Locus 5239

Sequence ID	2R_DroMel_CAF1
Location	17,048,104 – 17,048,254
Length	150
Max. P	0.992323

overview

Window 9

Location	17,048,104 – 17,048,215
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.15
Mean single sequence MFE	-34.26
Consensus MFE	-22.73
Energy contribution	-21.77
Covariance contribution	-0.96
Combinations/Pair	1.43
Mean z-score	-2.04
Structure conservation index	0.66
SVM decision value	1.26
SVM RNA-class probability	0.936813
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17048104 111 - 20766785
AAACGAA-ACCUCCCAGUGGCAAACUUUG-----UUCAACCAUCA---GUAUGUUUGUACAGCUGGGAUAUGAAAAACACUAAGAUCUUUGUAGUGGUCGUACUUUUGGCCGCCAGUUCA
....(((-...(((((((.((((((.(((-----.........))---)...))))))...))))))).........................(((((((......)))))))...))). ( -28.90)
>DroSec_CAF1 141592 114 - 1
AAGGGAA-ACAUCCCAGUUGCGAACUUUA-----UUCAACCAUUAGCUGUAUGUUUAUACAGCUGGGGUAUGAAAAACACUGAGAUCUUUGUACUGGCCGUACUUUUGGCCAGCAGUUCA
..((((.-...))))......(((((...-----(((((((.((((((((((....))))))))))))).))))...................(((((((......))))))).))))). ( -40.00)
>DroSim_CAF1 150136 114 - 1
AAGCGAA-ACAUCCCAGUUGCGAACUUUA-----UUCAACCAUUAGCUGUAUGUUCAUACAGCUGGGGUAUGAAAAACACUGAGAUCUUUGUACUGGCCGUACUUUUGGCCAGCAGUUCA
..((((.-.........))))(((((...-----(((((((.((((((((((....))))))))))))).))))...................(((((((......))))))).))))). ( -37.20)
>DroEre_CAF1 145698 116 - 1
CAUCGAACAGCUCCCAGUUGCGAGCUUCGAACAGCUCA-GCAUCA---GUAUGCUUGCACUGCUGGAAUAUGAGAAACACUGAAAUCUUGGUACUGGCCGUGCCUUUGGCUGCCUGCUCA
.......(((((.(((((((((((((......)))))(-((((..---..))))).)))..))))).......................(((((.....)))))...)))))........ ( -31.70)
>DroYak_CAF1 155186 112 - 1
UAGGAAACACAUCCCAGUUGCGUGAUGUG-----CUCAACCAUCA---GUAUGCUCGCACUGCUGGGAUAUGGAAAACAUGGAAAUCUUCGUACUGGCCGUGCUUUUGGCUGCCUGUUCA
((((...((.((((((((.(.((((((((-----((........)---))))).)))).).)))))))).))......(((((....)))))...(((((......))))).)))).... ( -33.50)
>consensus
AAGCGAA_ACAUCCCAGUUGCGAACUUUG_____UUCAACCAUCA___GUAUGUUUGUACAGCUGGGAUAUGAAAAACACUGAGAUCUUUGUACUGGCCGUACUUUUGGCCGCCAGUUCA
..........(((((((((((((((...........................)))))))..)))))))).((((....((.((....)).)).(((((((......)))))))...)))) (-22.73 = -21.77 +  -0.96)

alignment

secondary structure

dotplot

Window 0

Location	17,048,144 – 17,048,254
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.46
Mean single sequence MFE	-29.30
Consensus MFE	-14.64
Energy contribution	-14.32
Covariance contribution	-0.32
Combinations/Pair	1.40
Mean z-score	-2.43
Structure conservation index	0.50
SVM decision value	2.32
SVM RNA-class probability	0.992323
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17048144 110 - 20766785
GCUCUCUUCUCUCCAACCGGCGAUA-AGCCAAUUCAUAAAAAACGAA-ACCUCCCAGUGGCAAACUUUG-----UUCAACCAUCA---GUAUGUUUGUACAGCUGGGAUAUGAAAAACAC
..................(((....-.)))..((((((.........-...(((((((.((((((.(((-----.........))---)...))))))...)))))))))))))...... ( -25.80)
>DroSec_CAF1 141632 113 - 1
UCUCUCUUCUCUUCGAGAGGAGAUA-AGCCAAUUCAUAAAAAGGGAA-ACAUCCCAGUUGCGAACUUUA-----UUCAACCAUUAGCUGUAUGUUUAUACAGCUGGGGUAUGAAAAACAC
..(((((((((...)))))))))..-......(((.(((...((((.-...))))..))).))).....-----(((((((.((((((((((....))))))))))))).))))...... ( -34.50)
>DroSim_CAF1 150176 113 - 1
GCUCUCUUCUCUCCGAGAGGCGAUA-AGCCAAUUCAUAAAAAGCGAA-ACAUCCCAGUUGCGAACUUUA-----UUCAACCAUUAGCUGUAUGUUCAUACAGCUGGGGUAUGAAAAACAC
..((((........))))(((....-.)))......((((...((.(-((......))).))...))))-----(((((((.((((((((((....))))))))))))).))))...... ( -29.00)
>DroEre_CAF1 145738 112 - 1
GCGCUCUUCCCUUCG----GCCUUAUCACAAAUCCACAAACAUCGAACAGCUCCCAGUUGCGAGCUUCGAACAGCUCA-GCAUCA---GUAUGCUUGCACUGCUGGAAUAUGAGAAACAC
...(((.....((((----((.....................((((..(((((.(....).)))))))))...((..(-((((..---..))))).))...))))))....)))...... ( -24.40)
>DroYak_CAF1 155226 108 - 1
GCUCUUUACUCUCCG----GCCUUAUCGCCAAUCCGUAAAUAGGAAACACAUCCCAGUUGCGUGAUGUG-----CUCAACCAUCA---GUAUGCUCGCACUGCUGGGAUAUGGAAAACAU
..............(----((......)))..((((((....(....)...(((((((.(.((((((((-----((........)---))))).)))).).)))))))))))))...... ( -32.80)
>consensus
GCUCUCUUCUCUCCGA__GGCGAUA_AGCCAAUUCAUAAAAAGCGAA_ACAUCCCAGUUGCGAACUUUG_____UUCAACCAUCA___GUAUGUUUGUACAGCUGGGAUAUGAAAAACAC
................................((((((.............((((((((((((((...........................)))))))..)))))))))))))...... (-14.64 = -14.32 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:56 2006