Locus 144

Sequence ID	X_DroMel_CAF1
Location	529,539 – 529,786
Length	247
Max. P	0.884728

overview

Window 6

Location	529,539 – 529,655
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.36
Mean single sequence MFE	-23.66
Consensus MFE	-20.52
Energy contribution	-20.32
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-1.21
Structure conservation index	0.87
SVM decision value	0.01
SVM RNA-class probability	0.540909
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 529539 116 - 22224390
UAU----AAGUACCUUUAAUAACUUUACUUACACGAUGCUCGUUUAUUGAAAUUCCCACCCAUGGGAUACCACGCGCGUCGUCGUUCUUGACUUGACUUUUCCUCAACCCAUCUUGAAUG
..(----(((((.............)))))).(((((((.(((..........(((((....)))))....))).)))))))(((((..((.((((.......))))....))..))))) ( -22.26)
>DroSec_CAF1 16259 116 - 1
UAU----AAGUACCUUUAAUAACUUUACUUACACGAUGCUCGUUUAUUGAAAUUUCCACCCAUGGGAUGCCUCGCGCGUCGUCGUUCUUGACUUGACUUUUCCUCAACUCAUCUUGAAUG
..(----(((((.............)))))).(((((((.((...........(((((....))))).....)).)))))))(((((.(((.((((.......)))).)))....))))) ( -20.51)
>DroSim_CAF1 16573 116 - 1
UAU----AAGUACCUUUAAUAACUUUACUUACACGAUGCUCGUUUAUUGAAAUUUCCACCCAUGGGAUGCCUCGCGCGUCGUCGUUCUUGACUUGACUUUUCCUCAACUCAUCUUGAAUG
..(----(((((.............)))))).(((((((.((...........(((((....))))).....)).)))))))(((((.(((.((((.......)))).)))....))))) ( -20.51)
>DroEre_CAF1 21249 120 - 1
UAUAUGUAAGUACCUUUAAUAACUUUACUUACACGAUGCUCGUUUAUUGAAAUUCCCACCCAUGGGAUGGCACACGCGUCGUCGUUCUUGACUUGACUUUGCCUCAACUCAUCUUGAAUG
.....(((((((.............)))))))((((((((((.....)))...(((((....)))))........)))))))(((((.(((.((((.......)))).)))....))))) ( -26.82)
>DroYak_CAF1 15680 120 - 1
UAUGUGUAAGUACCUUUAAUAACUUUACUUACGCGAUGCUCGUUUAUUGAAAUUCCCACCCAUGGGAUGGCACACGCGUCGUCGUUCUUGACUUGACUUUGCCUCAACUCAUCUUGAAUG
...(((((((((.............)))))))))((((((((.....)))...(((((....)))))........)))))..(((((.(((.((((.......)))).)))....))))) ( -28.22)
>consensus
UAU____AAGUACCUUUAAUAACUUUACUUACACGAUGCUCGUUUAUUGAAAUUCCCACCCAUGGGAUGCCACGCGCGUCGUCGUUCUUGACUUGACUUUUCCUCAACUCAUCUUGAAUG
.......(((((.............)))))..((((((((((.....)))...(((((....)))))........)))))))(((((.(((.((((.......)))).)))....))))) (-20.52 = -20.32 +  -0.20)

alignment

secondary structure

dotplot

Window 7

Location	529,619 – 529,727
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.58
Mean single sequence MFE	-19.72
Consensus MFE	-13.01
Energy contribution	-14.81
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.66
SVM decision value	-0.05
SVM RNA-class probability	0.505577
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 529619 108 + 22224390
AGCAUCGUGUAAGUAAAGUUAUUAAAGGUACUU----AUACAACCGAACUACCAGUAGCAACAGCAACAGCCCCACGGCAAUCC----AUAU----ACACAUAGUUACUUACUUACCCGU
.....((.((((((((.((.((((..((((.((----.........)).)))).(((((....))....(((....))).....----...)----))...)))).)))))))))).)). ( -20.10)
>DroSec_CAF1 16339 104 + 1
AGCAUCGUGUAAGUAAAGUUAUUAAAGGUACUU----AUACAACCGACCUACCAGCAGCAACAGCAACAGCCCCAGGGCAACCC----AUAU----ACACAUAGUUAC----UUACCCGU
.....((.((((((((.(((......((((...----............))))....((....))))).(((....))).....----....----........))))----)))).)). ( -19.36)
>DroSim_CAF1 16653 104 + 1
AGCAUCGUGUAAGUAAAGUUAUUAAAGGUACUU----AUACAACCGACCUACCAGUAGCAACAGCAACAGCCCCAGGGCAACCC----AUAU----ACACAUAGUUAC----UUACCCGU
.....((.((((((((.((((((..((((....----.........))))...))))))..........(((....))).....----....----........))))----)))).)). ( -21.32)
>DroEre_CAF1 21329 106 + 1
AGCAUCGUGUAAGUAAAGUUAUUAAAGGUACUUACAUAUACAACCCAACUACCAGUAGCU------ACAGCCCCACGGCAACCU----AUAU----ACACACAGUUACUUACUUACCCGU
.....((.(((((((((((((((...((((...................)))))))))))------...(((....))).....----....----............)))))))).)). ( -18.31)
>DroYak_CAF1 15760 114 + 1
AGCAUCGCGUAAGUAAAGUUAUUAAAGGUACUUACACAUACAACCCAACUACCAGUAGCA------ACAGCCCCACGGCAACCUCUGUAUAUACACACACACAGUUACUUACUUACCCGU
.....((.((((((((..........((((...................)))).(((((.------...(((....)))......(((....)))........))))))))))))).)). ( -19.51)
>consensus
AGCAUCGUGUAAGUAAAGUUAUUAAAGGUACUU____AUACAACCGAACUACCAGUAGCAACAGCAACAGCCCCACGGCAACCC____AUAU____ACACAUAGUUACUUACUUACCCGU
.....((.((((((((.((((((...((((...................))))))))))..........(((....))).............................)))))))).)). (-13.01 = -14.81 +   1.80)

alignment

secondary structure

dotplot

Window 8

Location	529,655 – 529,746
Length	91
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	80.71
Mean single sequence MFE	-15.11
Consensus MFE	-10.73
Energy contribution	-11.07
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.71
SVM decision value	0.93
SVM RNA-class probability	0.884728
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 529655 91 + 22224390
CAACCGAACUACCAGUAGCAACAGCAACAGCCCCACGGCAAUCCAUAUACACAUAGUUACUUACUUACCCGUGUAACUACUU---------------------ACAUUAUGC
..............((.((....)).)).(((....)))....((((......(((((((............)))))))...---------------------....)))). ( -12.72)
>DroSec_CAF1 16375 108 + 1
CAACCGACCUACCAGCAGCAACAGCAACAGCCCCAGGGCAACCCAUAUACACAUAGUUAC----UUACCCGUGUAACUACUUAUGAAUAUUUACAUUAUGAAUACAUUAUGA
.................((....))....(((....)))....((((......(((((((----........)))))))..))))........(((.(((....))).))). ( -16.10)
>DroSim_CAF1 16689 87 + 1
CAACCGACCUACCAGUAGCAACAGCAACAGCCCCAGGGCAACCCAUAUACACAUAGUUAC----UUACCCGUGUAACUACUU---------------------ACAUUAUGA
..............((.((....)).)).(((....)))....((((......(((((((----........)))))))...---------------------....)))). ( -16.52)
>consensus
CAACCGACCUACCAGUAGCAACAGCAACAGCCCCAGGGCAACCCAUAUACACAUAGUUAC____UUACCCGUGUAACUACUU_____________________ACAUUAUGA
..............((.((....)).)).(((....)))..............(((((((............)))))))................................. (-10.73 = -11.07 +   0.33)

alignment

secondary structure

dotplot

Window 9

Location	529,695 – 529,786
Length	91
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.42
Mean single sequence MFE	-11.98
Consensus MFE	-9.08
Energy contribution	-8.89
Covariance contribution	-0.19
Combinations/Pair	1.08
Mean z-score	-1.53
Structure conservation index	0.76
SVM decision value	0.12
SVM RNA-class probability	0.594621
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 529695 91 + 22224390
AUCC----AUAU----ACACAUAGUUACUUACUUACCCGUGUAACUACUU---------------------ACAUUAUGCAUAUUACUAUCACCCACUUUCCACGGGAUUUUUGACUGUU
....----....----....(((((((........((((((.........---------------------..............................)))))).....))))))). ( -10.25)
>DroSec_CAF1 16415 106 + 1
ACCC----AUAU----ACACAUAGUUAC----UUACCCGUGUAACUACUUAUGAAUAUUUACAUUAUGAAUACAUUAUGAAUAUUACUAUCACCCACUUUCCACGGGAUUUUUGACUG--
.(((----....----.....(((((((----........)))))))......((((((((....(((....)))..))))))))...................)))...........-- ( -15.50)
>DroSim_CAF1 16729 85 + 1
ACCC----AUAU----ACACAUAGUUAC----UUACCCGUGUAACUACUU---------------------ACAUUAUGAAUAUUACUAUCACCCACUUUCCACGGGAUUUUUGACUG--
...(----(((.----.....(((((((----........)))))))...---------------------....)))).............(((.........)))...........-- ( -11.62)
>DroYak_CAF1 15834 97 + 1
ACCUCUGUAUAUACACACACACAGUUACUUACUUACCCGUGUAACUACUU---------------------ACAUUAUGCAUAUUACUAUCACCCACUUUCCACGGGAUUUUUGACUG--
.....................((((((........((((((.........---------------------..............................)))))).....))))))-- ( -10.55)
>consensus
ACCC____AUAU____ACACAUAGUUAC____UUACCCGUGUAACUACUU_____________________ACAUUAUGAAUAUUACUAUCACCCACUUUCCACGGGAUUUUUGACUG__
.....................((((((........((((((............................................................)))))).....)))))).. ( -9.08 =  -8.89 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:30 2006