Locus 4380

Sequence ID	X_DroMel_CAF1
Location	11,522,996 – 11,523,146
Length	150
Max. P	0.861923

overview

Window 1

Location	11,522,996 – 11,523,106
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.57
Mean single sequence MFE	-37.37
Consensus MFE	-18.98
Energy contribution	-21.85
Covariance contribution	2.87
Combinations/Pair	1.07
Mean z-score	-2.67
Structure conservation index	0.51
SVM decision value	0.83
SVM RNA-class probability	0.861923
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11522996 110 + 22224390
ACAGUCGGUUAAUCACAACAAUACGGCGAUCUGGCAGAUCAGUUGGGGGGAUCUGCCACU------GCCACUGCCAUUGCUGGUGC----UAUUGCUUUAGGAAGUGGCAAACCCCUAAU
...((((................))))((((.....)))).((((((((....(((((((------.((...((((....))))((----....))....)).)))))))..)))))))) ( -38.89)
>DroSec_CAF1 4387 110 + 1
ACAGUCGGUUAAUCACAACAAUACGGCGAUCUGGCAGAUCAGUUGGGGGGAUCUGCCACU------GCCACUGCCAUUGCUGGUGC----UAUUGCUUUAGGAAGUGGCAAACCCCUAAU
...((((................))))((((.....)))).((((((((....(((((((------.((...((((....))))((----....))....)).)))))))..)))))))) ( -38.89)
>DroSim_CAF1 5926 98 + 1
ACAGUCGGUUAAUCACAACAAUACGGCGAUCUGGCAGAUCAGUUGGGGGGAUCUG------------------CCAUUGCUGGUGC----UAUUGCUUUAGGAAGUGGCAAACCCCUAAU
...((((................))))((((.....)))).((((((((....((------------------(((((.((((.((----....)).))))..)))))))..)))))))) ( -33.79)
>DroYak_CAF1 4712 108 + 1
--------UUAAUU--AACAAUUCAGCGAUUUGGCAGAUCAACUAU--GCAUCUGCCACUGUCAUUGCCACUGCCAUUGGUGGUGCGCUACACUGCUGUAGGAAGUGGCAAACCCCUAAU
--------......--...........(((.((((((((((....)--).))))))))..))).((((((((.((..(((..(((.....)))..)))..)).))))))))......... ( -37.90)
>consensus
ACAGUCGGUUAAUCACAACAAUACGGCGAUCUGGCAGAUCAGUUGGGGGGAUCUGCCACU______GCCACUGCCAUUGCUGGUGC____UAUUGCUUUAGGAAGUGGCAAACCCCUAAU
......((((.....................(((((((((.........)))))))))........((((((.(((..((.((((.....))))))..).)).)))))).))))...... (-18.98 = -21.85 +   2.87)

alignment

secondary structure

dotplot

Window 2

Location	11,522,996 – 11,523,106
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	79.57
Mean single sequence MFE	-33.84
Consensus MFE	-22.29
Energy contribution	-23.60
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.66
SVM decision value	0.69
SVM RNA-class probability	0.825057
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11522996 110 - 22224390
AUUAGGGGUUUGCCACUUCCUAAAGCAAUA----GCACCAGCAAUGGCAGUGGC------AGUGGCAGAUCCCCCCAACUGAUCUGCCAGAUCGCCGUAUUGUUGUGAUUAACCGACUGU
..(((.(((((((((((.......((....----)).(((....))).))))))------).(((((((((.........)))))))))((((((.........))))))))))..))). ( -36.70)
>DroSec_CAF1 4387 110 - 1
AUUAGGGGUUUGCCACUUCCUAAAGCAAUA----GCACCAGCAAUGGCAGUGGC------AGUGGCAGAUCCCCCCAACUGAUCUGCCAGAUCGCCGUAUUGUUGUGAUUAACCGACUGU
..(((.(((((((((((.......((....----)).(((....))).))))))------).(((((((((.........)))))))))((((((.........))))))))))..))). ( -36.70)
>DroSim_CAF1 5926 98 - 1
AUUAGGGGUUUGCCACUUCCUAAAGCAAUA----GCACCAGCAAUGG------------------CAGAUCCCCCCAACUGAUCUGCCAGAUCGCCGUAUUGUUGUGAUUAACCGACUGU
.(((((((........))))))).((((((----(.((..((..(((------------------((((((.........)))))))))....)).)).))))))).............. ( -26.30)
>DroYak_CAF1 4712 108 - 1
AUUAGGGGUUUGCCACUUCCUACAGCAGUGUAGCGCACCACCAAUGGCAGUGGCAAUGACAGUGGCAGAUGC--AUAGUUGAUCUGCCAAAUCGCUGAAUUGUU--AAUUAA--------
.((((.(((((((((((.((.......(((.....))).......)).))))))).......((((((((.(--(....)))))))))))))).))))......--......-------- ( -35.64)
>consensus
AUUAGGGGUUUGCCACUUCCUAAAGCAAUA____GCACCAGCAAUGGCAGUGGC______AGUGGCAGAUCCCCCCAACUGAUCUGCCAGAUCGCCGUAUUGUUGUGAUUAACCGACUGU
.(((((((........)))))))(((((((....((.(((....)))...............(((((((((.........)))))))))....))..)))))))................ (-22.29 = -23.60 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	11,523,036 – 11,523,146
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.37
Mean single sequence MFE	-32.11
Consensus MFE	-21.16
Energy contribution	-23.46
Covariance contribution	2.30
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.66
SVM decision value	0.76
SVM RNA-class probability	0.842465
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11523036 110 - 22224390
CAUCGAACUAUUCGCAGCUGUGAUGCAAGCUUCGAUCUCUAUUAGGGGUUUGCCACUUCCUAAAGCAAUA----GCACCAGCAAUGGCAGUGGC------AGUGGCAGAUCCCCCCAACU
.((((((((..((((....))))....)).))))))........(((((((((((((.((....((....----)).(((....)))....)).------)))))))))))))....... ( -39.30)
>DroSec_CAF1 4427 110 - 1
CAUCGAACUAUUCGCAGCUGUGAUGCAAGCCUCGAUCUCUAUUAGGGGUUUGCCACUUCCUAAAGCAAUA----GCACCAGCAAUGGCAGUGGC------AGUGGCAGAUCCCCCCAACU
.(((((.((..((((....))))....))..)))))........(((((((((((((.((....((....----)).(((....)))....)).------)))))))))))))....... ( -37.50)
>DroSim_CAF1 5966 98 - 1
CAUCGAACUAUUCGCAGCUGUGAUGCAAGCCUCGAUCUCUAUUAGGGGUUUGCCACUUCCUAAAGCAAUA----GCACCAGCAAUGG------------------CAGAUCCCCCCAACU
.(((((.((..((((....))))....))..)))))........(((((((((((.((.((...((....----))...)).)))))------------------))))))))....... ( -25.70)
>DroEre_CAF1 4406 85 - 1
CAUCGAACUAUUCGCAGCCGUGAUGCAAGUCUCGAUCUCUAUUAGGGGUUUGCCACUUCCUAAAGCAAAG----GCAC---------------------CAGUGGCAGAU----------
.((((((((..((((....))))....))).)))))(((.....)))((((((((((.(((.......))----)...---------------------.))))))))))---------- ( -23.60)
>DroYak_CAF1 4742 118 - 1
CAUCGAACUAUUCGCAGCUGUGAUGCAAGCUUCGAUCUCUAUUAGGGGUUUGCCACUUCCUACAGCAGUGUAGCGCACCACCAAUGGCAGUGGCAAUGACAGUGGCAGAUGC--AUAGUU
.....((((((..(((.((((.((.((......((((((.....))))))(((((((.((.......(((.....))).......)).))))))).))...)).)))).)))--)))))) ( -34.44)
>consensus
CAUCGAACUAUUCGCAGCUGUGAUGCAAGCCUCGAUCUCUAUUAGGGGUUUGCCACUUCCUAAAGCAAUA____GCACCAGCAAUGGCAGUGGC______AGUGGCAGAUCCCCCCAACU
.(((((.....((((....))))........)))))........(((((((((((((.......((........)).(((....))).............)))))))))))))....... (-21.16 = -23.46 +   2.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:33 2006