Locus 3932

Sequence ID	3R_DroMel_CAF1
Location	10,667,979 – 10,668,085
Length	106
Max. P	0.970474

overview

Window 7

Location	10,667,979 – 10,668,085
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	73.59
Mean single sequence MFE	-22.91
Consensus MFE	-11.76
Energy contribution	-12.60
Covariance contribution	0.84
Combinations/Pair	1.07
Mean z-score	-2.13
Structure conservation index	0.51
SVM decision value	1.58
SVM RNA-class probability	0.965288
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10667979 106 + 27905053
UUUUGUUCCUUAACAAAUCUAUCAUCGGGCUACCAAUAAGCUAAAUGUAUUUGAUAGAUUUGUUUAAGUGUUUUCCUAGUCUUCGUAGACAAAUUAUUUUCUGA--------------AU
....((((((((((((((((((((..((....)).....((.....))...))))))))))).)))))..........((((....))))............))--------------)) ( -22.50)
>DroSec_CAF1 9581 106 + 1
UUUCGUUCCCUGACAAAUCUAUCAUAGGGCUACCAAUAAGCUCAAUGAAUUUGAUAGAUUUGCUUAAGUGUUUUACUCGUCUUCAUAGACAAAUUCUUUUCUGA--------------AU
..........((((((((((((((..(((((.......)))))........))))))))))).)))............((((....))))..((((......))--------------)) ( -20.40)
>DroSim_CAF1 9712 106 + 1
UUUCGUUCCUUGGCAAAUCUAUCAUCGGGCUACCAAUAAGCUAAAUGAAUUUGAUAGAUUUGCUUAAGUGUUUUCCUCGUCUUCAUAGACAAAUUCUUUUCUGA--------------AU
........(((((((((((((((((((((((.......))))...)))...)))))))))))).))))..........((((....))))..((((......))--------------)) ( -25.30)
>DroEre_CAF1 6510 117 + 1
UUCUGUUCCUUUGCAAAUCUAUCAUCGGGCUACCAAAAAACUAAUUGAAUCUGAUAGAUUUGC-AAAGUGUUU--CUUUUUUGCUUCAACAAAUUCCUUGCUGAGUCCCAGUACAUGAGU
........((((((((((((((((..((....))......(.....)....))))))))))))-)))).....--.................((((..(((((.....)))))...)))) ( -27.20)
>DroYak_CAF1 1150 105 + 1
UUCUGUUCCUUGGAAAAUCUUUCAUCGGGCUACCAAGAAACUAAAUGAAUCUGAUAGAUUCG------UUUUU--CUUUUCUA-------AAGCUACUUUCUGAAUCCCAGUACAUGAGU
((((((..((.(((...((........((((....(((((..(((((((((.....))))))------)))..--..))))).-------.)))).......)).))).)).))).))). ( -19.16)
>consensus
UUUUGUUCCUUGGCAAAUCUAUCAUCGGGCUACCAAUAAGCUAAAUGAAUUUGAUAGAUUUGCUUAAGUGUUUU_CUCGUCUUCAUAGACAAAUUCUUUUCUGA______________AU
............((((((((((((..((....))......(.....)....))))))))))))......................................................... (-11.76 = -12.60 +   0.84)

alignment

secondary structure

dotplot

Window 8

Location	10,667,979 – 10,668,085
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.59
Mean single sequence MFE	-23.71
Consensus MFE	-13.50
Energy contribution	-14.30
Covariance contribution	0.80
Combinations/Pair	1.27
Mean z-score	-2.09
Structure conservation index	0.57
SVM decision value	1.66
SVM RNA-class probability	0.970474
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10667979 106 - 27905053
AU--------------UCAGAAAAUAAUUUGUCUACGAAGACUAGGAAAACACUUAAACAAAUCUAUCAAAUACAUUUAGCUUAUUGGUAGCCCGAUGAUAGAUUUGUUAAGGAACAAAA
.(--------------((............((((....))))..........(((((.(((((((((((...............((((....)))))))))))))))))))))))..... ( -20.36)
>DroSec_CAF1 9581 106 - 1
AU--------------UCAGAAAAGAAUUUGUCUAUGAAGACGAGUAAAACACUUAAGCAAAUCUAUCAAAUUCAUUGAGCUUAUUGGUAGCCCUAUGAUAGAUUUGUCAGGGAACGAAA
.(--------------((........((((((((....))))))))......(((..((((((((((((.....((..(.....)..)).......))))))))))))..)))...))). ( -23.60)
>DroSim_CAF1 9712 106 - 1
AU--------------UCAGAAAAGAAUUUGUCUAUGAAGACGAGGAAAACACUUAAGCAAAUCUAUCAAAUUCAUUUAGCUUAUUGGUAGCCCGAUGAUAGAUUUGCCAAGGAACGAAA
.(--------------((.........(((((((....))))))).......(((..((((((((((((...............((((....))))))))))))))))..)))...))). ( -24.06)
>DroEre_CAF1 6510 117 - 1
ACUCAUGUACUGGGACUCAGCAAGGAAUUUGUUGAAGCAAAAAAG--AAACACUUU-GCAAAUCUAUCAGAUUCAAUUAGUUUUUUGGUAGCCCGAUGAUAGAUUUGCAAAGGAACAGAA
.........(((.(..((((((((...))))))))..).......--.....((((-((((((((((((......(((((....))))).......))))))))))))))))...))).. ( -32.12)
>DroYak_CAF1 1150 105 - 1
ACUCAUGUACUGGGAUUCAGAAAGUAGCUU-------UAGAAAAG--AAAAA------CGAAUCUAUCAGAUUCAUUUAGUUUCUUGGUAGCCCGAUGAAAGAUUUUCCAAGGAACAGAA
..((.(((.((((((((((....((.(((.-------.(((((..--(((..------.(((((.....))))).)))..))))).))).))....)))).....)))).))..))))). ( -18.40)
>consensus
AU______________UCAGAAAAGAAUUUGUCUAUGAAGACAAG_AAAACACUUAAGCAAAUCUAUCAAAUUCAUUUAGCUUAUUGGUAGCCCGAUGAUAGAUUUGCCAAGGAACAAAA
...........................((((((......))))))............((((((((((((...............((((....))))))))))))))))............ (-13.50 = -14.30 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:43 2006