Locus 6061

Sequence ID	2L_DroMel_CAF1
Location	17,049,746 – 17,049,986
Length	240
Max. P	0.992879

overview

Window 1

Location	17,049,746 – 17,049,866
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.17
Mean single sequence MFE	-26.10
Consensus MFE	-25.10
Energy contribution	-25.10
Covariance contribution	-0.00
Combinations/Pair	1.06
Mean z-score	-1.69
Structure conservation index	0.96
SVM decision value	2.36
SVM RNA-class probability	0.992879
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049746 120 + 22407834
GUGCACAAAAGUACACAGAAGUUUUAUGAAAGAAAAUGAAAUGAAAAUCCGGUUGCAAUCCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAA
((((......))))......(((((((........))))))).........(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))..... ( -26.30)
>DroSec_CAF1 13636 120 + 1
GUGCACAGAAGUACACAGAAGUUUUAUGAAAGAAAAUGAAAUGAAAAUCCGGUUGCAAUCCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAA
((((......))))......(((((((........))))))).........(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))..... ( -26.30)
>DroSim_CAF1 7901 120 + 1
GUGCACAAAAGUACACAGAAGUUUUAUGAAAGAAAAUGAAAUGAAAAUCCGGUUGCAAUUCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAA
((((......))))......(((((((........))))))).........(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))..... ( -26.30)
>DroEre_CAF1 13590 120 + 1
GUGCACAAAAGUACACAGAAGUUUUAUGAAAGAAAAUGAAAUGAAAAUCCGGUUGCAGUCCCUCAAAGCUUCGUAAACUGAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAA
((((......))))......(((((((........))))))).........(((((.((..((.((((((....((((((((......))))))))..)))))).))...)).))))).. ( -26.70)
>DroYak_CAF1 11595 116 + 1
GUGCACAAAAGUACACAGAAGUUUUAUGAAAGAAAAUGAAAUGAAAAUCCGGUUGCAGUCCCUCAAAGCU----AAACCAAGGAAAUCUUUAGUUUUUGGCUUUAAGCUCGCGGCAACAA
((((......))))......(((((((........))))))).........(((((.((..((.((((((----((((.((((....)))).))..)))))))).))...)).))))).. ( -24.90)
>consensus
GUGCACAAAAGUACACAGAAGUUUUAUGAAAGAAAAUGAAAUGAAAAUCCGGUUGCAAUCCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAA
((((......))))......(((((((........))))))).........(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))..... (-25.10 = -25.10 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	17,049,746 – 17,049,866
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.17
Mean single sequence MFE	-24.30
Consensus MFE	-24.20
Energy contribution	-24.24
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.04
Structure conservation index	1.00
SVM decision value	0.13
SVM RNA-class probability	0.600214
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049746 120 - 22407834
UUGUUGCCGCAAGCUUAAAGCCAAAAACUAAAGAUUUUCUUAGUUUACGAAGCUUUGAGGGAUUGCAACCGGAUUUUCAUUUCAUUUUCUUUCAUAAAACUUCUGUGUACUUUUGUGCAC
..((((((....)((((((((...(((((((........))))))).....)))))))).....)))))...................................((((((....)))))) ( -24.70)
>DroSec_CAF1 13636 120 - 1
UUGUUGCCGCAAGCUUAAAGCCAAAAACUAAAGAUUUUCUUAGUUUACGAAGCUUUGAGGGAUUGCAACCGGAUUUUCAUUUCAUUUUCUUUCAUAAAACUUCUGUGUACUUCUGUGCAC
..((((((....)((((((((...(((((((........))))))).....)))))))).....)))))...................................((((((....)))))) ( -24.70)
>DroSim_CAF1 7901 120 - 1
UUGUUGCCGCAAGCUUAAAGCCAAAAACUAAAGAUUUUCUUAGUUUACGAAGCUUUGAGGAAUUGCAACCGGAUUUUCAUUUCAUUUUCUUUCAUAAAACUUCUGUGUACUUUUGUGCAC
..((((((....)((((((((...(((((((........))))))).....)))))))).....)))))...................................((((((....)))))) ( -24.70)
>DroEre_CAF1 13590 120 - 1
UUGUUGCCGCAAGCUUAAAGCCAAAAACUAAAGAUUUUCUCAGUUUACGAAGCUUUGAGGGACUGCAACCGGAUUUUCAUUUCAUUUUCUUUCAUAAAACUUCUGUGUACUUUUGUGCAC
..((((((....)((((((((...(((((..((.....)).))))).....)))))))).....)))))...................................((((((....)))))) ( -22.40)
>DroYak_CAF1 11595 116 - 1
UUGUUGCCGCGAGCUUAAAGCCAAAAACUAAAGAUUUCCUUGGUUU----AGCUUUGAGGGACUGCAACCGGAUUUUCAUUUCAUUUUCUUUCAUAAAACUUCUGUGUACUUUUGUGCAC
..((((((....)((((((((...(((((((.(....).)))))))----.)))))))).....)))))...................................((((((....)))))) ( -25.00)
>consensus
UUGUUGCCGCAAGCUUAAAGCCAAAAACUAAAGAUUUUCUUAGUUUACGAAGCUUUGAGGGAUUGCAACCGGAUUUUCAUUUCAUUUUCUUUCAUAAAACUUCUGUGUACUUUUGUGCAC
..((((((....)((((((((...(((((((........))))))).....)))))))).....)))))...................................((((((....)))))) (-24.20 = -24.24 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	17,049,786 – 17,049,906
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.67
Mean single sequence MFE	-26.90
Consensus MFE	-24.00
Energy contribution	-25.50
Covariance contribution	1.50
Combinations/Pair	1.06
Mean z-score	-1.41
Structure conservation index	0.89
SVM decision value	0.78
SVM RNA-class probability	0.848603
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049786 120 + 22407834
AUGAAAAUCCGGUUGCAAUCCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAAUUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGC
........((.(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))...........((((((...((....))........)))))))). ( -26.70)
>DroSec_CAF1 13676 120 + 1
AUGAAAAUCCGGUUGCAAUCCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAAUUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGC
........((.(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))...........((((((...((....))........)))))))). ( -26.70)
>DroSim_CAF1 7941 120 + 1
AUGAAAAUCCGGUUGCAAUUCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAAUUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGC
........((.(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))...........((((((...((....))........)))))))). ( -26.70)
>DroEre_CAF1 13630 120 + 1
AUGAAAAUCCGGUUGCAGUCCCUCAAAGCUUCGUAAACUGAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAAUUAAAUGGGAAUAAGCUGAAAAGAAAAUGAGAUUUCCGGC
........((.(((((.((..((.((((((....((((((((......))))))))..)))))).))...)).)))))........((((((...((....))........)))))))). ( -27.10)
>DroYak_CAF1 11635 116 + 1
AUGAAAAUCCGGUUGCAGUCCCUCAAAGCU----AAACCAAGGAAAUCUUUAGUUUUUGGCUUUAAGCUCGCGGCAACAAUUAAAUGGGAAUAAGCUGAAAAGAAAAUAAGAUUUCCGGC
........((((((..(((........)))----.))))..(((((((((...((((..((((....((((.(....).......))))...))))..))))......))))))))))). ( -27.30)
>consensus
AUGAAAAUCCGGUUGCAAUCCCUCAAAGCUUCGUAAACUAAGAAAAUCUUUAGUUUUUGGCUUUAAGCUUGCGGCAACAAUUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGC
........((.(((((((...((.((((((....((((((((......))))))))..)))))).)).)))))))...........((((((...((....))........)))))))). (-24.00 = -25.50 +   1.50)

alignment

secondary structure

dotplot

Window 4

Location	17,049,866 – 17,049,986
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-26.86
Consensus MFE	-23.55
Energy contribution	-23.59
Covariance contribution	0.04
Combinations/Pair	1.09
Mean z-score	-1.48
Structure conservation index	0.88
SVM decision value	0.91
SVM RNA-class probability	0.878982
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17049866 120 + 22407834
UUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGCUUGGAAUCCUUUGACAAAACACUUUCUGGAAGCACAGAAAACAGGGAAAAUCAAUUUGGAACUGUGAGGGAUUUUCCACU
.......(((.(((((((....((((......)))))))))))(((((((((..........((((((......))))))((((....((.....))....))))))))))))))))... ( -27.40)
>DroSec_CAF1 13756 120 + 1
UUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGCUUGGAAUCCUUUGACAAAACACUUUCUGGAAGCACAGAAAACAGGGAAAAUCAAUUUGGAACUGUGAGGGAUUUUCCACU
.......(((.(((((((....((((......)))))))))))(((((((((..........((((((......))))))((((....((.....))....))))))))))))))))... ( -27.40)
>DroSim_CAF1 8021 120 + 1
UUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGCUUGGAAUCCUUUGACAAAACACUUUCUGGAAGCACAGAAAACAGGGAAAAUCAAUUUGGAACUGUGAGGGAUUUUCCACU
.......(((.(((((((....((((......)))))))))))(((((((((..........((((((......))))))((((....((.....))....))))))))))))))))... ( -27.40)
>DroEre_CAF1 13710 120 + 1
UUAAAUGGGAAUAAGCUGAAAAGAAAAUGAGAUUUCCGGCUUGGAAUCCUUUGACAAAACACUUUCUGGAAUAACAGAAAACAGGGACAAUCAAUUUGGGACUGUAGGGGAUUUUCCACU
.......(((.(((((((....((((......)))))))))))(((((((((..........((((((......))))))((((...(((.....)))...))))))))))))))))... ( -29.70)
>DroYak_CAF1 11711 120 + 1
UUAAAUGGGAAUAAGCUGAAAAGAAAAUAAGAUUUCCGGCUGGGAAUGCUUUGACAAAACACUUUCUGGAAUAACAGAAAACAGGGACAAUCAAUUUGGGACAGCAAGGGAUUUUCCACU
.....(((((((...((....))........)))))))..(((((((.(((((.(.......((((((......))))))...(...(((.....)))...).)))))).).)))))).. ( -22.40)
>consensus
UUAAAUGGGAAUAAGCUGAAAAGAAAAUACGAUUUCCGGCUUGGAAUCCUUUGACAAAACACUUUCUGGAAGCACAGAAAACAGGGAAAAUCAAUUUGGAACUGUGAGGGAUUUUCCACU
.......(((.(((((((....((((......)))))))))))((((((((((.........((((((......)))))).(((.................))))))))))))))))... (-23.55 = -23.59 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:12 2006