Locus 4064

Sequence ID dm3.chr2R
Location 10,097,838 – 10,098,003
Length 165
Max. P 0.999686
window5567 window5568 window5569 window5570 window5571

overview

Window 7

Location 10,097,838 – 10,097,956
Length 118
Sequences 9
Columns 121
Reading direction reverse
Mean pairwise identity 78.33
Shannon entropy 0.44849
G+C content 0.38026
Mean single sequence MFE -26.23
Consensus MFE -11.44
Energy contribution -11.14
Covariance contribution -0.30
Combinations/Pair 1.61
Mean z-score -2.26
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.859647
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10097838 118 - 21146708
GCCAUUUCAGCUGACUGACUUU-CGUAGUUUCCGA-CGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCU
((..(((((.(((....((((.-..(((((((.((-((((.....)))))).......(((((...(((.........)))..))))).)))))))....)))).))).))))).-))... ( -32.20, z-score =  -2.80, R)
>droPer1.super_4 6718496 113 + 7162766
-----UAUGACUGACUGA-UUC-CGCGGUUUCCGA-CGGGAAACUCUCGGCUACAAAUUGGCCGGAAUUAUGAAUGGAAAUGAAGCCAUGAAACGAAAUUAAAUACUGAUGAAAACGAUUU
-----..........(((-(((-(..(((((((..-..)))))))...(((((.....))))))))))))...((((........))))................................ ( -24.40, z-score =  -1.72, R)
>dp4.chr3 16320272 113 - 19779522
-----UAUGACUGACUGA-UUC-CGCGGUUUCCGA-CGGGAAACUCUCGGCUACAAAUUGGCUGAAAUUAUGAAUGGAAAUGAAGCCAUGAAACGAAAUUAAAUACUGAUGAAAACGAUUU
-----((((.((......-(((-((.(((((((..-..))))))).(((((((.....))))))).........)))))....)).))))............................... ( -21.20, z-score =  -1.43, R)
>droAna3.scaffold_13266 14059369 114 + 19884421
-----UACACCCGACUGACUUU-CGUAGUUUCCGA-CGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAACGCUUU
-----......((.(((((((.-..(((((((.((-((((.....)))))).......(((((...(((.........)))..))))).)))))))....)))).))).)).......... ( -28.50, z-score =  -2.67, R)
>droEre2.scaffold_4845 6844363 113 + 22589142
-----UUCAGCUGACUGACUUU-CGUAGUUUCCGA-CGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCU
-----...((((..(((((((.-..(((((((.((-((((.....)))))).......(((((...(((.........)))..))))).)))))))....)))).)))......)-))).. ( -30.40, z-score =  -3.24, R)
>droYak2.chr2R 10035529 113 - 21139217
-----UUCAGCUGAAUGACUUU-CGUAGUUUCCGA-CGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAUGAAGCCGUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCU
-----((((.(((....((((.-..((((((((((-((((.....))))))........((((...(((.........)))..))))).)))))))....)))).))).))))..-..... ( -29.90, z-score =  -2.97, R)
>droSim1.chr2R 8861118 113 - 19596830
-----UUCAGCUGACUGACUUU-CGUAGUUUCCGA-CGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA-GCUCU
-----...((((..(((((((.-..(((((((.((-((((.....)))))).......(((((...(((.........)))..))))).)))))))....)))).)))......)-))).. ( -30.40, z-score =  -2.81, R)
>droSec1.super_1 7606156 113 - 14215200
-----UUCAGCUGACUGACUUU-CGUAGUUUCCGA-CGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAACUAAGUACAGAUGAAAA-GCUCU
-----...((((..(((((((.-..(((((((.((-((((.....)))))).......(((((...(((.........)))..))))).)))))))....)))).)))......)-))).. ( -30.40, z-score =  -2.84, R)
>droVir3.scaffold_12875 2991325 95 + 20611582
-----AACAUUUAAACAACCUUACGUUGCGUCCGGUUCAGAUAUCAUUUUAUAUAUACGGAAU-AUAUUAGGAA-AGAAGCAUACAUACACACACACACUCA-------------------
-----...................(((((.((...(((.(((((.(((((........)))))-))))).))).-.)).))).)).................------------------- (  -8.70, z-score =   0.10, R)
>consensus
_____UUCAGCUGACUGACUUU_CGUAGUUUCCGA_CGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAUGAAGCCAUGAAAUUAAAUUAAGUACAGAUGAAAA_GCUCU
.......(((((((............(((((((.....)))))))............))))))).........((((........))))................................ (-11.44 = -11.14 +  -0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 10,097,877 – 10,097,980
Length 103
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 85.55
Shannon entropy 0.28303
G+C content 0.40595
Mean single sequence MFE -30.87
Consensus MFE -21.22
Energy contribution -22.42
Covariance contribution 1.20
Combinations/Pair 1.05
Mean z-score -3.71
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.30
SVM RNA-class probability 0.998257
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10097877 103 + 21146708
AUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAAAUGGCUAGCUAAUACGUAUAAAGGGGAAA
.(..((............(((((.((((((((((((.....))))))(....)))))))..((((....))))..))))).((......)).....))..).. ( -31.60, z-score =  -3.40, R)
>droAna3.scaffold_13266 14059409 90 - 19884421
AUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCGGGUGUA--CCUCAGUUACUAUAUA-----------
.....(((((....((((.((......)).((((((.....))))))))))(((((....)).))).)))))..--................----------- ( -22.30, z-score =  -1.94, R)
>droEre2.scaffold_4845 6844402 94 - 22589142
AUUUCCAUUCAUAAUUUCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-UGGCUAA--------UAUAUAGGGGAAG
..((((.(..(((..((.(((((.((((((((((((.....))))))(....)))))))..((((....)))).-)))))))--------..)))..))))). ( -30.90, z-score =  -4.23, R)
>droYak2.chr2R 10035568 102 + 21139217
AUUUCCAUUCAUAAUUUCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAUUCAGCUGAA-UGUCUAAUACAUAUGUAUAUAGGGGAAG
..((((.........((((((.........((((((.....)))))).(((...((....))..))).))))))-..((((((((....)))).)))))))). ( -30.20, z-score =  -3.88, R)
>droSim1.chr2R 8861157 100 + 19596830
AUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-UGGCUAAU--ACGUAUAUAUGGGGGAAG
.(..((((..(((.....(((((.((((((((((((.....))))))(....)))))))..((((....)))).-)))))...--...)))..))))..)... ( -35.10, z-score =  -4.40, R)
>droSec1.super_1 7606195 100 + 14215200
AUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-UGGCUAAU--ACGUAUAUAUGGGGGAAG
.(..((((..(((.....(((((.((((((((((((.....))))))(....)))))))..((((....)))).-)))))...--...)))..))))..)... ( -35.10, z-score =  -4.40, R)
>consensus
AUUUCCAUUCAUAAUUCCAGCCAAUUUGUAGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA_UGGCUAAU__AUAUAUAUAUAGGGGAAG
..................(((((.((((((((((((.....))))))(....)))))))..((((....))))..)))))....................... (-21.22 = -22.42 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,097,877 – 10,097,980
Length 103
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 85.55
Shannon entropy 0.28303
G+C content 0.40595
Mean single sequence MFE -27.33
Consensus MFE -21.65
Energy contribution -22.27
Covariance contribution 0.61
Combinations/Pair 1.11
Mean z-score -2.86
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.65
SVM RNA-class probability 0.993858
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10097877 103 - 21146708
UUUCCCCUUUAUACGUAUUAGCUAGCCAUUUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAU
.......(((((.((((....(((((((..((((....))))..............((((((.....)))))).......)))))))...)))).)))))... ( -29.30, z-score =  -2.91, R)
>droAna3.scaffold_13266 14059409 90 + 19884421
-----------UAUAUAGUAACUGAGG--UACACCCGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAU
-----------....((((...((.((--....)))))))).(.(((((((((((.((((((.....))))))..(.....)...))))))))))).)..... ( -21.80, z-score =  -1.12, R)
>droEre2.scaffold_4845 6844402 94 + 22589142
CUUCCCCUAUAUA--------UUAGCCA-UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAU
.((((..((((..--------(((((((-.((((....))))..............((((((.....)))))).......)))))))...))))...)))).. ( -27.20, z-score =  -3.69, R)
>droYak2.chr2R 10035568 102 - 21139217
CUUCCCCUAUAUACAUAUGUAUUAGACA-UUCAGCUGAAUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGAAAUUAUGAAUGGAAAU
.((((.(((.((((....))))))).((-(((....)))))...(((((((((((.((((((.....))))))..(.....)...))))))))))).)))).. ( -29.50, z-score =  -3.90, R)
>droSim1.chr2R 8861157 100 - 19596830
CUUCCCCCAUAUAUACGU--AUUAGCCA-UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAU
......((((.((((.((--.(((((((-.((((....))))..............((((((.....)))))).......))))))).)))))).)))).... ( -28.10, z-score =  -2.78, R)
>droSec1.super_1 7606195 100 - 14215200
CUUCCCCCAUAUAUACGU--AUUAGCCA-UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAU
......((((.((((.((--.(((((((-.((((....))))..............((((((.....)))))).......))))))).)))))).)))).... ( -28.10, z-score =  -2.78, R)
>consensus
CUUCCCCUAUAUAUAUAU__AUUAGCCA_UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCUACAAAUUGGCUGGAAUUAUGAAUGGAAAU
.((((................(((((.......)))))......(((((((((((.((((((.....))))))..(.....)...))))))))))).)))).. (-21.65 = -22.27 +   0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 10,097,906 – 10,098,003
Length 97
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 75.60
Shannon entropy 0.45047
G+C content 0.39449
Mean single sequence MFE -28.42
Consensus MFE -17.76
Energy contribution -18.43
Covariance contribution 0.67
Combinations/Pair 1.27
Mean z-score -3.77
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.19
SVM RNA-class probability 0.999686
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10097906 97 + 21146708
AGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAAAUGGCUAGCUAAUACGUAUAAAGGGGAAAUAC-UUAUAUACAGUCAUAUACUU
.((((((.....))))))(....).((....)).((..((((.....))))..)).....(((((.(((.......)-)).)))))............ ( -26.60, z-score =  -2.99, R)
>droAna3.scaffold_13266 14059438 82 - 19884421
AGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCGGGUGUA--CCUCAGUUACUAUAUAACUUAGAUAUAGACGUUAUAU--------------
.((((((.....))))))....(((((....)).)))((..((((--.((.(((((.....))))).)).))))..))......-------------- ( -23.20, z-score =  -1.95, R)
>droEre2.scaffold_4845 6844431 78 - 22589142
AGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-UGGCUA--------AUAUAUAGGGGAAGUAC-UUAUAUACGA----------
.((((((.....))))))(....)..((..(((((.((....)).-))))).--------.((((((((.......)-))))))))).---------- ( -25.50, z-score =  -3.59, R)
>droYak2.chr2R 10035597 86 + 21139217
AGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAUUCAGCUGAA-UGUCUAAUACAUAUGUAUAUAGGGGAAGUAC-UUAUAUACAG----------
.((((((.....))))))(....)......((.(((((....)))-)).))........((((((((((.......)-))))))))).---------- ( -29.50, z-score =  -4.86, R)
>droSim1.chr2R 8861186 94 + 19596830
AGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-UGGCUAAU--ACGUAUAUAUGGGGGAAGUAC-UUUUAUAUAUGUAUAUACUU
.((((((.....))))))(....).((....)).(((((......-))))).((--(((((((((..((.......)-)..)))))))))))...... ( -31.20, z-score =  -4.09, R)
>droSec1.super_1 7606224 94 + 14215200
AGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA-UGGCUAAU--ACGUAUAUAUGGGGGAAGUAC-UUAUAUAUAUGUAUAUACUU
.((((((.....))))))(....).((....)).(((((......-))))).((--(((((((((((((.......)-))))))))))))))...... ( -34.50, z-score =  -5.15, R)
>consensus
AGACGGGAAUUUCCCGUCGGAAACUACGAAAGUCAGUCAGCUGAA_UGGCUAAU__AUAUAUAUAUAGGGGAAGUAC_UUAUAUACAG__________
.((((((.....))))))(....).((....)).....((((.....)))).........((((((((.(......).))))))))............ (-17.76 = -18.43 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,097,906 – 10,098,003
Length 97
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 75.60
Shannon entropy 0.45047
G+C content 0.39449
Mean single sequence MFE -20.17
Consensus MFE -13.05
Energy contribution -12.88
Covariance contribution -0.16
Combinations/Pair 1.14
Mean z-score -2.11
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.17
SVM RNA-class probability 0.984655
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10097906 97 - 21146708
AAGUAUAUGACUGUAUAUAA-GUAUUUCCCCUUUAUACGUAUUAGCUAGCCAUUUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCU
.....(((((..(((((.((-(........))))))))...((((.((((.......)))).))))...)))))......((((((.....)))))). ( -22.60, z-score =  -2.22, R)
>droAna3.scaffold_13266 14059438 82 + 19884421
--------------AUAUAACGUCUAUAUCUAAGUUAUAUAGUAACUGAGG--UACACCCGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCU
--------------......((..(.(((((.((((((...)))))).)))--)).)..))...((((.....))))...((((((.....)))))). ( -20.20, z-score =  -1.40, R)
>droEre2.scaffold_4845 6844431 78 + 22589142
----------UCGUAUAUAA-GUACUUCCCCUAUAUAU--------UAGCCA-UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCU
----------..((((....-))))............(--------((((..-....)))))..((((.....))))...((((((.....)))))). ( -17.20, z-score =  -1.96, R)
>droYak2.chr2R 10035597 86 - 21139217
----------CUGUAUAUAA-GUACUUCCCCUAUAUACAUAUGUAUUAGACA-UUCAGCUGAAUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCU
----------.((((((((.-(.......).))))))))((((....((.((-(((....))))).))..))))......((((((.....)))))). ( -22.60, z-score =  -3.21, R)
>droSim1.chr2R 8861186 94 - 19596830
AAGUAUAUACAUAUAUAAAA-GUACUUCCCCCAUAUAUACGU--AUUAGCCA-UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCU
..(((((((...........-............)))))))..--.(((((..-....)))))..((((.....))))...((((((.....)))))). ( -18.80, z-score =  -1.89, R)
>droSec1.super_1 7606224 94 - 14215200
AAGUAUAUACAUAUAUAUAA-GUACUUCCCCCAUAUAUACGU--AUUAGCCA-UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCU
((((...(((.(((((((..-...........))))))).))--)(((((..-....)))))...))))...........((((((.....)))))). ( -19.62, z-score =  -1.99, R)
>consensus
__________AUGUAUAUAA_GUACUUCCCCUAUAUAUAUAU__AUUAGCCA_UUCAGCUGACUGACUUUCGUAGUUUCCGACGGGAAAUUCCCGUCU
..............................................((((.......))))...((((.....))))...((((((.....)))))). (-13.05 = -12.88 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:22:04 2011