Locus 4081

Sequence ID	dm3.chr2R
Location	10,250,521 – 10,250,579
Length	58
Max. P	0.982117

overview

Window 7

Location	10,250,521 – 10,250,579
Length	58
Sequences	7
Columns	69
Reading direction	forward
Mean pairwise identity	74.07
Shannon entropy	0.46660
G+C content	0.46314
Mean single sequence MFE	-17.37
Consensus MFE	-8.31
Energy contribution	-9.66
Covariance contribution	1.35
Combinations/Pair	1.14
Mean z-score	-2.60
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.09
SVM RNA-class probability	0.982117
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10250521 58 + 21146708
----------AUGGGCACGGUA-CAUCGAUUCUCGAUACAUCGAUGUAUUCUUACAUCCCUAGCCUGAC
----------..((((..(((.-.((((.....))))..)))((((((....))))))....))))... ( -16.70, z-score =  -2.56, R)
>droSim1.chr2R 9014853 58 + 19596830
----------ACUGGCACGGGA-CAUCGAUUCUCGAUGCAUCGAUAUAUUCUUACAUCCCUAGCCUGAC
----------...(((..((((-(((((.....)))))....((.....)).....))))..))).... ( -15.50, z-score =  -2.47, R)
>droSec1.super_1 7758232 58 + 14215200
----------ACUGGCACGGGA-CAUCGAUUCUCGAUGCAUCGAUGUAUUCUUACAUCCCUAGCCUGAC
----------...(((..((..-(((((.....)))))..))((((((....))))))....))).... ( -18.30, z-score =  -2.96, R)
>droYak2.chr2R 10187943 57 + 21139217
----------ACGGGCACGGUA-CAUCGAUUGUGGAUGCAUCGAUGUGUU-UUACAUCCCUAGGCUGAC
----------.(((.(..((((-(((((((.((....)))))))))))..-.......))..).))).. ( -13.90, z-score =  -0.03, R)
>droEre2.scaffold_4845 6998384 55 - 22589142
----------AAGGGCACGGAA-CAUCGAUUCUCGAUGCAUCG---UGUUUUUACAUCCCUAGCCUGGC
----------((((((((((..-(((((.....)))))..)))---))))))).....((......)). ( -16.60, z-score =  -1.98, R)
>dp4.chrXL_group1e 6499613 66 + 12523060
AUCAGUAAACAUCGGCAGAAAAACAUCGCUGCUCGAUGCAUCGAUGUUUUUUUACAUCACUAAUCU---
..............(.((((((((((((.(((.....))).)))))))))))).)...........--- ( -17.10, z-score =  -3.60, R)
>droPer1.super_2 3166322 68 + 9036312
AUCAGUAAACAUCGGCAGAAAAACAUCGAUGCUCGAUGCAUCGAUGUUUUUUUACAUCACUGGCAAGA-
.(((((........(.((((((((((((((((.....)))))))))))))))).)...))))).....- ( -23.50, z-score =  -4.62, R)
>consensus
__________ACGGGCACGGAA_CAUCGAUUCUCGAUGCAUCGAUGUAUUCUUACAUCCCUAGCCUGAC
.............(((.......(((((.....)))))....((((((....))))))....))).... ( -8.31 =  -9.66 +   1.35)

alignment

secondary structure

dotplot

Window 8

Location	10,250,521 – 10,250,579
Length	58
Sequences	7
Columns	69
Reading direction	reverse
Mean pairwise identity	74.07
Shannon entropy	0.46660
G+C content	0.46314
Mean single sequence MFE	-18.71
Consensus MFE	-9.20
Energy contribution	-9.94
Covariance contribution	0.74
Combinations/Pair	1.27
Mean z-score	-2.55
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.08
SVM RNA-class probability	0.981782
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10250521 58 - 21146708
GUCAGGCUAGGGAUGUAAGAAUACAUCGAUGUAUCGAGAAUCGAUG-UACCGUGCCCAU----------
....(((..((((((((....))))))....(((((.....)))))-..))..)))...---------- ( -16.10, z-score =  -1.57, R)
>droSim1.chr2R 9014853 58 - 19596830
GUCAGGCUAGGGAUGUAAGAAUAUAUCGAUGCAUCGAGAAUCGAUG-UCCCGUGCCAGU----------
....(((..((((((((....))))))...((((((.....)))))-).))..)))...---------- ( -18.00, z-score =  -2.17, R)
>droSec1.super_1 7758232 58 - 14215200
GUCAGGCUAGGGAUGUAAGAAUACAUCGAUGCAUCGAGAAUCGAUG-UCCCGUGCCAGU----------
....(((..((((((((....))))))...((((((.....)))))-).))..)))...---------- ( -19.90, z-score =  -2.66, R)
>droYak2.chr2R 10187943 57 - 21139217
GUCAGCCUAGGGAUGUAA-AACACAUCGAUGCAUCCACAAUCGAUG-UACCGUGCCCGU----------
.........((((((...-...((((((((.........)))))))-)..))).)))..---------- ( -13.60, z-score =  -0.90, R)
>droEre2.scaffold_4845 6998384 55 + 22589142
GCCAGGCUAGGGAUGUAAAAACA---CGAUGCAUCGAGAAUCGAUG-UUCCGUGCCCUU----------
........((((.........((---((..((((((.....)))))-)..)))))))).---------- ( -16.40, z-score =  -1.78, R)
>dp4.chrXL_group1e 6499613 66 - 12523060
---AGAUUAGUGAUGUAAAAAAACAUCGAUGCAUCGAGCAGCGAUGUUUUUCUGCCGAUGUUUACUGAU
---..((((((((.(((.((((((((((.(((.....))).)))))))))).)))......)))))))) ( -21.10, z-score =  -3.54, R)
>droPer1.super_2 3166322 68 - 9036312
-UCUUGCCAGUGAUGUAAAAAAACAUCGAUGCAUCGAGCAUCGAUGUUUUUCUGCCGAUGUUUACUGAU
-......((((((.(((.((((((((((((((.....)))))))))))))).)))......)))))).. ( -25.90, z-score =  -5.25, R)
>consensus
GUCAGGCUAGGGAUGUAAAAAUACAUCGAUGCAUCGAGAAUCGAUG_UUCCGUGCCCAU__________
....(((..(((((((......)))))....(((((.....)))))...))..)))............. ( -9.20 =  -9.94 +   0.74)

alignment

secondary structure

dotplot

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