Locus 8612

Sequence ID	3L_DroMel_CAF1
Location	22,407,987 – 22,408,079
Length	92
Max. P	0.923942

overview

Window 9

Location	22,407,987 – 22,408,079
Length	92
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	68.17
Mean single sequence MFE	-25.98
Consensus MFE	-13.84
Energy contribution	-13.51
Covariance contribution	-0.33
Combinations/Pair	1.33
Mean z-score	-1.52
Structure conservation index	0.53
SVM decision value	0.54
SVM RNA-class probability	0.773564
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22407987 92 + 23771897
GAUUUUGUGCUGCGUCAGAGGUUACUUGGGCGCAGCACAGUAACUUGGGAGGUUCAAGA---G---------GUCAGCUUCUCCCGAAAUC------CUCUACAACGAUC
((((((((((((((((.(((....))).))))))))))))....(((((((((((.(((---(---------(....)))))...)))..)------)))).))).)))) ( -35.00)
>DroGri_CAF1 8812 102 + 1
UAUUUUGUGCUGCGUCAUACUC-------AAGUGGCACAAAAAAGAG-UAAGCUGAAUUUAUGUUCAUAUUUGUUGUUGUUGGCGAAGCUUUUGUAUUUUUUGUAUGAUC
...(((((((..(.........-------..)..)))))))((((((-((((((((((....)))))..((((((......)))))))))....))))))))........ ( -22.00)
>DroSec_CAF1 7365 85 + 1
GAUUUUGUGCUGCGUCAGAGUU-------GCGCAGCACUGUAACUUGGGAGGUUCAAGA---G---------GUCAGCUUCUCCCGAAAUC------CUCUACAACGAUC
(((((((((((((((.......-------)))))))))........((((((..(....---.---------....)..))))))))))))------............. ( -27.40)
>DroSim_CAF1 7381 85 + 1
GAUUUUGUGCUGCGUCAGAGUU-------GCGCAGCACUGUAACUUGGGAGGUUCAAGA---G---------GUCAGCUUCUCCCGAAAUC------CUCUACAACGAUC
(((((((((((((((.......-------)))))))))........((((((..(....---.---------....)..))))))))))))------............. ( -27.40)
>DroEre_CAF1 7654 78 + 1
GAUUUUGUGCUGCGUCAGAGGU-------GCGCGGCACU------ACGUAAGUCCAAAA---G---------GUCAGCUUCUACCGCAAUG------CUCCACAACGUU-
......(((((((((.......-------))))))))).------((((..(.((....---)---------).).((.......))....------.......)))).- ( -19.90)
>DroYak_CAF1 7101 83 + 1
GAUUUUGUGCUGCGUCAGAGGU-------GCGCAGCACUAUA--UACAUAAGUCGAAGA---G---------GUCAGCUUCUGCCGAAAUA------CUCUACAACGAUC
......(((((((((.......-------)))))))))....--.......((((.(((---(---------.((.((....)).))....------))))....)))). ( -24.20)
>consensus
GAUUUUGUGCUGCGUCAGAGGU_______GCGCAGCACUGUAACUAGGGAAGUUCAAGA___G_________GUCAGCUUCUCCCGAAAUC______CUCUACAACGAUC
......(((((((((..............)))))))))........................................................................ (-13.84 = -13.51 +  -0.33)

alignment

secondary structure

dotplot

Window 0

Location	22,407,987 – 22,408,079
Length	92
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	68.17
Mean single sequence MFE	-25.03
Consensus MFE	-10.98
Energy contribution	-11.87
Covariance contribution	0.89
Combinations/Pair	1.08
Mean z-score	-1.95
Structure conservation index	0.44
SVM decision value	1.16
SVM RNA-class probability	0.923942
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22407987 92 - 23771897
GAUCGUUGUAGAG------GAUUUCGGGAGAAGCUGAC---------C---UCUUGAACCUCCCAAGUUACUGUGCUGCGCCCAAGUAACCUCUGACGCAGCACAAAAUC
..........(((------(..((((((((........---------)---))))))))))).........(((((((((....((......))..)))))))))..... ( -29.00)
>DroGri_CAF1 8812 102 - 1
GAUCAUACAAAAAAUACAAAAGCUUCGCCAACAACAACAAAUAUGAACAUAAAUUCAGCUUA-CUCUUUUUUGUGCCACUU-------GAGUAUGACGCAGCACAAAAUA
.....................(((.((.((.............((((......))))...((-(((...............-------))))))).)).)))........ ( -10.46)
>DroSec_CAF1 7365 85 - 1
GAUCGUUGUAGAG------GAUUUCGGGAGAAGCUGAC---------C---UCUUGAACCUCCCAAGUUACAGUGCUGCGC-------AACUCUGACGCAGCACAAAAUC
......(((((.(------((.((((((((........---------)---)))))))..)))....)))))(((((((((-------(....)).))))))))...... ( -29.70)
>DroSim_CAF1 7381 85 - 1
GAUCGUUGUAGAG------GAUUUCGGGAGAAGCUGAC---------C---UCUUGAACCUCCCAAGUUACAGUGCUGCGC-------AACUCUGACGCAGCACAAAAUC
......(((((.(------((.((((((((........---------)---)))))))..)))....)))))(((((((((-------(....)).))))))))...... ( -29.70)
>DroEre_CAF1 7654 78 - 1
-AACGUUGUGGAG------CAUUGCGGUAGAAGCUGAC---------C---UUUUGGACUUACGU------AGUGCCGCGC-------ACCUCUGACGCAGCACAAAAUC
-....((((((.(------(((((((....((((..(.---------.---..)..).))).)))------))))))((((-------(....)).)))..))))).... ( -22.30)
>DroYak_CAF1 7101 83 - 1
GAUCGUUGUAGAG------UAUUUCGGCAGAAGCUGAC---------C---UCUUCGACUUAUGUA--UAUAGUGCUGCGC-------ACCUCUGACGCAGCACAAAAUC
....((((.((((------....(((((....))))).---------)---))).)))).......--....(((((((((-------(....)).))))))))...... ( -29.00)
>consensus
GAUCGUUGUAGAG______GAUUUCGGGAGAAGCUGAC_________C___UCUUGAACCUACCAAGUUACAGUGCUGCGC_______AACUCUGACGCAGCACAAAAUC
.......................((((......))))...................................((((((((................))))))))...... (-10.98 = -11.87 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:20 2006