Locus 4341

Sequence ID	dm3.chr2R
Location	12,334,892 – 12,335,044
Length	152
Max. P	0.992845

overview

Window 0

Location	12,334,892 – 12,335,044
Length	152
Sequences	6
Columns	184
Reading direction	forward
Mean pairwise identity	79.41
Shannon entropy	0.35289
G+C content	0.42584
Mean single sequence MFE	-46.87
Consensus MFE	-30.07
Energy contribution	-30.25
Covariance contribution	0.17
Combinations/Pair	1.26
Mean z-score	-2.38
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.74
SVM RNA-class probability	0.964678
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12334892 152 + 21146708
UAUCCUGUGACCUUGAACUGC---AGCAGAGCUCUGUUGCCGACUUCAGU---UCGAUAUUCCA--CUGCAGUCGGCAACAGAAC----------UCAGUGACAGGCAUCU---------GUAAUGUGUGAAAUGAAAUCGAUUUGUAUCUUAACUCUUCU-----CAGAGAUUCUAUCUUCUC
...(((((.((.(((.....)---))..(((.(((((((((((((.((((---..(.....).)--))).))))))))))))).)----------)).)).))))).....---------.(((.(((..((.((....)).))..))).))).((((...-----.))))............. ( -45.40, z-score =  -2.18, R)
>droAna3.scaffold_13266 15710357 180 + 19884421
UGUCCUGUGACCUUCGACUGUCAAAAGGGAUUUUUAUUACCGACUUUAGUCUGUUGAUAUCACAAACUAAAGUCGACAAAAAAAAAAUCCUUUUGCCAGUUACUGGCAUACAGGCAUCAAGUUAUGUGCGAAAUGAAAUCGAUCUGUGUUGAAAACAUUUUA----CAAGGAUUUGAUCUUAUU
.(.((((((.((...(((((.((((((((.(((((.((..((((((((((.(((.(....)))).))))))))))...)).))))).)))))))).)))))...))..)))))))((((((((...((..(((((...(((((....)))))...)))))..----))..))))))))...... ( -55.80, z-score =  -5.31, R)
>droEre2.scaffold_4845 9065451 151 - 22589142
UAUCCUGUGACCUUGAACUGC---AACCGAGCUGUGUUGCCGACUUCAGU---UUGAU-UUUCA--CUGCAGUCGGCAACAGAAC----------UCAGUGACAGGCAUCU---------GUGGUGUGCGAAAUGAAAUCGAUUUGUGUCCUAACUCUUCU-----CAGAGAUUCCAUCUUCCU
...(((((.((.(((.....)---))..(((.(.(((((((((((.((((---.....-....)--))).))))))))))).).)----------)).)).))))).....---------.(((..((((((.((....)).))))))..))).((((...-----.))))............. ( -44.70, z-score =  -1.56, R)
>droYak2.chr2R 4488101 155 - 21139217
CAUCCUGUGACCUUAAGCUGC---AACCGAGCUCUGUUGCCGACUUCAGU---UUGAU-UUUCA--GUGGAGUCGGCGACAGAAC----------UCAGUGACAGGCAUCU---------GUAAUGUGUGAAAUGAAAUCGAUUUGUGUCUCAACUCUUUUAACUUCAGAGAUUCUAACUUCU-
....((.(((..(((((((..---.((.(((.((((((((((((((((..---(((..-...))--))))))))))))))))).)----------)).))....)))....---------......((.((.(..((.....))..).)).))......))))..))).))............- ( -45.20, z-score =  -1.53, R)
>droSec1.super_1 9832474 152 + 14215200
UAUCCUGUGACCUUGAACUGC---AGCAGAUCUCUGUUGCCGACUUCAGU---UUGAUAUCCCA--CUGCAGUCGGCAACAGGAC----------UCAGUGACAGGCAUCU---------GUAAUGUGUGAAAUGAAAUCGAUUUGUGUCUUAACUCUUCU-----CAGAGAUUCUAUCUUCUC
.((((((.((.........((---(.(((((((((((((((((((.((((---..(....)..)--))).)))))))))))))((----------.((...((((....))---------))..)).))...........))))))))).........)).-----))).)))........... ( -45.07, z-score =  -1.79, R)
>droSim1.chr2R 11070835 152 + 19596830
UAUCCUGUGACCUUGAACUGC---AGCAGAUCUCUGUUGCCGACUUCAGU---UUGAUAUCCCA--CUGCAGUCGGCAACAGGAC----------UCAGUGACAGGCAUCU---------GUAAUGUGUGAAAUGAAAUCGAUUUGUGUCUUAACUCUUCU-----CAGAGAUUCUAUUUUCUC
.((((((.((.........((---(.(((((((((((((((((((.((((---..(....)..)--))).)))))))))))))((----------.((...((((....))---------))..)).))...........))))))))).........)).-----))).)))........... ( -45.07, z-score =  -1.91, R)
>consensus
UAUCCUGUGACCUUGAACUGC___AACAGAGCUCUGUUGCCGACUUCAGU___UUGAUAUCCCA__CUGCAGUCGGCAACAGAAC__________UCAGUGACAGGCAUCU_________GUAAUGUGUGAAAUGAAAUCGAUUUGUGUCUUAACUCUUCU_____CAGAGAUUCUAUCUUCUC
...(((((.((......(((......)))...(((((((((((((.(((.................))).)))))))))))))...............)).))))).......................((((((.(((((((....)))........(((......))))))).))).))).. (-30.07 = -30.25 +   0.17)

alignment

secondary structure

dotplot

Window 1

Location	12,334,892 – 12,335,044
Length	152
Sequences	6
Columns	184
Reading direction	reverse
Mean pairwise identity	79.41
Shannon entropy	0.35289
G+C content	0.42584
Mean single sequence MFE	-50.15
Consensus MFE	-31.94
Energy contribution	-32.42
Covariance contribution	0.48
Combinations/Pair	1.24
Mean z-score	-2.90
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.57
SVM RNA-class probability	0.992845
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12334892 152 - 21146708
GAGAAGAUAGAAUCUCUG-----AGAAGAGUUAAGAUACAAAUCGAUUUCAUUUCACACAUUAC---------AGAUGCCUGUCACUGA----------GUUCUGUUGCCGACUGCAG--UGGAAUAUCGA---ACUGAAGUCGGCAACAGAGCUCUGCU---GCAGUUCAAGGUCACAGGAUA
((((........))))((-----(((.(((....(((....)))...))).)))))........---------.....(((((.(((((----------(((((((((((((((.(((--(..........---)))).))))))))))))))))).((.---...))....))).)))))... ( -52.50, z-score =  -3.23, R)
>droAna3.scaffold_13266 15710357 180 - 19884421
AAUAAGAUCAAAUCCUUG----UAAAAUGUUUUCAACACAGAUCGAUUUCAUUUCGCACAUAACUUGAUGCCUGUAUGCCAGUAACUGGCAAAAGGAUUUUUUUUUUGUCGACUUUAGUUUGUGAUAUCAACAGACUAAAGUCGGUAAUAAAAAUCCCUUUUGACAGUCGAAGGUCACAGGACA
......(((((.....((----..(((((...((..........))...)))))..))......))))).(((((..(((..(.((((.(((((((((((((...((..((((((((((((((.......))))))))))))))..)).)))))).))))))).)))).)..))).)))))... ( -56.00, z-score =  -5.47, R)
>droEre2.scaffold_4845 9065451 151 + 22589142
AGGAAGAUGGAAUCUCUG-----AGAAGAGUUAGGACACAAAUCGAUUUCAUUUCGCACACCAC---------AGAUGCCUGUCACUGA----------GUUCUGUUGCCGACUGCAG--UGAAA-AUCAA---ACUGAAGUCGGCAACACAGCUCGGUU---GCAGUUCAAGGUCACAGGAUA
.(..(((((((((((((.-----...)))((....)).......))))))))))..)..(((..---------.((...((((.(((((----------(((.(((((((((((.(((--(....-.....---)))).))))))))))).)))))))).---)))).))..)))......... ( -52.30, z-score =  -2.85, R)
>droYak2.chr2R 4488101 155 + 21139217
-AGAAGUUAGAAUCUCUGAAGUUAAAAGAGUUGAGACACAAAUCGAUUUCAUUUCACACAUUAC---------AGAUGCCUGUCACUGA----------GUUCUGUCGCCGACUCCAC--UGAAA-AUCAA---ACUGAAGUCGGCAACAGAGCUCGGUU---GCAGCUUAAGGUCACAGGAUG
-..........(((.(((..((.(((.(((((((........)))))))..))).)).......---------....((.(((.(((((----------(((((((.(((((((.((.--((...-..)).---..)).))))))).)))))))))))).---))))).........)))))). ( -47.30, z-score =  -2.29, R)
>droSec1.super_1 9832474 152 - 14215200
GAGAAGAUAGAAUCUCUG-----AGAAGAGUUAAGACACAAAUCGAUUUCAUUUCACACAUUAC---------AGAUGCCUGUCACUGA----------GUCCUGUUGCCGACUGCAG--UGGGAUAUCAA---ACUGAAGUCGGCAACAGAGAUCUGCU---GCAGUUCAAGGUCACAGGAUA
((((........))))((-----(((.(((....((......))...))).)))))........---------.....(((((.(((..----------...((((((((((((.(((--(..(....)..---)))).)))))))))))).((.(((..---.))).))..))).)))))... ( -46.40, z-score =  -1.63, R)
>droSim1.chr2R 11070835 152 - 19596830
GAGAAAAUAGAAUCUCUG-----AGAAGAGUUAAGACACAAAUCGAUUUCAUUUCACACAUUAC---------AGAUGCCUGUCACUGA----------GUCCUGUUGCCGACUGCAG--UGGGAUAUCAA---ACUGAAGUCGGCAACAGAGAUCUGCU---GCAGUUCAAGGUCACAGGAUA
((((........))))((-----(((.(((....((......))...))).)))))........---------.....(((((.(((..----------...((((((((((((.(((--(..(....)..---)))).)))))))))))).((.(((..---.))).))..))).)))))... ( -46.40, z-score =  -1.93, R)
>consensus
GAGAAGAUAGAAUCUCUG_____AGAAGAGUUAAGACACAAAUCGAUUUCAUUUCACACAUUAC_________AGAUGCCUGUCACUGA__________GUUCUGUUGCCGACUGCAG__UGGAAUAUCAA___ACUGAAGUCGGCAACAGAGAUCUGCU___GCAGUUCAAGGUCACAGGAUA
...........(((.(((..........................((.......))......................((((...((((...........(((((((((((((((.(((..(((....))).....))).)))))))))))))))..........))))...))))..)))))). (-31.94 = -32.42 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:27:20 2011