Locus 1112

Sequence ID dm3.chr2L
Location 8,364,601 – 8,364,697
Length 96
Max. P 0.927598
window1516 window1517

overview

Window 6

Location 8,364,601 – 8,364,697
Length 96
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 81.08
Shannon entropy 0.37081
G+C content 0.42477
Mean single sequence MFE -24.02
Consensus MFE -15.90
Energy contribution -16.68
Covariance contribution 0.78
Combinations/Pair 1.13
Mean z-score -1.46
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.641864
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8364601 96 + 23011544
GACUUUUGGCACGUUGACAGCUCUACGAU-GUGGAGACCUGUCAAAGCAGCUAUCGAUAACGGGAUGCUUAGCGAUAUUUUUU--UUAAU-GCGCUUACA
........((...(((((((((((((...-))))))..))))))).))(((..(((....)))...))).((((.((((....--..)))-))))).... ( -24.30, z-score =  -1.17, R)
>droAna3.scaffold_12916 5449642 86 + 16180835
GACUUUUAGCACGUUGACAGCUCUGCUAUUGUGGAGACCUGUCAAAA-AACUAUCGAUAACAG--CGAUUGGUAUUAUCUUUUCAAGAA-----------
......(((....((((((((((..(....)..)))..)))))))..-..)))..(((((..(--(.....)).)))))..........----------- ( -18.20, z-score =  -0.92, R)
>droYak2.chr2L 11002643 98 + 22324452
GACUUUUGGCACGUUGACAGCUCUACGAUUGUGGAGACCUGUCAAAGCAACUAUCGAUAAGGGGAGGGUAAGCGAUAUUUUUUUGUAAAUCGCGUACA--
..(((((.((...(((((((((((((....))))))..))))))).))..((........)))))))(((.(((((............))))).))).-- ( -25.40, z-score =  -1.11, R)
>droEre2.scaffold_4929 17273924 95 + 26641161
GACUUUUGGCACGUUGACAGCUCUACGAUUGUGGAGACCUGUCAAAGCAACUAUCGAUAACAGAAUGCUAAGCGAUAUUUCUUUUCUAAU-GCGUG----
.....((((((..(((((((((((((....))))))..)))))))........((.......)).))))))(((.((((........)))-)))).---- ( -22.10, z-score =  -0.95, R)
>droSec1.super_3 3860000 99 + 7220098
GACUUUUGGCACGUUGACAGCUCUACGAUUGUGGAGACCUGUCAAAGCAGCUAUCGAUAACGGCAUGCUUAAAGAUAUUUUUUUUGGAAU-GCGCAUAAC
......((((...(((((((((((((....))))))..)))))))....)))).........((((..(((((((.....))))))).))-))....... ( -25.70, z-score =  -1.67, R)
>droSim1.chr2L 8150158 97 + 22036055
GACUUUUGGCACGUUGACAGCUCUACGAUUGUGGAGACCUGUCAAAGCAGCUAUCGAUAACGGGAUGCUUAACGAUAUUUUUU--AGACU-GCGCUUACA
.......(((...(((((((((((((....))))))..))))))).(((((((..((((.((..(....)..)).))))...)--)).))-))))).... ( -28.40, z-score =  -2.95, R)
>consensus
GACUUUUGGCACGUUGACAGCUCUACGAUUGUGGAGACCUGUCAAAGCAACUAUCGAUAACGGGAUGCUUAGCGAUAUUUUUUU_AGAAU_GCGCAUA__
........((...(((((((((((((....))))))..))))))).))...(((((.(((........))).)))))....................... (-15.90 = -16.68 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 8,364,601 – 8,364,697
Length 96
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 81.08
Shannon entropy 0.37081
G+C content 0.42477
Mean single sequence MFE -22.50
Consensus MFE -14.41
Energy contribution -15.05
Covariance contribution 0.64
Combinations/Pair 1.13
Mean z-score -2.06
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.927598
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 8364601 96 - 23011544
UGUAAGCGC-AUUAA--AAAAAAUAUCGCUAAGCAUCCCGUUAUCGAUAGCUGCUUUGACAGGUCUCCAC-AUCGUAGAGCUGUCAACGUGCCAAAAGUC
.....((((-.....--..........((..((((((........))).))))).(((((((.(((.(..-...).))).))))))).))))........ ( -22.20, z-score =  -1.75, R)
>droAna3.scaffold_12916 5449642 86 - 16180835
-----------UUCUUGAAAAGAUAAUACCAAUCG--CUGUUAUCGAUAGUU-UUUUGACAGGUCUCCACAAUAGCAGAGCUGUCAACGUGCUAAAAGUC
-----------..........(((((((.(....)--.)))))))..((((.-..(((((((.(((.(......).))).)))))))...))))...... ( -20.90, z-score =  -2.23, R)
>droYak2.chr2L 11002643 98 - 22324452
--UGUACGCGAUUUACAAAAAAAUAUCGCUUACCCUCCCCUUAUCGAUAGUUGCUUUGACAGGUCUCCACAAUCGUAGAGCUGUCAACGUGCCAAAAGUC
--.(((.(((((............))))).)))................(..((.(((((((.(((.(......).))).))))))).))..)....... ( -21.80, z-score =  -2.35, R)
>droEre2.scaffold_4929 17273924 95 - 26641161
----CACGC-AUUAGAAAAGAAAUAUCGCUUAGCAUUCUGUUAUCGAUAGUUGCUUUGACAGGUCUCCACAAUCGUAGAGCUGUCAACGUGCCAAAAGUC
----((((.-......((((...(((((..((((.....)))).)))))....))))(((((.(((.(......).))).)))))..))))......... ( -23.30, z-score =  -1.75, R)
>droSec1.super_3 3860000 99 - 7220098
GUUAUGCGC-AUUCCAAAAAAAAUAUCUUUAAGCAUGCCGUUAUCGAUAGCUGCUUUGACAGGUCUCCACAAUCGUAGAGCUGUCAACGUGCCAAAAGUC
.....((((-....................(((((.((..((...))..)))))))((((((.(((.(......).))).))))))..))))........ ( -23.00, z-score =  -1.89, R)
>droSim1.chr2L 8150158 97 - 22036055
UGUAAGCGC-AGUCU--AAAAAAUAUCGUUAAGCAUCCCGUUAUCGAUAGCUGCUUUGACAGGUCUCCACAAUCGUAGAGCUGUCAACGUGCCAAAAGUC
.....((((-(((..--......(((((...(((.....)))..)))))))))).(((((((.(((.(......).))).)))))))...))........ ( -23.80, z-score =  -2.38, R)
>consensus
__UAAGCGC_AUUCA_AAAAAAAUAUCGCUAAGCAUCCCGUUAUCGAUAGCUGCUUUGACAGGUCUCCACAAUCGUAGAGCUGUCAACGUGCCAAAAGUC
.......................(((((.(((........))).)))))((.((.(((((((.(((.(......).))).))))))).))))........ (-14.41 = -15.05 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:25:48 2011