Locus 71

Sequence ID dm3.chr2L
Location 541,402 – 541,546
Length 144
Max. P 0.982474
window105 window106 window107 window108

overview

Window 5

Location 541,402 – 541,520
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.52
Shannon entropy 0.18705
G+C content 0.42488
Mean single sequence MFE -34.62
Consensus MFE -27.08
Energy contribution -27.40
Covariance contribution 0.32
Combinations/Pair 1.14
Mean z-score -2.55
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.60
SVM RNA-class probability 0.953793
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 541402 118 + 23011544
AAUUUUUAUUGAAAUUACAUAGGUUUGUACGUAGUACUCGCGAUACAAAAUAGCCCGUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGAAA--AGAGCGUCGAAUUCUGGGUGCC
((((((....))))))....((((((((((((.......))).)))))....(((.((......)).)))))))(((((((((((.((.(((....--..))).))..))))))))))). ( -36.70, z-score =  -3.52, R)
>droEre2.scaffold_4929 596449 118 + 26641161
CAUUUUUAUUGAAAUUACAUGUGUUUGUACGUAGUACUUGCGAUACAAAAUAGACCGUAGAAUAAUCAG-AUAUGCACCCAGAAUCGAAGAUGAGA-AUGAGCUUCGGUUACUGGGUGCC
..............((((.....(((((((((((...))))).)))))).......)))).........-....((((((((((((((((......-.....)))))))).)))))))). ( -31.70, z-score =  -3.00, R)
>droYak2.chr2L 528704 118 + 22324452
CAUUUUUAUUGAAAUUACAUAUGUUUGUACGUAGUACUUGCGAUACAAAAUAGCCCGUAGAACAAUCGG-ACAUGCACCCAGAAUCGAAGAUGGAA-GGGAGCGUCGGCUUCUGGGUGCC
.((((((((((.((.(((.(((((....)))))))).)).))))).))))).(.(((.........)))-.)..((((((((((.(...((((...-.....)))).).)))))))))). ( -31.10, z-score =  -1.25, R)
>droSec1.super_14 523974 119 + 2068291
CAUUUUUAUUGAAAUUACAUAGGUUUGUACGUAGUACUUGCGGUACAAAAUAGCCCAUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGCAA-UGGAGCGUCGAAUUCUGGGUGCC
....................((((((((((((((...)))).))))))....(((.((......)).)))))))(((((((((((.((.(((.(..-.).))).))..))))))))))). ( -36.90, z-score =  -2.59, R)
>droSim1.chr2L 549899 120 + 22036055
CAUUUUUAUUGAAAUUACAUAGGUUUGUACGUAGUACUUGCGGUACAAAAUAGCCCAUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGCAAGCUGAGCGUCGAAUUCUGGGUGCC
....................((((((((((((((...)))).))))))....(((.((......)).)))))))(((((((((((.((.(((........))).))..))))))))))). ( -36.70, z-score =  -2.37, R)
>consensus
CAUUUUUAUUGAAAUUACAUAGGUUUGUACGUAGUACUUGCGAUACAAAAUAGCCCGUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGAAA__GGAGCGUCGAAUUCUGGGUGCC
....................((((((((((((((...))))).))))))...(((.((......)).))).)))(((((((((((.((.(((........))).)).).)))))))))). (-27.08 = -27.40 +   0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 541,402 – 541,520
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.52
Shannon entropy 0.18705
G+C content 0.42488
Mean single sequence MFE -33.15
Consensus MFE -24.68
Energy contribution -24.56
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -3.05
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.10
SVM RNA-class probability 0.982474
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 541402 118 - 23011544
GGCACCCAGAAUUCGACGCUCU--UUUCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUACGGGCUAUUUUGUAUCGCGAGUACUACGUACAAACCUAUGUAAUUUCAAUAAAAAUU
.(((((((((((..((.(((..--....))).)).))))))))))).(((((.((.((..(....)..)).)).)))))..(((...((((((......))))))..))).......... ( -35.00, z-score =  -3.53, R)
>droEre2.scaffold_4929 596449 118 - 26641161
GGCACCCAGUAACCGAAGCUCAU-UCUCAUCUUCGAUUCUGGGUGCAUAU-CUGAUUAUUCUACGGUCUAUUUUGUAUCGCAAGUACUACGUACAAACACAUGUAAUUUCAAUAAAAAUG
.((((((((.((.(((((.....-......))))).))))))))))....-..........((((......((((((((....)......)))))))....))))............... ( -25.30, z-score =  -2.51, R)
>droYak2.chr2L 528704 118 - 22324452
GGCACCCAGAAGCCGACGCUCCC-UUCCAUCUUCGAUUCUGGGUGCAUGU-CCGAUUGUUCUACGGGCUAUUUUGUAUCGCAAGUACUACGUACAAACAUAUGUAAUUUCAAUAAAAAUG
.((((((((((..(((.......-........))).))))))))))..((-(((.........)))))(((((((((.(....))))((((((......)))))).........)))))) ( -31.46, z-score =  -2.56, R)
>droSec1.super_14 523974 119 - 2068291
GGCACCCAGAAUUCGACGCUCCA-UUGCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUAUGGGCUAUUUUGUACCGCAAGUACUACGUACAAACCUAUGUAAUUUCAAUAAAAAUG
.(((((((((((..((.(((...-....))).)).)))))))))))(((((((.((......)).)))....(((((((....)......)))))))))).................... ( -36.70, z-score =  -3.41, R)
>droSim1.chr2L 549899 120 - 22036055
GGCACCCAGAAUUCGACGCUCAGCUUGCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUAUGGGCUAUUUUGUACCGCAAGUACUACGUACAAACCUAUGUAAUUUCAAUAAAAAUG
.(((((((((((..((.((((.....).))).)).)))))))))))(((((((.((......)).)))....(((((((....)......)))))))))).................... ( -37.30, z-score =  -3.23, R)
>consensus
GGCACCCAGAAUUCGACGCUCA__UUGCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUACGGGCUAUUUUGUAUCGCAAGUACUACGUACAAACCUAUGUAAUUUCAAUAAAAAUG
.((((((((((...((.(((........))).))..))))))))))((((.(((.........)))......(((((((....)......)))))))))).................... (-24.68 = -24.56 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 541,428 – 541,546
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.15
Shannon entropy 0.22608
G+C content 0.51278
Mean single sequence MFE -38.52
Consensus MFE -28.64
Energy contribution -30.00
Covariance contribution 1.36
Combinations/Pair 1.08
Mean z-score -1.71
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.542893
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 541428 118 + 23011544
GUACGUAGUACUCGCGAUACAAAAUAGCCCGUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGAAA--AGAGCGUCGAAUUCUGGGUGCCACGUGGCCACUUUGGGCCUCAUCGAA
((((...))))...((((........(((.((......)).)))....(((((((((((.((.(((....--..))).))..)))))))))))...(.((((......)))).))))).. ( -40.40, z-score =  -2.45, R)
>droEre2.scaffold_4929 596475 118 + 26641161
GUACGUAGUACUUGCGAUACAAAAUAGACCGUAGAAUAAUCAG-AUAUGCACCCAGAAUCGAAGAUGAGA-AUGAGCUUCGGUUACUGGGUGCCACGUAGCCACUUUGGGGCUCUUCAAA
.(((((.....(((((.............))))).........-....((((((((((((((((......-.....)))))))).)))))))).)))))(((.(....))))........ ( -34.12, z-score =  -1.99, R)
>droYak2.chr2L 528730 118 + 22324452
GUACGUAGUACUUGCGAUACAAAAUAGCCCGUAGAACAAUCGG-ACAUGCACCCAGAAUCGAAGAUGGAA-GGGAGCGUCGGCUUCUGGGUGCCACGUAGCCACUUUGGGGCUCAUCAUA
((((((((...))))).))).....(((((...((....))((-..((((((((((((.(...((((...-.....)))).).))))))))))...))..))......)))))....... ( -34.30, z-score =  -0.25, R)
>droSec1.super_14 524000 117 + 2068291
GUACGUAGUACUUGCGGUACAAAAUAGCCCAUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGCAA-UGGAGCGUCGAAUUCUGGGUGCCACGUGGCCACUUUGGGCCCCAUCG--
((((((((...)))).))))......(((((..((....))(((((..(((((((((((.((.(((.(..-.).))).))..)))))))))))...)).)))....))))).......-- ( -42.00, z-score =  -1.96, R)
>droSim1.chr2L 549925 118 + 22036055
GUACGUAGUACUUGCGGUACAAAAUAGCCCAUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGCAAGCUGAGCGUCGAAUUCUGGGUGCCACGUGGCCACUUUGGGCCCCAUCG--
((((((((...)))).))))......(((((..((....))(((((..(((((((((((.((.(((........))).))..)))))))))))...)).)))....))))).......-- ( -41.80, z-score =  -1.87, R)
>consensus
GUACGUAGUACUUGCGAUACAAAAUAGCCCGUAGAAUAAUCGGCACCUGCACCCAGAAUGGAAGCUGAAA__GGAGCGUCGAAUUCUGGGUGCCACGUGGCCACUUUGGGCCUCAUCG_A
((((((((...))))).)))......(((((..((....))(((((..(((((((((((.((.(((........))).)).).))))))))))...)).)))....)))))......... (-28.64 = -30.00 +   1.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 541,428 – 541,546
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.15
Shannon entropy 0.22608
G+C content 0.51278
Mean single sequence MFE -40.61
Consensus MFE -34.62
Energy contribution -34.46
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -2.31
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.90
SVM RNA-class probability 0.974116
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 541428 118 - 23011544
UUCGAUGAGGCCCAAAGUGGCCACGUGGCACCCAGAAUUCGACGCUCU--UUUCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUACGGGCUAUUUUGUAUCGCGAGUACUACGUAC
((((.(((....((((((((((.(((((((((((((((..((.(((..--....))).)).))))))))))).......((....))))))))))))))))..))))))).......... ( -44.80, z-score =  -3.45, R)
>droEre2.scaffold_4929 596475 118 - 26641161
UUUGAAGAGCCCCAAAGUGGCUACGUGGCACCCAGUAACCGAAGCUCAU-UCUCAUCUUCGAUUCUGGGUGCAUAU-CUGAUUAUUCUACGGUCUAUUUUGUAUCGCAAGUACUACGUAC
.......((((.......))))(((((((((((((.((.(((((.....-......))))).))))))))))....-.......................(((.(....))))))))).. ( -31.30, z-score =  -1.61, R)
>droYak2.chr2L 528730 118 - 22324452
UAUGAUGAGCCCCAAAGUGGCUACGUGGCACCCAGAAGCCGACGCUCCC-UUCCAUCUUCGAUUCUGGGUGCAUGU-CCGAUUGUUCUACGGGCUAUUUUGUAUCGCAAGUACUACGUAC
.......((((.......))))(((((((((((((((..(((.......-........))).))))))))))..((-(((.........)))))......(((.(....))))))))).. ( -36.36, z-score =  -1.51, R)
>droSec1.super_14 524000 117 - 2068291
--CGAUGGGGCCCAAAGUGGCCACGUGGCACCCAGAAUUCGACGCUCCA-UUGCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUAUGGGCUAUUUUGUACCGCAAGUACUACGUAC
--...((.((..((((((((((.(((((((((((((((..((.(((...-....))).)).))))))))))).......((....))))))))))))))))..)).)).((((...)))) ( -45.00, z-score =  -2.54, R)
>droSim1.chr2L 549925 118 - 22036055
--CGAUGGGGCCCAAAGUGGCCACGUGGCACCCAGAAUUCGACGCUCAGCUUGCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUAUGGGCUAUUUUGUACCGCAAGUACUACGUAC
--...((.((..((((((((((.(((((((((((((((..((.((((.....).))).)).))))))))))).......((....))))))))))))))))..)).)).((((...)))) ( -45.60, z-score =  -2.44, R)
>consensus
U_CGAUGAGGCCCAAAGUGGCCACGUGGCACCCAGAAUUCGACGCUCA__UUGCAGCUUCCAUUCUGGGUGCAGGUGCCGAUUAUUCUACGGGCUAUUUUGUAUCGCAAGUACUACGUAC
......((....((((((((((.((((((((((((((...((.(((........))).))..)))))))))).......((....))))))))))))))))..))....((((...)))) (-34.62 = -34.46 +  -0.16)

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 21:06:08 2011