Locus 10255

Sequence ID dm3.chr3R
Location 12,511,492 – 12,511,583
Length 91
Max. P 0.904626
window14098 window14099

overview

Window 8

Location 12,511,492 – 12,511,583
Length 91
Sequences 12
Columns 112
Reading direction forward
Mean pairwise identity 79.37
Shannon entropy 0.42193
G+C content 0.33186
Mean single sequence MFE -15.93
Consensus MFE -8.06
Energy contribution -8.22
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.904626
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12511492 91 + 27905053
------------CAUCUGCCUUGGACA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGC--------
------------...(((((((.....-....(((........))).................(((((((((......))))))))).........))))))).-------- ( -18.70, z-score =  -3.50, R)
>droSim1.chr3R 18559098 91 - 27517382
------------CAUCUGCCUUGGACA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGC--------
------------...(((((((.....-....(((........))).................(((((((((......))))))))).........))))))).-------- ( -18.70, z-score =  -3.50, R)
>droSec1.super_12 487478 91 - 2123299
------------CAUCUGCCUUGGACA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGC--------
------------...(((((((.....-....(((........))).................(((((((((......))))))))).........))))))).-------- ( -18.70, z-score =  -3.50, R)
>droYak2.chr3R 16953612 98 - 28832112
------------CCUCUGCCUCGGACA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGCAGACAGC-
------------.((((((((((....-.)))(((........))).................(((((((((......)))))))))...........))))).)).....- ( -19.60, z-score =  -3.01, R)
>droEre2.scaffold_4770 8626825 98 - 17746568
------------CAUCUGCCGCGGACA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGCAGACAGC-
------------..(((((.((.....-....(((........))).................(((((((((......)))))))))............)).)))))....- ( -18.80, z-score =  -2.57, R)
>droAna3.scaffold_13340 16325846 89 - 23697760
-------------GAGACAA-CGGACA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGC--------
-------------.((.((.-((....-.)).)))).......((.....((........)).(((((((((......)))))))))............))...-------- ( -10.10, z-score =  -1.40, R)
>dp4.chr2 17493957 106 + 30794189
GCCCCUCGG-----ACCCGUUCGGUCA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGCGAGCAGCG
((..(((((-----(((.....)))).-....((((..............((........)).(((((((((......)))))))))...........)))).))))..)). ( -22.00, z-score =  -1.75, R)
>droPer1.super_0 11342479 110 + 11822988
GCCCCUCGGCUCUGACCCGUUCGGUCA-ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGCGAGCAGC-
((..(((((((.(((((.....)))))-..(((((........))..................(((((((((......))))))))).))).......)))..))))..))- ( -21.80, z-score =  -1.14, R)
>droWil1.scaffold_181130 11550408 101 - 16660200
--------GACCAGCCGGGACCAGCAAAACGAUAGUAUACAACGCGAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGUUGAGCAGA---
--------(..(((((.............((...((.....)).)).................(((((((((......)))))))))...........)))))..)...--- ( -14.80, z-score =  -0.91, R)
>droVir3.scaffold_13047 13469842 75 - 19223366
----------------------------ACGAUGCAAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAA-AAACGC--------
----------------------------..(((((........))..................(((((((((......))))))))).)))......-......-------- (  -8.90, z-score =  -2.02, R)
>droMoj3.scaffold_6540 17991151 81 - 34148556
-----------------------CACCAACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAAAACGC--------
-----------------------.......(((((........))..................(((((((((......))))))))).))).............-------- (  -8.80, z-score =  -1.98, R)
>droGri2.scaffold_14906 3055018 90 - 14172833
--------------AGACAGCCGCACAAACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAGAAACGC--------
--------------........((........(((........))).......((.((((...(((((((((......))))))))).....)))).))...))-------- ( -10.30, z-score =  -1.11, R)
>consensus
______________UCUGCCUCGGACA_ACGAUGCUAUACAACGCAAAACACAUCAUUAAGUAUAAAAUUCUUAAAAUGGAAUUUUAAAUCAUUAAAAGGCAGC________
..............................(((((........))..................(((((((((......))))))))).)))..................... ( -8.06 =  -8.22 +   0.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,511,492 – 12,511,583
Length 91
Sequences 12
Columns 112
Reading direction reverse
Mean pairwise identity 79.37
Shannon entropy 0.42193
G+C content 0.33186
Mean single sequence MFE -20.47
Consensus MFE -9.43
Energy contribution -9.52
Covariance contribution 0.09
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.541787
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12511492 91 - 27905053
--------GCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGUCCAAGGCAGAUG------------
--------.(((((((.........((((((((........))))))))....(((((((((....(((...)))..)))))))-))...)))))))...------------ ( -22.90, z-score =  -3.24, R)
>droSim1.chr3R 18559098 91 + 27517382
--------GCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGUCCAAGGCAGAUG------------
--------.(((((((.........((((((((........))))))))....(((((((((....(((...)))..)))))))-))...)))))))...------------ ( -22.90, z-score =  -3.24, R)
>droSec1.super_12 487478 91 + 2123299
--------GCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGUCCAAGGCAGAUG------------
--------.(((((((.........((((((((........))))))))....(((((((((....(((...)))..)))))))-))...)))))))...------------ ( -22.90, z-score =  -3.24, R)
>droYak2.chr3R 16953612 98 + 28832112
-GCUGUCUGCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGUCCGAGGCAGAGG------------
-.....((.(((((((.........((((((((........))))))))....(((((((((....(((...)))..)))))))-))...))))))))).------------ ( -24.10, z-score =  -2.24, R)
>droEre2.scaffold_4770 8626825 98 + 17746568
-GCUGUCUGCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGUCCGCGGCAGAUG------------
-...(((((((((............((((((((........))))))))....(((((((((....(((...)))..)))))))-))...))))))))).------------ ( -27.60, z-score =  -3.89, R)
>droAna3.scaffold_13340 16325846 89 + 23697760
--------GCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGUCCG-UUGUCUC-------------
--------.........(((((...((((((((........))))))))....(((((((((....(((...)))..)))))))-))..))-)))....------------- ( -14.20, z-score =  -1.53, R)
>dp4.chr2 17493957 106 - 30794189
CGCUGCUCGCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGACCGAACGGGU-----CCGAGGGGC
.(((.((((..((((..........((((((((........))))))))...((((((((((....(((...)))..)))))))-)))......))))-----.)))).))) ( -27.40, z-score =  -1.46, R)
>droPer1.super_0 11342479 110 - 11822988
-GCUGCUCGCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU-UGACCGAACGGGUCAGAGCCGAGGGGC
-(((.((((((((((..........((((((((........))))))))...((((((((((....(((...)))..)))))))-)))......))).)))...)))).))) ( -28.20, z-score =  -1.16, R)
>droWil1.scaffold_181130 11550408 101 + 16660200
---UCUGCUCAACCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUCGCGUUGUAUACUAUCGUUUUGCUGGUCCCGGCUGGUC--------
---........(((....((((((.((((((((........))))))))......(..(((((...)))))..).....))))))..((((....)))).))).-------- ( -17.70, z-score =  -1.19, R)
>droVir3.scaffold_13047 13469842 75 + 19223366
--------GCGUUU-UUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUUGCAUCGU----------------------------
--------(((((.-.((((.(...((((((((........))))))))..))))).)))))....((((......))))....---------------------------- (  -9.90, z-score =  -0.13, R)
>droMoj3.scaffold_6540 17991151 81 + 34148556
--------GCGUUUUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGUUGGUG-----------------------
--------.((((.....))))...((((((((........))))))))((((.((((((((....(((...)))..))))))))))))----------------------- ( -13.60, z-score =  -1.06, R)
>droGri2.scaffold_14906 3055018 90 + 14172833
--------GCGUUUCUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGUUUGUGCGGCUGUCU--------------
--------((...............((((((((........))))))))(((..((((((((....(((...)))..)))))))).)))..)).....-------------- ( -14.30, z-score =  -0.16, R)
>consensus
________GCUGCCUUUUAAUGAUUUAAAAUUCCAUUUUAAGAAUUUUAUACUUAAUGAUGUGUUUUGCGUUGUAUAGCAUCGU_UGUCCGAGGCAGA______________
.........................((((((((........))))))))......(((((((....(((...)))..)))))))............................ ( -9.43 =  -9.52 +   0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:20:24 2011