Locus 8901

Sequence ID dm3.chr3R
Location 2,594,064 – 2,594,212
Length 148
Max. P 0.992641
window12214 window12215 window12216 window12217

overview

Window 4

Location 2,594,064 – 2,594,172
Length 108
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 63.67
Shannon entropy 0.67336
G+C content 0.37753
Mean single sequence MFE -19.97
Consensus MFE -8.07
Energy contribution -7.93
Covariance contribution -0.14
Combinations/Pair 1.42
Mean z-score -1.76
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.62
SVM RNA-class probability 0.955405
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2594064 108 + 27905053
AAUGCACAAGCAUUUCAUCUAAUUAACGUCAGCUGCUUAAUUUCCCUCCAACCGAUCAAAAGAUCCCUGGUCAAGCAGUUUUGCAAACGAAAUUC--ACCA--CAUACUGCU
(((((....))))).............((.((((((((.........(((...((((....))))..)))..))))))))..))...........--....--......... ( -16.10, z-score =  -0.82, R)
>droEre2.scaffold_4770 2836932 108 + 17746568
CUUUUACGAUAAUUCAAUUUAAUUGACACUAGCCUAGUAAUUUUCCUCCAACCGAUCAAAAGAUCGCCGGACAAGCAGUUUGUCAAACAAUAUUC--ACCA--CGAACUGCU
.............(((((...)))))....................(((...(((((....)))))..)))..((((((((((............--...)--))))))))) ( -18.86, z-score =  -2.40, R)
>droYak2.chr3R 21011859 107 - 28832112
CUUUUCCAAUUAUUAAAUUUAAUUGACAUUAGUCUUGUAAUUUUCCUCUAGCAGAUCGAAAGAUCCCUGGAAAAGCAGUUCGGCAAUCAA-AUUC--ACCA--CGAACUGCU
.(((((((......(((.(((...(((....)))...))).))).........((((....))))..)))))))((((((((........-....--....--)))))))). ( -27.69, z-score =  -4.23, R)
>droSec1.super_6 2685063 98 + 4358794
AAUGUACAAGCAUUUAAUUUAAUUGACGCCAACUGCG----------CCAACCGAUCAAUAGAUCACUGGUCAAGCAGUUUUGCAAACGAAAUUC--ACCG--CAAACUGCU
(((((....)))))........(((((((.....)).----------......((((....))))....)))))(((((((.((...........--...)--)))))))). ( -20.14, z-score =  -1.25, R)
>droSim1.chr3R 2624844 98 + 27517382
AAUGUACAAGCAUUUAAUUUAAUUGACGCCAACUGAG----------CCAACCGAUCAAUAGAUCACUGGUCAAGCAGUUUUGCAAACGAAAUUC--ACCA--CAAACUGCU
(((((....)))))........((((((((....).)----------).....((((....))))....)))))(((((((((............--..))--.))))))). ( -16.44, z-score =  -0.67, R)
>droMoj3.scaffold_6540 17591712 107 - 34148556
AGAUUACAAACUACGAUUCCCGUUG--UUUAAUUGUCCGAAUAA---UUGAGGGAUUUAACAUUUGAGCAACUAACUGUUCAGCUAACUAGAUUCUAGUCAGUUAAACUAUU
.(((...((((.(((.....))).)--)))....)))....(((---((((((((((((....(((((((......))))))).....))))))))..)))))))....... ( -20.60, z-score =  -1.20, R)
>consensus
AAUGUACAAGCAUUUAAUUUAAUUGACGCCAACUGAGUAAUUU____CCAACCGAUCAAAAGAUCACUGGACAAGCAGUUUUGCAAACGAAAUUC__ACCA__CAAACUGCU
.....................................................((((....))))........((((((((.......................)))))))) ( -8.07 =  -7.93 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,594,064 – 2,594,172
Length 108
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 63.67
Shannon entropy 0.67336
G+C content 0.37753
Mean single sequence MFE -25.21
Consensus MFE -9.37
Energy contribution -9.52
Covariance contribution 0.15
Combinations/Pair 1.59
Mean z-score -1.15
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.506476
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2594064 108 - 27905053
AGCAGUAUG--UGGU--GAAUUUCGUUUGCAAAACUGCUUGACCAGGGAUCUUUUGAUCGGUUGGAGGGAAAUUAAGCAGCUGACGUUAAUUAGAUGAAAUGCUUGUGCAUU
..((((.((--(...--.((((((.((((((....)))..((((...((((....)))))))).))).))))))..))))))).((((.....)))).(((((....))))) ( -24.50, z-score =   0.20, R)
>droEre2.scaffold_4770 2836932 108 - 17746568
AGCAGUUCG--UGGU--GAAUAUUGUUUGACAAACUGCUUGUCCGGCGAUCUUUUGAUCGGUUGGAGGAAAAUUACUAGGCUAGUGUCAAUUAAAUUGAAUUAUCGUAAAAG
.....((..--((((--((..(((..((((((....(((((((((((((((....)))).))))))(........))))))...))))))...)))....))))))..)).. ( -25.00, z-score =  -1.02, R)
>droYak2.chr3R 21011859 107 + 28832112
AGCAGUUCG--UGGU--GAAU-UUGAUUGCCGAACUGCUUUUCCAGGGAUCUUUCGAUCUGCUAGAGGAAAAUUACAAGACUAAUGUCAAUUAAAUUUAAUAAUUGGAAAAG
.(((((((.--.((.--.(..-....)..)))))))))(((((((((((((....)))))..................(((....)))...............)))))))). ( -28.60, z-score =  -2.58, R)
>droSec1.super_6 2685063 98 - 4358794
AGCAGUUUG--CGGU--GAAUUUCGUUUGCAAAACUGCUUGACCAGUGAUCUAUUGAUCGGUUGG----------CGCAGUUGGCGUCAAUUAAAUUAAAUGCUUGUACAUU
((((((((.--..(.--.(((...)))..).))))))))((((.(((((((....))))((((((----------(((.....))))))))).........))).)).)).. ( -29.60, z-score =  -1.96, R)
>droSim1.chr3R 2624844 98 - 27517382
AGCAGUUUG--UGGU--GAAUUUCGUUUGCAAAACUGCUUGACCAGUGAUCUAUUGAUCGGUUGG----------CUCAGUUGGCGUCAAUUAAAUUAAAUGCUUGUACAUU
((((((((.--..(.--.(((...)))..).))))))))((((((.(((((....))))).).))----------.)))((.(((((............)))))...))... ( -24.40, z-score =  -0.91, R)
>droMoj3.scaffold_6540 17591712 107 + 34148556
AAUAGUUUAACUGACUAGAAUCUAGUUAGCUGAACAGUUAGUUGCUCAAAUGUUAAAUCCCUCAA---UUAUUCGGACAAUUAAA--CAACGGGAAUCGUAGUUUGUAAUCU
....(((((.((((((((...)))))))).)))))..(((((((..(.((((.............---.)))).)..)))))))(--(.(((.....))).))......... ( -19.14, z-score =  -0.63, R)
>consensus
AGCAGUUUG__UGGU__GAAUUUCGUUUGCAAAACUGCUUGACCAGCGAUCUUUUGAUCGGUUGG____AAAUUACACAGCUAACGUCAAUUAAAUUAAAUGCUUGUAAAUU
((((((((.......................))))))))...(((((((((....))))).))))............................................... ( -9.37 =  -9.52 +   0.15)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,594,104 – 2,594,212
Length 108
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 67.43
Shannon entropy 0.61173
G+C content 0.45249
Mean single sequence MFE -27.25
Consensus MFE -15.38
Energy contribution -14.78
Covariance contribution -0.60
Combinations/Pair 1.54
Mean z-score -1.80
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.56
SVM RNA-class probability 0.992641
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2594104 108 + 27905053
UUUCCCUCCAACCGAUCAAAAGAUC-CCUGGUCAAGCAGUUUUGCAAACGAAAUUCACCACAUACUGCUUGCAUCGACAACUGCUUGUCUGC-CGUAGCGCGCCAUGUUC
.............((((....))))-..(((((((((((((.(((((.((...............)).))))).....)))))))))...((-......))))))..... ( -21.06, z-score =  -0.43, R)
>droEre2.scaffold_4770 2836972 108 + 17746568
UUUUCCUCCAACCGAUCAAAAGAUC-GCCGGACAAGCAGUUUGUCAAACAAUAUUCACCACGAACUGCUUGUAUUUGCAACUGCUUGUCUGC-AGUAGCGCGCCAUGUUC
............(((((....))))-)..(((((((((((((((...............)))))))))))))....((.(((((......))-))).))...))...... ( -33.96, z-score =  -4.07, R)
>droYak2.chr3R 21011899 107 - 28832112
UUUUCCUCUAGCAGAUCGAAAGAUC-CCUGGAAAAGCAGUUCGGCAAUCAA-AUUCACCACGAACUGCUUGCAUAUUCAACUGCUUGGCUGC-CUUAGCGCGCCACUUUC
......(((((..((((....))))-.))))).((((((((((........-........))))))))))(((........))).(((((((-....))).))))..... ( -34.59, z-score =  -3.71, R)
>droSec1.super_6 2685098 103 + 4358794
-----CGCCAACCGAUCAAUAGAUC-ACUGGUCAAGCAGUUUUGCAAACGAAAUUCACCGCAAACUGCUUGCAUAGGAAACUGCUUGUCUGC-AGUAGCGCGCCAUGUUC
-----((((..((((((....))))-....(.((((((((((.((..............)))))))))))))...))..(((((......))-))).).)))........ ( -30.24, z-score =  -1.64, R)
>droSim1.chr3R 2624879 103 + 27517382
-----AGCCAACCGAUCAAUAGAUC-ACUGGUCAAGCAGUUUUGCAAACGAAAUUCACCACAAACUGCUUGCAUAGGAAACUGCUUGUCUGU-AGUAGCGCGCCAUGUUC
-----.(((....((((....))))-(((((.(((((((((((((((.((...............)).)))))....)))))))))).))..-))).).))......... ( -24.16, z-score =  -0.30, R)
>droMoj3.scaffold_6540 17591742 105 - 34148556
---UUGUCCGAAUAAUUGAGGGAUUUAACAUUUGAGCAACUAACUGUUCAG--CUAACUAGAUUCUAGUCAGUUAAACUAUUACUCAAAAGUGCUUAACGUCUCGCAUUU
---.............((.(((((((((((((((((((......)))))((--((.(((((...))))).))))..............))))).)))).))))).))... ( -19.50, z-score =  -0.64, R)
>consensus
___UCCUCCAACCGAUCAAAAGAUC_ACUGGUCAAGCAGUUUUGCAAACAAAAUUCACCACAAACUGCUUGCAUAGGCAACUGCUUGUCUGC_AGUAGCGCGCCAUGUUC
......((((...((((....))))...))))(((((((((.(((((.((...............)).))))).....)))))))))....................... (-15.38 = -14.78 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,594,104 – 2,594,212
Length 108
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 67.43
Shannon entropy 0.61173
G+C content 0.45249
Mean single sequence MFE -31.48
Consensus MFE -20.17
Energy contribution -18.30
Covariance contribution -1.88
Combinations/Pair 1.71
Mean z-score -1.26
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.04
SVM RNA-class probability 0.980313
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2594104 108 - 27905053
GAACAUGGCGCGCUACG-GCAGACAAGCAGUUGUCGAUGCAAGCAGUAUGUGGUGAAUUUCGUUUGCAAAACUGCUUGACCAGG-GAUCUUUUGAUCGGUUGGAGGGAAA
.(((.(((...((....-))...(((((((((.....(((((((...((.......))...))))))).))))))))).)))..-((((....)))).)))......... ( -30.50, z-score =  -0.13, R)
>droEre2.scaffold_4770 2836972 108 - 17746568
GAACAUGGCGCGCUACU-GCAGACAAGCAGUUGCAAAUACAAGCAGUUCGUGGUGAAUAUUGUUUGACAAACUGCUUGUCCGGC-GAUCUUUUGAUCGGUUGGAGGAAAA
...........((.(((-((......))))).)).....(((((((((....((.((......)).)).)))))))))((((((-((((....)))).))))))...... ( -34.90, z-score =  -1.88, R)
>droYak2.chr3R 21011899 107 + 28832112
GAAAGUGGCGCGCUAAG-GCAGCCAAGCAGUUGAAUAUGCAAGCAGUUCGUGGUGAAU-UUGAUUGCCGAACUGCUUUUCCAGG-GAUCUUUCGAUCUGCUAGAGGAAAA
.....((((..((....-)).))))((((((((((.....(((((((((..((..(..-....)..))))))))))).((....-))...))))).)))))......... ( -33.90, z-score =  -0.93, R)
>droSec1.super_6 2685098 103 - 4358794
GAACAUGGCGCGCUACU-GCAGACAAGCAGUUUCCUAUGCAAGCAGUUUGCGGUGAAUUUCGUUUGCAAAACUGCUUGACCAGU-GAUCUAUUGAUCGGUUGGCG-----
...(((((.(....(((-((......)))))..))))))((((((((((...(..(((...)))..).)))))))))).(((.(-((((....))))).).))..----- ( -33.00, z-score =  -1.13, R)
>droSim1.chr3R 2624879 103 - 27517382
GAACAUGGCGCGCUACU-ACAGACAAGCAGUUUCCUAUGCAAGCAGUUUGUGGUGAAUUUCGUUUGCAAAACUGCUUGACCAGU-GAUCUAUUGAUCGGUUGGCU-----
...........((((((-.....((((((((((....((((((((((((.....)))))..)))))))))))))))))......-((((....)))))).)))).----- ( -29.70, z-score =  -0.76, R)
>droMoj3.scaffold_6540 17591742 105 + 34148556
AAAUGCGAGACGUUAAGCACUUUUGAGUAAUAGUUUAACUGACUAGAAUCUAGUUAG--CUGAACAGUUAGUUGCUCAAAUGUUAAAUCCCUCAAUUAUUCGGACAA---
......(((..(((.((((..((((((((((.(((((.((((((((...))))))))--.))))).....)))))))))))))).)))..)))..............--- ( -26.90, z-score =  -2.73, R)
>consensus
GAACAUGGCGCGCUACG_GCAGACAAGCAGUUGCCUAUGCAAGCAGUUUGUGGUGAAUUUCGUUUGCAAAACUGCUUGACCAGU_GAUCUUUUGAUCGGUUGGAGGA___
.....((((..............(((((((((.....(((((((.................))))))).))))))))).......((((....)))).))))........ (-20.17 = -18.30 +  -1.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:54:18 2011