Locus 8603

Sequence ID	3R_DroMel_CAF1
Location	22,997,390 – 22,997,506
Length	116
Max. P	0.995142

overview

Window 2

Location	22,997,390 – 22,997,481
Length	91
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	74.36
Mean single sequence MFE	-24.61
Consensus MFE	-11.73
Energy contribution	-11.92
Covariance contribution	0.19
Combinations/Pair	1.20
Mean z-score	-2.82
Structure conservation index	0.48
SVM decision value	2.55
SVM RNA-class probability	0.995142
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22997390 91 - 27905053
AUCGAAAUCGAA-AUCGACCAGCGAGCAGCCUUGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACCAAAAAGAGCC-----GG-----CCGAAAC
.(((....))).-.(((.((.(((((((((...((((......)))))))))))(((.............))).......)).-----))-----.)))... ( -23.62)
>DroPse_CAF1 1339 94 - 1
AGCGAAAUCGGGAAUUGG-------GAAUCG-AGCAAUGCAUUUUGCGUUGUUUGGUUUCUAAUUAAAAUACCAAAAAGAGCCGAGCCGAGCCAGCCGACAC
.......((((.((((((-------((((((-((((((((.....)))))))))))))))))))).............(.((((...)).)))..))))... ( -30.70)
>DroGri_CAF1 3703 70 - 1
AGCAAAAC--------GG-------CCAGAG-AGCAAUGCAUUUUGCGUUGUUUGGUUUCUAAUUAAAAUACCAAAAAAA---------------CCGAAA-
.......(--------((-------.....(-((((((((.....)))))))))(((.............))).......---------------)))...- ( -15.12)
>DroEre_CAF1 3634 77 - 1
AUCGAAAUCGACCA--------------GCG-AGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACCAAAAAGAGCC-----GG-----CCGAAAC
.......(((.((.--------------(((-((((((((.....)))))))))(((.............))).......)).-----))-----.)))... ( -23.02)
>DroAna_CAF1 1552 80 - 1
AGCGAAAUCGACCG--------------GCG-AGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACCAAAAAGAGCC-----AGAGCCGCCG--AC
.......(((..((--------------(((-((((((((.....)))))))))(((((...................)))))-----...)))).))--). ( -24.91)
>DroPer_CAF1 1375 89 - 1
AGCGAAAUCGGGAAUUGG-------GAAUCG-AGCAAUGCAUUUUGCGUUGUUUGGUUUCUAAUUAAAAUACCAAAAAGAGCC-----GAGCCAGCCGACAC
.((....((((.((((((-------((((((-((((((((.....)))))))))))))))))))).......(.....)..))-----))....))...... ( -30.30)
>consensus
AGCGAAAUCGAC_A__GG_______G_AGCG_AGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACCAAAAAGAGCC_____GG_____CCGAAAC
...((((((((......................(((((((.....))))))))))))))).......................................... (-11.73 = -11.92 +   0.19)

alignment

secondary structure

dotplot

Window 3

Location	22,997,409 – 22,997,506
Length	97
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	78.18
Mean single sequence MFE	-25.07
Consensus MFE	-12.36
Energy contribution	-12.52
Covariance contribution	0.17
Combinations/Pair	1.13
Mean z-score	-2.79
Structure conservation index	0.49
SVM decision value	1.58
SVM RNA-class probability	0.965541
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22997409 97 - 27905053
AGAUCAGA---AGGCCAGAAG----GAAAGAAAUCGAAAUCGAA-AUCGACCAGCGAGCAGCCUUGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACC
.(((.(((---((.((....(----(...((..(((....))).-.))..))...(((((((...((((......)))))))))))))))))).)))........ ( -23.10)
>DroPse_CAF1 1368 93 - 1
AGAUCAGAAAAAGGCCCAAAG----CAGAGAAAGCGAAAUCGGGAAUUGG-------GAAUCG-AGCAAUGCAUUUUGCGUUGUUUGGUUUCUAAUUAAAAUACC
..............(((...(----(.......))(....))))((((((-------((((((-((((((((.....))))))))))))))))))))........ ( -29.10)
>DroEre_CAF1 3653 83 - 1
AGAUCAGA---AGGCCAGGAG----GAAAGAAAUCGAAAUCGACCA--------------GCG-AGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACC
.(((.(((---((.((.....----........(((....)))...--------------..(-((((((((.....)))))))))))))))).)))........ ( -21.10)
>DroMoj_CAF1 3345 86 - 1
GGAUCGAA---CGGCCGAAAGGCUCGAAAGAAAGCGAAAU--------GG-------CCAAAG-AGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACC
((((((((---(((((....)))((....))..(((((((--------((-------(.....-.))....))))))))..)))))))))).............. ( -27.40)
>DroAna_CAF1 1574 83 - 1
AGAUCAGA---AGGCCAAAAG----GAAAGAAAGCGAAAUCGACCG--------------GCG-AGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACC
.(((.(((---((.((....(----(...((........))..)).--------------..(-((((((((.....)))))))))))))))).)))........ ( -20.60)
>DroPer_CAF1 1399 93 - 1
AGAUCAGAAAAAGGCCCAAAG----CAGAGAAAGCGAAAUCGGGAAUUGG-------GAAUCG-AGCAAUGCAUUUUGCGUUGUUUGGUUUCUAAUUAAAAUACC
..............(((...(----(.......))(....))))((((((-------((((((-((((((((.....))))))))))))))))))))........ ( -29.10)
>consensus
AGAUCAGA___AGGCCAAAAG____GAAAGAAAGCGAAAUCGAC_A__GG_______G_AGCG_AGCAAUGCAUUUUGCGUUGUUCGGUUUCUAAUUAAAAUACC
...................................((((((((......................(((((((.....)))))))))))))))............. (-12.36 = -12.52 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:21 2006