Locus 2949

Sequence ID	dm3.chr2RHet
Location	3,145,343 – 3,145,406
Length	63
Max. P	0.993184

overview

Window 0

Location	3,145,343 – 3,145,406
Length	63
Sequences	10
Columns	69
Reading direction	forward
Mean pairwise identity	61.81
Shannon entropy	0.79699
G+C content	0.38799
Mean single sequence MFE	-11.87
Consensus MFE	-5.85
Energy contribution	-4.81
Covariance contribution	-1.04
Combinations/Pair	2.29
Mean z-score	-1.38
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.59
SVM RNA-class probability	0.993184
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 3145343 63 + 3288761
---UUUAUUAUUCGCAACAGCUAUUGAAAAAGCUCAAUAGCUAAACAUU--GGUGACCCC-GACGUGAU
---........((((...(((((((((......))))))))).....((--((.....))-)).)))). ( -16.70, z-score =  -3.75, R)
>droSim1.chrU 6574800 64 + 15797150
---UCCGUCGUCCACACACGCUAAUGAUAAAGCUCUUUGGCUACACAUU--GGUGGCCCUAGACGUGAU
---((((((..........(((........))).....((((((.....--.))))))...)))).)). ( -17.00, z-score =  -1.41, R)
>droSec1.super_81 106974 58 + 123496
--------UUUAUUCUAAAGCUAAUAAAAAGGCUCAUUGGUUUAACAUU--UCUGACCAC-GACGCGAU
--------.......................((((..(((((.......--...))))).-)).))... (  -6.00, z-score =   0.07, R)
>droYak2.chr2R 266274 64 + 21139217
----UUCAUUUGCAAAAAGGCUAAUACAAAUUCUUAUUAGCUCAAUAUUUUGGUGACCCC-GACUGGAU
----.(((((........((((((((........)))))))).........)))))((..-....)).. (  -9.43, z-score =  -0.34, R)
>droAna3.scaffold_13417 6814960 62 + 6960332
----UUAUUUUGGAUAAAAGUCAUUGAAAAAUCUCAAUGACCAAACAUU--GGUGACCCC-GACAUGAU
----((((.((((......((((((((......))))))))........--(....).))-)).)))). ( -14.50, z-score =  -2.36, R)
>dp4.Unknown_group_284 5815 67 - 17202
UUAACUUCAAAUUGCAACAUUUAUUAAAAACGCUUAAUAGCUUAACAUUU-GGUAACCCC-GACGUGAU
..........((..(................(((....))).......((-((.....))-)).)..)) (  -6.00, z-score =  -0.06, R)
>droPer1.super_226 23616 67 + 38019
UUAACUUCAAAUUGCAACAGUUAUUAAAAACGCUUAAUAGCUUAACAUUU-GGUGACCCC-GACGUGAU
..........((..(...(((((((((......)))))))))......((-((.....))-)).)..)) (  -9.50, z-score =  -0.89, R)
>droGri2.scaffold_14948 4364 59 + 44767
-------AUUGAAAUUAAAGCUAUCAAAAAG--CUGAUAGCGCAAACCUCUGGUGACCCC-GACGUGAU
-------............(((((((.....--.)))))))....((.((.((....)).-)).))... ( -11.70, z-score =  -2.05, R)
>droVir3.scaffold_12958 3369160 60 - 3547706
-------CUAUUUGUGAAAGCUAUUGAAAAAGCUCAAUAGCGCAACAUUU-GGUGACCCC-GACGUGAU
-------(((..(((....((((((((......))))))))...)))..)-)).......-........ ( -14.60, z-score =  -2.48, R)
>droEre2.scaffold_4784 25734147 59 + 25762168
-------UUAUUGAAAAGGGCUGUCAAACCAGUCAGUCCUCGUAACAUU--GGUGACCCC-GACGUGAU
-------.........(((((((.(......).)))))))....((.((--((.....))-)).))... ( -13.30, z-score =  -0.56, R)
>consensus
_____U_UUAUUUACAAAAGCUAUUAAAAAAGCUCAAUAGCUUAACAUU__GGUGACCCC_GACGUGAU
...................(((((((........)))))))............................ ( -5.85 =  -4.81 +  -1.04)

alignment

secondary structure

dotplot

Window 1

Location	3,145,343 – 3,145,406
Length	63
Sequences	10
Columns	69
Reading direction	reverse
Mean pairwise identity	61.81
Shannon entropy	0.79699
G+C content	0.38799
Mean single sequence MFE	-11.69
Consensus MFE	-5.77
Energy contribution	-5.58
Covariance contribution	-0.19
Combinations/Pair	1.87
Mean z-score	-0.47
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.80
SVM RNA-class probability	0.822524
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2RHet 3145343 63 - 3288761
AUCACGUC-GGGGUCACC--AAUGUUUAGCUAUUGAGCUUUUUCAAUAGCUGUUGCGAAUAAUAAA---
.((((((.-((.....))--.)))).(((((((((((....)))))))))))....))........--- ( -16.20, z-score =  -2.29, R)
>droSim1.chrU 6574800 64 - 15797150
AUCACGUCUAGGGCCACC--AAUGUGUAGCCAAAGAGCUUUAUCAUUAGCGUGUGUGGACGACGGA---
....((((((.((((((.--...)))..))).....(((........))).....)))))).....--- ( -15.30, z-score =   0.15, R)
>droSec1.super_81 106974 58 - 123496
AUCGCGUC-GUGGUCAGA--AAUGUUAAACCAAUGAGCCUUUUUAUUAGCUUUAGAAUAAA--------
...((.((-(((((((..--..))....))).)))))).......................-------- (  -7.30, z-score =   0.19, R)
>droYak2.chr2R 266274 64 - 21139217
AUCCAGUC-GGGGUCACCAAAAUAUUGAGCUAAUAAGAAUUUGUAUUAGCCUUUUUGCAAAUGAA----
((((....-.))))...(((((....(.(((((((........)))))))).)))))........---- (  -8.80, z-score =   0.46, R)
>droAna3.scaffold_13417 6814960 62 - 6960332
AUCAUGUC-GGGGUCACC--AAUGUUUGGUCAUUGAGAUUUUUCAAUGACUUUUAUCCAAAAUAA----
..(((...-.((....))--.)))...((((((((((....))))))))))..............---- ( -12.60, z-score =  -0.69, R)
>dp4.Unknown_group_284 5815 67 + 17202
AUCACGUC-GGGGUUACC-AAAUGUUAAGCUAUUAAGCGUUUUUAAUAAAUGUUGCAAUUUGAAGUUAA
...((((.-.((....))-..))))..(((((((.(((((((.....)))))))..)))....)))).. (  -8.30, z-score =   0.61, R)
>droPer1.super_226 23616 67 - 38019
AUCACGUC-GGGGUCACC-AAAUGUUAAGCUAUUAAGCGUUUUUAAUAACUGUUGCAAUUUGAAGUUAA
...((((.-.((....))-..))))...(((....)))........(((((............))))). (  -8.50, z-score =   0.69, R)
>droGri2.scaffold_14948 4364 59 - 44767
AUCACGUC-GGGGUCACCAGAGGUUUGCGCUAUCAG--CUUUUUGAUAGCUUUAAUUUCAAU-------
........-((.....)).((((((...((((((((--....))))))))...))))))...------- ( -15.40, z-score =  -2.51, R)
>droVir3.scaffold_12958 3369160 60 + 3547706
AUCACGUC-GGGGUCACC-AAAUGUUGCGCUAUUGAGCUUUUUCAAUAGCUUUCACAAAUAG-------
...((((.-.((....))-..))))...(((((((((....)))))))))............------- ( -14.40, z-score =  -2.54, R)
>droEre2.scaffold_4784 25734147 59 - 25762168
AUCACGUC-GGGGUCACC--AAUGUUACGAGGACUGACUGGUUUGACAGCCCUUUUCAAUAA-------
...((((.-((.....))--.))))...((((.(((.(......).))).))))........------- ( -10.10, z-score =   1.21, R)
>consensus
AUCACGUC_GGGGUCACC__AAUGUUAAGCUAUUGAGCUUUUUUAAUAGCUUUUGUAAAUAA_A_____
...((((...((....))...))))...(((((((((....)))))))))................... ( -5.77 =  -5.58 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:00:51 2011