Locus 3492

Sequence ID	3L_DroMel_CAF1
Location	10,259,817 – 10,259,927
Length	110
Max. P	0.935454

overview

Window 2

Location	10,259,817 – 10,259,927
Length	110
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	95.24
Mean single sequence MFE	-25.95
Consensus MFE	-23.44
Energy contribution	-23.22
Covariance contribution	-0.22
Combinations/Pair	1.12
Mean z-score	-1.52
Structure conservation index	0.90
SVM decision value	1.10
SVM RNA-class probability	0.915732
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10259817 110 + 23771897
UAAUUUUUGCGCAGCGUCAUCAAAUUGCGAAAUUGCAGAACUGCGCAAGC--AACCAGAACAAGCGAAAAUAUUAAUUUUCACAGUUUGACAUGUCGCA----CUCGCAUCUGCCU
.......((((..(((.((((((((((..............(((....))--)............((((((....)))))).))))))))..)).))).----..))))....... ( -26.00)
>DroSec_CAF1 135163 110 + 1
UAAUUUUUGCGCAGCGUCAUCAAAUUGCGAAAUUGCAGAACUGCGCAAGC--AACCAGAACAAGCGAAAAUAUUAAUUUUCACAGUUUGACAUGUCGCA----CUCGCAUCUGCCU
.......((((..(((.((((((((((..............(((....))--)............((((((....)))))).))))))))..)).))).----..))))....... ( -26.00)
>DroSim_CAF1 140525 110 + 1
UAAUUUUUGCGCAGCGUCAUCAAAUUGCGAAAUUGCAGAACUGCGCAAGC--AACCAGAACAAGCGAAAAUAUUAAUUUUCACAGUUUGACAUGUCGCA----CUCGCAUCUGCCU
.......((((..(((.((((((((((..............(((....))--)............((((((....)))))).))))))))..)).))).----..))))....... ( -26.00)
>DroEre_CAF1 144823 110 + 1
UAAUUUUUGCGCAGCGUCAUCAAAUUGCGAAAUUGCAGAACUGCGCAAGC--AACCAGAACAAGCGAAAAUAUUAAUUUUCACAGUUUGACAUGUCGCA----CUCGCAUCUGCCU
.......((((..(((.((((((((((..............(((....))--)............((((((....)))))).))))))))..)).))).----..))))....... ( -26.00)
>DroYak_CAF1 142161 109 + 1
UAAUUUUUGCGCAGCGUCAUCAAAUUGCGA-AUUGCAGAACUGCGCAAGC--AACCAGAACAAGCGAAAAUAUUAAUUUUCACAGUUUGACAUGUCGCA----CUCGCAUCUGCCU
.......((((..(((.((((((((((...-..........(((....))--)............((((((....)))))).))))))))..)).))).----..))))....... ( -26.00)
>DroAna_CAF1 148641 116 + 1
UAAUUUUUGCGCAGCGUCAUCAAAUUGGGAAAUUGCGAAACUGCGCGAAUAAAACCAGAACAAGCAAAAAUAUUAAUUUUCACAGUUUGACAUGUCGCGGUGGUUCGCAUCUGCCU
.............(((.((((((((((((((((((((....)))((.................)).........))))))).))))))))..)).)))((..(.......)..)). ( -25.73)
>consensus
UAAUUUUUGCGCAGCGUCAUCAAAUUGCGAAAUUGCAGAACUGCGCAAGC__AACCAGAACAAGCGAAAAUAUUAAUUUUCACAGUUUGACAUGUCGCA____CUCGCAUCUGCCU
.....(((((((((.(....)...(((((....)))))..)))))))))......((((.(((((((((((....))))))...))))).......((........)).))))... (-23.44 = -23.22 +  -0.22)

alignment

secondary structure

dotplot

Window 3

Location	10,259,817 – 10,259,927
Length	110
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	95.24
Mean single sequence MFE	-30.22
Consensus MFE	-27.63
Energy contribution	-27.38
Covariance contribution	-0.25
Combinations/Pair	1.09
Mean z-score	-1.48
Structure conservation index	0.91
SVM decision value	1.24
SVM RNA-class probability	0.935454
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10259817 110 - 23771897
AGGCAGAUGCGAG----UGCGACAUGUCAAACUGUGAAAAUUAAUAUUUUCGCUUGUUCUGGUU--GCUUGCGCAGUUCUGCAAUUUCGCAAUUUGAUGACGCUGCGCAAAAAUUA
..(((((((((..----.(((((......(((.((((((((....))))))))..)))...)))--))...))))..)))))..(((((((............)))).)))..... ( -30.30)
>DroSec_CAF1 135163 110 - 1
AGGCAGAUGCGAG----UGCGACAUGUCAAACUGUGAAAAUUAAUAUUUUCGCUUGUUCUGGUU--GCUUGCGCAGUUCUGCAAUUUCGCAAUUUGAUGACGCUGCGCAAAAAUUA
..(((((((((..----.(((((......(((.((((((((....))))))))..)))...)))--))...))))..)))))..(((((((............)))).)))..... ( -30.30)
>DroSim_CAF1 140525 110 - 1
AGGCAGAUGCGAG----UGCGACAUGUCAAACUGUGAAAAUUAAUAUUUUCGCUUGUUCUGGUU--GCUUGCGCAGUUCUGCAAUUUCGCAAUUUGAUGACGCUGCGCAAAAAUUA
..(((((((((..----.(((((......(((.((((((((....))))))))..)))...)))--))...))))..)))))..(((((((............)))).)))..... ( -30.30)
>DroEre_CAF1 144823 110 - 1
AGGCAGAUGCGAG----UGCGACAUGUCAAACUGUGAAAAUUAAUAUUUUCGCUUGUUCUGGUU--GCUUGCGCAGUUCUGCAAUUUCGCAAUUUGAUGACGCUGCGCAAAAAUUA
..(((((((((..----.(((((......(((.((((((((....))))))))..)))...)))--))...))))..)))))..(((((((............)))).)))..... ( -30.30)
>DroYak_CAF1 142161 109 - 1
AGGCAGAUGCGAG----UGCGACAUGUCAAACUGUGAAAAUUAAUAUUUUCGCUUGUUCUGGUU--GCUUGCGCAGUUCUGCAAU-UCGCAAUUUGAUGACGCUGCGCAAAAAUUA
..((((...((((----(((((..(((..((((((((((((....))))))((..((.......--))..))))))))..)))..-)))).)))))......)))).......... ( -30.30)
>DroAna_CAF1 148641 116 - 1
AGGCAGAUGCGAACCACCGCGACAUGUCAAACUGUGAAAAUUAAUAUUUUUGCUUGUUCUGGUUUUAUUCGCGCAGUUUCGCAAUUUCCCAAUUUGAUGACGCUGCGCAAAAAUUA
.((((..((((......))))...)))).(((.(..(((((....)))))..)..)))............(((((((.((((((.........))).))).)))))))........ ( -29.80)
>consensus
AGGCAGAUGCGAG____UGCGACAUGUCAAACUGUGAAAAUUAAUAUUUUCGCUUGUUCUGGUU__GCUUGCGCAGUUCUGCAAUUUCGCAAUUUGAUGACGCUGCGCAAAAAUUA
.((((..((((......))))...)))).(((.((((((((....))))))))..)))..........(((((((((((..(((.........)))..)).)))))))))...... (-27.63 = -27.38 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:27 2006