAGGCGACAAAAAAGAUGCACACUAGCAUGUGUU-------CGCACACGAAU---AUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCA
.............(((........(((((......)))((((((-------((....)))))---))).))((((((((((.....))))))))))......))). ( -19.70, z-score =  -2.37, R)
>droSec1.super_3 5547184 96 - 7220098
ACAAAGGAAGGAGGCGACAAAAAAGAUGCACACUAGCAUGUGUU-------CGCACACGAAU---AUUUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCA
.............(((.........((((......))))(((((-------((....)))))---))....((((((((((.....))))))))))......))). ( -19.00, z-score =  -1.92, R)
>droYak2.chr2L 12793336 96 - 22324452
ACAAAGGAUGGAGGCGACAAAAAAGAUGCACACUAGCAUGUGUG-------CGCACACGAAU---AUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCA
.............(((........(.(((((((......)))))-------)))........---......((((((((((.....))))))))))......))). ( -21.90, z-score =  -2.44, R)
>droEre2.scaffold_4929 10724639 96 - 26641161
ACAAAGGAAGGAGGCGACAAAAAAGAUGCACACUAGCAUGUGUU-------CGCACACGAAU---AUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCA
.............(((........(((((......)))((((((-------((....)))))---))).))((((((((((.....))))))))))......))). ( -19.70, z-score =  -2.37, R)
>droAna3.scaffold_12916 13942541 104 - 16180835
--ACAAAAGGAAGGCCACAAAAAAGAUGCACAUACAUACAUAGUAUAGUGGCAUGUGUGUAUGUCGUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCA
--......((....))..........(((..((((((((((.((......))))))))))))(((((....((((((((((.....))))))))))..)))))))) ( -27.40, z-score =  -3.46, R)
>dp4.chr4_group3 11609481 75 + 11692001
--AUGAAAGGAAGGCGGCAAAAAGGAUGUACACAGACAUAU------------------------GUAUGUAUUUCAAUUAAAUUUUAAUUGAAGUACGCA-----
--..............((.........(((((........)------------------------))))((((((((((((.....)))))))))))))).----- ( -15.90, z-score =  -2.94, R)
>droPer1.super_1 8726399 75 + 10282868
--AUGAAAGGAAGGCGGCAAAAAGGAUGUACACAGACAUAU------------------------GUAUGUAUUUCAAUUAAAUUUUAAUUGAAGUACGCA-----
--..............((.........(((((........)------------------------))))((((((((((((.....)))))))))))))).----- ( -15.90, z-score =  -2.94, R)
>consensus
ACAAAGAAAGGAGGCGACAAAAAAGAUGCACACUAGCAUGUGUU_______CGCACACGAAU___AUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCA
.........................((((......))))................................((((((((((.....)))))))))).......... ( -8.70 =  -8.53 +  -0.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:29:37 2011