Locus 3084

Sequence ID	2L_DroMel_CAF1
Location	8,789,955 – 8,790,115
Length	160
Max. P	0.565738

overview

Window 3

Location	8,789,955 – 8,790,075
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.94
Mean single sequence MFE	-33.73
Consensus MFE	-27.43
Energy contribution	-28.32
Covariance contribution	0.89
Combinations/Pair	1.07
Mean z-score	-1.95
Structure conservation index	0.81
SVM decision value	-0.00
SVM RNA-class probability	0.532401
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8789955 120 + 22407834
GCGGUUUACACCGACCCGCAAACAACAAACACAGAAAACAGAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGAGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCGC
((((..((..............(((((((............((((.....))))......(((.....))).)))))))..((((((.(((((.....))))))))))).))..)))).. ( -34.30)
>DroSec_CAF1 92642 120 + 1
GCGGUUUACACCGACCCGCAAACAACAAACACAGAAAAAAGAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACGUUUGCCAGCCUAUUCCGCGC
(((((..((((((((..........................((((.....))))......(((.....)))....))))))))..)))..((((((...((......))...)))))))) ( -33.20)
>DroSim_CAF1 96227 120 + 1
GCGGUUUACACCGACCCGCAAACAACAAACGCUGAAAAAAGAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCGC
((((..((.((((((...............(((........((((.....))))..))).(((.....)))....))))))((((((.(((((.....))))))))))).))..)))).. ( -36.00)
>DroEre_CAF1 99152 120 + 1
GCGGUUUACACCGACCCGCAAACAACAAGCACGGAAAACAGAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCAC
((((..((.((((((..((.........))((((.......((((.....))))....)))).............))))))((((((.(((((.....))))))))))).))..)))).. ( -37.80)
>DroYak_CAF1 97981 120 + 1
GCGGUUUACACCGACCCACAAACAACAAACACAGAAAACAGAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCAC
((((..((.((((((..........................((((.....))))......(((.....)))....))))))((((((.(((((.....))))))))))).))..)))).. ( -34.70)
>DroAna_CAF1 117067 109 + 1
GCGCUCCACACCGGGCCG------ACAAAC-----AAACAAAGUGAAAACCCCUAAAGCCAUCACAAAGACUGUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCAGAC
............((((((------((((.(-----(......((((...............))))......))))))))))((((((.(((((.....))))))))))).....)).... ( -26.36)
>consensus
GCGGUUUACACCGACCCGCAAACAACAAACACAGAAAACAGAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCAC
((((.....((((((..........................((((.....))))......(((.....)))....))))))((((((.(((((.....))))))))))).....)))).. (-27.43 = -28.32 +   0.89)

alignment

secondary structure

dotplot

Window 4

Location	8,789,995 – 8,790,115
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	95.39
Mean single sequence MFE	-38.18
Consensus MFE	-31.69
Energy contribution	-32.72
Covariance contribution	1.03
Combinations/Pair	1.03
Mean z-score	-1.83
Structure conservation index	0.83
SVM decision value	0.06
SVM RNA-class probability	0.565738
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8789995 120 + 22407834
GAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGAGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCGCUCGGCUUUGGGCCAUUAGACCAGCAAAUUGUUGGUAAAAC
..(((....)))(((((((((((.....)))....((.(((((.(((((((((.....))))))...))).)))))))....))))))))........((((((.....))))))..... ( -41.30)
>DroSec_CAF1 92682 120 + 1
GAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACGUUUGCCAGCCUAUUCCGCGCUCGGCUUUGGGCCAUUAGACCAGCAAAUUGUUGGUAAAAC
.((((.....))))...((((((.....))).(((((((((.((((((..((.....))....(((((((......).))).)))....)))))..).))))))))).....)))..... ( -38.40)
>DroSim_CAF1 96267 120 + 1
GAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCGCUCGGCUUUGGGCCAUUAGACCAGCAAAUUGUUGGUAAAAC
.((((.....))))...((((((.....))).(((((((((.(((((((((((.....)))))(((((((......).))).)))....)))))..).))))))))).....)))..... ( -40.80)
>DroEre_CAF1 99192 120 + 1
GAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCACUCUGCUGUGGGCCAUUAGACCAGCAAAUUGUUGGUAAAAC
.((((.....))))...((((((.....))).(((((((((((((((.(((((.....)))))))))))(((.((((((......))))))....)))))))))))).....)))..... ( -40.70)
>DroYak_CAF1 98021 120 + 1
GAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCACUCUGCUCUGGGCCAUUAGACCAGCAAAUUGUUGGUAAAAC
.((((.....))))...((((((.....))).(((((((((..((((.(((((.....)))))))))(((((....((.....))..)))))......))))))))).....)))..... ( -37.60)
>DroAna_CAF1 117096 120 + 1
AAGUGAAAACCCCUAAAGCCAUCACAAAGACUGUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCAGACUCGACUGUGGGCCAUUAGACGAGCAAAUUGUUGGUAAAAC
..((....))..((((.(((..((((..(((((..((.((.((((((.(((((.....)))))))))))))))..)))..))...)))))))..))))((.(((.....))).))..... ( -30.30)
>consensus
GAGGGAAAGCCCCUAAAGCCGUCACAAAGACUUUUGUUGGUGUUGGCCAAGUGGAAAACAUUUGCCAGCCUAUUCCGCACUCGGCUUUGGGCCAUUAGACCAGCAAAUUGUUGGUAAAAC
.((((.....))))...((((((.....))).(((((((((..((((.(((((.....)))))))))(((((....((.....))..)))))......))))))))).....)))..... (-31.69 = -32.72 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:03 2006