Locus 909

Sequence ID	X_DroMel_CAF1
Location	2,539,220 – 2,539,361
Length	141
Max. P	0.988398

overview

Window 4

Location	2,539,220 – 2,539,323
Length	103
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	72.36
Mean single sequence MFE	-26.92
Consensus MFE	-15.58
Energy contribution	-16.97
Covariance contribution	1.39
Combinations/Pair	1.12
Mean z-score	-2.23
Structure conservation index	0.58
SVM decision value	2.12
SVM RNA-class probability	0.988398
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2539220 103 + 22224390
CCUUGUUUUC------CCCCUCGAAGCAGAUGUUAA-UCCCAACU-UGGGAUUAAGGUUC---UUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUUCGUCGUCCUAC
..........------......((((..(((.((((-((((....-.)))))))).))))---)))...((..(.(((((.((((((((....))))))))))))).)..)).. ( -35.60)
>DroSec_CAF1 2587 103 + 1
CCUUGUUUCC------CCCCUCGCAGAAGAUGUUAA-UCCCAACU-UGGGAUUAUGGACC---CUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUCCGUCGUCUUAC
....(..(((------......(((.....)))(((-((((....-.))))))).)))..---)...........((((.(((((((((....)))))))))...))))..... ( -29.00)
>DroSim_CAF1 2576 103 + 1
CCUUGUUUUC------CCCCUCGCAGAAGAUGUUAA-UCCCAACU-UGGGUUUAAGGACC---CUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUCCGUCGUCUUAC
..........------..........((((((....-....((((-((((((....))))---)....)))))..(((..(((((((((....))))))))).))))))))).. ( -27.10)
>DroEre_CAF1 2759 101 + 1
CCUCGUUUUUUU---CACU-CC---GAAGAUGUUAA-ACCCAACU-UGGGAUUAAG-GUC---CGUCAAAGUUUCGCGAAAGGCGUUGAAAUUUCCACGCCUCCGUCGUCUUGC
............---.(((-..---((.(((.((((-.(((....-.))).)))).-)))---..))..)))...((((.((((((.((....)).))))))...))))..... ( -24.90)
>DroYak_CAF1 2802 95 + 1
CCUUGUUUUUUA---CCCCCUC---GAAGAUGUUCA-ACUCAACU-UGGGAUUAAGGGUC---CUGCAAAGUUUCUCGAAAGGCGUUGAAAUUUCAACGCCUCCUC--------
............---.....((---((.((......-....((((-((((((.....)))---))...))))))))))).(((((((((....)))))))))....-------- ( -21.90)
>DroAna_CAF1 2409 102 + 1
CCUUAUUUUCUUUUCUUUU-CC---GGAAAUCUCGAGAACCAUCGCGGGGAUUAAUAUUUCCAGUUAAAAGUUUUCCUUAAGGCGUUGAAAUUUCAACGCUUUUUC--------
...................-..---(((((.(((((......))).((..((....))..)).......)).)))))..((((((((((....))))))))))...-------- ( -23.00)
>consensus
CCUUGUUUUC______CCCCUC___GAAGAUGUUAA_ACCCAACU_UGGGAUUAAGGAUC___CUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUCCGUCGUCUUAC
......................................(((......))).........................((((.(((((((((....)))))))))...))))..... (-15.58 = -16.97 +   1.39)

alignment

secondary structure

dotplot

Window 5

Location	2,539,220 – 2,539,323
Length	103
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	72.36
Mean single sequence MFE	-29.95
Consensus MFE	-15.04
Energy contribution	-15.65
Covariance contribution	0.61
Combinations/Pair	1.07
Mean z-score	-2.08
Structure conservation index	0.50
SVM decision value	1.45
SVM RNA-class probability	0.954802
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2539220 103 - 22224390
GUAGGACGACGAAGGCGUUGAAAUUUCAACGCCUUUCGCGAAACUUUUGAA---GAACCUUAAUCCCA-AGUUGGGA-UUAACAUCUGCUUCGAGGGG------GAAAACAAGG
......((.((((((((((((....)))))))).))))))...((((((((---(....((((((((.-....))))-))))......))))))))).------.......... ( -38.40)
>DroSec_CAF1 2587 103 - 1
GUAAGACGACGGAGGCGUUGAAAUUUCAACGCCUUUCGCGAAACUUUUGAG---GGUCCAUAAUCCCA-AGUUGGGA-UUAACAUCUUCUGCGAGGGG------GGAAACAAGG
......((.((((((((((((....)))))))).))))))...((((.(((---(((...(((((((.-....))))-)))..))))))...))))..------(....).... ( -35.90)
>DroSim_CAF1 2576 103 - 1
GUAAGACGACGGAGGCGUUGAAAUUUCAACGCCUUUCGCGAAACUUUUGAG---GGUCCUUAAACCCA-AGUUGGGA-UUAACAUCUUCUGCGAGGGG------GAAAACAAGG
......((.((((((((((((....)))))))).)))))).....((((((---....))))))(((.-....))).-......((((((....))))------))........ ( -31.00)
>DroEre_CAF1 2759 101 - 1
GCAAGACGACGGAGGCGUGGAAAUUUCAACGCCUUUCGCGAAACUUUGACG---GAC-CUUAAUCCCA-AGUUGGGU-UUAACAUCUUC---GG-AGUG---AAAAAAACGAGG
......((.(((((((((.((....)).))))).))))))..(((((((.(---((.-.((((.(((.-....))).-))))..)))))---))-))).---............ ( -28.80)
>DroYak_CAF1 2802 95 - 1
--------GAGGAGGCGUUGAAAUUUCAACGCCUUUCGAGAAACUUUGCAG---GACCCUUAAUCCCA-AGUUGAGU-UGAACAUCUUC---GAGGGGG---UAAAAAACAAGG
--------(((.(((((((((....))))))))))))......(((((...---.((((((..((...-....)).(-((((....)))---)))))))---)......))))) ( -25.10)
>DroAna_CAF1 2409 102 - 1
--------GAAAAAGCGUUGAAAUUUCAACGCCUUAAGGAAAACUUUUAACUGGAAAUAUUAAUCCCCGCGAUGGUUCUCGAGAUUUCC---GG-AAAAGAAAAGAAAAUAAGG
--------......(((((((....)))))))...........(((((..((((((((........((.....))........))))))---))-))))).............. ( -20.49)
>consensus
GUAAGACGACGGAGGCGUUGAAAUUUCAACGCCUUUCGCGAAACUUUUGAG___GAACCUUAAUCCCA_AGUUGGGA_UUAACAUCUUC___GAGGGG______GAAAACAAGG
..........(((((((((((....)))))))))))............................(((......)))...................................... (-15.04 = -15.65 +   0.61)

alignment

secondary structure

dotplot

Window 6

Location	2,539,253 – 2,539,361
Length	108
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	70.35
Mean single sequence MFE	-28.13
Consensus MFE	-11.11
Energy contribution	-12.90
Covariance contribution	1.79
Combinations/Pair	1.19
Mean z-score	-1.73
Structure conservation index	0.39
SVM decision value	-0.03
SVM RNA-class probability	0.516883
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2539253 108 + 22224390
CAACUUGGGAUUAAGGUUCUUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUUCGUCGUCCUACAACGGGCCAUCUCCGA-UUUUUUCACGCCUUAAACUGUG-
.......((.(((((((.....(((((((..(((((.((((((((....))))))))))))).((((......)))).......))-)))))....))))))).))...- ( -31.80)
>DroPse_CAF1 2359 89 + 1
-------AGAAGAAGGUCCGGCAAAACUUUU-CCAAAAGCGUGAAAAUUUCCACGGA------------AA-UUUGCCUACGCGGAUUCCCUUCACGCCCCAUGCCACGC
-------.((((..(((((((.((....)).-))....(((((.(((((((....))------------))-)))...))))))))))..))))................ ( -23.00)
>DroSec_CAF1 2620 107 + 1
CAACUUGGGAUUAUGGACCCUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUCCGUCGUCUUACA-CAGGCCAUCUCGGA-UUUUUUCACGCCUUAAACUGUG-
.((((((((........)))....)))))..((((.(((((((((....)))))))))...))))....((-(((.......((((-.....)).)).......)))))- ( -28.74)
>DroSim_CAF1 2609 107 + 1
CAACUUGGGUUUAAGGACCCUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUCCGUCGUCUUACA-CAGGCCAUCUCGGA-UUUUUUCACGCCCCAAACUGUG-
.((((((((((....)))))....)))))..((((.(((((((((....)))))))))...))))....((-(((.......((((-.....)).)).......)))))- ( -31.74)
>DroEre_CAF1 2791 105 + 1
CAACUUGGGAUUAAG-GUCCGUCAAAGUUUCGCGAAAGGCGUUGAAAUUUCCACGCCUCCGUCGUCUUGCA-CUGGACUGCUCG-C-CUUUUUCACGCCUUGAACUGUG-
.......((.(((((-(..(((.((((....((((.((((((.((....)).))))))..((.((((....-..)))).)))))-)-..)))).))))))))).))...- ( -28.00)
>DroYak_CAF1 2835 88 + 1
CAACUUGGGAUUAAGGGUCCUGCAAAGUUUCUCGAAAGGCGUUGAAAUUUCAACGCCUCCUC------------GGAC---------UUUUUUCACGCCUUAAACAGUG-
..(((.(...((((((((.....((((((...(((.(((((((((....)))))))))..))------------))))---------)))....)).)))))).)))).- ( -25.50)
>consensus
CAACUUGGGAUUAAGGACCCUCAAAAGUUUCGCGAAAGGCGUUGAAAUUUCAACGCCUCCGUCGUCUUACA_CAGGCCAUCUCGGA_UUUUUUCACGCCUUAAACUGUG_
......(((........)))...........((((.(((((((((....)))))))))...))))............................................. (-11.11 = -12.90 +   1.79)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:01 2006