Locus 7259

Sequence ID dm3.chr3L
Location 13,426,740 – 13,426,839
Length 99
Max. P 0.935850
window9994 window9995

overview

Window 4

Location 13,426,740 – 13,426,839
Length 99
Sequences 13
Columns 99
Reading direction forward
Mean pairwise identity 82.04
Shannon entropy 0.40010
G+C content 0.56669
Mean single sequence MFE -33.42
Consensus MFE -29.11
Energy contribution -27.91
Covariance contribution -1.20
Combinations/Pair 1.24
Mean z-score -1.32
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.935850
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13426740 99 + 24543557
UCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAAUAUAGUCCGUCCGA
(((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))............... ( -34.90, z-score =  -1.43, R)
>droSim1.chr3L 12829617 97 + 22553184
--ACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGCUGAGCAUAGUUCGUCCGA
--..((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))..((((...))))...... ( -33.40, z-score =  -0.75, R)
>droSec1.super_0 5601814 99 + 21120651
UCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGCUGAGCGUGGUUCGUCCGA
(((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))...(((.....))). ( -36.00, z-score =  -0.59, R)
>droYak2.chr3L 13528768 99 + 24197627
CAGCCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAGCUGAGCGCGUCCAA
((((((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))....))))........... ( -36.30, z-score =  -0.91, R)
>droEre2.scaffold_4784 13437547 99 + 25762168
UAACAUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAGCUGAGUGCGUCCAA
((((.(((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))))).((.....))...... ( -33.50, z-score =  -0.82, R)
>droAna3.scaffold_13337 1846395 99 - 23293914
CAUCCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGCUGAAAGCCGUGCGCCCAA
....((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).)))))))))................... ( -31.90, z-score =   0.09, R)
>dp4.chrXR_group8 2849465 99 - 9212921
UCAUCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGCUGAACGUCGUGCGGCCAU
(((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))..(((....)))... ( -36.40, z-score =  -1.03, R)
>droPer1.super_45 119116 99 + 618639
UCAUCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGCUGAACGUCGUGCGGCCAU
(((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).)))..(((....)))... ( -36.40, z-score =  -1.03, R)
>droWil1.scaffold_180698 7115582 80 - 11422946
---CAUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGAUG----------------
---..(((((((((((((.......))))).....(((((.......))))).(((.....))).......))))))))....---------------- ( -28.60, z-score =  -3.32, R)
>droVir3.scaffold_13049 17111829 96 - 25233164
CCACUUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGUUGAGCACCGUCUGUC---
.((.((((((((((((((.......))))).....(((((.......))))).(((.....))).......))))))))).)).............--- ( -30.40, z-score =  -1.50, R)
>droMoj3.scaffold_6680 11784331 84 + 24764193
CAACAUGGUUCCAUCCGGGAUCGAACCGGAGACCUUCUGCGUGUAAAGCAGACGUGAUAACCGCUACACUAUGGAACCAGUUAA---------------
.(((.(((((((((((((.......))))).....(((((.......))))).(((.....))).......)))))))))))..--------------- ( -29.90, z-score =  -3.55, R)
>droGri2.scaffold_15110 6689306 99 - 24565398
UCAUCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAACGCAGGUCGGCCAA
(((.((((((((((((((.......)))))((......(((.((((.((....))..)))))))....)).))))))))).))).....((....)).. ( -36.80, z-score =  -1.28, R)
>anoGam1.chr2L 19555540 85 - 48795086
-AACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCCGCGUGUUAGGCGGAUGUGAUAACCACUACACCACGGAAACCGAUGAAU-------------
-...(.((((((((((((.......)))))((...(((((.......))))).(((.....)))....)).))))))).)......------------- ( -29.90, z-score =  -0.99, R)
>consensus
UCACCUGUUUCCGCCCGGGAUCGAACCGGGGGCCUUCUGCGUGUUAGGCAGAUGUGAUAACCGCUACACCACGGAAACAGUUGAACGUAGUGCGUCCAA
.....(((((((((((((.......))))).....(((((.......))))).(((.....))).......)))))))).................... (-29.11 = -27.91 +  -1.20)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 13,426,740 – 13,426,839
Length 99
Sequences 13
Columns 99
Reading direction reverse
Mean pairwise identity 82.04
Shannon entropy 0.40010
G+C content 0.56669
Mean single sequence MFE -32.50
Consensus MFE -26.69
Energy contribution -25.56
Covariance contribution -1.13
Combinations/Pair 1.24
Mean z-score -0.86
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.678932
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13426740 99 - 24543557
UCGGACGGACUAUAUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGA
...............(((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).))) ( -33.60, z-score =  -0.71, R)
>droSim1.chr3L 12829617 97 - 22553184
UCGGACGAACUAUGCUCAGCUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGU--
...................((((((((((((((.......)))))).(((((.......)))))..((((..((......)).))))))))))))..-- ( -32.00, z-score =  -0.23, R)
>droSec1.super_0 5601814 99 - 21120651
UCGGACGAACCACGCUCAGCUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGA
..((.....))....(((.((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).))) ( -36.40, z-score =  -0.94, R)
>droYak2.chr3L 13528768 99 - 24197627
UUGGACGCGCUCAGCUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGCUG
...((.((.....))))..((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).... ( -34.70, z-score =  -0.62, R)
>droEre2.scaffold_4784 13437547 99 - 25762168
UUGGACGCACUCAGCUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAUGUUA
...((.((.....))))((((((((((((((((.......)))))).(((((.......)))))..((((..((......)).))))))))))).))). ( -32.00, z-score =  -0.71, R)
>droAna3.scaffold_13337 1846395 99 + 23293914
UUGGGCGCACGGCUUUCAGCUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGAUG
..((((.....))))....((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).... ( -33.80, z-score =   0.07, R)
>dp4.chrXR_group8 2849465 99 + 9212921
AUGGCCGCACGACGUUCAGCUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGAUGA
.((..((.....))..)).((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).... ( -33.90, z-score =  -0.31, R)
>droPer1.super_45 119116 99 - 618639
AUGGCCGCACGACGUUCAGCUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGAUGA
.((..((.....))..)).((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).... ( -33.90, z-score =  -0.31, R)
>droWil1.scaffold_180698 7115582 80 + 11422946
----------------CAUCUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAUG---
----------------....((((((((..(((((((((.........)))))..))))..........(((((.......)))))))))))))..--- ( -27.70, z-score =  -2.41, R)
>droVir3.scaffold_13049 17111829 96 + 25233164
---GACAGACGGUGCUCAACUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAAGUGG
---.............((..((((((((..(((((((((.........)))))..))))..........(((((.......)))))))))))))..)). ( -29.60, z-score =  -0.43, R)
>droMoj3.scaffold_6680 11784331 84 - 24764193
---------------UUAACUGGUUCCAUAGUGUAGCGGUUAUCACGUCUGCUUUACACGCAGAAGGUCUCCGGUUCGAUCCCGGAUGGAACCAUGUUG
---------------.((((((((((((..(((((((((.........)))))..))))..........(((((.......))))))))))))).)))) ( -29.60, z-score =  -2.81, R)
>droGri2.scaffold_15110 6689306 99 + 24565398
UUGGCCGACCUGCGUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGAUGA
(((..((.....))..)))((((((((((((((.......)))))).(((((.......)))))..((((..((......)).)))))))))))).... ( -34.70, z-score =  -0.88, R)
>anoGam1.chr2L 19555540 85 + 48795086
-------------AUUCAUCGGUUUCCGUGGUGUAGUGGUUAUCACAUCCGCCUAACACGCGGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUU-
-------------....(((.(((((((.(((.(.(((.....))).(((((.......)))))).)))(((((.......)))))))))))).))).- ( -30.60, z-score =  -0.85, R)
>consensus
UUGGACGCACUACGUUCAACUGUUUCCGUGGUGUAGCGGUUAUCACAUCUGCCUAACACGCAGAAGGCCCCCGGUUCGAUCCCGGGCGGAAACAGGUGA
....................((((((((..((((.((((.........))))...))))..........(((((.......)))))))))))))..... (-26.69 = -25.56 +  -1.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:23:31 2011