Locus 3596

Sequence ID	dm3.chr2R
Location	6,604,916 – 6,605,050
Length	134
Max. P	0.997226

overview

Window 5

Location	6,604,916 – 6,605,050
Length	134
Sequences	5
Columns	164
Reading direction	forward
Mean pairwise identity	71.72
Shannon entropy	0.44922
G+C content	0.46511
Mean single sequence MFE	-48.98
Consensus MFE	-25.92
Energy contribution	-25.52
Covariance contribution	-0.40
Combinations/Pair	1.14
Mean z-score	-3.09
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.06
SVM RNA-class probability	0.997226
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6604916 134 + 21146708
CAAAAGGUCUGCAGCAAGAUUGUCCAACCC--------AGUGUGUCGCAGAAGUCUCGAA--------UUUUGUACCAAAUUCCCUGGAAAAUC-----------GUAUGGCACCAUUGGUAACAUUCGGUUUUGGGAGAUUUCUGUGACAUGCCUGCUCC---
.....((...((((...(......).....--------.(((((((((((((((((((((--------(((......))))))((...((((((-----------(.(((..(((...)))..))).))))))))))))))))))))))))))))))).))--- ( -45.60, z-score =  -3.34, R)
>droEre2.scaffold_4845 3416768 150 - 22589142
CAGAAGCUCUGCAGCCAGAUUGCCCAUCC---------AGUAUGUCACAGAAGUCUCUGGUGAUCGGUUUCGGCACUCACUUGCCUGAAAAAUCUUAUAGACUUAGUCGGGCACCAGUGGAAACAUUUGGUUUUGGGAGAUUUCUGUGACAUGUGGGCU-----
.......((((....))))..((((((..---------...(((((((((((((((((((((.(((....))))))).....((((((....((.....)).....))))))(((((((....)).)))))....))))))))))))))))))))))).----- ( -59.40, z-score =  -3.78, R)
>droYak2.chr2R 18579400 159 - 21139217
CAGAAGAUGUGCAGCAAGAUUGCCCAACCCAGUGUCACAGUGUGUCACAGAAGUCUCUGGAGAUCGCUUUUGGUACCCACUUUCCAGAAAAAUCUUUUGGACUUGGUCUGGCACCAUUUGUAACAUUUGGUUUUGGGAGAUUUCUGUGACAUGCCUGCU-----
(((....(((((((((....))).........)).))))(((((((((((((((((((.((((((((...((((.((.(((.(((((((.....)))))))...)))..)).))))...)).......)))))).))))))))))))))))))))))..----- ( -54.91, z-score =  -2.31, R)
>droSec1.super_1 4185330 118 + 14215200
CAGAAGGUCUGCAGCAAGAUUGU--------------------GUCACAGAAGUCUCUAG--------UUUGGUACC-------CUGGAAAAUC-----------GUAUGGCACCAUUGGUAACAUUCGGUUUUGGGAGAUUUCUGUGACAUGCCUACUGCUCU
(((.((((((......))...((--------------------(((((((((((((((..--------.(..(....-------)..)((((((-----------(.(((..(((...)))..))).))))))).))))))))))))))))))))).))).... ( -43.00, z-score =  -3.20, R)
>droSim1.chr2R 5211549 118 + 19596830
CAGAAGGUCUGCAGCAAGAUUGU--------------------GUCACAGAAGUCUCGAG--------UUUGGUACC-------CUGGAAAAUC-----------GUAUGGCACCAUUGGUAACAUUCGGUUUUGGGAGAUUUCUGUGACAUGCCUACUGCUCU
(((.((((((......))...((--------------------((((((((((((((...--------.(..(....-------)..)((((((-----------(.(((..(((...)))..))).)))))))..)))))))))))))))))))).))).... ( -42.00, z-score =  -2.82, R)
>consensus
CAGAAGGUCUGCAGCAAGAUUGUCCA_CC_________AGU_UGUCACAGAAGUCUCUAG________UUUGGUACC_A_UU_CCUGGAAAAUC___________GUAUGGCACCAUUGGUAACAUUCGGUUUUGGGAGAUUUCUGUGACAUGCCUGCU_C___
.....(((..(((((......))....................((((((((((((((................................................(.....).(((.....(((.....))).))))))))))))))))).)))..)))..... (-25.92 = -25.52 +  -0.40)

alignment

secondary structure

dotplot

Window 6

Location	6,604,916 – 6,605,050
Length	134
Sequences	5
Columns	164
Reading direction	reverse
Mean pairwise identity	71.72
Shannon entropy	0.44922
G+C content	0.46511
Mean single sequence MFE	-42.14
Consensus MFE	-24.84
Energy contribution	-25.36
Covariance contribution	0.52
Combinations/Pair	1.13
Mean z-score	-2.67
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.76
SVM RNA-class probability	0.995041
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6604916 134 - 21146708
---GGAGCAGGCAUGUCACAGAAAUCUCCCAAAACCGAAUGUUACCAAUGGUGCCAUAC-----------GAUUUUCCAGGGAAUUUGGUACAAAA--------UUCGAGACUUCUGCGACACACU--------GGGUUGGACAAUCUUGCUGCAGACCUUUUG
---(.((((((..((((.(((((.((((((((((.((.(((.((((...)))).))).)-----------).))))...))((((((......)))--------))))))).)))))((((.....--------..))))))))..)))))).).......... ( -37.20, z-score =  -1.21, R)
>droEre2.scaffold_4845 3416768 150 + 22589142
-----AGCCCACAUGUCACAGAAAUCUCCCAAAACCAAAUGUUUCCACUGGUGCCCGACUAAGUCUAUAAGAUUUUUCAGGCAAGUGAGUGCCGAAACCGAUCACCAGAGACUUCUGUGACAUACU---------GGAUGGGCAAUCUGGCUGCAGAGCUUCUG
-----.(((((((((((((((((.((((............(((((((((..((((.((..(((((.....))))).)).))))....))))..))))).........)))).)))))))))))...---------.).)))))..((((....))))....... ( -47.40, z-score =  -2.53, R)
>droYak2.chr2R 18579400 159 + 21139217
-----AGCAGGCAUGUCACAGAAAUCUCCCAAAACCAAAUGUUACAAAUGGUGCCAGACCAAGUCCAAAAGAUUUUUCUGGAAAGUGGGUACCAAAAGCGAUCUCCAGAGACUUCUGUGACACACUGUGACACUGGGUUGGGCAAUCUUGCUGCACAUCUUCUG
-----.((((...((((((((((.((((....(((.....))).....(((((((..((....((((...((....))))))..)).))))))).............)))).))))))))))..))))..((..((((((((((....)))).)).))))..)) ( -44.40, z-score =  -0.47, R)
>droSec1.super_1 4185330 118 - 14215200
AGAGCAGUAGGCAUGUCACAGAAAUCUCCCAAAACCGAAUGUUACCAAUGGUGCCAUAC-----------GAUUUUCCAG-------GGUACCAAA--------CUAGAGACUUCUGUGAC--------------------ACAAUCUUGCUGCAGACCUUCUG
...((((((((..((((((((((.((((....(((.....))).....(((((((....-----------(.....)...-------)))))))..--------...)))).)))))))))--------------------)....)))))))).......... ( -40.80, z-score =  -4.52, R)
>droSim1.chr2R 5211549 118 - 19596830
AGAGCAGUAGGCAUGUCACAGAAAUCUCCCAAAACCGAAUGUUACCAAUGGUGCCAUAC-----------GAUUUUCCAG-------GGUACCAAA--------CUCGAGACUUCUGUGAC--------------------ACAAUCUUGCUGCAGACCUUCUG
...((((((((..((((((((((.((((....(((.....))).....(((((((....-----------(.....)...-------)))))))..--------...)))).)))))))))--------------------)....)))))))).......... ( -40.90, z-score =  -4.59, R)
>consensus
___G_AGCAGGCAUGUCACAGAAAUCUCCCAAAACCGAAUGUUACCAAUGGUGCCAUAC___________GAUUUUCCAGG_AA_U_GGUACCAAA________CUAGAGACUUCUGUGACA_ACU_________GG_UGGACAAUCUUGCUGCAGACCUUCUG
.....((((((..((((((((((.((((....(((.....))).....(((((((................................))))))).............)))).))))))))))........................))))))............ (-24.84 = -25.36 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:13:11 2011