Locus 5408

Sequence ID dm3.chr2R
Location 20,127,984 – 20,128,129
Length 145
Max. P 0.985003
window7416 window7417

overview

Window 6

Location 20,127,984 – 20,128,089
Length 105
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 71.51
Shannon entropy 0.52184
G+C content 0.54930
Mean single sequence MFE -33.60
Consensus MFE -18.52
Energy contribution -19.18
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.10
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.647047
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20127984 105 - 21146708
------AGCUGGGAGCUGGGAGCUAAG---GGAGCAGGGGAC-UGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGU-AAAGGAAUCGUUUAAAAUAAAUGACAGGCGGACCCCC-
------.(((...(((.....)))...---..))).((((.(-((.(...(((((.(((....))).)))))......-.......(((((((...)))))))..).))).)))).- ( -37.30, z-score =  -1.64, R)
>droSim1.chr2R 18610584 98 - 19596830
-------------AGCUGGGAGCUAAG---GGAGCAGGGGAC-CGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGU-AAAGGAAUCGUUUAAAAUAAAUGACAGGCGAGCCCCC-
-------------........(((...---..))).((((..-((.(...(((((.(((....))).)))))......-.......(((((((...)))))))..).))..)))).- ( -34.20, z-score =  -1.30, R)
>droYak2.chr2R 20093660 115 - 21139217
GCAAGUGGCAGGGGGUAGGGGCAUGGGGCAGGGGCAGGGGAC-UGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUGU-AAAGGAAUCGUUUAAAAUAAAUGACAGGCGGGCCCCCC
((.....)).((((((....((.((..(((.((.(((....)-)).)...(((((.(((....))).))))).).)))-.......(((((((...))))))))).))..)))))). ( -44.90, z-score =  -1.89, R)
>droWil1.scaffold_180701 3683641 108 + 3904529
-----UGUGUGUGGAGGGGGGAAUGGGACGUCAGCGGUGG---CGGCAACGUUGGCGGCGACAGCCUCCGACAUGUGUAAAAGGAAUCGUUUAAAAUAAAUGACAGCAGCGCCCCC-
-----..........(((((........(((((....)))---))((...(((((.(((....))).)))))..............(((((((...)))))))..))....)))))- ( -33.50, z-score =   0.32, R)
>droPer1.super_34 422534 109 + 916997
---GGCAUCAGAAAGGACAACAGCAAAACAACAAUAAAUGCG---GCAACGUUGGCGGCGACAGACUCCGACAUGUGU-AAAGGAAUCGUUUAAAAUAAAUGACAGCGGCGCCCCC-
---(((...........((((.(((.............)))(---....)))))((.((.......(((.((....))-...))).(((((((...)))))))..)).)))))...- ( -24.42, z-score =  -0.22, R)
>droAna3.scaffold_13266 5604110 101 + 19884421
------------AACAUCAACAGC--AACAACAAUAAAUGCGGCAGCAACGUUGGCGGCGAAAGCCUCCGACAUGUGU-AAAGGAAUCGUUUAAAAUAAAUGACAGGCGAGCCCCC-
------------..........((--(...........)))(((.((...(((((.(((....))).)))))......-.......(((((((...)))))))...))..)))...- ( -27.30, z-score =  -1.85, R)
>consensus
________C_G_GAGCUGGGAAAUAAGACAGCAGCAGGGGAC_CGGCAACGUUGGCGGCGAAAGCCUCCGACAUGUGU_AAAGGAAUCGUUUAAAAUAAAUGACAGGCGAGCCCCC_
............................................(((...(((((.(((....))).)))))..............(((((((...))))))).......))).... (-18.52 = -19.18 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,128,022 – 20,128,129
Length 107
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 65.57
Shannon entropy 0.53934
G+C content 0.57954
Mean single sequence MFE -38.50
Consensus MFE -21.94
Energy contribution -22.88
Covariance contribution 0.94
Combinations/Pair 1.20
Mean z-score -1.91
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.19
SVM RNA-class probability 0.985003
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 20128022 107 - 21146708
AGCCGAGCUGUACUACUAUAUAGCUGAAACUGAAGCUG------GAAGCUGGGAGCUGGGAGCUAAG---GGAGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUG
.(((.(((((((......)))))))(...((..((((.------..(((.....)))...))))..)---)...)((....)))))...(((((.(((....))).)))))..... ( -40.00, z-score =  -2.00, R)
>droSim1.chr2R 18610622 100 - 19596830
AGCCGAGCUGUACUACUAUAUAGCUGAAAACGAA-------------GCUGGGAGCUGGGAGCUAAG---GGAGCAGGGGACCGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUG
.((((((((...(((((...(((((........)-------------))))..)).))).))))...---......(....)))))...(((((.(((....))).)))))..... ( -37.50, z-score =  -1.89, R)
>droYak2.chr2R 20093699 113 - 21139217
AGCCGCGC---AGUACUAUAUAGCUGAAACUGAAGCUGUGGCAAGUGGCAGGGGGUAGGGGCAUGGGGCAGGGGCAGGGGACUGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUG
.(((.(((---..((((.(((((((........)))))))((.....))....))))...))..).)))...(.(((....))).)...(((((.(((....))).)))))..... ( -43.20, z-score =  -1.25, R)
>droAna3.scaffold_13266 5604148 98 + 19884421
-----AGCUAUAUGGCUAUAUAGCCCUGCCUGCC-------------ACCAGCAACAUCAACAGCAACAACAAUAAAUGCGGCAGCAACGUUGGCGGCGAAAGCCUCCGACAUGUG
-----.(((((((....))))))).((((((((.-------------....))).........(((...........))))))))....(((((.(((....))).)))))..... ( -33.30, z-score =  -2.48, R)
>consensus
AGCCGAGCUGUACUACUAUAUAGCUGAAACUGAA_____________GCUGGGAGCAGGGACAUAAG___GGAGCAGGGGACCGGCGACGUUGGCGGCGAAAGCCUCCGACAUGUG
......((((((......))))))...........................(..(((((......................)))))..)(((((.(((....))).)))))..... (-21.94 = -22.88 +   0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:47:43 2011