Locus 8042

Sequence ID dm3.chr3L
Location 19,711,209 – 19,711,301
Length 92
Max. P 0.999272
window11067 window11068

overview

Window 7

Location 19,711,209 – 19,711,301
Length 92
Sequences 12
Columns 112
Reading direction forward
Mean pairwise identity 67.55
Shannon entropy 0.65214
G+C content 0.48382
Mean single sequence MFE -26.45
Consensus MFE -14.87
Energy contribution -14.92
Covariance contribution 0.05
Combinations/Pair 1.55
Mean z-score -0.87
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.904689
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19711209 92 + 24543557
GUUGUUGUUCUCCGUGCUAA--CUUUCUUUUGCCCG----CCCAGUCGACAUGCAAAAGAAGAAUCCGCACAGGCGCAACAA-GCAAUCGGGGGAGGGG-------------
....((.(((((((((((..--.((((((((((.((----......))....))))))))))....(((....))).....)-)))..))))))).)).------------- ( -24.80, z-score =   0.59, R)
>droGri2.scaffold_15110 15532711 98 + 24565398
GUAGUUGCU-CCCGUGUAGAGUUUUUCUUUUGCUAUG-UUUGGCUCCAACAUGCAAAAGAA-AUUCUACACGCACGCAACAG-GCAAUCGACUCUUGGGUAA----------
...(((((.-..(((((((((((..((((((((.(((-((.(....)))))))))))))))-))))))))))...)))))..-.......(((....)))..---------- ( -36.20, z-score =  -4.72, R)
>droVir3.scaffold_13049 11529057 95 - 25233164
GUUGUUCCC-UCAGUGUAGAGAUUUUCCUUUGCUGUG-UUCG-CUCCAACAUGCAAAAGAA-AUUCCACACUAACGCAGCAG-GCAAACGAAAAUUGGUU------------
(((((....-..(((((.(.((.((((.(((((.(((-((..-....)))))))))).)))-).))))))))...)))))..-.................------------ ( -21.00, z-score =  -0.64, R)
>droMoj3.scaffold_6680 13642634 93 + 24764193
GUAGUUGCC-UCAGUGUAGAGAUUUCCUUUUGCUUUA-GUUU-CUCCAACAUGCAAAAGAA-AUUCCACACACACGCAACAG-GCAAACGAAACUUGG--------------
...(((((.-...((((.(..(((((.((((((....-(((.-....)))..)))))))))-))..)))))....)))))..-...............-------------- ( -21.10, z-score =  -1.65, R)
>droWil1.scaffold_180949 4853084 109 + 6375548
---CCUGUUGUUGUUGUAGAGAUUUUCCUUUGCCCUGUUUCUGGUUCAACAUGCAAAAGGAAAAUAUCUACAGCAAUGUCAACACAAGCCAACAAUUAGAUGGGAUUAUAUA
---..(((((((((((((((.((((((((((((..((((........)))).)).)))))))))).))))))))))...)))))....(((.(.....).)))......... ( -31.70, z-score =  -3.13, R)
>droPer1.super_48 566602 101 + 581423
GUUGUUGUUCUGCGUGUAAAAACUUUCCUUUGCUUGUCGUCCAGGUCAACAUGCAAAGGAAGAAUCUACACAAGCGCAACAA-GCAGACGGGGAAGGGGAUC----------
.(((((((.((..(((((.....((((((((((.(((.(.......).))).))))))))))....))))).)).)))))))-...................---------- ( -28.60, z-score =  -1.13, R)
>dp4.chrXR_group8 7785194 101 + 9212921
GUUGUUGUUCUGCGUGUAAAAACUUUCCUUUGCUUGUCGUCCAGGUCAACAUGCAAAGGAAGAAUCUACACAAGCGCAACAA-GCAGACGGGGAAGGGGAUC----------
.(((((((.((..(((((.....((((((((((.(((.(.......).))).))))))))))....))))).)).)))))))-...................---------- ( -28.60, z-score =  -1.13, R)
>droAna3.scaffold_13337 6109105 97 - 23293914
UUGGUUGUUCUCCGUGCAAA--CUAUCUUUUGCCCU--GUCCCGCGAAACAUGCAAAAGAA-AAUCUACACAGGGGCAACAA-GCAAACGGGGUAUGGGAACA---------
.....(((((.((((((...--...((.(((((..(--((((((((.....)))...((..-...)).....))))))....-))))).)).)))))))))))--------- ( -27.30, z-score =  -0.97, R)
>droEre2.scaffold_4784 19504142 92 + 25762168
GUUGUUGUUCUCCGUGCUAA--CUUUCUUCUGCUCG----CCCAGUCGACAUGCAAAAGAAGAAUCCGCACAGGCGCAACAA-GCGAUCGGGGGAAGGG-------------
.....(.((((((((((...--..((((((((((((----......)))...))...)))))))...)))).(((((.....-))).)).)))))).).------------- ( -25.10, z-score =   0.39, R)
>droYak2.chr3L 3381832 92 - 24197627
GUUGUUGUUCUCCGUGCUAA--CUUUCUUCUGCCCG----CCCAGUCGACAUGCAAAAGAAGAAUCCGCACAGGUGCAACAA-GCAAUCGGGGGAGGGG-------------
....((.(((((((((((..--..(((((((....(----(...........))...)))))))...(((....)))....)-)))..))))))).)).------------- ( -23.50, z-score =   0.95, R)
>droSec1.super_29 409241 89 + 700605
GUUGUUGUUCUCCGUGCUAA--CUUUCUUUUGCCCG----CCCAGACGACAUGCAAAAGA---AUCCGCACAGGCGCAACAA-GCAAUCGGGGGAGGGG-------------
....((.(((((((((((..--..(((((((((.((----......))....))))))))---)..(((....))).....)-)))..))))))).)).------------- ( -24.70, z-score =   0.36, R)
>droSim1.chr3L 19037288 92 + 22553184
GUUGUUGUUCUCCGUGCUAA--CUUUCUUUUGCCCG----CCCAGUCGACAUGCAAAAGAAGAAUCCGCACAGGCGCAACAA-GCAAUCGGGGGAGGGG-------------
....((.(((((((((((..--.((((((((((.((----......))....))))))))))....(((....))).....)-)))..))))))).)).------------- ( -24.80, z-score =   0.59, R)
>consensus
GUUGUUGUUCUCCGUGCAAA__CUUUCUUUUGCCCG___UCCCAGUCAACAUGCAAAAGAAGAAUCCACACAGGCGCAACAA_GCAAUCGGGGGAGGGG_____________
...(((((.((..((((.......(((((((((...................)))))))))......)))).)).)))))................................ (-14.87 = -14.92 +   0.05)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 8

Location 19,711,209 – 19,711,301
Length 92
Sequences 12
Columns 112
Reading direction reverse
Mean pairwise identity 67.55
Shannon entropy 0.65214
G+C content 0.48382
Mean single sequence MFE -32.10
Consensus MFE -14.27
Energy contribution -14.19
Covariance contribution -0.08
Combinations/Pair 1.45
Mean z-score -2.89
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.75
SVM RNA-class probability 0.999272
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19711209 92 - 24543557
-------------CCCCUCCCCCGAUUGC-UUGUUGCGCCUGUGCGGAUUCUUCUUUUGCAUGUCGACUGGG----CGGGCAAAAGAAAG--UUAGCACGGAGAACAACAAC
-------------................-((((((..(((((((.((((.(((((((((.((((.....))----)).)))))))))))--)).)))))).)..)))))). ( -32.30, z-score =  -2.04, R)
>droGri2.scaffold_15110 15532711 98 - 24565398
----------UUACCCAAGAGUCGAUUGC-CUGUUGCGUGCGUGUAGAAU-UUCUUUUGCAUGUUGGAGCCAAA-CAUAGCAAAAGAAAAACUCUACACGGG-AGCAACUAC
----------...................-..(((((.(.((((((((.(-(((((((((((((((....).))-))).))))))))))...)))))))).)-.)))))... ( -35.00, z-score =  -4.41, R)
>droVir3.scaffold_13049 11529057 95 + 25233164
------------AACCAAUUUUCGUUUGC-CUGCUGCGUUAGUGUGGAAU-UUCUUUUGCAUGUUGGAG-CGAA-CACAGCAAAGGAAAAUCUCUACACUGA-GGGAACAAC
------------.................-.((.(.(.((((((((((.(-(((((((((.((((....-..))-))..))))))))))...))))))))))-.).).)).. ( -27.50, z-score =  -1.86, R)
>droMoj3.scaffold_6680 13642634 93 - 24764193
--------------CCAAGUUUCGUUUGC-CUGUUGCGUGUGUGUGGAAU-UUCUUUUGCAUGUUGGAG-AAAC-UAAAGCAAAAGGAAAUCUCUACACUGA-GGCAACUAC
--------------...............-..(((((.(..(((((((.(-(((((((((...((((..-...)-))).))))))))))...)))))))..)-.)))))... ( -28.40, z-score =  -2.63, R)
>droWil1.scaffold_180949 4853084 109 - 6375548
UAUAUAAUCCCAUCUAAUUGUUGGCUUGUGUUGACAUUGCUGUAGAUAUUUUCCUUUUGCAUGUUGAACCAGAAACAGGGCAAAGGAAAAUCUCUACAACAACAACAGG---
.........((.......(((..((....))..)))(((.((((((.((((((((((.((.((((........))))..)))))))))))).)))))).))).....))--- ( -32.80, z-score =  -3.82, R)
>droPer1.super_48 566602 101 - 581423
----------GAUCCCCUUCCCCGUCUGC-UUGUUGCGCUUGUGUAGAUUCUUCCUUUGCAUGUUGACCUGGACGACAAGCAAAGGAAAGUUUUUACACGCAGAACAACAAC
----------...................-((((((..((((((((((..((((((((((.(((((.......))))).))))))).)))..)))))))).))..)))))). ( -34.50, z-score =  -4.53, R)
>dp4.chrXR_group8 7785194 101 - 9212921
----------GAUCCCCUUCCCCGUCUGC-UUGUUGCGCUUGUGUAGAUUCUUCCUUUGCAUGUUGACCUGGACGACAAGCAAAGGAAAGUUUUUACACGCAGAACAACAAC
----------...................-((((((..((((((((((..((((((((((.(((((.......))))).))))))).)))..)))))))).))..)))))). ( -34.50, z-score =  -4.53, R)
>droAna3.scaffold_13337 6109105 97 + 23293914
---------UGUUCCCAUACCCCGUUUGC-UUGUUGCCCCUGUGUAGAUU-UUCUUUUGCAUGUUUCGCGGGAC--AGGGCAAAAGAUAG--UUUGCACGGAGAACAACCAA
---------(((((((...........((-.....))....(((((((((-.((((((((.(((((....))))--)..)))))))).))--))))))))).)))))..... ( -34.30, z-score =  -3.42, R)
>droEre2.scaffold_4784 19504142 92 - 25762168
-------------CCCUUCCCCCGAUCGC-UUGUUGCGCCUGUGCGGAUUCUUCUUUUGCAUGUCGACUGGG----CGAGCAGAAGAAAG--UUAGCACGGAGAACAACAAC
-------------................-((((((..(((((((.((((.(((((((((.((((.....))----)).)))))))))))--)).)))))).)..)))))). ( -32.40, z-score =  -2.30, R)
>droYak2.chr3L 3381832 92 + 24197627
-------------CCCCUCCCCCGAUUGC-UUGUUGCACCUGUGCGGAUUCUUCUUUUGCAUGUCGACUGGG----CGGGCAGAAGAAAG--UUAGCACGGAGAACAACAAC
-------------................-((((((..(((((((.((((.(((((((((.((((.....))----)).)))))))))))--)).)))))).)..)))))). ( -31.10, z-score =  -1.75, R)
>droSec1.super_29 409241 89 - 700605
-------------CCCCUCCCCCGAUUGC-UUGUUGCGCCUGUGCGGAU---UCUUUUGCAUGUCGUCUGGG----CGGGCAAAAGAAAG--UUAGCACGGAGAACAACAAC
-------------................-((((((..(((((((...(---((((((((.((((.....))----)).)))))))))..--...)))))).)..)))))). ( -30.10, z-score =  -1.36, R)
>droSim1.chr3L 19037288 92 - 22553184
-------------CCCCUCCCCCGAUUGC-UUGUUGCGCCUGUGCGGAUUCUUCUUUUGCAUGUCGACUGGG----CGGGCAAAAGAAAG--UUAGCACGGAGAACAACAAC
-------------................-((((((..(((((((.((((.(((((((((.((((.....))----)).)))))))))))--)).)))))).)..)))))). ( -32.30, z-score =  -2.04, R)
>consensus
_____________CCCCUCCCCCGAUUGC_UUGUUGCGCCUGUGUGGAUUCUUCUUUUGCAUGUUGACUGGGA___CGAGCAAAAGAAAG__UUUACACGGAGAACAACAAC
................................((((....(((((.((...(((((((((...................)))))))))....)).))))).....))))... (-14.27 = -14.19 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:38:19 2011