Locus 300

Sequence ID	3R_DroMel_CAF1
Location	1,146,997 – 1,147,097
Length	100
Max. P	0.725467

overview

Window 8

Location	1,146,997 – 1,147,097
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	71.81
Mean single sequence MFE	-14.72
Consensus MFE	-1.66
Energy contribution	-1.70
Covariance contribution	0.04
Combinations/Pair	1.45
Mean z-score	-1.68
Structure conservation index	0.11
SVM decision value	0.41
SVM RNA-class probability	0.725467
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1146997 100 + 27905053
UUUUAAUUUUCCCACUUCCAUUUCUCCCCAUCGCUUCCUGACACUUUCAAUUGAUUUGCAUAGUCAGUCAGUCGCACUUUUAGGUGGGCCACCCCACCUU
................................((...((((((((..(((.....)))...)))..)))))..))......(((((((....))))))). ( -20.30)
>DroSec_CAF1 82508 96 + 1
UUUUAAUUUUCCCACACCCAUUUCUCCCCACCGCUUCCUGACACUUUCAAUUGAUUUGCAUAGUC----AGUCGCACUUUUGCGUGGGCCACCCCACCAU
..........(((((......................(((((.....(((.....)))....)))----))..(((....))))))))............ ( -16.20)
>DroSim_CAF1 78380 89 + 1
UU-UAAUUUUCCCACAC-CAUUUCUCCCCACCGCUUCCUGACACU-UCAAUUGAU-UGCAUAGUC----AGUCGCACUUUUGCGUGGGCCACCC-A-CA-
..-.......(((((..-...................(((((...-.(((....)-))....)))----))..(((....))))))))......-.-..- ( -16.00)
>DroYak_CAF1 103760 95 + 1
UU-GAAUUUUCCAAUUCUAUUUUCUCUUCAACGCUUCCUGACAGUUUUAAUUGAUUUGCAUAGUC----AAUCGCACUUUUACAAGAGCCACCCCGCCUU
..-(((((....)))))...............((((..(((.(((....(((((((.....))))----)))...))).)))...))))........... (  -9.70)
>DroAna_CAF1 77216 87 + 1
UU--A-UAUUUCUUCUUAUAUUUCUUACAACUGUUUCCUGACAAGUUUAAUU-----GCCGAGUG----GAUUGUGGGCUUACGUGAACCACGCC-CUGU
..--.-......................(((((((....))).)))).....-----.....(((----(.(..((......))..).))))...-.... ( -11.40)
>consensus
UU_UAAUUUUCCCACUCCCAUUUCUCCCCACCGCUUCCUGACACUUUCAAUUGAUUUGCAUAGUC____AGUCGCACUUUUACGUGGGCCACCCCACCAU
..........(((((.......................(((.....))).......(((..............))).......)))))............ ( -1.66 =  -1.70 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	1,146,997 – 1,147,097
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	71.81
Mean single sequence MFE	-20.68
Consensus MFE	-4.83
Energy contribution	-4.95
Covariance contribution	0.12
Combinations/Pair	1.33
Mean z-score	-1.74
Structure conservation index	0.23
SVM decision value	0.35
SVM RNA-class probability	0.698305
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1146997 100 - 27905053
AAGGUGGGGUGGCCCACCUAAAAGUGCGACUGACUGACUAUGCAAAUCAAUUGAAAGUGUCAGGAAGCGAUGGGGAGAAAUGGAAGUGGGAAAAUUAAAA
.(((((((....))))))).......((.((..(((((....(((.....))).....)))))..))))............................... ( -24.30)
>DroSec_CAF1 82508 96 - 1
AUGGUGGGGUGGCCCACGCAAAAGUGCGACU----GACUAUGCAAAUCAAUUGAAAGUGUCAGGAAGCGGUGGGGAGAAAUGGGUGUGGGAAAAUUAAAA
.......(((..(((((((...(.(((..((----(((....(((.....))).....)))))...))).)....(....)..)))))))...))).... ( -22.70)
>DroSim_CAF1 78380 89 - 1
-UG-U-GGGUGGCCCACGCAAAAGUGCGACU----GACUAUGCA-AUCAAUUGA-AGUGUCAGGAAGCGGUGGGGAGAAAUG-GUGUGGGAAAAUUA-AA
-..-.-.(((..(((((((...(.(((..((----(((....((-(....))).-...)))))...))).)....(....).-)))))))...))).-.. ( -23.30)
>DroYak_CAF1 103760 95 - 1
AAGGCGGGGUGGCUCUUGUAAAAGUGCGAUU----GACUAUGCAAAUCAAUUAAAACUGUCAGGAAGCGUUGAAGAGAAAAUAGAAUUGGAAAAUUC-AA
..(((((....((.(((....))).))((((----((.........))))))....)))))......................(((((....)))))-.. ( -17.30)
>DroAna_CAF1 77216 87 - 1
ACAG-GGCGUGGUUCACGUAAGCCCACAAUC----CACUCGGC-----AAUUAAACUUGUCAGGAAACAGUUGUAAGAAAUAUAAGAAGAAAUA-U--AA
...(-(((.((.....))...))))(((((.----.....(((-----((......))))).(....).)))))....................-.--.. ( -15.80)
>consensus
AAGGUGGGGUGGCCCACGUAAAAGUGCGACU____GACUAUGCAAAUCAAUUGAAAGUGUCAGGAAGCGGUGGGGAGAAAUGGGAGUGGGAAAAUUA_AA
............(((((..................(((....................))).(....).................))))).......... ( -4.83 =  -4.95 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:50 2006