Locus 11038

Sequence ID dm3.chr3R
Location 18,222,246 – 18,222,346
Length 100
Max. P 0.989470
window15165 window15166

overview

Window 5

Location 18,222,246 – 18,222,346
Length 100
Sequences 13
Columns 102
Reading direction forward
Mean pairwise identity 83.31
Shannon entropy 0.39444
G+C content 0.54020
Mean single sequence MFE -35.58
Consensus MFE -33.44
Energy contribution -32.02
Covariance contribution -1.42
Combinations/Pair 1.41
Mean z-score -1.92
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989470
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18222246 100 + 27905053
GAAGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGGAAAAUAUCCUUUUU-
...((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......))))))))))))(((.....))).....- ( -37.30, z-score =  -2.44, R)
>droSim1.chr3L 15030562 99 - 22553184
AUAGUCAGGAUGGCCGAGUGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUACUCUGUAGGCGUGGGUUCGAAUCCCACUUCUGACAAGACUUUUUUUAU---
...(((((((..(((((((((.((..(((.(((....))))))..)).))))))....)))(((((.......))))))))))))..............--- ( -36.10, z-score =  -2.54, R)
>droSec1.super_0 18578278 98 + 21120651
GAAGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCG--AAAUAUCCUUUAU-
...((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......)))))))))))).--.............- ( -35.40, z-score =  -2.29, R)
>droYak2.chr3R 19065908 100 + 28832112
GAAGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGUUAAAUAUCCUUUUU-
...((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......))))))))))))................- ( -35.40, z-score =  -2.27, R)
>droEre2.scaffold_4820 614917 100 - 10470090
GAAGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGGAGGAUACCCUUUUU-
...((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......))))))))))))(((((....)))))..- ( -38.40, z-score =  -1.96, R)
>droAna3.scaffold_13340 14777878 98 + 23697760
AGAGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGAACCCUAUUUUUU---
...((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......))))))))))))..............--- ( -35.40, z-score =  -1.95, R)
>dp4.chr2 16931290 98 - 30794189
AGAGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGAGUUGCAAUUUUU---
...((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......))))))))))))..............--- ( -35.40, z-score =  -1.69, R)
>droPer1.super_0 6581235 98 + 11822988
AGAGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGAGUUGCAAUUUUU---
...((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......))))))))))))..............--- ( -35.40, z-score =  -1.69, R)
>droWil1.scaffold_181130 12558288 100 + 16660200
CAUGACGAGGUGGCCGAGUGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGAGA-ACUUUCUCUGAU
...(((((((((((.((((...-....((((((((.......)))))))))))).)).)))(((((.......))))).))))))((((-....)))).... ( -36.61, z-score =  -1.96, R)
>droVir3.scaffold_13047 14022111 87 + 19223366
CAUGACGAGGUGGCCGAGUGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGCA--------------
...(((((((((((.((((...-....((((((((.......)))))))))))).)).)))(((((.......))))).))))))...-------------- ( -33.51, z-score =  -1.64, R)
>droMoj3.scaffold_6540 8084199 87 - 34148556
GAAGACGAGGUGGCCGAGUGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGCA--------------
...(((((((((((.((((...-....((((((((.......)))))))))))).)).)))(((((.......))))).))))))...-------------- ( -33.71, z-score =  -1.74, R)
>droGri2.scaffold_14830 335854 87 - 6267026
GAAGACGAGGUGGCCGAGUGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGGA--------------
...(((((((((((.((((...-....((((((((.......)))))))))))).)).)))(((((.......))))).))))))...-------------- ( -33.71, z-score =  -1.67, R)
>anoGam1.chr2R 36059751 98 - 62725911
--AGACGAGGUGGCCGAGAGGU-UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGGGCGAUGCUUUUUGU-
--.((((((((((((....)))-))..((((((((.......))))))((((...))))))(((((.......))))))))))))..((((......))))- ( -36.20, z-score =  -1.12, R)
>consensus
GAAGACGAGGUGGCCGAGAGGU_UAAGGCGUUGGACUGCUAAUCCAAUGUGCUCUGCACGCGUGGGUUCGAAUCCCAUCCUCGUCGAAA_AUAUUCUUU___
...(((((((..(((....))).....((((((((.......))))))((((...))))))(((((.......))))))))))))................. (-33.44 = -32.02 +  -1.42)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,222,246 – 18,222,346
Length 100
Sequences 13
Columns 102
Reading direction reverse
Mean pairwise identity 83.31
Shannon entropy 0.39444
G+C content 0.54020
Mean single sequence MFE -29.41
Consensus MFE -29.14
Energy contribution -28.02
Covariance contribution -1.12
Combinations/Pair 1.39
Mean z-score -1.74
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.25
SVM RNA-class probability 0.986644
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18222246 100 - 27905053
-AAAAAGGAUAUUUUCCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCUUC
-.....(((.....)))(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -31.90, z-score =  -2.28, R)
>droSim1.chr3L 15030562 99 + 22553184
---AUAAAAAAAGUCUUGUCAGAAGUGGGAUUCGAACCCACGCCUACAGAGUAGACUGCGACCUGAACGCAGCGCCUUAGACCACUCGGCCAUCCUGACUAU
---..............(((((..(((((.......)))))(((....(((..(.(((((.......))))))..))).((....)))))....)))))... ( -26.90, z-score =  -1.96, R)
>droSec1.super_0 18578278 98 - 21120651
-AUAAAGGAUAUUU--CGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCUUC
-.............--.(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -28.80, z-score =  -1.46, R)
>droYak2.chr3R 19065908 100 - 28832112
-AAAAAGGAUAUUUAACGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCUUC
-................(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -28.80, z-score =  -1.63, R)
>droEre2.scaffold_4820 614917 100 + 10470090
-AAAAAGGGUAUCCUCCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCUUC
-.....(((.....)))(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -30.20, z-score =  -1.04, R)
>droAna3.scaffold_13340 14777878 98 - 23697760
---AAAAAAUAGGGUUCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCUCU
---.......((((..(((.((((.((((.......)))).((((((...)))).((((((.....)))))).))....-.)))))))..).)))....... ( -29.60, z-score =  -1.18, R)
>dp4.chr2 16931290 98 + 30794189
---AAAAAUUGCAACUCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCUCU
---..............(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -28.80, z-score =  -1.59, R)
>droPer1.super_0 6581235 98 - 11822988
---AAAAAUUGCAACUCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCUCU
---..............(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -28.80, z-score =  -1.59, R)
>droWil1.scaffold_181130 12558288 100 - 16660200
AUCAGAGAAAGU-UCUCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCACUCGGCCACCUCGUCAUG
....((((....-))))(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -32.80, z-score =  -2.41, R)
>droVir3.scaffold_13047 14022111 87 - 19223366
--------------UGCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCACUCGGCCACCUCGUCAUG
--------------...(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -29.30, z-score =  -2.09, R)
>droMoj3.scaffold_6540 8084199 87 + 34148556
--------------UGCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCACUCGGCCACCUCGUCUUC
--------------...(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -28.80, z-score =  -1.89, R)
>droGri2.scaffold_14830 335854 87 + 6267026
--------------UCCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCACUCGGCCACCUCGUCUUC
--------------...(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............)))))))... ( -28.80, z-score =  -2.16, R)
>anoGam1.chr2R 36059751 98 + 62725911
-ACAAAAAGCAUCGCCCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA-ACCUCUCGGCCACCUCGUCU--
-................(((((((.((((.......)))).((((((...)))).((((((.....)))))).))....-............))))))).-- ( -28.80, z-score =  -1.29, R)
>consensus
___AAAAAAUAU_UUUCGACGAGGAUGGGAUUCGAACCCACGCGUGCAGAGCACAUUGGAUUAGCAGUCCAACGCCUUA_ACCUCUCGGCCACCUCGUCUUC
.................(((((((.((((.......)))).((((((...)))).((((((.....)))))).)).................)))))))... (-29.14 = -28.02 +  -1.12)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:35:12 2011