Locus 9148

Sequence ID	3R_DroMel_CAF1
Location	24,400,199 – 24,400,328
Length	129
Max. P	0.911723

overview

Window 7

Location	24,400,199 – 24,400,291
Length	92
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	85.40
Mean single sequence MFE	-16.90
Consensus MFE	-14.04
Energy contribution	-14.02
Covariance contribution	-0.03
Combinations/Pair	1.10
Mean z-score	-1.51
Structure conservation index	0.83
SVM decision value	-0.04
SVM RNA-class probability	0.510753
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24400199 92 - 27905053
AUCUUUAGCCAAUAAAGAAAACAGGAUAAGCCAUCAUUUCCGAAUUGCAAGUCAAAAGGAUGUAAGCAGGCGGAAUUCCCCGCAA------------------AACAUCA
.((((((.....))))))......(((..((..((......))...))..))).....(((((......((((......))))..------------------.))))). ( -17.30)
>DroVir_CAF1 214506 110 - 1
AUCUUUAACCAAUAAAGAAAACAGGAUAAGCCAGCAUUUCCGAAUUGCAAGUCAAAAAGAUUUAAGUAGGCGGAAUUCCCCACAACCAAAUAAUAAUGCAAACAACAACA
.((((((.....)))))).....((....(((.(((.........)))(((((.....))))).....)))((......))....))....................... ( -16.20)
>DroEre_CAF1 236763 92 - 1
AUCUUUAGCCAAUAAAGAAAACAGGAUAAGCCAUCAUUUCCGAUUUGCAAGUCAAAAGGAUGUAAGCAGGCGGAAUUCCCCGCAA------------------AACAUCA
.((((((.....))))))......(((..((.(((......)))..))..))).....(((((......((((......))))..------------------.))))). ( -18.40)
>DroWil_CAF1 206062 95 - 1
-UCUUUAGCCAAUAAAGAAAACAGGAUAAUCCACUAUUUCCGAAUUGCAAGUCAAAAAGAUUUAAGCAAGCGGAAUUCCCCGCAAUUGA--------------AGAAUGA
-(((((((...............(((............)))...(((((((((.....)))))..))))((((......))))..))))--------------))).... ( -17.90)
>DroYak_CAF1 230723 92 - 1
AUCUUAAGCCAAUAAAGAAAACAGGAUAAGCCAUCAUUUCCGAAUUGCAAGUCAAAAGGAUGUAAGCAGGCGGAAUUCCCCGCAA------------------AACAUCA
.......((.(((...((((...((.....))....))))...)))))..........(((((......((((......))))..------------------.))))). ( -13.90)
>DroAna_CAF1 225908 91 - 1
AUCUUUAACCAAUAAAGAAAACAGGAUAAGCCAUCAUUUCCGAAUUGCAAGUCAAAAAGAUGUAAGCAAGCGGAAUUC-CCGCAG------------------CACAUCA
.((((((.....))))))......(((..((..((......))...))..))).....(((((..((..((((.....-)))).)------------------)))))). ( -17.70)
>consensus
AUCUUUAGCCAAUAAAGAAAACAGGAUAAGCCAUCAUUUCCGAAUUGCAAGUCAAAAAGAUGUAAGCAGGCGGAAUUCCCCGCAA__________________AACAUCA
.((((((.....)))))).....(((............)))...((((..(((.....)))....))))((((......))))........................... (-14.04 = -14.02 +  -0.03)

alignment

secondary structure

dotplot

Window 8

Location	24,400,212 – 24,400,328
Length	116
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.58
Mean single sequence MFE	-18.60
Consensus MFE	-14.38
Energy contribution	-14.10
Covariance contribution	-0.28
Combinations/Pair	1.14
Mean z-score	-1.68
Structure conservation index	0.77
SVM decision value	1.08
SVM RNA-class probability	0.911723
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24400212 116 - 27905053
AAAACAAGGACCAUUCAAAGCAGCGACGACUCACGGCAUCUUUAGCCAAUAAAGAAAACAGGAUAAGCCAUCAUUUCCGAAUUGCAAGUCAAA-AGGAUGUAAGCAGGCGGAAUUCC
.......((...((((...((.(.((....)).).)).((((((.....)))))).....))))...)).....(((((..((((..(((...-..)))....)))).))))).... ( -20.70)
>DroVir_CAF1 214537 109 - 1
AAAACAAAGCGUACAUUAGGCAACAA-------CAGAAUCUUUAACCAAUAAAGAAAACAGGAUAAGCCAGCAUUUCCGAAUUGCAAGUCAAA-AAGAUUUAAGUAGGCGGAAUUCC
........((.(((.....((((...-------.....((((((.....)))))).....(((...(....)...)))...))))(((((...-..)))))..))).))((....)) ( -18.00)
>DroGri_CAF1 209952 109 - 1
AAAACAAAGCAAACAUUAAGCAACAA-------CAGAAUCUUUAACCAAUAAAGAAAACAGGAUAAGCCAGUAUUUCCGAAUUGCAAGUCAAA-AAGAUUUAAGUAGGCGGAAUUCC
........((..((.....((((...-------.....((((((.....)))))).....(((............)))...))))(((((...-..)))))..))..))((....)) ( -14.50)
>DroWil_CAF1 206079 92 - 1
ACAACAAAG-CCAUU-----------------------UCUUUAGCCAAUAAAGAAAACAGGAUAAUCCACUAUUUCCGAAUUGCAAGUCAAA-AAGAUUUAAGCAAGCGGAAUUCC
.........-...((-----------------------((((((.....))))))))...((.....)).....(((((..(((((((((...-..)))))..)))).))))).... ( -18.30)
>DroMoj_CAF1 190466 110 - 1
AAAACAAAGCGUACAUUAAGCAACAA-------CAGAUUCUUUAACCAAUAAAGAAAAUAGGAUAAGCCAGAGUUUCCGAAUUGCAAGUCAAAAAAGACUUAAGUAGGCGGAAUUCC
........((.(((.....((((...-------....(((((((.....)))))))....(((..(((....))))))...))))(((((......)))))..))).))((....)) ( -21.50)
>DroAna_CAF1 225921 111 - 1
AAAACAAAAACAUUGCAGACC---G-AGACACACUGCAUCUUUAACCAAUAAAGAAAACAGGAUAAGCCAUCAUUUCCGAAUUGCAAGUCAAA-AAGAUGUAAGCAAGCGGAAUUC-
.............(((((...---.-.......)))))((((((.....)))))).....((.....)).....(((((..((((..(((...-..)))....)))).)))))...- ( -18.60)
>consensus
AAAACAAAGCCAACAUUAAGCAACAA_______CAGAAUCUUUAACCAAUAAAGAAAACAGGAUAAGCCAGCAUUUCCGAAUUGCAAGUCAAA_AAGAUUUAAGCAGGCGGAAUUCC
......................................((((((.....)))))).....((.....)).....(((((..(((((((((......)))))..)))).))))).... (-14.38 = -14.10 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:27:40 2006