Locus 12171

Sequence ID dm3.chr3R
Location 26,201,573 – 26,201,708
Length 135
Max. P 0.999425
window16737 window16738 window16739 window16740

overview

Window 7

Location 26,201,573 – 26,201,679
Length 106
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 56.31
Shannon entropy 0.74819
G+C content 0.47787
Mean single sequence MFE -32.62
Consensus MFE -19.62
Energy contribution -19.70
Covariance contribution 0.08
Combinations/Pair 1.27
Mean z-score -1.79
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.68
SVM RNA-class probability 0.999155
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26201573 106 + 27905053
--UAAGCCUAGAUAUAUAAGAUAUACAUAAGAACGCCGCUCCGCUGCUGGCGUACCCGGCAGCGCAGCUACGCGGAUU-AGCCU----AAGUCCAAAUAUAUAAAAAACUGUA
--..........((((((................((.(((.(((((((((.....))))))))).)))...))(((((-.....----.)))))...)))))).......... ( -29.90, z-score =  -1.65, R)
>droSim1.chr3h_random 862046 96 + 1452968
--UAACUAUAUAUAUGUAGGAAACGCAAAUAAGCGUCGCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUGGACUUAGGCUA----AGAAACCAUUGUAU-----------
--........((..(.(((((.((((......)))).((.(((((((.(((...))).))))))).))))))).)..))((...----.....)).......----------- ( -32.10, z-score =  -1.43, R)
>droSec1.super_16 19895 96 + 1878335
--AAUAUAUAUAUAUGUAGGAAACGCAAAUAAGCGUCGCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUCGACUUAGGCUA----AGAAACCAUUGUAU-----------
--.(((((......((.((((.((((......)))).((.(((((((.(((...))).))))))).)))))))).....((...----.....))..)))))----------- ( -31.10, z-score =  -1.36, R)
>droEre2.scaffold_4855 234970 96 - 242605
------------UA-AGCACAGAUAUAUAAGAGAGCCGCUCCGCUGCUGGCGUAGCUGGCAGCGCAGCUACGCGGUUUUAGGUU----UAGCCGAAAUAUACUUAAGAAUGUA
------------..-...(((......((((((((((((..((((((..((...))..)))))).......)))))))).((..----...))........))))....))). ( -29.20, z-score =  -0.22, R)
>droPer1.super_81 10284 106 + 277874
UACUAACAUAUAAGGGAUAAGAACACAUAGUUCUGCCGCUCCGCUGCCGGCGUCACUGGCAGCGCAGCUCCGCGGCUUUUGGCUUACAAAAGCCCAAAAAAUUCAG-------
..............((...(((((.....))))).))(((.(((((((((.....))))))))).)))...(.((((((((.....)))))))))...........------- ( -40.80, z-score =  -4.30, R)
>consensus
__UAAACAUAUAUAUGUAAGAAACACAUAAAAGCGCCGCUCCGCUGCAGGCGUAGCCGGCAGCGCAGCUCCGCGGCUUAAGCUU____AAAACCCAAUAUAU__A________
..................................((((((.(((((((((.....))))))))).))).....)))..................................... (-19.62 = -19.70 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 26,201,573 – 26,201,679
Length 106
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 56.31
Shannon entropy 0.74819
G+C content 0.47787
Mean single sequence MFE -33.26
Consensus MFE -18.18
Energy contribution -18.98
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.13
SVM RNA-class probability 0.997592
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26201573 106 - 27905053
UACAGUUUUUUAUAUAUUUGGACUU----AGGCU-AAUCCGCGUAGCUGCGCUGCCGGGUACGCCAGCAGCGGAGCGGCGUUCUUAUGUAUAUCUUAUAUAUCUAGGCUUA--
..........(((((((..((((..----..((.-.....))((.(((.((((((.((.....)).)))))).))).))))))..)))))))...................-- ( -32.20, z-score =  -0.55, R)
>droSim1.chr3h_random 862046 96 - 1452968
-----------AUACAAUGGUUUCU----UAGCCUAAGUCCAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGCGACGCUUAUUUGCGUUUCCUACAUAUAUAUAGUUA--
-----------.......((((...----.)))).......((((((.(((((((.(((...))).))))))).))(((((......)))))))))...............-- ( -34.40, z-score =  -2.72, R)
>droSec1.super_16 19895 96 - 1878335
-----------AUACAAUGGUUUCU----UAGCCUAAGUCGAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGCGACGCUUAUUUGCGUUUCCUACAUAUAUAUAUAUU--
-----------.......((((...----.)))).......((((((.(((((((.(((...))).))))))).))(((((......)))))))))...............-- ( -34.50, z-score =  -2.77, R)
>droEre2.scaffold_4855 234970 96 + 242605
UACAUUCUUAAGUAUAUUUCGGCUA----AACCUAAAACCGCGUAGCUGCGCUGCCAGCUACGCCAGCAGCGGAGCGGCUCUCUUAUAUAUCUGUGCU-UA------------
........((((((((....((...----..)).......((...(((.((((((..((...))..)))))).))).)).............))))))-))------------ ( -25.60, z-score =   0.00, R)
>droPer1.super_81 10284 106 - 277874
-------CUGAAUUUUUUGGGCUUUUGUAAGCCAAAAGCCGCGGAGCUGCGCUGCCAGUGACGCCGGCAGCGGAGCGGCAGAACUAUGUGUUCUUAUCCCUUAUAUGUUAGUA
-------((((........((((((((.....))))))))..((((((.(((((((.(.....).))))))).)))...(((((.....)))))..)))........)))).. ( -39.60, z-score =  -1.94, R)
>consensus
________U__AUAUAUUGGGUUUU____AAGCCAAAGCCGCGGAGCUGCGCUGCCGGCAACGCCAGCAGCGGAGCGGCGCUCAUAUGUGUUUCUUACAUAUAUAUAUUUA__
..........................................(..(((.((((((.((.....)).)))))).)))..).................................. (-18.18 = -18.98 +   0.80)

alignment

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secondary structure

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dotplot

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Window 9

Location 26,201,608 – 26,201,708
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 59.92
Shannon entropy 0.71647
G+C content 0.49166
Mean single sequence MFE -30.78
Consensus MFE -18.70
Energy contribution -19.18
Covariance contribution 0.48
Combinations/Pair 1.17
Mean z-score -2.03
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.88
SVM RNA-class probability 0.999425
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26201608 100 + 27905053
GCUCCGCUGCUGGCGUACCCGGCAGCGCAGCUACGCGGAUUA-GCCUAAGUCCAAAUAUAUAAAAAACUGUAAAAUCGGAGAGACUCUGUAGACGUUGAGC
(((.(((((((((.....))))))))).)))...(((((((.-.....)))))............(((.((.....(((((...)))))...)))))..)) ( -31.20, z-score =  -1.50, R)
>droSim1.chr3h_random 862081 97 + 1452968
GCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUGGACUUAGGCUAAGAAACCAUUGUAUUUA-GAUCGCCAAAU--GAUUGACGAAUUAA-CUUCGAAU
((.(((((((.(((...))).))))))).)).((((....))))...........(((...(((-(.(((.(((..--..))).))).))))-...))).. ( -27.40, z-score =  -0.84, R)
>droSec1.super_16 19930 97 + 1878335
GCUGCGCUGCAGGCUAUGCCGGCAGCGCUGCUCCUCGACUUAGGCUAAGAAACCAUUGUAUUUA-GAUCGCCAAAU--CAUUGACGAAUUAA-CUUCGAAU
((.(((((((.(((...))).))))))).))...((((....((........)).......(((-(.(((.(((..--..))).))).))))-..)))).. ( -28.90, z-score =  -1.58, R)
>droEre2.scaffold_4855 234994 99 - 242605
GCUCCGCUGCUGGCGUAGCUGGCAGCGCAGCUACGCGGUUUUAGGUUUAGCCGAAAUAUACUUAAGAAUGUAUCGC--CAGAUACUUGUGAAUGUUUGAAC
(((.((((((..((...))..)))))).)))..(((((((((((((.((.......)).))))))))..(((((..--..))))))))))........... ( -33.20, z-score =  -1.59, R)
>droPer1.super_81 10321 89 + 277874
GCUCCGCUGCCGGCGUCACUGGCAGCGCAGCUCCGCGGCUU---UUGGCUUACAAAAGCCCAAAAAAUU-CAGAAU-AUAAAAACCAAUAAAAC-------
(((.(((((((((.....))))))))).)))...(.(((((---(((.....)))))))))........-......-.................------- ( -33.20, z-score =  -4.61, R)
>consensus
GCUCCGCUGCAGGCGUAGCCGGCAGCGCAGCUCCGCGGCUUA_GCUAAAAAACAAAUGUAUUUAAGAUUGCAAAAU__CAGAGACGAAUUAA_CUUCGAAC
(((.(((((((((.....))))))))).)))...................................................................... (-18.70 = -19.18 +   0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 26,201,608 – 26,201,708
Length 100
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 59.92
Shannon entropy 0.71647
G+C content 0.49166
Mean single sequence MFE -30.81
Consensus MFE -16.22
Energy contribution -17.70
Covariance contribution 1.48
Combinations/Pair 1.25
Mean z-score -1.62
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.84
SVM RNA-class probability 0.995742
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26201608 100 - 27905053
GCUCAACGUCUACAGAGUCUCUCCGAUUUUACAGUUUUUUAUAUAUUUGGACUUAGGC-UAAUCCGCGUAGCUGCGCUGCCGGGUACGCCAGCAGCGGAGC
.....((((......(((((.(((((....................)))))...))))-).....)))).(((.((((((.((.....)).)))))).))) ( -29.35, z-score =  -0.67, R)
>droSim1.chr3h_random 862081 97 - 1452968
AUUCGAAG-UUAAUUCGUCAAUC--AUUUGGCGAUC-UAAAUACAAUGGUUUCUUAGCCUAAGUCCAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGC
........-(((..(((((((..--..)))))))..-)))........((((((..((....))..)))))).(((((((.(((...))).)))))))... ( -33.10, z-score =  -2.67, R)
>droSec1.super_16 19930 97 - 1878335
AUUCGAAG-UUAAUUCGUCAAUG--AUUUGGCGAUC-UAAAUACAAUGGUUUCUUAGCCUAAGUCGAGGAGCAGCGCUGCCGGCAUAGCCUGCAGCGCAGC
........-(((..(((((((..--..)))))))..-)))........((((((..((....))..)))))).(((((((.(((...))).)))))))... ( -35.90, z-score =  -2.89, R)
>droEre2.scaffold_4855 234994 99 + 242605
GUUCAAACAUUCACAAGUAUCUG--GCGAUACAUUCUUAAGUAUAUUUCGGCUAAACCUAAAACCGCGUAGCUGCGCUGCCAGCUACGCCAGCAGCGGAGC
((((............(((((..--..)))))................((((((..(........)..))))))((((((..((...))..)))))))))) ( -23.90, z-score =  -0.20, R)
>droPer1.super_81 10321 89 - 277874
-------GUUUUAUUGGUUUUUAU-AUUCUG-AAUUUUUUGGGCUUUUGUAAGCCAA---AAGCCGCGGAGCUGCGCUGCCAGUGACGCCGGCAGCGGAGC
-------.................-......-.....((((((((((((.....)))---))))).))))(((.(((((((.(.....).))))))).))) ( -31.80, z-score =  -1.68, R)
>consensus
AUUCAAAG_UUAAUUAGUCUAUC__AUUUUGCAAUCUUAAAUACAUUUGUACCUAAGC_UAAGCCGCGGAGCUGCGCUGCCGGCAACGCCAGCAGCGGAGC
................(((((......)))))......................................(((.((((((.((.....)).)))))).))) (-16.22 = -17.70 +   1.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:57:09 2011