Locus 2300

Sequence ID	3R_DroMel_CAF1
Location	6,541,705 – 6,541,853
Length	148
Max. P	0.743244

overview

Window 8

Location	6,541,705 – 6,541,825
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.08
Mean single sequence MFE	-29.52
Consensus MFE	-20.39
Energy contribution	-20.52
Covariance contribution	0.13
Combinations/Pair	1.14
Mean z-score	-2.17
Structure conservation index	0.69
SVM decision value	0.46
SVM RNA-class probability	0.743244
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6541705 120 - 27905053
AUGAGAGUUCGAUAACCGGAUUCCGAACUGAACCCGGCGGCCUAAAGGCUUGCCAAUGUUGGUCAAAACAACUGCACACGUCAGCAAAUAAGAAUAAAUUUGUAAAAAAUUACGGAACUA
.((.(((((((.....)))))))))..((((....(((((((....))).))))...((((.......))))........))))..............(((((((....))))))).... ( -27.40)
>DroSec_CAF1 18587 120 - 1
AUGAGAGUUCGAUAACCGGAUUCCGAACCGAACCCGGCGGCCUAAAGGCUUGCCAAUGUUGGCCAAAACAACUGCACACGUCGGCAAAUAAGAAUAAAUUCGUAAAAAAUCACGGAACUA
.((.(((((((.....)))))))))..(((...(((((((((....))).(((....((((.......)))).)))..)))))).......(((....)))...........)))..... ( -30.00)
>DroSim_CAF1 18031 108 - 1
AUUAAAAUUCGACAACCGGAUUCCGAACCGAACCCGGCGGCCUAAAGGCUUGCCAAUUUUGG------------CACACGUCGGCAAAUAAGAAUAAAUUCGUAAAAAAUCACGGAACUA
.......((((.....))))(((((........(((((((((....))).(((((....)))------------))..)))))).......(((....)))...........)))))... ( -27.50)
>DroEre_CAF1 20805 118 - 1
--GAGAGUUCGAUAACCGGAUUUCGAACCAAGUCCGGCGGCCUAAAGGAUUGCCAAUGUUGGCCAAAACAACUGCACACGUCGGCAAAUAAGAAUAAAUACGUGAAAAAUCACGGAACUA
--...((((((((..((((((((......)))))))).((((....((....))......))))...............)))..................(((((....)))))))))). ( -30.70)
>DroYak_CAF1 19005 120 - 1
ACGAGAGUUCGAUAACCGGAUUUCGAACCAAACCCCGUGGCCCAAAGGCUUGCCAAUGUUGGCCAAAACAACUGCACACGUUGGCAAAUAAGAAAAAAUACGUUAAAAAUCACGGAACUA
.(((((.((((.....))))))))).........((((((((....)))((((((((((..((..........))..)))))))))).......................)))))..... ( -32.00)
>consensus
AUGAGAGUUCGAUAACCGGAUUCCGAACCGAACCCGGCGGCCUAAAGGCUUGCCAAUGUUGGCCAAAACAACUGCACACGUCGGCAAAUAAGAAUAAAUUCGUAAAAAAUCACGGAACUA
.....(((((.....((((.(((......))).))))(((((....)))(((((.((((..((..........))..)))).))))).........................))))))). (-20.39 = -20.52 +   0.13)

alignment

secondary structure

dotplot

Window 9

Location	6,541,745 – 6,541,853
Length	108
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	81.61
Mean single sequence MFE	-34.15
Consensus MFE	-20.86
Energy contribution	-21.06
Covariance contribution	0.20
Combinations/Pair	1.15
Mean z-score	-1.81
Structure conservation index	0.61
SVM decision value	0.10
SVM RNA-class probability	0.585822
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6541745 108 + 27905053
CGUGUGCAGUUGUUUUGACCAACAUUGGCAAGCCUUUAGGCCGCCGGGUUCAGUUCGGAAUCCGGUUAUCGAACUCUCAUCCAGAAGGAUGUUUGCAUGUG------UAUUCAU
((..(((((..(((((((((......(((..(((....))).)))((((((......)))))))))))..))))...(((((....))))).)))))..))------....... ( -36.90)
>DroSec_CAF1 18627 108 + 1
CGUGUGCAGUUGUUUUGGCCAACAUUGGCAAGCCUUUAGGCCGCCGGGUUCGGUUCGGAAUCCGGUUAUCGAACUCUCAUCCAGAAGGAUGUUGGCAUGUG------UAUUUAU
.(((..((.........((((((((((((..(((....))).)))(((((((((((((...))))..)))))))))...........))))))))).))..------))).... ( -38.80)
>DroSim_CAF1 18071 96 + 1
CGUGUG------------CCAAAAUUGGCAAGCCUUUAGGCCGCCGGGUUCGGUUCGGAAUCCGGUUGUCGAAUUUUAAUAAAGAAGGAUGUUGGCAUGUG------UAUUUAU
((..((------------((((..((((((.(((....))).(((((((((......)))))))))))))))(((((........))))).))))))..))------....... ( -33.60)
>DroEre_CAF1 20845 104 + 1
CGUGUGCAGUUGUUUUGGCCAACAUUGGCAAUCCUUUAGGCCGCCGGACUUGGUUCGAAAUCCGGUUAUCGAACUCUC----------AUGUUUGCAUGGGUACAAGUAUCUAU
.(((.((..........((((....))))..........)))))...(((((((((((.(......).)))))).(((----------(((....))))))..)))))...... ( -27.15)
>DroYak_CAF1 19045 108 + 1
CGUGUGCAGUUGUUUUGGCCAACAUUGGCAAGCCUUUGGGCCACGGGGUUUGGUUCGAAAUCCGGUUAUCGAACUCUCGUACAGAAGGAUGUUUGCAUGUG------UAUUUAU
((..(((((((.(((((((((....))))..(((....))).(((((((((((((((.....)))..))))))).))))).))))).)))...))))..))------....... ( -34.30)
>consensus
CGUGUGCAGUUGUUUUGGCCAACAUUGGCAAGCCUUUAGGCCGCCGGGUUCGGUUCGGAAUCCGGUUAUCGAACUCUCAUACAGAAGGAUGUUUGCAUGUG______UAUUUAU
(((((...........((((......((....))....))))(((((((((......)))))))))............................)))))............... (-20.86 = -21.06 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:59 2006