Locus 4351

Sequence ID dm3.chr2R
Location 12,399,265 – 12,399,430
Length 165
Max. P 0.986472
window5963 window5964 window5965

overview

Window 3

Location 12,399,265 – 12,399,382
Length 117
Sequences 8
Columns 120
Reading direction forward
Mean pairwise identity 84.77
Shannon entropy 0.29253
G+C content 0.50819
Mean single sequence MFE -38.52
Consensus MFE -25.70
Energy contribution -26.09
Covariance contribution 0.39
Combinations/Pair 1.21
Mean z-score -2.78
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.07
SVM RNA-class probability 0.981282
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12399265 117 + 21146708
GAGCCGGAUUUUCCCAGACUUUGCUGACAUGCGGCUUGAAGCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAUCAACCUU-
(((((((......)).......((......)))))))(((((((.(..(((((-(....))))))..).)))))))(((((((....-.))))))).....((((....))))......- ( -41.20, z-score =  -3.66, R)
>droSim1.chr2R 11138409 117 + 19596830
GAGCCGGAUUUUCCCAGACGUUGCUGACAUGCGGCUUGAAGCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAUCCACCUU-
(((((((......)).......((......)))))))(((((((.(..(((((-(....))))))..).)))))))(((((((....-.)))))))...(.((((....))))).....- ( -40.60, z-score =  -3.16, R)
>droSec1.super_1 9903117 117 + 14215200
GAGCCGGAUUUUCCCAGACUUUGCUGACAUGCGGCUUGAAGCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAUCCACCUU-
(((((((......)).......((......)))))))(((((((.(..(((((-(....))))))..).)))))))(((((((....-.)))))))...(.((((....))))).....- ( -40.60, z-score =  -3.48, R)
>droYak2.chr2R 4556571 117 - 21139217
GAGCCGGAUUUUCCCAGACUUUGCUGACAUGCGGCUGGAAGCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAUCCACCUU-
.....((((.......((.(((.((((..((.((..((((((....)))))).-.)))))))).))).)).((((.(((((((....-.))))))).)))).........)))).....- ( -40.00, z-score =  -2.80, R)
>droEre2.scaffold_4845 9132209 117 - 22589142
GAGCCGGAUUUUCCCAGACUUUGCUGACAUGCGGCUGGAAGCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAUCCACCUU-
.....((((.......((.(((.((((..((.((..((((((....)))))).-.)))))))).))).)).((((.(((((((....-.))))))).)))).........)))).....- ( -40.00, z-score =  -2.80, R)
>droAna3.scaffold_13266 15773588 116 + 19884421
GAGCCAGAUUU-CCCAGACUUUGCUGACAUGCGGCUGGAAACUGUGGCUUCUG-ACCCAUCAGAAAACUCAACUUUGCUGCGGUUUC-AACGUAGCUAAGCGAUAAAAUUAUACUCCUU-
..((((.(.((-.((((....(((......))).)))).)).).))))(((((-(....)))))).......(((.((((((.....-..)))))).)))...................- ( -30.20, z-score =  -1.57, R)
>dp4.chr3 16037557 114 - 19779522
-AGCCCGGGUUUUCC----UCUGAUGACAUGCGGCUUUCC-CUGCGGUUUCCGGACCCAUCAGAACCGAAAGCUUUGCUGUGGUCUCCGCCGCAGCUAAACGAUCAAAUUAUUCCGACUU
-....(((((((((.----(((((((....((((......-))))((((....)))))))))))...))))))...((((((((....)))))))).................))).... ( -37.80, z-score =  -2.38, R)
>droPer1.super_2 5107285 114 - 9036312
-AGCCCGGGUUUUCC----UCUGAUGACAUGCGGCUUUCC-CUGCGGUUUCCGGACCCAUCAGAACCGAAAGCUUUGCUGUGGUCUCCGCCGCAGCUAAACGAUCAAAUUAUUCCGACUU
-....(((((((((.----(((((((....((((......-))))((((....)))))))))))...))))))...((((((((....)))))))).................))).... ( -37.80, z-score =  -2.38, R)
>consensus
GAGCCGGAUUUUCCCAGACUUUGCUGACAUGCGGCUUGAAGCUGCGGCUUCUG_ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC_ACCGUAGCUAAGCGAUAAAAUUAUCCACCUU_
(((((.........(((......)))....((((.......))))))))).....................((((.((((((((....)))))))).))))................... (-25.70 = -26.09 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,399,305 – 12,399,416
Length 111
Sequences 7
Columns 116
Reading direction forward
Mean pairwise identity 82.87
Shannon entropy 0.30669
G+C content 0.47312
Mean single sequence MFE -30.24
Consensus MFE -22.83
Energy contribution -22.59
Covariance contribution -0.24
Combinations/Pair 1.20
Mean z-score -2.57
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.24
SVM RNA-class probability 0.986472
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12399305 111 + 21146708
GCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CAACCUUUUUUUUUCAAGCCUUUUA--CCCCCGACAAAUGGCA
((((.(..(((((-(....))))))..).))))...(((((((....-.))))))).....((((....)))-)................(((.....--............))). ( -30.43, z-score =  -3.29, R)
>droSim1.chr2R 11138449 108 + 19596830
GCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUAA-ACCUCGACAAAUGGCA
((((.(..(((((-(....))))))..).))))...(((((((....-.)))))))...(.((((....)))-)).........----..(((......-............))). ( -29.77, z-score =  -3.04, R)
>droSec1.super_1 9903157 108 + 14215200
GCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUAA-ACCUUGACAAAUGGCA
((((.(..(((((-(....))))))..).))))...(((((((....-.)))))))...(.((((....)))-)).........----..(((......-............))). ( -29.77, z-score =  -2.98, R)
>droYak2.chr2R 4556611 109 - 21139217
GCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUGCUCCCCCGACAAAUGGCA
((((.(..(((((-(....))))))..).))))...(((((((....-.)))))))...(.((((....)))-)).........----..(((.((((.((....)))))).))). ( -33.80, z-score =  -3.87, R)
>droEre2.scaffold_4845 9132249 107 - 22589142
GCUGCGGCUUCUG-ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUG--CCCCCGACAAAUGGCA
((((.(..(((((-(....))))))..).))))...(((((((....-.)))))))...(.((((....)))-)).........----..(((.((((--.......)))).))). ( -32.90, z-score =  -3.62, R)
>dp4.chr3 16037592 111 - 19779522
-CUGCGGUUUCCGGACCCAUCAGAACCGAAAGCUUUGCUGUGGUCUCCGCCGCAGCUAAACGAUCAAAUUAUUCCGACUUUUUCCUCCAUGCCAGGUA----CUUUUAAAGUGGCA
-(((((((....(((((((.((((..(....).)))).)).)))))..)))))))..................((.(((((.....((......))..----.....))))))).. ( -27.50, z-score =  -0.57, R)
>droPer1.super_2 5107320 111 - 9036312
-CUGCGGUUUCCGGACCCAUCAGAACCGAAAGCUUUGCUGUGGUCUCCGCCGCAGCUAAACGAUCAAAUUAUUCCGACUUUUUUCUCCAUGCCAGGUA----CUUUUAAAGUGGCA
-(((((((....(((((((.((((..(....).)))).)).)))))..)))))))..................((.(((((.....((......))..----.....))))))).. ( -27.50, z-score =  -0.59, R)
>consensus
GCUGCGGCUUCUG_ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC_ACCGUAGCUAAGCGAUAAAAUUAU_CCACCUUUUUU____AAGCCUUUUA__CCCUCGACAAAUGGCA
.....((((((((.......)))))......((((.((((((((....)))))))).)))).............................)))....................... (-22.83 = -22.59 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 12,399,318 – 12,399,430
Length 112
Sequences 7
Columns 116
Reading direction forward
Mean pairwise identity 81.85
Shannon entropy 0.32667
G+C content 0.45976
Mean single sequence MFE -27.07
Consensus MFE -21.81
Energy contribution -21.08
Covariance contribution -0.73
Combinations/Pair 1.24
Mean z-score -2.00
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.79
SVM RNA-class probability 0.967632
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12399318 112 + 21146708
ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CAACCUUUUUUUUUCAAGCCUUUUA--CCCCCGACAAAUGGCAGCUGACAUCGCAGA
........(((((....((((.(((((((....-.))))))).))))((((....)))-).........)))))..(((.....--............)))..(((......))). ( -27.23, z-score =  -2.85, R)
>droSim1.chr2R 11138462 109 + 19596830
ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUAA-ACCUCGACAAAUGGCAGCUGACAUCGCAGA
.....((((........((((.(((((((....-.))))))).))))((((....)))-)..........----..(((......-............)))..))))......... ( -25.47, z-score =  -2.13, R)
>droSec1.super_1 9903170 109 + 14215200
ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUAA-ACCUUGACAAAUGGCAGCUGACAUCGCAGA
.....((((........((((.(((((((....-.))))))).))))((((....)))-)..........----..(((......-............)))..))))......... ( -25.47, z-score =  -2.04, R)
>droYak2.chr2R 4556624 110 - 21139217
ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUGCUCCCCCGACAAAUGGCAGCUGACAUCGCAGA
.....((((........((((.(((((((....-.))))))).))))((((....)))-)..........----..(((.((((.((....)))))).)))..))))......... ( -29.50, z-score =  -3.13, R)
>droEre2.scaffold_4845 9132262 108 - 22589142
ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC-ACCGUAGCUAAGCGAUAAAAUUAU-CCACCUUUUUU----AAGCCUUUUG--CCCCCGACAAAUGGCAGCUGACAUCGCACA
.....((((........((((.(((((((....-.))))))).))))((((....)))-)..........----..(((.((((--.......)))).)))..))))......... ( -28.60, z-score =  -3.28, R)
>dp4.chr3 16037605 112 - 19779522
ACCCAUCAGAACCGAAAGCUUUGCUGUGGUCUCCGCCGCAGCUAAACGAUCAAAUUAUUCCGACUUUUUCCUCCAUGCCAGGUA----CUUUUAAAGUGGCAGGGUACAUUCCGGA
(((((((.(((.(....).)))((((((((....)))))))).....))).........................(((((..(.----......)..))))))))).......... ( -26.60, z-score =  -0.25, R)
>droPer1.super_2 5107333 112 - 9036312
ACCCAUCAGAACCGAAAGCUUUGCUGUGGUCUCCGCCGCAGCUAAACGAUCAAAUUAUUCCGACUUUUUUCUCCAUGCCAGGUA----CUUUUAAAGUGGCAGGGUACAUUCCGGA
(((((((.(((.(....).)))((((((((....)))))))).....))).........................(((((..(.----......)..))))))))).......... ( -26.60, z-score =  -0.31, R)
>consensus
ACCCAUCAGAAAACUCAGCUUUGCUGCGGUCUC_ACCGUAGCUAAGCGAUAAAAUUAU_CCACCUUUUUU____AAGCCUUUUA__CCCUCGACAAAUGGCAGCUGACAUCGCAGA
.................((((.((((((((....)))))))).)))).............................(((...................))).((.......))... (-21.81 = -21.08 +  -0.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:27:31 2011