Locus 4030

Sequence ID	X_DroMel_CAF1
Location	10,650,302 – 10,650,435
Length	133
Max. P	0.984516

overview

Window 6

Location	10,650,302 – 10,650,413
Length	111
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	92.68
Mean single sequence MFE	-20.64
Consensus MFE	-17.02
Energy contribution	-16.98
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.82
SVM decision value	0.68
SVM RNA-class probability	0.819737
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10650302 111 - 22224390
UAAACACUAAAUACUUUA-AGCGGCUCAAAUACCACACUUUUGAACCACUGUGCGCAUAUGUGUACUUCAAUUUCAAUCAUGCCC-----AGCAAAAGGUGCGAAUCCAUCAAAGUC
............(((((.-.((((.(((((.........))))).))...((((((....))))))...................-----.))....((((......))))))))). ( -18.80)
>DroSec_CAF1 7756 111 - 1
UAAACACUAAAUACUUUA-AGCGGCUCAAAUACCACACUUUUGAACCACUGUGCGCACAUGUGUACUUCAAUUUCAAUCAUGCCC-----AGCAAAAGGUGCGAAUCCAUCAAAGUC
............(((((.-.((((.(((((.........))))).))...((((((....))))))...................-----.))....((((......))))))))). ( -18.80)
>DroSim_CAF1 6044 111 - 1
UAAACACUAAAUACUUUA-AGCGGUUCAAAUACCACACUUUCGAACCACUGUGCGCACAUGUGUACUUCAAUUUCAAUCAUGCCC-----AGCAAAAGGUGCGAAUCCAUCAAAGUC
............(((((.-.(.(((......))).)...((((.(((...((((((....))))))..............(((..-----.)))...))).))))......))))). ( -20.10)
>DroEre_CAF1 7810 112 - 1
UAAACACCAAAUACUUUAAAGUGGCUCAAAUACUACACUUUUGACCCACUGUGCGCACAUGUGUACUUCACAUUCAAUCAUUCAC-----AGCAAAAGGUGCGAAUCCAUCAAAGUC
....((((...........(((((.(((((.........))))).)))))((((((....))))))...................-----.......))))................ ( -22.90)
>DroYak_CAF1 8085 116 - 1
UAAACACUAAAUACUUUA-AGUGGCUCAAACACUAUACUUUUGAUCCACUGUGCGCACAUGUGUACUUCAAUUUCAAUCAUGCCCAAGUGAGCAAAAGGUGCGAAUCCAUCAAAGUC
............(((((.-(((((.(((((.........))))).)))))((((((....))))))......(((..((((......))))(((.....))))))......))))). ( -22.60)
>consensus
UAAACACUAAAUACUUUA_AGCGGCUCAAAUACCACACUUUUGAACCACUGUGCGCACAUGUGUACUUCAAUUUCAAUCAUGCCC_____AGCAAAAGGUGCGAAUCCAUCAAAGUC
............(((((...((((.(((((.........))))).))...((((((....)))))).........................))....((((......))))))))). (-17.02 = -16.98 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	10,650,337 – 10,650,435
Length	98
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	87.22
Mean single sequence MFE	-23.96
Consensus MFE	-20.30
Energy contribution	-20.66
Covariance contribution	0.36
Combinations/Pair	1.17
Mean z-score	-1.60
Structure conservation index	0.85
SVM decision value	0.50
SVM RNA-class probability	0.762084
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10650337 98 + 22224390
UUGAAAUUGAAGUACACAUAUGCGCACAGUGGUUCAAAAGUGUGGUAUUUGAGCCGCU-UAAAGUAUUUAGUGUUUACCAUGGAAAUGUGGGUAUUUU-------U
........(((((((((((((((....(((((((((((.........)))))))))))-....))))...))))...((((......)))))))))))-------. ( -25.20)
>DroSec_CAF1 7791 105 + 1
UUGAAAUUGAAGUACACAUGUGCGCACAGUGGUUCAAAAGUGUGGUAUUUGAGCCGCU-UAAAGUAUUUAGUGUUUACCAUGGAAAUGUGGGGAUUUUAUUAUAUU
.(((((((.....((((..((((....(((((((((((.........)))))))))))-....))))...))))...((((......)))).)))))))....... ( -26.30)
>DroSim_CAF1 6079 105 + 1
UUGAAAUUGAAGUACACAUGUGCGCACAGUGGUUCGAAAGUGUGGUAUUUGAACCGCU-UAAAGUAUUUAGUGUUUACCAUGGAAAUGUGGGGAUUUUAUUAUUUU
.(((((((.....((((..((((....(((((((((((.........)))))))))))-....))))...))))...((((......)))).)))))))....... ( -26.00)
>DroEre_CAF1 7845 96 + 1
UUGAAUGUGAAGUACACAUGUGCGCACAGUGGGUCAAAAGUGUAGUAUUUGAGCCACUUUAAAGUAUUUGGUGUUUACCAUGGAAAUG---AGAAUUU-------U
.((((..(.((((((...(((....)))((((.(((((.........))))).))))......)))))).)..)))).(((....)))---.......-------. ( -22.20)
>DroYak_CAF1 8125 98 + 1
UUGAAAUUGAAGUACACAUGUGCGCACAGUGGAUCAAAAGUAUAGUGUUUGAGCCACU-UAAAGUAUUUAGUGUUUACCAUGGUAAUGUGGGGAAUUU-------A
...(((((.....((((..((((....(((((.(((((.........))))).)))))-....))))...))))...((((......))))..)))))-------. ( -20.10)
>consensus
UUGAAAUUGAAGUACACAUGUGCGCACAGUGGUUCAAAAGUGUGGUAUUUGAGCCGCU_UAAAGUAUUUAGUGUUUACCAUGGAAAUGUGGGGAUUUU_______U
.............((((..((((....(((((((((((.........))))))))))).....))))...))))...((((......))))............... (-20.30 = -20.66 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	10,650,337 – 10,650,435
Length	98
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	87.22
Mean single sequence MFE	-16.34
Consensus MFE	-12.88
Energy contribution	-12.92
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-2.57
Structure conservation index	0.79
SVM decision value	1.98
SVM RNA-class probability	0.984516
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10650337 98 - 22224390
A-------AAAAUACCCACAUUUCCAUGGUAAACACUAAAUACUUUA-AGCGGCUCAAAUACCACACUUUUGAACCACUGUGCGCAUAUGUGUACUUCAAUUUCAA
.-------....((((...........))))................-((.((.(((((.........))))).)).))((((((....))))))........... ( -14.80)
>DroSec_CAF1 7791 105 - 1
AAUAUAAUAAAAUCCCCACAUUUCCAUGGUAAACACUAAAUACUUUA-AGCGGCUCAAAUACCACACUUUUGAACCACUGUGCGCACAUGUGUACUUCAAUUUCAA
...............(((........)))..................-((.((.(((((.........))))).)).))((((((....))))))........... ( -14.00)
>DroSim_CAF1 6079 105 - 1
AAAAUAAUAAAAUCCCCACAUUUCCAUGGUAAACACUAAAUACUUUA-AGCGGUUCAAAUACCACACUUUCGAACCACUGUGCGCACAUGUGUACUUCAAUUUCAA
...............(((........)))..................-((.((((((((........))).))))).))((((((....))))))........... ( -14.40)
>DroEre_CAF1 7845 96 - 1
A-------AAAUUCU---CAUUUCCAUGGUAAACACCAAAUACUUUAAAGUGGCUCAAAUACUACACUUUUGACCCACUGUGCGCACAUGUGUACUUCACAUUCAA
.-------.......---........((((....))))..........(((((.(((((.........))))).)))))((((((....))))))........... ( -20.00)
>DroYak_CAF1 8125 98 - 1
U-------AAAUUCCCCACAUUACCAUGGUAAACACUAAAUACUUUA-AGUGGCUCAAACACUAUACUUUUGAUCCACUGUGCGCACAUGUGUACUUCAAUUUCAA
.-------............((((....))))...............-(((((.(((((.........))))).)))))((((((....))))))........... ( -18.50)
>consensus
A_______AAAAUCCCCACAUUUCCAUGGUAAACACUAAAUACUUUA_AGCGGCUCAAAUACCACACUUUUGAACCACUGUGCGCACAUGUGUACUUCAAUUUCAA
..........................((((....))))..........((.((.(((((.........))))).)).))((((((....))))))........... (-12.88 = -12.92 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:42 2006