Locus 5241

Sequence ID	3R_DroMel_CAF1
Location	13,693,312 – 13,693,467
Length	155
Max. P	0.977206

overview

Window 3

Location	13,693,312 – 13,693,432
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.50
Mean single sequence MFE	-30.45
Consensus MFE	-26.78
Energy contribution	-26.66
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.87
Structure conservation index	0.88
SVM decision value	1.79
SVM RNA-class probability	0.977206
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13693312 120 - 27905053
AAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGACGUGCAGAGAAAACACACCGAUAAAGUACAAAAUGAAUGA
.....((((((........((((((..............((((.((((........)))).)))).((((......)))).))))))......))))))..................... ( -31.74)
>DroSec_CAF1 3208 120 - 1
AAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGACGUGCAGAGGAAACACACCGAUAAAGUACAAAAUGAAUGA
.....((((((......(.((((((..............((((.((((........)))).)))).((((......)))).)))))).)....))))))..................... ( -32.20)
>DroSim_CAF1 3222 120 - 1
AAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGACGUGCAGAGGAAACACACCGAUAAAGUACAAAAUGAAUGA
.....((((((......(.((((((..............((((.((((........)))).)))).((((......)))).)))))).)....))))))..................... ( -32.20)
>DroEre_CAF1 3213 120 - 1
AAUUUGGUGUGGCAAAACGCACCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGACAAUGGGACGUGCAGAGGAAACACACCAAUAAAGUGCAAAAUGAAUGA
...((((((((.(.....(((((((((.....)))))..((((.((((........)))).)))).((((......)))).))))....)...))))))))................... ( -31.00)
>DroYak_CAF1 3266 120 - 1
AAUUAUGUGAGGCAAAACGCAGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGACGUGCAGAGGAAACACACCGAUAAAGUACAAAAUCAAUGA
......(((........(.((((((((.....)))))))).)......((((((.......((.(.((((......)))).).))...)))))).)))...................... ( -25.10)
>consensus
AAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGACGUGCAGAGGAAACACACCGAUAAAGUACAAAAUGAAUGA
.....((((..((.....))..))))..(((((..((((((.......((((((.......((.(.((((......)))).).))...))))))...)))))).))).)).......... (-26.78 = -26.66 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	13,693,352 – 13,693,467
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.77
Mean single sequence MFE	-30.31
Consensus MFE	-25.96
Energy contribution	-26.16
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.86
SVM decision value	0.64
SVM RNA-class probability	0.808873
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13693352 115 - 27905053
AAACUGA-----AGAGUACAGUGCUGGUAAAUGUGGGGUAAAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGA
(((((((-----...(..(((..(((((.............(((((.((..((.....))..))))))).)))))..)))..)..)))))))..............((((......)))) ( -29.44)
>DroSec_CAF1 3248 115 - 1
AAACUGA-----AGAGUACAGUGCUGGUAAAUGUGGGGUAAAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGA
(((((((-----...(..(((..(((((.............(((((.((..((.....))..))))))).)))))..)))..)..)))))))..............((((......)))) ( -29.44)
>DroSim_CAF1 3262 115 - 1
AAACUGA-----AGAGUACAGUGCUGGUAAAUGUGGGGUAAAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGA
(((((((-----...(..(((..(((((.............(((((.((..((.....))..))))))).)))))..)))..)..)))))))..............((((......)))) ( -29.44)
>DroEre_CAF1 3253 120 - 1
AAACUAAAACUGAGAGUACAGUGCUGGUAAAUGUGGGGUAAAUUUGGUGUGGCAAAACGCACCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGACAAUGGGA
.....((((((((..(..(((..(((((.....(((........(((((((......))))))))))...)))))..)))..)..)))))))).............((((......)))) ( -34.20)
>DroYak_CAF1 3306 120 - 1
AAACUAAAACUGAGAGUACAGUGCUGGUAAAUGUGGGGUAAAUUAUGUGAGGCAAAACGCAGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGA
.....((((((((..(..(((..(((((.............((((.(((..((.....))..))))))).)))))..)))..)..)))))))).............((((......)))) ( -29.04)
>consensus
AAACUGA_____AGAGUACAGUGCUGGUAAAUGUGGGGUAAAUUAGGUGUGGCAAAACGCUGCACUAAUGACUAGUGUUGGGCAAUUAGUUUUCAAUAAUGGCUCUUCCCGAAAAUGGGA
............(((((.(((..(((((.............((((.(((..((.....))..))))))).)))))..)))....((((........)))).)))))((((......)))) (-25.96 = -26.16 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:59 2006