Locus 8088

Sequence ID	X_DroMel_CAF1
Location	20,130,511 – 20,130,605
Length	94
Max. P	0.954236

overview

Window 8

Location	20,130,511 – 20,130,605
Length	94
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	73.33
Mean single sequence MFE	-27.16
Consensus MFE	-15.24
Energy contribution	-16.10
Covariance contribution	0.86
Combinations/Pair	1.05
Mean z-score	-1.74
Structure conservation index	0.56
SVM decision value	0.54
SVM RNA-class probability	0.775278
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20130511 94 + 22224390
CGAAC--UCAGCCGUU------------UUCACCUGGCCAACCCAGUUAGGGAUUAUUUCCGGGUAAACUACGGCGAUAAC-----CAACUGGCAAAUGCCAGGAAGGUGAAA
.....--...(((((.------------((.((((((....(((.....))).......)))))).))..)))))....((-----(..(((((....)))))...))).... ( -32.20)
>DroSec_CAF1 31904 83 + 1
CGAAC--UCAGCCGCG------------UUCACCUGGCCAACCCAGUUAGGGAUUAUUUCC-----------GGCGAUAAC-----CAACUGGCAAAUGCCAGGAAGUUGGAA
.((((--.(....).)------------))).((((((....((((((.((((....))))-----------((......)-----))))))).....))))))......... ( -27.30)
>DroSim_CAF1 15358 83 + 1
UGAAC--UCAGCCGCU------------UUCACCUGGCCAACCCAGUUAGGGAUUAUUUCC-----------GGCGAUAAC-----CAACUGGCAAAUGCCAGGAAGUUGGAA
.....--....(((((------------(...((((((....((((((.((((....))))-----------((......)-----))))))).....))))))))).))).. ( -26.30)
>DroEre_CAF1 26136 89 + 1
CGAAC--UCGGCAGUU------------UCCUUGUGGCCA-CCCAGUUAGGGAUUAUAUCCGAGAAAACUACGGCGAUAACCAAACCAACUGCCAAAUGCCAGG---------
.....--..(((((((------------......(((...-(((.....))).((((..(((((....)).)))..)))))))....)))))))..........--------- ( -21.60)
>DroYak_CAF1 11180 108 + 1
UCAAGUUUCAGCAGUUUCAGCAGUUUUCUCCUUCUGACCAACCCAGUUGGGGAUUAUUUCCGGGUAAACUACGGCGAUAAC-----CAACUGCCAAAUGCCAGGAAGGUGAAA
(((..((((.(((......((((((.(((((..(((.......)))..)))))(((((.(((((....)).))).))))).-----.))))))....)))..))))..))).. ( -28.40)
>consensus
CGAAC__UCAGCCGUU____________UUCACCUGGCCAACCCAGUUAGGGAUUAUUUCCG_G_AAACUACGGCGAUAAC_____CAACUGGCAAAUGCCAGGAAGGUGAAA
................................((((((....((((((.....(((((.(((.........))).))))).......)))))).....))))))......... (-15.24 = -16.10 +   0.86)

alignment

secondary structure

dotplot

Window 9

Location	20,130,511 – 20,130,605
Length	94
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	73.33
Mean single sequence MFE	-30.20
Consensus MFE	-19.34
Energy contribution	-20.12
Covariance contribution	0.78
Combinations/Pair	1.10
Mean z-score	-1.87
Structure conservation index	0.64
SVM decision value	1.44
SVM RNA-class probability	0.954236
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20130511 94 - 22224390
UUUCACCUUCCUGGCAUUUGCCAGUUG-----GUUAUCGCCGUAGUUUACCCGGAAAUAAUCCCUAACUGGGUUGGCCAGGUGAA------------AACGGCUGA--GUUCG
.((((((...(((((....)))))..)-----))....(((((..((((((.((...((((((......)))))).)).))))))------------.))))).))--).... ( -34.90)
>DroSec_CAF1 31904 83 - 1
UUCCAACUUCCUGGCAUUUGCCAGUUG-----GUUAUCGCC-----------GGAAAUAAUCCCUAACUGGGUUGGCCAGGUGAA------------CGCGGCUGA--GUUCG
..((((((..(((((....)))))..)-----))).(((((-----------((...((((((......)))))).)).))))).------------...))....--..... ( -28.40)
>DroSim_CAF1 15358 83 - 1
UUCCAACUUCCUGGCAUUUGCCAGUUG-----GUUAUCGCC-----------GGAAAUAAUCCCUAACUGGGUUGGCCAGGUGAA------------AGCGGCUGA--GUUCA
..((((((..(((((....)))))..)-----))).(((((-----------((...((((((......)))))).)).))))).------------...))....--..... ( -28.40)
>DroEre_CAF1 26136 89 - 1
---------CCUGGCAUUUGGCAGUUGGUUUGGUUAUCGCCGUAGUUUUCUCGGAUAUAAUCCCUAACUGGG-UGGCCACAAGGA------------AACUGCCGA--GUUCG
---------...((.(((((((((((..((((....(((((.(((((.....((((...))))..)))))))-)))...))))..------------)))))))))--)))). ( -29.80)
>DroYak_CAF1 11180 108 - 1
UUUCACCUUCCUGGCAUUUGGCAGUUG-----GUUAUCGCCGUAGUUUACCCGGAAAUAAUCCCCAACUGGGUUGGUCAGAAGGAGAAAACUGCUGAAACUGCUGAAACUUGA
.....((.....))..((..(((((((-----((....)))(((((((.((((((.....)))(((((...)))))......)).).)))))))...))))))..))...... ( -29.50)
>consensus
UUCCAACUUCCUGGCAUUUGCCAGUUG_____GUUAUCGCCGUAGUUU_C_CGGAAAUAAUCCCUAACUGGGUUGGCCAGGUGAA____________AACGGCUGA__GUUCG
.........((((((.....(((((((.....(((((..(((.........)))..)))))...)))))))....))))))................................ (-19.34 = -20.12 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:11 2006