Locus 7258

Sequence ID dm3.chr3L
Location 13,426,142 – 13,426,229
Length 87
Max. P 0.988153
window9992 window9993

overview

Window 2

Location 13,426,142 – 13,426,229
Length 87
Sequences 13
Columns 97
Reading direction forward
Mean pairwise identity 85.80
Shannon entropy 0.31231
G+C content 0.55732
Mean single sequence MFE -31.83
Consensus MFE -27.11
Energy contribution -26.57
Covariance contribution -0.54
Combinations/Pair 1.21
Mean z-score -1.92
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.77
SVM RNA-class probability 0.966780
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13426142 87 + 24543557
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGAUAAA----------
((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).)).....---------- ( -32.60, z-score =  -2.19, R)
>droGri2.scaffold_15110 17875141 87 + 24565398
CGACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGAAGCUAAU----------
...((((((((((((((.......)))))).(((((.......)))))..((((..((......)).))))))))))))........---------- ( -32.10, z-score =  -2.15, R)
>droMoj3.scaffold_6680 5130360 84 - 24764193
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGAUAAC-------------
...((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).....------------- ( -32.10, z-score =  -2.81, R)
>droVir3.scaffold_13049 17111495 89 - 25233164
CAGCUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGACCCCGGAUGGAACCAUGGCGUAUAAC--------
..((((((((((..(((((((((.........)))))..))))..........(((((.......))))))))))))..))).......-------- ( -29.50, z-score =  -1.44, R)
>droWil1.scaffold_180698 7114884 96 - 11422946
CAACUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCA-GGAUUCUGGUUGAGUCAA
...(((((((((..(((((((((.........)))))..))))..........(((((.......)))))))))))))-)(((((.....))))).. ( -36.30, z-score =  -2.96, R)
>droPer1.super_45 118515 85 + 618639
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACA-UGAUUGG-----------
(((((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))-.).))).----------- ( -29.40, z-score =  -1.32, R)
>dp4.chrXR_group8 2848906 85 - 9212921
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACA-UGAUUGG-----------
(((((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))-.).))).----------- ( -29.40, z-score =  -1.32, R)
>droAna3.scaffold_13337 1845583 88 - 23293914
CAGCUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACA--GGAUGAUUAA-------
((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))--)..)).....------- ( -32.10, z-score =  -1.72, R)
>droEre2.scaffold_4784 13437001 84 + 25762168
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGAU-------------
((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).))..------------- ( -32.60, z-score =  -2.14, R)
>droYak2.chr3L 13528204 85 + 24197627
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGAAG------------
((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).))...------------ ( -32.60, z-score =  -2.21, R)
>droSec1.super_0 5600852 87 + 21120651
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGAUAAA----------
((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).)).....---------- ( -32.60, z-score =  -2.19, R)
>droSim1.chr3L 12827177 87 + 22553184
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGAUAAA----------
((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).)).....---------- ( -32.60, z-score =  -2.19, R)
>anoGam1.chr2L 19552281 84 - 48795086
---CGGUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAAUGGAUGUU----------
---..(((((((.(((.(.(((.....))).(((((.......)))))).)))(((((.......))))))))))))..........---------- ( -29.90, z-score =  -0.34, R)
>consensus
CAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGGGAUAA___________
....(((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))................... (-27.11 = -26.57 +  -0.54)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,426,142 – 13,426,229
Length 87
Sequences 13
Columns 97
Reading direction reverse
Mean pairwise identity 85.80
Shannon entropy 0.31231
G+C content 0.55732
Mean single sequence MFE -31.35
Consensus MFE -29.48
Energy contribution -28.58
Covariance contribution -0.89
Combinations/Pair 1.26
Mean z-score -2.04
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.31
SVM RNA-class probability 0.988153
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13426142 87 - 24543557
----------UUUAUCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
----------.....((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)) ( -32.30, z-score =  -2.35, R)
>droGri2.scaffold_15110 17875141 87 - 24565398
----------AUUAGCUUCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUCG
----------........((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))... ( -31.90, z-score =  -1.88, R)
>droMoj3.scaffold_6680 5130360 84 + 24764193
-------------GUUAUCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
-------------.....((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))... ( -31.90, z-score =  -2.22, R)
>droVir3.scaffold_13049 17111495 89 + 25233164
--------GUUAUACGCCAUGGUUCCAUCCGGGGUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGCUG
--------.......((..(((((((((((((.......))))).....(((((.......))))).(((.....))).......)))))))))).. ( -29.60, z-score =  -1.95, R)
>droWil1.scaffold_180698 7114884 96 + 11422946
UUGACUCAACCAGAAUCC-UGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGUUG
.................(-(((((((((((((.......))))).....(((((.......))))).(((.....))).......)))))))))... ( -31.00, z-score =  -2.73, R)
>droPer1.super_45 118515 85 - 618639
-----------CCAAUCA-UGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
-----------.((((..-(((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))))) ( -30.00, z-score =  -1.57, R)
>dp4.chrXR_group8 2848906 85 + 9212921
-----------CCAAUCA-UGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
-----------.((((..-(((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))))) ( -30.00, z-score =  -1.57, R)
>droAna3.scaffold_13337 1845583 88 + 23293914
-------UUAAUCAUCC--UGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGCUG
-------.........(--(((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))... ( -31.90, z-score =  -2.10, R)
>droEre2.scaffold_4784 13437001 84 - 25762168
-------------AUCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
-------------..((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)) ( -32.30, z-score =  -2.22, R)
>droYak2.chr3L 13528204 85 - 24197627
------------CUUCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
------------...((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)) ( -32.30, z-score =  -2.20, R)
>droSec1.super_0 5600852 87 - 21120651
----------UUUAUCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
----------.....((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)) ( -32.30, z-score =  -2.35, R)
>droSim1.chr3L 12827177 87 - 22553184
----------UUUAUCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
----------.....((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)) ( -32.30, z-score =  -2.35, R)
>anoGam1.chr2L 19552281 84 + 48795086
----------AACAUCCAUUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAACCG---
----------..........((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).)))))))..--- ( -29.70, z-score =  -1.09, R)
>consensus
___________UCAUCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUG
...................(((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).)))))))).... (-29.48 = -28.58 +  -0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:23:30 2011