Locus 3266

Sequence ID	2L_DroMel_CAF1
Location	9,446,812 – 9,446,946
Length	134
Max. P	0.975646

overview

Window 4

Location	9,446,812 – 9,446,911
Length	99
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	78.77
Mean single sequence MFE	-35.22
Consensus MFE	-20.40
Energy contribution	-20.98
Covariance contribution	0.59
Combinations/Pair	1.21
Mean z-score	-2.84
Structure conservation index	0.58
SVM decision value	1.75
SVM RNA-class probability	0.975646
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9446812 99 + 22407834
CAUUGUCAGCUGAGUGCCCAAGUGUGAAUGUGCAUGCA-------UUGGGUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUCAAGCAUUGCCAGA
.........(((.(..((((((((((......))))).-------)))))..)..(((((((((((((((((((....))))))))))))....))).))))))). ( -34.90)
>DroSec_CAF1 11290 106 + 1
CAUUGUUAGCUGAGUGCCCAAGUGUGAAUGUGCACAUGUGUGUACUUGGUUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUCAAGCAUUGCCAGA
......((((..(((((.((.(((((......))))).)).)))))..))))...(((((((((((((((((((....))))))))))))....))).)))).... ( -38.40)
>DroSim_CAF1 11445 106 + 1
CAUUGUCAGCUGAGUGCCCAAGUGUGAAUGUGCAUGUGUGUGUACUUGGUUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUCAAGCAUUGCCAGC
..(((.((((..(((((.((.((((......))))...)).)))))..)))))))(((((((((((((((((((....))))))))))))....))).)))).... ( -37.80)
>DroEre_CAF1 11676 106 + 1
CAUUGUCAGCUGAGUGCCCAAGUGUGAAUGUGCAUGUGUGUACUUGUGUGUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUCGAGCGUUGCCAGA
..(((.((((.((((((.((.((((......)))).)).))))))((.(((....))).)).((((((((((((....)))))))))))).......)))).))). ( -32.20)
>DroYak_CAF1 11487 106 + 1
CAUUGUCAGCUGAGUGCCCAUGUGUGAAUGUGCAUGGGUACGCCUGUGUAUGUAAGCUGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUAAAGCGUUGCCAGA
..(((.((((...(((((((((..(....)..)))))))))..............(((....((((((((((((....))))))))))))....))))))).))). ( -41.60)
>DroAna_CAF1 10612 84 + 1
CAUUGCCGCUUGAGUGUC----UGUGAGUGUUCUC------------------GAGCAAGCUCUUAAGUUUUGUUUAAGAGAGGCCCCAGAGCCGGCGUUGCCAGC
((.(((((((((((...(----.......)..)))------------------))))...((((((((.....)))))))).(((......))))))).))..... ( -26.40)
>consensus
CAUUGUCAGCUGAGUGCCCAAGUGUGAAUGUGCAUGUGUGUG___UUGGGUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUCAAGCAUUGCCAGA
.........(((.((((.((........)).))))....................(((((((((((((((((((....))))))))))))....))).))))))). (-20.40 = -20.98 +   0.59)

alignment

secondary structure

dotplot

Window 5

Location	9,446,849 – 9,446,946
Length	97
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	77.85
Mean single sequence MFE	-25.73
Consensus MFE	-16.54
Energy contribution	-16.52
Covariance contribution	-0.02
Combinations/Pair	1.26
Mean z-score	-1.59
Structure conservation index	0.64
SVM decision value	0.62
SVM RNA-class probability	0.802097
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9446849 97 + 22407834
A-------UUGGGUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUC-AAGCAUUGCCAGA--UU--AAAAACAUUUUUAAAAUUUUGUAACGGAAACAG
.-------...((((...((..(..((((((((((((....))))))))))))..)-..))..))))...--((--((((....))))))...........(....).. ( -22.00)
>DroSec_CAF1 11327 104 + 1
GUGUGUACUUGGUUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUC-AAGCAUUGCCAGA--UU--AAAAGCAUUUUUAAAAUUUUGUAACGGAAACAG
..((((..((((((....(((((((((((((((((((....))))))))))))...-.))).))))..))--))--))..)))).................(....).. ( -25.60)
>DroSim_CAF1 11482 104 + 1
GUGUGUACUUGGUUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUC-AAGCAUUGCCAGC--UU--AAAAGCAUUUUUAAAAUUUUGUAACGGAAACAG
((((......(((((...(((((((((((((((((((....))))))))))))...-.))).))))))))--).--....)))).................(....).. ( -26.90)
>DroEre_CAF1 11713 104 + 1
GUGUACUUGUGUGUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUC-GAGCGUUGCCAGA--GU--AAAAGCAUUUUUAAAAUUUUGUAACGGCAACAG
(..(((....)))..)..((..(..((((((((((((....))))))))))))..)-..))((((((...--.(--((((............)))))....)))))).. ( -27.20)
>DroYak_CAF1 11524 104 + 1
GUACGCCUGUGUAUGUAAGCUGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUA-AAGCGUUGCCAGA--AU--AAAAGCAUGUUUUAAAUAUUGUAACGGUUAGAG
(((((....))))).....((((((((((((((((((....))))))))))))(((-((((((.((....--..--....)))))))))))..........)))))).. ( -26.80)
>DroPer_CAF1 10893 108 + 1
GUGUGUAAACACAAGAGAGCAAGCUCUUAAGUUCUUGUUAAGAGUAUCUUGGGCCGGAGGCAUUGCCAGCCCUUAGAAAAGUGGUGUUUGAAUUUU-UAACCGACAUUU
.....(((((((..((((....((((((((.......)))))))).))))((((.((........)).))))...........)))))))......-............ ( -25.90)
>consensus
GUGUGUACUUGGAUGUAAGCAGGCUCUUAAGUUUCUUUUAAGAGAGACUUGAGUUC_AAGCAUUGCCAGA__UU__AAAAGCAUUUUUAAAAUUUUGUAACGGAAACAG
..................(((((((((((((((((((....)))))))))))).....))).))))........................................... (-16.54 = -16.52 +  -0.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:21 2006