Locus 3501

Sequence ID	X_DroMel_CAF1
Location	9,396,098 – 9,396,257
Length	159
Max. P	0.582094

overview

Window 3

Location	9,396,098 – 9,396,217
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.22
Mean single sequence MFE	-34.76
Consensus MFE	-28.06
Energy contribution	-30.62
Covariance contribution	2.56
Combinations/Pair	1.19
Mean z-score	-1.48
Structure conservation index	0.81
SVM decision value	0.10
SVM RNA-class probability	0.582094
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9396098 119 - 22224390
UAGUUUUCUUGAAAUUGCAUCGGCUAAGCUUUCAGUUGAGCAGAGCUUUCAGCGCUGUUAAGAUGUACCCACUC-CACAGUGCUCGUUAGCAUCGCUGUUAAGGACACGGCAACUUGUUG
..((.(((((((....((.((.(((.(((.....))).))).))(((..(((((((((..((.((....)))).-.)))))))).)..)))...))..))))))).))(....)...... ( -32.70)
>DroSec_CAF1 10048 119 - 1
AUGUUUCUUUGAAAUUGCAUCGGCUAAGCUUUCGGUUUAGCAGAGCUUGCAGCGCUGUUAAGGUGCACCCACUC-CACAGUGCCCGUUAGCAGAGCUGUUAAGGACACGACAACUUGUUG
.(((.((((((.....((.((.(((((((.....))))))).))))..(((((.(((((((((.((((......-....)))))).))))))).))))))))))).)))........... ( -40.10)
>DroSim_CAF1 14214 119 - 1
AAGUUUCUUUGAAAUUGCAUCGGCUAAGCUUUCAGUUUAGCAGAGCUUGCAGCGCUGUUAAGGUGCUCCCACUC-CACAGUGUCCGUUUGCAGCGCUGUUAAGGACACGGCAACUUGUUG
..((.((((((.....((.((.(((((((.....))))))).))))..((((((((((...((......((((.-...)))).))....)))))))))))))))).))(....)...... ( -38.90)
>DroYak_CAF1 14033 119 - 1
AAGUUAACAUAAAACUGCAUCGGCUAAACUUAAAUUUUAGCAGAGCUUUCACCGCUGUUAAAAUUCGCCCACUCCCACAG-ACCCGUUAGCAGCGCUGUUAAGCCCAUGGCAACUUGUUG
(((((..(((.........((.((((((.......)))))).))((((.((.(((((((((...((.............)-)....))))))))).))..))))..)))..))))).... ( -27.32)
>consensus
AAGUUUCCUUGAAAUUGCAUCGGCUAAGCUUUCAGUUUAGCAGAGCUUGCAGCGCUGUUAAGAUGCACCCACUC_CACAGUGCCCGUUAGCAGCGCUGUUAAGGACACGGCAACUUGUUG
..((.(((((((....((.((.(((((((.....))))))).))))...((((((((((((.(.((((...........)))).).))))))))))))))))))).))............ (-28.06 = -30.62 +   2.56)

alignment

secondary structure

dotplot

Window 4

Location	9,396,138 – 9,396,257
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.36
Mean single sequence MFE	-33.73
Consensus MFE	-24.42
Energy contribution	-24.67
Covariance contribution	0.25
Combinations/Pair	1.15
Mean z-score	-1.52
Structure conservation index	0.72
SVM decision value	0.09
SVM RNA-class probability	0.580389
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9396138 119 - 22224390
AUAAACUUGCUCUGCGGCGCCAUCUGUUGGCGACGACUAGUAGUUUUCUUGAAAUUGCAUCGGCUAAGCUUUCAGUUGAGCAGAGCUUUCAGCGCUGUUAAGAUGUACCCACUC-CACAG
........(((((((..(((((.....))))).(((((...(((((..((((.......))))..)))))...))))).)))))))........((((..((.((....)))).-.)))) ( -33.40)
>DroSec_CAF1 10088 119 - 1
AUAAACUUGCUCUGCACCGCCAUCUGUUGGCGACCACUCGAUGUUUCUUUGAAAUUGCAUCGGCUAAGCUUUCGGUUUAGCAGAGCUUGCAGCGCUGUUAAGGUGCACCCACUC-CACAG
.....(..(((((((..(((((.....)))))(((...((((((............))))))((...))....)))...)))))))..)..(((((.....)))))........-..... ( -36.50)
>DroSim_CAF1 14254 119 - 1
AUAAACUUGCUCUGCACCGCCAUCUGUUGGCGACCACUCGAAGUUUCUUUGAAAUUGCAUCGGCUAAGCUUUCAGUUUAGCAGAGCUUGCAGCGCUGUUAAGGUGCUCCCACUC-CACAG
.....(..(((((((..(((((.....)))))...(((.(((((((..((((.......))))..))))))).)))...)))))))..).((((((.....)))))).......-..... ( -36.10)
>DroYak_CAF1 14072 119 - 1
AUAAACUU-UUGUGCGGCGCCAUCUGUUGGCGACCAUGCUAAGUUAACAUAAAACUGCAUCGGCUAAACUUAAAUUUUAGCAGAGCUUUCACCGCUGUUAAAAUUCGCCCACUCCCACAG
........-..(((.(((((((.....))))(.((((((..((((.......)))))))).)))........(((((((((((.(.......).))))))))))).))))))........ ( -28.90)
>consensus
AUAAACUUGCUCUGCACCGCCAUCUGUUGGCGACCACUCGAAGUUUCCUUGAAAUUGCAUCGGCUAAGCUUUCAGUUUAGCAGAGCUUGCAGCGCUGUUAAGAUGCACCCACUC_CACAG
...(((..((.(((((.(((((.....)))))........................((.((.(((((((.....))))))).)))).))))).)).)))..................... (-24.42 = -24.67 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:00 2006