Locus 10854

Sequence ID dm3.chr3R
Location 17,077,143 – 17,077,312
Length 169
Max. P 0.917418
window14911 window14912 window14913

overview

Window 1

Location 17,077,143 – 17,077,235
Length 92
Sequences 11
Columns 116
Reading direction reverse
Mean pairwise identity 74.89
Shannon entropy 0.50920
G+C content 0.44765
Mean single sequence MFE -25.30
Consensus MFE -15.09
Energy contribution -14.74
Covariance contribution -0.35
Combinations/Pair 1.28
Mean z-score -1.45
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.917418
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17077143 92 - 27905053
CCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUUACUCGGCGUGUGGCUCAUUUGUCAGGGAUUG----GGAUUUGGACGA-ACUGGGACUU------------------
(((((..-.((((((..((((((..((.......))..))))))((((.(((...))).))))..))))))----(........)..-.)))))....------------------ ( -28.50, z-score =  -2.19, R)
>droSim1.chr3R 23135536 92 + 27517382
CCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUUACUCGGCGUGUGGCUCAUUUGUCAGGGAUUG----GGAUUAGGAAGA-ACUGGGCCCU------------------
(((....-......((.((((((..((.......))..))))))..))..((((......)))))))...(----((.((((.....-.)))).))).------------------ ( -28.10, z-score =  -1.75, R)
>droSec1.super_38 348902 92 + 400794
CCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUUACUCGGCGUGUGGCUCAUUUGUCAGGGAUUG----GGAUUAGGACGA-ACUGGGACUU------------------
(((((..-.((...((.((((((..((.......))..))))))..))..)).....((((((...(((..----..)))..)))))-))))))....------------------ ( -28.50, z-score =  -2.36, R)
>droYak2.chr3R 5868447 92 - 28832112
CCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUUACUCGGCGUGUGGCUCAUUUGUCAGGGAUUG----GGAUUAGGACGC-ACUUGGAAUU------------------
.((((..-.........((((((..((.......))..)))))).((((.(..((((.((......)).))----))....).))))-..))))....------------------ ( -24.30, z-score =  -1.12, R)
>droEre2.scaffold_4770 13163551 92 + 17746568
CCCAGAA-ACAAUUCGAGAGUAAUGAUGAAGAAAGUUGUUACUCGGCGUGUGGCUCAUUUGUCAGGGAUUG----GGAUUAGGACGC-ACUGGGGCUU------------------
(((((..-.........((((((..((.......))..)))))).((((.(..((((.((......)).))----))....).))))-.)))))....------------------ ( -28.00, z-score =  -1.91, R)
>droAna3.scaffold_13340 3739233 95 - 23697760
CCCAGAA-ACAAUUUGAGAGUAAUGACGAAGAAAGUUGUUACUCGGCGUGUGGCUCAUUUGUCAGGGAUUG----GGAUUAGAGGAG-ACUGAGACCCAGG---------------
(((....-.........((((((..((.......))..))))))((((.(((...))).)))).))).(((----((.((..((...-.))..))))))).--------------- ( -29.70, z-score =  -2.63, R)
>dp4.chr2 5580102 77 - 30794189
CCCAAAA-ACCAUUUGAAAGUAAUGAUGAAGAAAGUUGUUACUUAGCAUGUGGCUCAUUUGUCAAGGAUUGUCGAGGA--------------------------------------
.((....-.((((.((.((((((..((.......))..))))))..)).)))).....(((.((.....)).))))).-------------------------------------- ( -14.60, z-score =  -0.42, R)
>droPer1.super_19 1296683 94 - 1869541
CCCAAAA-ACCAUUUGAAAGUAAUGAUGAAGAAAGUUGUUACUUAGCGUGUGGCUCAUUUGUCAAGGAUUGUCGAGGAUUGGCAGUGGGCCUGGG---------------------
((((...-.........((((((..((.......))..)))))).......((((((((.(((((.............)))))))))))))))))--------------------- ( -26.42, z-score =  -1.57, R)
>droWil1.scaffold_181130 16053523 100 - 16660200
CCCAGAAUACAAUUUGAAAGUAAUGACGAAGAAAGUUGUUACUUAGCGUGUGGCUCAUUUGUCAGGAAUUG----GGAUUGGGAUUCUGAUGGGAGGGGGGCGG------------
(((....((((......((((((..((.......))..))))))....)))).(((.((..((((.((((.----.......))))))))..)).))))))...------------ ( -24.80, z-score =  -1.24, R)
>droMoj3.scaffold_6540 264435 115 + 34148556
CCCAGAA-ACAAUUUGAAGGUAAUGAGGAAGAAAGUUGUUACUUAGCUUGUGCCUCAUUUGUCAGCGAUUGCUCAGAGCUGAGAUGAGAAAAAGACAAAAAGAUGCUGAGAGACGA
.......-.((((((((....(((((((....((((((.....))))))...)))))))..)))..)))))(((((..((....................))...)))))...... ( -23.85, z-score =  -0.31, R)
>droGri2.scaffold_15074 2594581 95 - 7742996
UCCAGAA-ACAAUUUGAACGUAAUGACGAAGAAAGUUGUUACUUAGCUUGUGGCUCAUUUGUCAGCGAUUGCUCAAAAGCAGGACAAGCAGACCUU--------------------
...((.(-(((((((...(((....)))....)))))))).))..(((((((((......))).....(((((....))))).)))))).......-------------------- ( -21.50, z-score =  -0.46, R)
>consensus
CCCAGAA_ACAAUUUGAGAGUAAUGACGAAGAAAGUUGUUACUCGGCGUGUGGCUCAUUUGUCAGGGAUUG____GGAUUAGGACGA_ACUGGGACUU__________________
.........((((((..((((((..((.......))..))))))......((((......)))).))))))............................................. (-15.09 = -14.74 +  -0.35)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,077,196 – 17,077,301
Length 105
Sequences 8
Columns 107
Reading direction reverse
Mean pairwise identity 78.34
Shannon entropy 0.45096
G+C content 0.44649
Mean single sequence MFE -25.48
Consensus MFE -16.76
Energy contribution -18.19
Covariance contribution 1.42
Combinations/Pair 1.21
Mean z-score -1.06
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.31
SVM RNA-class probability 0.640540
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17077196 105 - 27905053
CAUUCAAUCCCAACCCUCUGCUCGCCAGGAUUGCGUGGGUGCUCACAGUUUUU-CAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUU
..........((((..(((((((....((((((..((((((((((.((((...-.)))).))).)))))))...-.))))))..))))........)))..)))).. ( -27.00, z-score =  -1.02, R)
>droSim1.chr3R 23135589 104 + 27517382
CAUACCAGCCC-AUCCUCCGCUCGCCAGGAUUGCGUGGGUGCUCACAGUUUUU-CAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUU
.....((((.(-.((.((.((((....((((((..((((((((((.((((...-.)))).))).)))))))...-.))))))..))))...)).)).)...)))).. ( -26.50, z-score =  -0.95, R)
>droSec1.super_38 348955 88 + 400794
-----------------CCGCUCGCCAGGAUUGCGUGGGUGCUCAAAGUUUUU-CAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUU
-----------------..((((....((((((..(((((((((((((((...-.)))))))).)))))))...-.))))))..))))((..((.......))..)) ( -29.50, z-score =  -3.01, R)
>droYak2.chr3R 5868500 104 - 28832112
CGGUUCACCCC-AUCCUCAGCUCACCAGGAUUGCGUGGGUGCUCACAGUUUUU-CAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUU
.((......))-.((.(((((((....((((((..((((((((((.((((...-.)))).))).)))))))...-.))))))..))))..))).))........... ( -26.30, z-score =  -0.63, R)
>droEre2.scaffold_4770 13163604 103 + 17746568
CAGUUCAUCCC-AUCCUCCGCUCGCCUGGAUUGCGUGGGUGCUCACAG-UUUU-CAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGAUGAAGAAAGUUGUU
..........(-(((....((((...(((((((..((((((((((.((-(...-..))).))).)))))))...-.))))))).))))...))))............ ( -26.70, z-score =  -0.86, R)
>droAna3.scaffold_13340 3739289 102 - 23697760
CGGUCGGAGUC-CCCAUCAUCUCGACA--AUUGCGUGGGUGCUCACAGUUUUU-CAAUUUUGAUGCGCCCAGAA-ACAAUUUGAGAGUAAUGACGAAGAAAGUUGUU
..(((((....-.))....((((((..--((((..((((((((((.((((...-.)))).))).)))))))...-.)))))))))).....)))............. ( -25.90, z-score =  -0.49, R)
>droWil1.scaffold_181130 16053583 98 - 16660200
------UGGUCUUCUUCCUUUUCAACA--AUUGCGUGGGUGCUCACAGUUUUU-CAAUUUUGAUGCGCCCAGAAUACAAUUUGAAAGUAAUGACGAAGAAAGUUGUU
------...(((((.((.(((((((..--((((..((((((((((.((((...-.)))).))).))))))).....)))))))))))....)).)))))........ ( -23.80, z-score =  -1.26, R)
>droVir3.scaffold_12822 2827569 87 + 4096053
-------------------GCAAGCCAAGCUUGUAUACGCUUACGUGUUUCUCACAAUUUGGAUGCGCCCAGAA-ACAAUUUGAACGUAAUGACGAAGAAAGUUGUU
-------------------(((..(((((.(((((((((....))))).....))))))))).))).......(-(((((((...(((....)))....)))))))) ( -18.10, z-score =  -0.25, R)
>consensus
C__U__A_CCC_ACCCUCCGCUCGCCAGGAUUGCGUGGGUGCUCACAGUUUUU_CAAUUUUGAUGCGCCCAGAA_ACAAUUCGAGAGUAAUGACGAAGAAAGUUGUU
...................((((....((((((..((((((((((.((((.....)))).))).))))))).....))))))..))))((..((.......))..)) (-16.76 = -18.19 +   1.42)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,077,207 – 17,077,312
Length 105
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.23
Shannon entropy 0.44265
G+C content 0.46564
Mean single sequence MFE -26.33
Consensus MFE -16.85
Energy contribution -16.80
Covariance contribution -0.05
Combinations/Pair 1.05
Mean z-score -1.07
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.551325
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17077207 105 - 27905053
GAUUCCCAUCCCAUUCAAUCCCAACCCUCUGC--UCGCCAGGAUUGCGUGGGUGCUCACAGUUUUUCAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGACGA
.............................(((--((....((((((..((((((((((.((((....)))).))).)))))))...-.))))))..)))))....... ( -25.30, z-score =  -1.05, R)
>droSim1.chr3R 23135600 104 + 27517382
GGUUUCCUUCCCAUACCAGCCC-AUCCUCCGC--UCGCCAGGAUUGCGUGGGUGCUCACAGUUUUUCAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGACGA
(((...........))).....-.......((--((....((((((..((((((((((.((((....)))).))).)))))))...-.))))))..))))........ ( -25.80, z-score =  -0.56, R)
>droYak2.chr3R 5868511 104 - 28832112
AAUCGUUUCAUCGGUUCACCCC-AUCCUCAGC--UCACCAGGAUUGCGUGGGUGCUCACAGUUUUUCAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGACGA
..(((((.....((......))-.......((--((....((((((..((((((((((.((((....)))).))).)))))))...-.))))))..))))...))))) ( -27.50, z-score =  -1.27, R)
>droEre2.scaffold_4770 13163615 102 + 17746568
-AUCGUUUCAGCAGUUCAUCCC-AUCCUCCGC--UCGCCUGGAUUGCGUGGGUGCUCACAG-UUUUCAAUUUUGAUGCGCCCAGAA-ACAAUUCGAGAGUAAUGAUGA
-((((((((.((((((((....-.........--.....)))))))).((((((((((.((-(.....))).))).))))))))))-)).((((....).)))))).. ( -27.97, z-score =  -1.08, R)
>droAna3.scaffold_13340 3739300 98 - 23697760
--------AAUCAACCGGUCGGAGUCCCCAUC-AUCUCGACAAUUGCGUGGGUGCUCACAGUUUUUCAAUUUUGAUGCGCCCAGAA-ACAAUUUGAGAGUAAUGACGA
--------.........(((((.....))...-.((((((..((((..((((((((((.((((....)))).))).)))))))...-.)))))))))).....))).. ( -25.90, z-score =  -0.86, R)
>droWil1.scaffold_181130 16053594 98 - 16660200
----------AGAAGGCAUUUUGGUCUUCUUCCUUUUCAACAAUUGCGUGGGUGCUCACAGUUUUUCAAUUUUGAUGCGCCCAGAAUACAAUUUGAAAGUAAUGACGA
----------(((((((......)))))))...(((((((..((((..((((((((((.((((....)))).))).))))))).....)))))))))))......... ( -25.50, z-score =  -1.62, R)
>consensus
_AU____UCACCAAUCCAUCCC_AUCCUCAGC__UCGCCAGGAUUGCGUGGGUGCUCACAGUUUUUCAAUUUUGAUGCGCCCAGAA_ACAAUUCGAGAGUAAUGACGA
..........................................(((((.((((((((((.((((....)))).))).)))))))(((.....)))....)))))..... (-16.85 = -16.80 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:31:43 2011