Locus 4780

Sequence ID	3L_DroMel_CAF1
Location	13,399,484 – 13,399,595
Length	111
Max. P	0.993502

overview

Window 8

Location	13,399,484 – 13,399,595
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	90.97
Mean single sequence MFE	-27.08
Consensus MFE	-23.22
Energy contribution	-23.10
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.86
SVM decision value	2.40
SVM RNA-class probability	0.993502
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13399484 111 + 23771897
UCAUCCGGUUCUCGCGGAGAAAGUUGCGUGAUGUGCCCAUCGAAGCCCGUUUCAUGGCCACGAGAAUCGAACAAAACAAGAGAUGAAAAAGAAAAAGAAACAAAUAUAAAA
(((((((((((((((((......)))).....(((.((((.((((....)))))))).)))))))))))..(.......).)))))......................... ( -26.20)
>DroSec_CAF1 15055 111 + 1
UCAUCCGGUUCUCGCGGAGAAAAUUGCGCGAUGUGCCCAUCGAUGCCCGUUUCAUGGCCACGAGAAUCGAUCAAAAUAAGAGAUGUAAAAGAAAAAGAAACAAAUAUAAAA
.(((((((((((((.((.((((...((((((((....))))).)))...))))....)).))))))))).((.......)))))).......................... ( -29.20)
>DroSim_CAF1 12046 111 + 1
UCAUCCGGUUCUCGCGGAGAAAAUUGCGCGAUGUGCCCAUCGAUGCCCGUUUCAUGGCCACGAGAAUCGAUCAAAACAAAAGAUGUAAAAGAAAAAGAAACAAAUAUAAAA
.....(((((((((.((.((((...((((((((....))))).)))...))))....)).))))))))).......................................... ( -27.90)
>DroEre_CAF1 12632 107 + 1
UCAUCCGGUUCUCGCGGAGAAAGUUGCGCGAUGUGCCCAUCGAGGCCCGUUUCAUGGCCACGAGAAUCGAUCUAAACAAGUAAUGAAAAAA----AAGAACAAAUAUAAAA
.....(((((((((.((.((((...((.(((((....)))))..))...))))....)).)))))))))......................----................ ( -25.90)
>DroYak_CAF1 12269 109 + 1
UCAUCCGGUUCUCGCGGAGAAAGUUGCGCGAUGUGCCCAUCGAGGCUCGUUUCAUGGCCACAAGAGUCGAUCAAAACAGGAGAUGAAAAAA--AAAAAAACAAAUAUAAAA
(((((((..(((((((.((....)).)))))((((.((((.((((....)))))))).)))).))..)).((.......))))))).....--.................. ( -26.20)
>consensus
UCAUCCGGUUCUCGCGGAGAAAGUUGCGCGAUGUGCCCAUCGAGGCCCGUUUCAUGGCCACGAGAAUCGAUCAAAACAAGAGAUGAAAAAGAAAAAGAAACAAAUAUAAAA
.....(((((((((.((.((((...((.(((((....)))))..))...))))....)).))))))))).......................................... (-23.22 = -23.10 +  -0.12)

alignment

secondary structure

dotplot

Window 9

Location	13,399,484 – 13,399,595
Length	111
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	90.97
Mean single sequence MFE	-26.98
Consensus MFE	-24.58
Energy contribution	-24.82
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.50
Structure conservation index	0.91
SVM decision value	1.18
SVM RNA-class probability	0.927140
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13399484 111 - 23771897
UUUUAUAUUUGUUUCUUUUUCUUUUUCAUCUCUUGUUUUGUUCGAUUCUCGUGGCCAUGAAACGGGCUUCGAUGGGCACAUCACGCAACUUUCUCCGCGAGAACCGGAUGA
.....................................(..((((.(((((((((....((((...((...((((....))))..))...)))).))))))))).))))..) ( -27.20)
>DroSec_CAF1 15055 111 - 1
UUUUAUAUUUGUUUCUUUUUCUUUUACAUCUCUUAUUUUGAUCGAUUCUCGUGGCCAUGAAACGGGCAUCGAUGGGCACAUCGCGCAAUUUUCUCCGCGAGAACCGGAUGA
..........................((((((.......)).((.(((((((((....((((...((..(((((....))))).))...)))).))))))))).)))))). ( -28.60)
>DroSim_CAF1 12046 111 - 1
UUUUAUAUUUGUUUCUUUUUCUUUUACAUCUUUUGUUUUGAUCGAUUCUCGUGGCCAUGAAACGGGCAUCGAUGGGCACAUCGCGCAAUUUUCUCCGCGAGAACCGGAUGA
...................((....(((.....)))...))(((.(((((((((....((((...((..(((((....))))).))...)))).))))))))).))).... ( -27.30)
>DroEre_CAF1 12632 107 - 1
UUUUAUAUUUGUUCUU----UUUUUUCAUUACUUGUUUAGAUCGAUUCUCGUGGCCAUGAAACGGGCCUCGAUGGGCACAUCGCGCAACUUUCUCCGCGAGAACCGGAUGA
................----.....(((((.((.....))..((.(((((((((....((((...((..(((((....))))).))...)))).))))))))).))))))) ( -27.60)
>DroYak_CAF1 12269 109 - 1
UUUUAUAUUUGUUUUUUU--UUUUUUCAUCUCCUGUUUUGAUCGACUCUUGUGGCCAUGAAACGAGCCUCGAUGGGCACAUCGCGCAACUUUCUCCGCGAGAACCGGAUGA
..................--.....((((((...(((......)))((((((((....((((...((..(((((....))))).))...)))).))))))))...)))))) ( -24.20)
>consensus
UUUUAUAUUUGUUUCUUUUUCUUUUUCAUCUCUUGUUUUGAUCGAUUCUCGUGGCCAUGAAACGGGCAUCGAUGGGCACAUCGCGCAACUUUCUCCGCGAGAACCGGAUGA
.........................................(((.(((((((((....((((...((..(((((....))))).))...)))).))))))))).))).... (-24.58 = -24.82 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:07 2006