Locus 10887

Sequence ID dm3.chr3R
Location 17,328,534 – 17,328,614
Length 80
Max. P 0.898017
window14958 window14959

overview

Window 8

Location 17,328,534 – 17,328,614
Length 80
Sequences 10
Columns 89
Reading direction forward
Mean pairwise identity 77.15
Shannon entropy 0.44714
G+C content 0.46999
Mean single sequence MFE -20.63
Consensus MFE -9.59
Energy contribution -10.09
Covariance contribution 0.50
Combinations/Pair 1.06
Mean z-score -2.27
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.898017
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17328534 80 + 27905053
AAUAAGCACGAUCAGAGAAGACUUUUAAGGCAACAUGCCUAUCGGCAUGUCAUUGUUG-GCCAACACAUUCGUGCACCAAG--------
.....((((((..((((....))))...(((.(((((((....)))))))((....))-))).......))))))......-------- ( -24.10, z-score =  -3.29, R)
>droSim1.chr3R 23377166 80 - 27517382
AAUAAGCACGAUCAGAGAAGACUUUUAAGGCAACAUGCCUAUCGGCAUGUCAUUGUUG-GCCAACACAUUCGUGCACCGAG--------
.....((((((..((((....))))...(((.(((((((....)))))))((....))-))).......))))))......-------- ( -24.10, z-score =  -3.04, R)
>droSec1.super_6 197875 80 - 4358794
AAUAAGCACGAUCAGAGAAGACUUUUAAGGCAACAUGCCUAUCGGCAUGUCAUUGUUG-GCCAACACAUUCGUGCACCGAG--------
.....((((((..((((....))))...(((.(((((((....)))))))((....))-))).......))))))......-------- ( -24.10, z-score =  -3.04, R)
>droYak2.chr3R 6163711 80 + 28832112
AAUAAGCACGAUCAGAGAAGACUUUUAAGGCAACAUGCCUAUCGGCAUGUCAUUGUUG-GCCAACACAUUCGUGCACCGAG--------
.....((((((..((((....))))...(((.(((((((....)))))))((....))-))).......))))))......-------- ( -24.10, z-score =  -3.04, R)
>droEre2.scaffold_4770 13408647 80 - 17746568
AAUAAGCACGAUCAGAGAAGACUUUUAAGGCAACAUGCCUAUCGGCAUGUCAUUGUUG-GCCAACACAUUCGUGCACCGCG--------
.....((((((..((((....))))...(((.(((((((....)))))))((....))-))).......))))))......-------- ( -24.10, z-score =  -2.68, R)
>droAna3.scaffold_13340 17668039 87 + 23697760
AAUAAGCGCGAUCACAGAAGUCUUUUAAGGCAACAAGCCUAUCGGCAUGUCAUUGGAG-GCCAACAU-CCCACAGACCUAUACACAGAG
.....((.((((...((....))....((((.....))))))))))..(((..(((.(-(......)-))))..)))............ ( -13.80, z-score =   0.28, R)
>dp4.chr2 10768859 63 + 30794189
AAUAAGCGCGAUCAGAGAAGUCUUUUAAGCCAACAUGCCUAUCGGCAUGUCAUUGCAG-ACCCA-------------------------
.....((((....((((....))))...))..(((((((....)))))))....))..-.....------------------------- ( -15.00, z-score =  -1.71, R)
>droPer1.super_0 2116699 63 - 11822988
AAUAAGCGCGAUCAGAGAAGUCUUUUAAGCCAACAUGCCUAUCGGCAUGUCAUUGCAG-GCCCA-------------------------
.....((((....((((....))))...))..(((((((....)))))))....))..-.....------------------------- ( -15.00, z-score =  -0.87, R)
>droVir3.scaffold_12822 3132384 62 - 4096053
AAUAAGCGCGAUCAGAGAAGUCUUUUAAGCCAACAUGCCUGUCGGCAUGUCAUUCGUGCUCA---------------------------
....(((((((..((((....)))).......(((((((....)))))))...)))))))..--------------------------- ( -20.10, z-score =  -2.86, R)
>droGri2.scaffold_15074 2843675 84 + 7742996
AAUAAGCGCGAUCAGAGAAGUCUUUUAAGCCAACAUGCCUGUCGGCAUGUCAUUCGCGCACCCAGAC-CUCACACGCACACUAAC----
.....((((((..((((....)))).......(((((((....)))))))...))))))........-.................---- ( -21.90, z-score =  -2.46, R)
>consensus
AAUAAGCACGAUCAGAGAAGACUUUUAAGGCAACAUGCCUAUCGGCAUGUCAUUGUUG_GCCAACAC_UUCGUGCACCGAG________
.......(((((.((((....)))).......(((((((....))))))).)))))................................. ( -9.59 = -10.09 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,328,534 – 17,328,614
Length 80
Sequences 10
Columns 89
Reading direction reverse
Mean pairwise identity 77.15
Shannon entropy 0.44714
G+C content 0.46999
Mean single sequence MFE -22.91
Consensus MFE -12.08
Energy contribution -12.18
Covariance contribution 0.10
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.849676
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17328534 80 - 27905053
--------CUUGGUGCACGAAUGUGUUGGC-CAACAAUGACAUGCCGAUAGGCAUGUUGCCUUAAAAGUCUUCUCUGAUCGUGCUUAUU
--------......((((((.......(((-.......((((((((....))))))))))).......((......))))))))..... ( -23.91, z-score =  -2.12, R)
>droSim1.chr3R 23377166 80 + 27517382
--------CUCGGUGCACGAAUGUGUUGGC-CAACAAUGACAUGCCGAUAGGCAUGUUGCCUUAAAAGUCUUCUCUGAUCGUGCUUAUU
--------......((((((.......(((-.......((((((((....))))))))))).......((......))))))))..... ( -23.91, z-score =  -2.03, R)
>droSec1.super_6 197875 80 + 4358794
--------CUCGGUGCACGAAUGUGUUGGC-CAACAAUGACAUGCCGAUAGGCAUGUUGCCUUAAAAGUCUUCUCUGAUCGUGCUUAUU
--------......((((((.......(((-.......((((((((....))))))))))).......((......))))))))..... ( -23.91, z-score =  -2.03, R)
>droYak2.chr3R 6163711 80 - 28832112
--------CUCGGUGCACGAAUGUGUUGGC-CAACAAUGACAUGCCGAUAGGCAUGUUGCCUUAAAAGUCUUCUCUGAUCGUGCUUAUU
--------......((((((.......(((-.......((((((((....))))))))))).......((......))))))))..... ( -23.91, z-score =  -2.03, R)
>droEre2.scaffold_4770 13408647 80 + 17746568
--------CGCGGUGCACGAAUGUGUUGGC-CAACAAUGACAUGCCGAUAGGCAUGUUGCCUUAAAAGUCUUCUCUGAUCGUGCUUAUU
--------......((((((.......(((-.......((((((((....))))))))))).......((......))))))))..... ( -23.91, z-score =  -1.48, R)
>droAna3.scaffold_13340 17668039 87 - 23697760
CUCUGUGUAUAGGUCUGUGGG-AUGUUGGC-CUCCAAUGACAUGCCGAUAGGCUUGUUGCCUUAAAAGACUUCUGUGAUCGCGCUUAUU
....((((((((((((..(((-..(((((.-..)))))((((.(((....))).)))).)))....))))..)))))..)))....... ( -21.80, z-score =  -0.45, R)
>dp4.chr2 10768859 63 - 30794189
-------------------------UGGGU-CUGCAAUGACAUGCCGAUAGGCAUGUUGGCUUAAAAGACUUCUCUGAUCGCGCUUAUU
-------------------------.((((-((((...((((((((....)))))))).)).....))))))................. ( -17.80, z-score =  -1.51, R)
>droPer1.super_0 2116699 63 + 11822988
-------------------------UGGGC-CUGCAAUGACAUGCCGAUAGGCAUGUUGGCUUAAAAGACUUCUCUGAUCGCGCUUAUU
-------------------------(((((-(......((((((((....))))))))))))))......................... ( -17.80, z-score =  -1.23, R)
>droVir3.scaffold_12822 3132384 62 + 4096053
---------------------------UGAGCACGAAUGACAUGCCGACAGGCAUGUUGGCUUAAAAGACUUCUCUGAUCGCGCUUAUU
---------------------------(((((.(((..((((((((....))))))))........(((....)))..))).))))).. ( -21.20, z-score =  -3.34, R)
>droGri2.scaffold_15074 2843675 84 - 7742996
----GUUAGUGUGCGUGUGAG-GUCUGGGUGCGCGAAUGACAUGCCGACAGGCAUGUUGGCUUAAAAGACUUCUCUGAUCGCGCUUAUU
----......(((((.(.(((-((((...((.((...(((((((((....))))))))))).))..))))))).)....)))))..... ( -31.00, z-score =  -2.26, R)
>consensus
________CUCGGUGCACGAA_GUGUUGGC_CAACAAUGACAUGCCGAUAGGCAUGUUGCCUUAAAAGACUUCUCUGAUCGCGCUUAUU
......................................((((((((....))))))))............................... (-12.08 = -12.18 +   0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:32:21 2011