Locus 3090

Sequence ID dm3.chr2R
Location 2,146,271 – 2,146,415
Length 144
Max. P 0.980575
window4241 window4242

overview

Window 1

Location 2,146,271 – 2,146,415
Length 144
Sequences 5
Columns 153
Reading direction forward
Mean pairwise identity 64.17
Shannon entropy 0.64151
G+C content 0.49180
Mean single sequence MFE -52.08
Consensus MFE -20.45
Energy contribution -21.93
Covariance contribution 1.48
Combinations/Pair 1.44
Mean z-score -2.16
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979150
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2146271 144 + 21146708
UUUAUGCCGUAAGCUUGCUGCGCG-CGGAGCUGA--AGUUCCAGUGUGUCCAGUCU--GACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAAAUCUUGGCGUUAGU----GUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACA
.....((((((.(....))))).)-)(((((...--.))))).((((((((((.((--((.((((((....))))))((((...((((....))))(((((((((----(....)))..))))))).....)))).)))).))))))).))). ( -55.40, z-score =  -2.65, R)
>droSim1.chrU 1857335 152 + 15797150
UUUCUGGCUGCAACUGGCUGGGGA-UGAAGCCGAGGAGGUUGAAUUGGCAUAUCCUCGGUCGCGAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAUUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACA
....((((.((..(((((((((((-(((.((((((((.(((.....)))...))))))))....(((....))).)))))).)))......(((.(((((..(........)..))))).)))))))).((((((....)))))))))))).. ( -62.20, z-score =  -2.05, R)
>droSec1.super_3 6919830 147 + 7220098
-UUAUGCCGUAAGCUUGUUGCGCG-CGGAGCUGA--AGUUCCAGUGUGCCCAGUCU--GACGAUAUCAGAAGAUAUCGUCCUCCAGGUAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUUAGUCUGGGCGCCACA
-....(((((((.....))))).)-)(((((...--.))))).((((((((((.((--(((((((((....)))))))))....((((..(((((.(((((((................))))))))))))..)))).)).))))))).))). ( -62.39, z-score =  -3.96, R)
>droEre2.scaffold_4929 21984477 148 + 26641161
UUGAUGCCGUAAGCUUGUUGCGCGGCAAGGCUGA--AGU-CGAGAGUGACCAGUCU--GACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACUUGCUUACGCCGUGUUGCCAGACUGGGCUUUAGUCUGGGCGCCACA
....((((((..((.....)))))))).(((...--.((-(.(((.((((((((((--(((((((((....)))))))))..........(((..((((((.(((....))).))))))....))))))))))...))).))).))))))... ( -60.80, z-score =  -2.99, R)
>dp4.Unknown_group_51 38428 126 - 55748
---------------------UAAACUAAGUUUU---CUUUAAGUUUGAACUUGUGAUAUAAAUACCAGA-GUUAUAGCAUUUUAUAAAAAGGGAUGGAUUUUGUA-UGAUCAUCUCUGAGAC-CUCGAUUGAACUGCAGUUUUUGGAUAAAA
---------------------.....(((((((.---..........)))))))...........(((((-(.....(((.((((.....(((((((.(((.....-.))))))))))((...-.))...)))).)))...))))))...... ( -19.60, z-score =   0.86, R)
>consensus
UUUAUGCCGUAAGCUUGCUGCGCG_CGAAGCUGA__AGUUCCAGUGUGACCAGUCU__GACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACA
..........................((((((..........................(((((((((....)))))))))..........(((((.(((((((................)))))))))))).))))))............... (-20.45 = -21.93 +   1.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,146,271 – 2,146,415
Length 144
Sequences 5
Columns 153
Reading direction reverse
Mean pairwise identity 64.17
Shannon entropy 0.64151
G+C content 0.49180
Mean single sequence MFE -44.73
Consensus MFE -17.62
Energy contribution -21.06
Covariance contribution 3.44
Combinations/Pair 1.08
Mean z-score -2.18
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.05
SVM RNA-class probability 0.980575
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2146271 144 - 21146708
UGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAAC----ACUAACGCCAAGAUUUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUC--AGACUGGACACACUGGAACU--UCAGCUCCG-CGCGCAGCAAGCUUACGGCAUAAA
(((.((((.(.((((((((.(((((.((.......((((.....----.....))))........(((.(...(((((((((....)))))))))--...).))))).)))))..))--)))).)).)-.)))).))).((.....))..... ( -51.40, z-score =  -2.93, R)
>droSim1.chrU 1857335 152 - 15797150
UGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAGGUAAUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUCGCGACCGAGGAUAUGCCAAUUCAACCUCCUCGGCUUCA-UCCCCAGCCAGUUGCAGCCAGAAA
.(((..(((.((((((.....)))))))))..)))(((...(((.(((......)))..........((((.(((((..(((....)))..)).(((((((..((......))...))))))).....-)))))))...)))...)))..... ( -50.80, z-score =  -1.68, R)
>droSec1.super_3 6919830 147 - 7220098
UGUGGCGCCCAGACUAAAGCCCGGUCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUACCUGGAGGACGAUAUCUUCUGAUAUCGUC--AGACUGGGCACACUGGAACU--UCAGCUCCG-CGCGCAACAAGCUUACGGCAUAA-
(((.((((.(........((((((((((((.....((((..............))))....((((.....))))..((((((....)))))))))--))))))))).....(((.(.--...).))))-.)))).))).((.....))....- ( -54.04, z-score =  -3.26, R)
>droEre2.scaffold_4929 21984477 148 - 26641161
UGUGGCGCCCAGACUAAAGCCCAGUCUGGCAACACGGCGUAAGCAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUC--AGACUGGUCACUCUCG-ACU--UCAGCCUUGCCGCGCAACAAGCUUACGGCAUCAA
.(((..(((.(((((.......))))))))..)))(((((.((......)).)))))..........(((((((((((((((....)))))))))--.((....)).......-.))--))))...(((((.((.....))...))))).... ( -52.20, z-score =  -3.03, R)
>dp4.Unknown_group_51 38428 126 + 55748
UUUUAUCCAAAAACUGCAGUUCAAUCGAG-GUCUCAGAGAUGAUCA-UACAAAAUCCAUCCCUUUUUAUAAAAUGCUAUAAC-UCUGGUAUUUAUAUCACAAGUUCAAACUUAAAG---AAAACUUAGUUUA---------------------
..........((((((.((((...(((((-(((........)))).-.......................((((((((....-..))))))))...))..((((....))))...)---).)))))))))).--------------------- ( -15.20, z-score =  -0.01, R)
>consensus
UGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUC__AGACUGGGCACACUCGAACU__UCAGCUUCG_CGCGCAACAAGCUUACGGCAUAAA
.(((..(((.((((((.....)))))))))..)))((((..............))))................(((((((((....))))))))).......................................................... (-17.62 = -21.06 +   3.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:28 2011