Locus 268

Sequence ID	dm3.chr2L
Location	1,986,505 – 1,986,601
Length	96
Max. P	0.998742

overview

Window 7

Location	1,986,505 – 1,986,601
Length	96
Sequences	8
Columns	110
Reading direction	forward
Mean pairwise identity	59.43
Shannon entropy	0.79764
G+C content	0.42851
Mean single sequence MFE	-22.95
Consensus MFE	-11.73
Energy contribution	-11.92
Covariance contribution	0.19
Combinations/Pair	1.46
Mean z-score	-1.79
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.47
SVM RNA-class probability	0.998742
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1986505 96 + 23011544
---AGUAUACA-AUAUAGAUCC--AUUUAAGCCUACGUCAGCGAUAACCUCGAUGAUUGU------UUGCUGACGUAGCCGGCUUUCCAAAUCUCCUUCUCAAUAUUC--
---........-....((((..--....(((((((((((((((((((.(.....).))).------)))))))))))...))))).....))))..............-- ( -23.20, z-score =  -3.17, R)
>droSim1.chr2L 1956161 95 + 22036055
---AGUAUACA-AUAUAGAUCC--AUUUAAGCCUACGUCAGCGAUAAGCUCGAUGAUUGU------UUGCUGACGUAGCCGGCAU-CAGAUUCUCCUUCUCGAUAUUC--
---........-..........--......(((((((((((((((((.(.....).))).------)))))))))))...)))((-((((.......))).)))....-- ( -22.50, z-score =  -1.26, R)
>droSec1.super_14 1930299 90 + 2068291
---AGUAUACA-AUAUAGAUCC--AUUUAAGCCUACGUCAGCGAUAAGCUCGAUGAU-----------GCUGACGUAGCCGGCAU-CCGAUUGUCCUGCUCGAUAUUC--
---((((.(((-((...(((((--......(.(((((((((((.((.......)).)-----------)))))))))).))).))-)..)))))..))))........-- ( -21.80, z-score =  -0.77, R)
>droYak2.chr2L 1968105 90 + 22324452
AGUAUACCAUAUACAUAGAUCC--ACUUGGGCCUACGUCAGCGAUAAGGUCGAUGGCUGU------UUGCUGACGUAGUCGGCUUCUUCUCCAUAUUU------------
.(((((...)))))........--....((((((((((((((((...(((.....)))..------)))))))))))...))))).............------------ ( -26.60, z-score =  -1.89, R)
>droEre2.scaffold_4929 2032331 98 + 26641161
---AGUAUACC-AUAUAGAUCCCCAUUUCAGCCUACGUCAGCGAUAAGGUCGAUGAUUGU------GUGCUGACGUAGCCGGCUUUCCGAGUCUCCUUCUCGAUAUUC--
---......((-.....((........)).(.((((((((((.(((..(((...)))..)------)))))))))))).))).....((((.......))))......-- ( -25.30, z-score =  -1.35, R)
>droAna3.scaffold_12916 9702033 93 - 16180835
------ACCUA-GUAUAGAUUU--AUUAAUUCCUACGUCAGUGAUAAGGUCGAUGAUUGUUCGCCACUGCUGACGUAGUCGACCUCCUCGGUCUCAUUCUAU--------
------.....-..(((((...--........(((((((((((....((.(((.......)))))..)))))))))))..((((.....))))....)))))-------- ( -26.60, z-score =  -2.72, R)
>dp4.chr4_group3 8757989 76 + 11692001
---AGAACAUGUGCAUAGAUCU--CACGGAGCCUACGUCAGUGAUAAUGUC--------U------CUGCUGACGUAUACGGUUUUGUC---ACAUUU------------
---.....(((((.........--.(((((((((((((((((((.......--------)------).)))))))))...)))))))))---))))..------------ ( -21.70, z-score =  -1.54, R)
>droWil1.scaffold_180772 1220577 107 - 8906247
---ACAGAAUAUAUAUAGUACACAAAUCGUGUCUACGUCAGUGAUAAGCCUUAUCCCUCUCUUUUCUCUUUUGCUGACGCAAUUUUUCUCCCAUAUUAUGCAAAAUGUUU
---.((.(((((...(((.((((.....)))))))((((((..(..........................)..)))))).............))))).)).......... ( -15.87, z-score =  -1.60, R)
>consensus
___AGUAUACA_AUAUAGAUCC__AUUUAAGCCUACGUCAGCGAUAAGCUCGAUGAUUGU______UUGCUGACGUAGCCGGCUUUCCCACUCUCCUUCUCGAUAUUC__
..............................(((((((((((((........................))))))))))...)))........................... (-11.73 = -11.92 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	1,986,505 – 1,986,601
Length	96
Sequences	8
Columns	110
Reading direction	reverse
Mean pairwise identity	59.43
Shannon entropy	0.79764
G+C content	0.42851
Mean single sequence MFE	-23.43
Consensus MFE	-9.41
Energy contribution	-10.41
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.40
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.62
SVM RNA-class probability	0.955387
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 1986505 96 - 23011544
--GAAUAUUGAGAAGGAGAUUUGGAAAGCCGGCUACGUCAGCAA------ACAAUCAUCGAGGUUAUCGCUGACGUAGGCUUAAAU--GGAUCUAUAU-UGUAUACU---
--..............((((..(..(((((...(((((((((..------..((((.....))))...))))))))))))))...)--..))))....-........--- ( -25.60, z-score =  -2.09, R)
>droSim1.chr2L 1956161 95 - 22036055
--GAAUAUCGAGAAGGAGAAUCUG-AUGCCGGCUACGUCAGCAA------ACAAUCAUCGAGCUUAUCGCUGACGUAGGCUUAAAU--GGAUCUAUAU-UGUAUACU---
--..(((.(((.....(((.(((.-.....(.((((((((((..------..................)))))))))).)......--))))))...)-)))))...--- ( -20.95, z-score =  -0.15, R)
>droSec1.super_14 1930299 90 - 2068291
--GAAUAUCGAGCAGGACAAUCGG-AUGCCGGCUACGUCAGC-----------AUCAUCGAGCUUAUCGCUGACGUAGGCUUAAAU--GGAUCUAUAU-UGUAUACU---
--...........((.(((((.((-((.(((.((((((((((-----------...............)))))))))).)......--))))))..))-)))...))--- ( -23.26, z-score =  -0.53, R)
>droYak2.chr2L 1968105 90 - 22324452
------------AAAUAUGGAGAAGAAGCCGACUACGUCAGCAA------ACAGCCAUCGACCUUAUCGCUGACGUAGGCCCAAGU--GGAUCUAUGUAUAUGGUAUACU
------------..(((((((......(((...(((((((((..------..................))))))))))))((....--)).)))))))............ ( -22.75, z-score =  -1.19, R)
>droEre2.scaffold_4929 2032331 98 - 26641161
--GAAUAUCGAGAAGGAGACUCGGAAAGCCGGCUACGUCAGCAC------ACAAUCAUCGACCUUAUCGCUGACGUAGGCUGAAAUGGGGAUCUAUAU-GGUAUACU---
--..((((((....(((..((((...((((...(((((((((..------..................)))))))))))))....))))..)))...)-)))))...--- ( -29.25, z-score =  -2.03, R)
>droAna3.scaffold_12916 9702033 93 + 16180835
--------AUAGAAUGAGACCGAGGAGGUCGACUACGUCAGCAGUGGCGAACAAUCAUCGACCUUAUCACUGACGUAGGAAUUAAU--AAAUCUAUAC-UAGGU------
--------(((((....((((.....))))..(((((((((....(((((.......))).))......)))))))))........--...)))))..-.....------ ( -27.40, z-score =  -2.75, R)
>dp4.chr4_group3 8757989 76 - 11692001
------------AAAUGU---GACAAAACCGUAUACGUCAGCAG------A--------GACAUUAUCACUGACGUAGGCUCCGUG--AGAUCUAUGCACAUGUUCU---
------------..((((---(.((.....((.((((((((..(------(--------.......)).)))))))).))..(...--.).....))))))).....--- ( -19.20, z-score =  -1.35, R)
>droWil1.scaffold_180772 1220577 107 + 8906247
AAACAUUUUGCAUAAUAUGGGAGAAAAAUUGCGUCAGCAAAAGAGAAAAGAGAGGGAUAAGGCUUAUCACUGACGUAGACACGAUUUGUGUACUAUAUAUAUUCUGU---
.........(((.((((((..((.....((((((((((......)..........((((.....)))).)))))))))((((.....)))).))...)))))).)))--- ( -19.00, z-score =  -0.57, R)
>consensus
__GAAUAUCGAGAAGGAGAAUCGGAAAGCCGGCUACGUCAGCAA______ACAAUCAUCGACCUUAUCGCUGACGUAGGCUUAAAU__GGAUCUAUAU_UAUAUACU___
..............................(.(((((((((............................))))))))).).............................. ( -9.41 = -10.41 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:09:46 2011