Locus 1853

Sequence ID	2L_DroMel_CAF1
Location	5,090,066 – 5,090,333
Length	267
Max. P	0.985844

overview

Window 6

Location	5,090,066 – 5,090,174
Length	108
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	94.44
Mean single sequence MFE	-26.20
Consensus MFE	-24.60
Energy contribution	-25.27
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-3.15
Structure conservation index	0.94
SVM decision value	2.02
SVM RNA-class probability	0.985844
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5090066 108 - 22407834
AAAAUCAACAAGAGUUUGGGGCCAACUGGAGCUACAAUUACAAGCAUCAUUGGCCUUAUUUCUUUUGUUUUUUUCGUUUUUUUUUUCAUUCCGCCAAUAUUAUUUUUG
.(((..((((((((..(((((((((.((..(((.........)))..)))))))))))...))))))))..))).................................. ( -24.60)
>DroSim_CAF1 22052 108 - 1
AAAACCAACAAGAGUUUGGGGCCAACUGGAGCUACAAUUACAAGCAUCAUUGGCCUUAUUUCUUUUGUUUUUUUCGGUUUUUUUUUCAUUCCGCCAAUAUUAUUUCUG
((((((((((((((..(((((((((.((..(((.........)))..)))))))))))...))))))))......))))))........................... ( -27.50)
>DroYak_CAF1 21060 107 - 1
AAAACCAACAAGAGUUGGGGGCCAACUGGAGCUACAAUUACAAGCAUCAUUGGCCUUAUUUCUUUUGUUUUUUUCGGUUUUUUUUUU-CUCUGCCAAUAUCAUUUCUG
((((((((((((((...((((((((.((..(((.........)))..))))))))))....))))))))......))))))......-.................... ( -26.50)
>consensus
AAAACCAACAAGAGUUUGGGGCCAACUGGAGCUACAAUUACAAGCAUCAUUGGCCUUAUUUCUUUUGUUUUUUUCGGUUUUUUUUUCAUUCCGCCAAUAUUAUUUCUG
((((((((((((((..(((((((((.((..(((.........)))..)))))))))))...))))))))......))))))........................... (-24.60 = -25.27 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	5,090,134 – 5,090,242
Length	108
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	89.74
Mean single sequence MFE	-26.83
Consensus MFE	-23.49
Energy contribution	-23.49
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.88
SVM decision value	0.92
SVM RNA-class probability	0.882920
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5090134 108 - 22407834
UCAAAAAGCUGCGAGAGGGGGGCUAAAAUCGUGUGGAAAACACACAUACAGCACAGCACAGCAGUUGCAAAAUCAACAAGAGUUUGGGGCCAACUGGAGCUACAAUUA
.......(((((....).............(((((.....)))))...))))..(((.(((..(((.((((.((.....)).)))).)))...)))..)))....... ( -24.90)
>DroSec_CAF1 19516 96 - 1
---AAGAGCUGCGAAAGG--GGCUAAAAUCGUGUGGAAAACACACA-------GAGCACAGCAGUUGCAAAACCAACAAGAGUUUGGGGCCAACUGGAGCUACAAUUA
---...((((.(....).--))))......(((((.....))))).-------.(((....(((((((....((((.......)))).).))))))..)))....... ( -27.80)
>DroSim_CAF1 22120 96 - 1
---AAGAGCUGCGAAAGG--GGCUAAAAUCGUGUGGAAAACACACA-------GAGCACAGCAGUUGCAAAACCAACAAGAGUUUGGGGCCAACUGGAGCUACAAUUA
---...((((.(....).--))))......(((((.....))))).-------.(((....(((((((....((((.......)))).).))))))..)))....... ( -27.80)
>consensus
___AAGAGCUGCGAAAGG__GGCUAAAAUCGUGUGGAAAACACACA_______GAGCACAGCAGUUGCAAAACCAACAAGAGUUUGGGGCCAACUGGAGCUACAAUUA
.......(((((....)....(((......(((((.....))))).........))).)))).((((......))))...(((((.((.....)).)))))....... (-23.49 = -23.49 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	5,090,242 – 5,090,333
Length	91
Sequences	3
Columns	91
Reading direction	forward
Mean pairwise identity	85.94
Mean single sequence MFE	-22.77
Consensus MFE	-18.60
Energy contribution	-18.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.82
SVM decision value	0.06
SVM RNA-class probability	0.562063
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5090242 91 + 22407834
CUGCUUUCGGCCAUGGCGGCCAAUUGCAAUUUCAAGGCUGCAGCUCCAACUCGAGCGAGCACUCCAUCUUCGUGGCCACCGCAUCCAUCGC
.(((....(((((((((((((..(((......))))))))).((((......))))..............)))))))...)))........ ( -30.10)
>DroSec_CAF1 19612 74 + 1
-----------------GGCCAAUUGCAAUUUCAAGGCUGCAGCUCCAACUCGAGCGAGCACUCCAUCUUCUUGGCCACCGCAUCCAUCGC
-----------------(((((((((......)))((.(((.((((......))))..)))..))......)))))).............. ( -19.10)
>DroSim_CAF1 22216 74 + 1
-----------------GGCCAAUUGCAAUUUCAAGGCUGCAGCUCCAACUCGAGCGAGCACUCCAUCUUCUUGGCCACCGCAUCCAUCGC
-----------------(((((((((......)))((.(((.((((......))))..)))..))......)))))).............. ( -19.10)
>consensus
_________________GGCCAAUUGCAAUUUCAAGGCUGCAGCUCCAACUCGAGCGAGCACUCCAUCUUCUUGGCCACCGCAUCCAUCGC
.................(((((.(((......)))((.(((.((((......))))..)))..)).......))))).............. (-18.60 = -18.60 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:02 2006