Locus 5334

Sequence ID dm3.chr2R
Location 19,597,316 – 19,597,437
Length 121
Max. P 0.856636
window7313 window7314

overview

Window 3

Location 19,597,316 – 19,597,437
Length 121
Sequences 7
Columns 128
Reading direction forward
Mean pairwise identity 63.45
Shannon entropy 0.67800
G+C content 0.47985
Mean single sequence MFE -35.56
Consensus MFE -12.34
Energy contribution -11.01
Covariance contribution -1.34
Combinations/Pair 1.67
Mean z-score -1.69
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.856636
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19597316 121 + 21146708
UUGCGCCUCCCAUCGAUAGCAGUCC-AACUGGAUUU-UGCAUGCUAUCGAUAUUUUCCCAAUUUAAAUUUGUAGUUCUAACAGC-GAGCACCAGUGGCGUCUUCCGCUUCCGGUUGUUGCUUGG----
.(((.......((((((((((((((-....))))..-....)))))))))).................((((.((....)).))-)))))((((..(((....(((....))).)))..).)))---- ( -31.40, z-score =  -1.43, R)
>droSim1.chr2R 18163367 121 + 19596830
UUGCGCCUCCCACCGAUAGCAGUCC-AAUUGGAUUU-UGCAUGCUAUCGAUACUUUCCCAAUUUAAAUUUUUAGUUCUAACAGC-GAGCACCAGUGGCGCCUUCCGUUUCCGGUGCUUGCUUGG----
.........(((.((((((((((((-....))))..-....))))))))................................(((-(((((((.(..(((.....)))..).)))))))))))))---- ( -36.10, z-score =  -3.08, R)
>droSec1.super_9 2876318 121 + 3197100
UUGCGCCUCCCACCGAUAGCAGUCC-AAUUGGAUUU-UGCAUGCUAUCGAUACUUUCCCAAUUUUAAUUUUUAGUUCUAACAGC-GAGCACCAGUGGCGCCUUCCGUUUCCGGUGCUUGCUUGG----
.........(((.((((((((((((-....))))..-....))))))))................................(((-(((((((.(..(((.....)))..).)))))))))))))---- ( -36.10, z-score =  -3.17, R)
>droYak2.chr2R 19574164 121 + 21139217
UUGCGCCUCCCACCGAUAGCAGUCCCAACUGGAUUU-UGCAUGCUAUCGAUAUUUUUAUAAUUCAAAUUUAUAGUUAUAAAAGC-AACCAUGCGGGGCGCCA-CCGCUUCCGGUUAUUGCUUUA----
..(((((((....((((((((((((.....))))..-....))))))))....((((((((((.........))))))))))((-(....)))))))))).(-(((....))))..........---- ( -34.50, z-score =  -2.61, R)
>droEre2.scaffold_4845 20959158 120 + 22589142
UUGCGCCUCCCACCGAUAGCGGUGC-AACUGGUUUU-UGCAUGCUAUCGAUAUUUUUGCAAUUUGAAUUUGUAGUACUAAAAGC-GGGCACGCGUGGCGCCA-CCGUUUCCGGUUGUUGCUUGA----
..(((...(((..((((((((.(((-((.......)-))))))))))))......((((((.......))))))..........-)))..)))(..(((..(-(((....)))))))..)....---- ( -36.50, z-score =  -0.32, R)
>dp4.chr3 10375364 127 - 19779522
UCGU-UCAUACAACGAACGUGUUGCGAGCGAACUUUCUGCGUACGCUCCCAGGUUCUUCGGCUCUAGCGUUCGGUUCGACUCGUUGUGUGCCGGUUGUGGGCACCAUACUUUACACGUGCAUAUUUUA
((((-(.....)))))((((((.((((((((((......((.(((((....((..(....)..))))))).))))))).)))))((.(((((.......)))))))......)))))).......... ( -38.20, z-score =  -0.50, R)
>droPer1.super_4 2436315 123 - 7162766
UCGU-UCAUACAACGAACGUGUUGCGAGCGAACUUUCUGCGUACGCUCCCAGGUUCUUCGGCUCUAGCGUUCGGCUCGACUCGUUGUGUGCCGGUUGUGUAC----UUUUUUACACGUGCAUAUUUUA
(((.-.((((((((((.((.((..(((((((((((...((....))....))))))....((....))))))))).))..)))))))))).))).(((((((----..........)))))))..... ( -36.10, z-score =  -0.72, R)
>consensus
UUGCGCCUCCCACCGAUAGCAGUCC_AACUGGAUUU_UGCAUGCUAUCGAUAUUUUUCCAAUUUAAAUUUUUAGUUCUAACAGC_GAGCACCAGUGGCGCCU_CCGUUUCCGGUUCUUGCUUGG____
..(((((.(....((((((((....................))))))))........................((.((........)).))..).)))))............................ (-12.34 = -11.01 +  -1.34)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,597,316 – 19,597,437
Length 121
Sequences 7
Columns 128
Reading direction reverse
Mean pairwise identity 63.45
Shannon entropy 0.67800
G+C content 0.47985
Mean single sequence MFE -36.05
Consensus MFE -14.35
Energy contribution -14.70
Covariance contribution 0.36
Combinations/Pair 1.50
Mean z-score -1.37
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.88
SVM RNA-class probability 0.841550
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19597316 121 - 21146708
----CCAAGCAACAACCGGAAGCGGAAGACGCCACUGGUGCUC-GCUGUUAGAACUACAAAUUUAAAUUGGGAAAAUAUCGAUAGCAUGCA-AAAUCCAGUU-GGACUGCUAUCGAUGGGAGGCGCAA
----....((....(((((..(((.....)))..)))))((((-.(..(((((........)))))...).))...((((((((((((.((-(.......))-).).)))))))))))....)))).. ( -32.90, z-score =  -1.18, R)
>droSim1.chr2R 18163367 121 - 19596830
----CCAAGCAAGCACCGGAAACGGAAGGCGCCACUGGUGCUC-GCUGUUAGAACUAAAAAUUUAAAUUGGGAAAGUAUCGAUAGCAUGCA-AAAUCCAAUU-GGACUGCUAUCGGUGGGAGGCGCAA
----...........(((....)))...((((((((....(((-(...(((((........)))))..))))..)))(((((((((((.((-(.......))-).).))))))))))....))))).. ( -36.90, z-score =  -1.62, R)
>droSec1.super_9 2876318 121 - 3197100
----CCAAGCAAGCACCGGAAACGGAAGGCGCCACUGGUGCUC-GCUGUUAGAACUAAAAAUUAAAAUUGGGAAAGUAUCGAUAGCAUGCA-AAAUCCAAUU-GGACUGCUAUCGGUGGGAGGCGCAA
----...........(((....)))...(((((.(..((....-....(((....)))........))..).....((((((((((((.((-(.......))-).).)))))))))))...))))).. ( -35.79, z-score =  -1.42, R)
>droYak2.chr2R 19574164 121 - 21139217
----UAAAGCAAUAACCGGAAGCGG-UGGCGCCCCGCAUGGUU-GCUUUUAUAACUAUAAAUUUGAAUUAUAAAAAUAUCGAUAGCAUGCA-AAAUCCAGUUGGGACUGCUAUCGGUGGGAGGCGCAA
----..........((((....)))-).(((((((..((((((-(......)))))))..................(((((((((((.(..-...(((.....))))))))))))))))).))))).. ( -37.90, z-score =  -2.09, R)
>droEre2.scaffold_4845 20959158 120 - 22589142
----UCAAGCAACAACCGGAAACGG-UGGCGCCACGCGUGCCC-GCUUUUAGUACUACAAAUUCAAAUUGCAAAAAUAUCGAUAGCAUGCA-AAAACCAGUU-GCACCGCUAUCGGUGGGAGGCGCAA
----....((....((((....)))-).)).....((((.(((-((.....(((..............)))........(((((((.((((-(.......))-)))..))))))))))))..)))).. ( -40.24, z-score =  -2.39, R)
>dp4.chr3 10375364 127 + 19779522
UAAAAUAUGCACGUGUAAAGUAUGGUGCCCACAACCGGCACACAACGAGUCGAACCGAACGCUAGAGCCGAAGAACCUGGGAGCGUACGCAGAAAGUUCGCUCGCAACACGUUCGUUGUAUGA-ACGA
..........((((((......(((((((.......))))).)).((((.(((((((.(((((....(((.......))).))))).))......)))))))))..))))))(((((.....)-)))) ( -36.50, z-score =  -0.70, R)
>droPer1.super_4 2436315 123 + 7162766
UAAAAUAUGCACGUGUAAAAAA----GUACACAACCGGCACACAACGAGUCGAGCCGAACGCUAGAGCCGAAGAACCUGGGAGCGUACGCAGAAAGUUCGCUCGCAACACGUUCGUUGUAUGA-ACGA
.......(((..(((((.....----.)))))..((((....(..((..((.(((.....))).))..))..)...))))(((((.((.......)).))))))))...(((((((...))))-))). ( -32.10, z-score =  -0.21, R)
>consensus
____CCAAGCAAGAACCGGAAACGG_AGGCGCCACUGGUGCUC_GCUGUUAGAACUAAAAAUUAAAAUUGGAAAAAUAUCGAUAGCAUGCA_AAAUCCAGUU_GGACUGCUAUCGGUGGGAGGCGCAA
........((.....(((....))).....(((..((((..............))))...................((((((((((......................))))))))))...))))).. (-14.35 = -14.70 +   0.36)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:46:16 2011