Locus 1540

Sequence ID	3R_DroMel_CAF1
Location	4,392,696 – 4,392,816
Length	120
Max. P	0.733980

overview

Window 9

Location	4,392,696 – 4,392,816
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.25
Mean single sequence MFE	-22.62
Consensus MFE	-14.20
Energy contribution	-14.57
Covariance contribution	0.38
Combinations/Pair	1.12
Mean z-score	-1.80
Structure conservation index	0.63
SVM decision value	-0.02
SVM RNA-class probability	0.523019
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4392696 120 + 27905053
AAGCAAGUAUACUGAGGAGAAGUGGAAAAAAAUUGCAGCACUCCAAACAGAGUGUACAAAAGUCCAAUAAGGAACAAAUUAUUGCACCUUCGUACGAAAAUAACGAAGACUAUGACAGUG
..((((...((((.......))))........)))).((((((......))))))......(((((((((........))))))...((((((.........)))))).....))).... ( -22.90)
>DroSec_CAF1 5051 120 + 1
AACCAAGUAUACUGAGGAGAGGUGGAAAAAAAUUGCAGCACUCCAAACAGAGUGUACAAAAGUCCAAUAAGAAACAAAUGGUUGCACCUUCGUACGAAAAUAACGAAGACUAUGACAGCG
(((((.(((((((..((((.(.((.((.....)).)).).))))......))))))).....((......))......)))))....((((((.........))))))............ ( -22.90)
>DroSim_CAF1 5037 120 + 1
AACCAAGUAUACUGAGGAGAGGUGGAAAAAAAAUGCAGCACUCCAAACAGAGUGUACAAAAGUCCAAUAAGAAACAUAUGGCUGCAUCUUCGUACGAAAAUAACGAAGACUAUGACAGCG
......(((((((..((((.(.((.(.......).)).).))))......))))))).......................(((((((((((((.........)))))))...)).)))). ( -26.30)
>DroEre_CAF1 4927 114 + 1
AACCAAGCAUAAU------GAGUCGAAAAAAAUUGAAACACUCCAAAAAGAGUGCACAAAAGUUCAAUAAUGAAAAAAGUAUUGCAACUUCGGGCGAAAAUAACGAAGAUUAUGACAGCG
......(((((((------...(((..............((((......))))((.(..((((((((((.(......).))))).)))))..)))........)))..)))))).).... ( -18.40)
>consensus
AACCAAGUAUACUGAGGAGAAGUGGAAAAAAAUUGCAGCACUCCAAACAGAGUGUACAAAAGUCCAAUAAGAAACAAAUGAUUGCACCUUCGUACGAAAAUAACGAAGACUAUGACAGCG
......................((((......(((..((((((......)))))).)))...))))..............((((((.(((((...........)))))....)).)))). (-14.20 = -14.57 +   0.38)

alignment

secondary structure

dotplot

Window 0

Location	4,392,696 – 4,392,816
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.25
Mean single sequence MFE	-24.55
Consensus MFE	-16.85
Energy contribution	-18.60
Covariance contribution	1.75
Combinations/Pair	1.12
Mean z-score	-1.91
Structure conservation index	0.69
SVM decision value	0.43
SVM RNA-class probability	0.733980
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4392696 120 - 27905053
CACUGUCAUAGUCUUCGUUAUUUUCGUACGAAGGUGCAAUAAUUUGUUCCUUAUUGGACUUUUGUACACUCUGUUUGGAGUGCUGCAAUUUUUUUCCACUUCUCCUCAGUAUACUUGCUU
.((((....(((.............((((((((((.((((((........)))))).))))))))))(((((....)))))................)))......)))).......... ( -26.30)
>DroSec_CAF1 5051 120 - 1
CGCUGUCAUAGUCUUCGUUAUUUUCGUACGAAGGUGCAACCAUUUGUUUCUUAUUGGACUUUUGUACACUCUGUUUGGAGUGCUGCAAUUUUUUUCCACCUCUCCUCAGUAUACUUGGUU
.((((......(((((((.........)))))))....................((((...(((((((((((....)))))).)))))......))))........)))).......... ( -23.80)
>DroSim_CAF1 5037 120 - 1
CGCUGUCAUAGUCUUCGUUAUUUUCGUACGAAGAUGCAGCCAUAUGUUUCUUAUUGGACUUUUGUACACUCUGUUUGGAGUGCUGCAUUUUUUUUCCACCUCUCCUCAGUAUACUUGGUU
.(((((....((((((((.........))))))))))))).((((.........((((....((((((((((....)))))).)))).......))))..........))))........ ( -28.11)
>DroEre_CAF1 4927 114 - 1
CGCUGUCAUAAUCUUCGUUAUUUUCGCCCGAAGUUGCAAUACUUUUUUCAUUAUUGAACUUUUGUGCACUCUUUUUGGAGUGUUUCAAUUUUUUUCGACUC------AUUAUGCUUGGUU
.((((.((((((..(((............((((((.(((((..........)))))))))))((.(((((((....)))))))..))........)))...------))))))..)))). ( -20.00)
>consensus
CGCUGUCAUAGUCUUCGUUAUUUUCGUACGAAGGUGCAACAAUUUGUUCCUUAUUGGACUUUUGUACACUCUGUUUGGAGUGCUGCAAUUUUUUUCCACCUCUCCUCAGUAUACUUGGUU
.((((....................((((((((((.((((((........)))))).))))))))))(((((....))))).........................)))).......... (-16.85 = -18.60 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:06 2006