Locus 10429

Sequence ID dm3.chr3R
Location 13,758,451 – 13,758,559
Length 108
Max. P 0.997908
window14343 window14344 window14345 window14346

overview

Window 3

Location 13,758,451 – 13,758,552
Length 101
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 67.41
Shannon entropy 0.57617
G+C content 0.31067
Mean single sequence MFE -24.05
Consensus MFE -13.49
Energy contribution -14.45
Covariance contribution 0.96
Combinations/Pair 1.28
Mean z-score -2.33
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.13
SVM RNA-class probability 0.997563
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13758451 101 + 27905053
AUUAAUAGGCAUUGGGUGCAUAUAUAUAAAAUUUGCAUAGGUACCUAAAAGUAUGCAACAAUAUAUAGUUGGCC------------------CAUUUUUUGUUGCAUACUUUUACACAC
.....((((.(((..(((((.............))))).))).))))((((((((((((((.............------------------......))))))))))))))....... ( -25.53, z-score =  -1.94, R)
>droSim1.chr3R 19784755 118 - 27517382
AUCAAAAAGCAUUAAUUGCAUAUUUAUAUCAUUUGUAUAGAUAUCUGAACGUAUGCAACAAUACAU-UCAAGCCAAUUUGAGAGAAACACACACUUUUUCGUUGCAUACUUUUACACAC
.(((....(((.....)))((((((((((.....)))))))))).)))..(((((((((.......-(((((....)))))((((((.......))))))))))))))).......... ( -26.10, z-score =  -4.44, R)
>droSec1.super_12 1726139 112 - 2123299
------AUAAAAAAAUUGCAUAUUUAUAUAAUUUGUAUAGAUAUUUAAACGUAUUCAACCAUACAU-UUAAGCCAAUUUGAGAGGCACACACACUUUUUCGUUGAAUACUUUUACACAC
------.(((((...(((.((((((((((.....)))))))))).)))..(((((((((.......-....(((.........)))..............))))))))))))))..... ( -17.71, z-score =  -2.75, R)
>droYak2.chr3R 2345318 118 + 28832112
AUAAGCAAGCAUUAAUUGGCUAUUUAUAUCAUGUCUAUGGGUAGCUAAAAGUAUGCAACAAUAUAU-GUAAGCCGUUUGAAUAGACCCACACGCUCUGUUGUUGCAUACUUUUACACAU
.................(((((((((((.......)))))))))))(((((((((((((((((...-...(((.((.((........)).))))).)))))))))))))))))...... ( -31.90, z-score =  -2.44, R)
>droEre2.scaffold_4770 9878277 99 - 17746568
AUUAAAAAGCGUUAACUGCAUAUUUUUAUCAUUUCUGUGGGGACCUAAAAGUAAGCAACAAGAAAU-GUAAGC-------------------GCUAUUUUGCUGCAUACUUUUGCACAC
.......((((((...(((.((((((((...(..(....)..)..)))))))).)))(((.....)-)).)))-------------------)))....((.((((......)))))). ( -19.00, z-score =  -0.08, R)
>consensus
AUUAAAAAGCAUUAAUUGCAUAUUUAUAUCAUUUGUAUAGGUACCUAAAAGUAUGCAACAAUACAU_GUAAGCC__UU__A_AG___CACACACUUUUUUGUUGCAUACUUUUACACAC
...................(((((((((.......))))))))).((((((((((((((((.....................................))))))))))))))))..... (-13.49 = -14.45 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,758,451 – 13,758,552
Length 101
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 67.41
Shannon entropy 0.57617
G+C content 0.31067
Mean single sequence MFE -23.01
Consensus MFE -13.67
Energy contribution -14.11
Covariance contribution 0.44
Combinations/Pair 1.29
Mean z-score -0.97
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.849250
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13758451 101 - 27905053
GUGUGUAAAAGUAUGCAACAAAAAAUG------------------GGCCAACUAUAUAUUGUUGCAUACUUUUAGGUACCUAUGCAAAUUUUAUAUAUAUGCACCCAAUGCCUAUUAAU
.....((((((((((((((((.(.(((------------------(.....)))).).))))))))))))))))((((....((((.((.......)).)))).....))))....... ( -28.30, z-score =  -3.03, R)
>droSim1.chr3R 19784755 118 + 27517382
GUGUGUAAAAGUAUGCAACGAAAAAGUGUGUGUUUCUCUCAAAUUGGCUUGA-AUGUAUUGUUGCAUACGUUCAGAUAUCUAUACAAAUGAUAUAAAUAUGCAAUUAAUGCUUUUUGAU
((((((....(((((((((((((.........))))..((((......))))-.......)))))))))......(((((.........)))))..))))))................. ( -20.50, z-score =   0.42, R)
>droSec1.super_12 1726139 112 + 2123299
GUGUGUAAAAGUAUUCAACGAAAAAGUGUGUGUGCCUCUCAAAUUGGCUUAA-AUGUAUGGUUGAAUACGUUUAAAUAUCUAUACAAAUUAUAUAAAUAUGCAAUUUUUUUAU------
...................(((((((((((((((((.........)))((((-((((((......)))))))))).....................)))))).))))))))..------ ( -18.90, z-score =  -0.97, R)
>droYak2.chr3R 2345318 118 - 28832112
AUGUGUAAAAGUAUGCAACAACAGAGCGUGUGGGUCUAUUCAAACGGCUUAC-AUAUAUUGUUGCAUACUUUUAGCUACCCAUAGACAUGAUAUAAAUAGCCAAUUAAUGCUUGCUUAU
.....((((((((((((((((...(..(((((((((.........)))))))-)).).))))))))))))))))((((...(((.......)))...)))).................. ( -30.10, z-score =  -1.65, R)
>droEre2.scaffold_4770 9878277 99 + 17746568
GUGUGCAAAAGUAUGCAGCAAAAUAGC-------------------GCUUAC-AUUUCUUGUUGCUUACUUUUAGGUCCCCACAGAAAUGAUAAAAAUAUGCAGUUAACGCUUUUUAAU
(((((((((((((.(((((((......-------------------......-.....))))))).))))))).........((....)).............))..))))........ ( -17.23, z-score =   0.39, R)
>consensus
GUGUGUAAAAGUAUGCAACAAAAAAGCGUGUG___CU_U__AA__GGCUUAC_AUAUAUUGUUGCAUACUUUUAGAUACCUAUACAAAUGAUAUAAAUAUGCAAUUAAUGCUUUUUAAU
(((((((((((((((((((((.....................................))))))))))))))))......))))).................................. (-13.67 = -14.11 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,758,458 – 13,758,559
Length 101
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 68.74
Shannon entropy 0.56138
G+C content 0.33486
Mean single sequence MFE -24.32
Consensus MFE -13.52
Energy contribution -14.48
Covariance contribution 0.96
Combinations/Pair 1.28
Mean z-score -2.46
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.21
SVM RNA-class probability 0.997908
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13758458 101 + 27905053
GGCAUUGGGUGCAUAUAUAUAAAAUUUGCAUAGGUACCUAAAAGUAUGCAACAAUAUAU-------AGUU-----GGCCCA-----UUUUUUGUUGCAUACUUUUACACACCUCUCGA
....(((((((((.............)))).((((...((((((((((((((((.....-------....-----......-----....))))))))))))))))...))))))))) ( -26.73, z-score =  -2.36, R)
>droSim1.chr3R 19784762 118 - 27517382
AGCAUUAAUUGCAUAUUUAUAUCAUUUGUAUAGAUAUCUGAACGUAUGCAACAAUACAUUCAAGCCAAUUUGAGAGAAACACACACUUUUUCGUUGCAUACUUUUACACACCUCUCGA
.(((.....)))((((((((((.....)))))))))).((((.(((((((((.......(((((....)))))((((((.......))))))))))))))).))))............ ( -25.90, z-score =  -4.17, R)
>droSec1.super_12 1726146 112 - 2123299
------AAUUGCAUAUUUAUAUAAUUUGUAUAGAUAUUUAAACGUAUUCAACCAUACAUUUAAGCCAAUUUGAGAGGCACACACACUUUUUCGUUGAAUACUUUUACACACCUCUCGA
------....((((((((((((.....))))))))))(((((.((((......)))).)))))))....((((((((............(((...)))............)))))))) ( -18.35, z-score =  -2.97, R)
>droYak2.chr3R 2345325 118 + 28832112
AGCAUUAAUUGGCUAUUUAUAUCAUGUCUAUGGGUAGCUAAAAGUAUGCAACAAUAUAUGUAAGCCGUUUGAAUAGACCCACACGCUCUGUUGUUGCAUACUUUUACACAUCUUUAAG
..........(((((((((((.......)))))))))))(((((((((((((((((......(((.((.((........)).))))).)))))))))))))))))............. ( -31.90, z-score =  -2.96, R)
>droEre2.scaffold_4770 9878284 99 - 17746568
AGCGUUAACUGCAUAUUUUUAUCAUUUCUGUGGGGACCUAAAAGUAAGCAACAAGAAAUGUAAGC-------------------GCUAUUUUGCUGCAUACUUUUGCACACCUCUAAA
((((((...(((.((((((((...(..(....)..)..)))))))).)))(((.....))).)))-------------------)))....((.((((......))))))........ ( -18.70, z-score =   0.17, R)
>consensus
AGCAUUAAUUGCAUAUUUAUAUCAUUUGUAUAGGUACCUAAAAGUAUGCAACAAUACAUGUAAGCCAAUU__A_AGACACACACACUUUUUUGUUGCAUACUUUUACACACCUCUCGA
............(((((((((.......))))))))).((((((((((((((((....................................))))))))))))))))............ (-13.52 = -14.48 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,758,458 – 13,758,559
Length 101
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 68.74
Shannon entropy 0.56138
G+C content 0.33486
Mean single sequence MFE -25.51
Consensus MFE -16.44
Energy contribution -17.32
Covariance contribution 0.88
Combinations/Pair 1.24
Mean z-score -1.66
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.32
SVM RNA-class probability 0.988361
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13758458 101 - 27905053
UCGAGAGGUGUGUAAAAGUAUGCAACAAAAAA-----UGGGCC-----AACU-------AUAUAUUGUUGCAUACUUUUAGGUACCUAUGCAAAUUUUAUAUAUAUGCACCCAAUGCC
.....(((((..((((((((((((((((.(.(-----(((...-----..))-------)).).))))))))))))))))..))))).((((.((.......)).))))......... ( -32.70, z-score =  -4.19, R)
>droSim1.chr3R 19784762 118 + 27517382
UCGAGAGGUGUGUAAAAGUAUGCAACGAAAAAGUGUGUGUUUCUCUCAAAUUGGCUUGAAUGUAUUGUUGCAUACGUUCAGAUAUCUAUACAAAUGAUAUAAAUAUGCAAUUAAUGCU
..((((((((((((....))))))((......)).......)))))).(((((..((((((((((......))))))))))(((((.........))))).......)))))...... ( -22.90, z-score =  -0.20, R)
>droSec1.super_12 1726146 112 + 2123299
UCGAGAGGUGUGUAAAAGUAUUCAACGAAAAAGUGUGUGUGCCUCUCAAAUUGGCUUAAAUGUAUGGUUGAAUACGUUUAAAUAUCUAUACAAAUUAUAUAAAUAUGCAAUU------
..((((((((..((......(((...)))......))..))))))))......((((((((((((......))))))))))((((.((((.......)))).))))))....------ ( -23.90, z-score =  -2.41, R)
>droYak2.chr3R 2345325 118 - 28832112
CUUAAAGAUGUGUAAAAGUAUGCAACAACAGAGCGUGUGGGUCUAUUCAAACGGCUUACAUAUAUUGUUGCAUACUUUUAGCUACCCAUAGACAUGAUAUAAAUAGCCAAUUAAUGCU
............((((((((((((((((...(..(((((((((.........))))))))).).))))))))))))))))((((...(((.......)))...))))........... ( -30.10, z-score =  -2.18, R)
>droEre2.scaffold_4770 9878284 99 + 17746568
UUUAGAGGUGUGCAAAAGUAUGCAGCAAAAUAGC-------------------GCUUACAUUUCUUGUUGCUUACUUUUAGGUCCCCACAGAAAUGAUAAAAAUAUGCAGUUAACGCU
......((((((((((((((.(((((((......-------------------...........))))))).))))))).........((....)).............))..))))) ( -17.93, z-score =   0.66, R)
>consensus
UCGAGAGGUGUGUAAAAGUAUGCAACAAAAAAGCGUGUGGGCCU_U__AAUUGGCUUAAAUAUAUUGUUGCAUACUUUUAGAUACCUAUACAAAUGAUAUAAAUAUGCAAUUAAUGCU
......(((((.((((((((((((((((....................................)))))))))))))))).)))))................................ (-16.44 = -17.32 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:23:50 2011