Locus 10346

Sequence ID	3R_DroMel_CAF1
Location	27,860,759 – 27,860,866
Length	107
Max. P	0.994882

overview

Window 4

Location	27,860,759 – 27,860,850
Length	91
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	93.96
Mean single sequence MFE	-21.06
Consensus MFE	-17.78
Energy contribution	-17.46
Covariance contribution	-0.32
Combinations/Pair	1.15
Mean z-score	-1.60
Structure conservation index	0.84
SVM decision value	0.91
SVM RNA-class probability	0.879684
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27860759 91 + 27905053
UUAAACAACUAAAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUAAAAGCACCUGUGCCUGCCGUAG
....((.(((......((((((.....))))))..........((((((..........)))))))))....(((....))).....)).. ( -17.30)
>DroSec_CAF1 169983 91 + 1
UUAAACAACUAAAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAGCACCUGUGCCAGCCACAG
..............((((((((.....)))))((((((.....((((((..........))))))..)))))))))(((((.....))))) ( -21.90)
>DroSim_CAF1 172208 91 + 1
UUAAACAACUAAAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAGCACCUGUGCCAGCCACAG
..............((((((((.....)))))((((((.....((((((..........))))))..)))))))))(((((.....))))) ( -21.90)
>DroEre_CAF1 200049 91 + 1
UUAAACAACUAAAAGUGUCACAAUUGUUGUGACUUGUAACCAGGACCAAUUGUUUAACUUUGGUUAGCACAAACACCUGUGCCUGCUGAAG
((((((((.........(((((.....)))))((((....)))).....))))))))(((..((..(((((......)))))..))..))) ( -23.70)
>DroYak_CAF1 173781 91 + 1
UUAAACAACUAAAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAACACCUGUGCCUUUCGGAG
........(..((((.((((((.....))))))..........((((((..........)))))).(((((......)))))))))..).. ( -20.50)
>consensus
UUAAACAACUAAAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAGCACCUGUGCCUGCCGCAG
(((((((((.....))((((((.....)))))).................)))))))((.((((..(((((......)))))..)))).)) (-17.78 = -17.46 +  -0.32)

alignment

secondary structure

dotplot

Window 5

Location	27,860,759 – 27,860,850
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	93.96
Mean single sequence MFE	-23.22
Consensus MFE	-19.76
Energy contribution	-19.84
Covariance contribution	0.08
Combinations/Pair	1.13
Mean z-score	-2.04
Structure conservation index	0.85
SVM decision value	2.06
SVM RNA-class probability	0.987040
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27860759 91 - 27905053
CUACGGCAGGCACAGGUGCUUUUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUUUAGUUGUUUAA
....((((((((....))).....))).))....((((((((((((....(((.....((((((.....))))))))).)))))))))))) ( -21.10)
>DroSec_CAF1 169983 91 - 1
CUGUGGCUGGCACAGGUGCUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUUUAGUUGUUUAA
(((((.....)))))(((((((((((((((((..........))))))..)).)))))).)))((((((((.........))))))))... ( -25.40)
>DroSim_CAF1 172208 91 - 1
CUGUGGCUGGCACAGGUGCUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUUUAGUUGUUUAA
(((((.....)))))(((((((((((((((((..........))))))..)).)))))).)))((((((((.........))))))))... ( -25.40)
>DroEre_CAF1 200049 91 - 1
CUUCAGCAGGCACAGGUGUUUGUGCUAACCAAAGUUAAACAAUUGGUCCUGGUUACAAGUCACAACAAUUGUGACACUUUUAGUUGUUUAA
........(((((((....)))))))........((((((((((((...((....)).((((((.....))))))....)))))))))))) ( -22.40)
>DroYak_CAF1 173781 91 - 1
CUCCGAAAGGCACAGGUGUUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUUUAGUUGUUUAA
..((....)).((((.((.(((((((((((((..........))))))..)).)))))((((((.....)))))).....)).)))).... ( -21.80)
>consensus
CUGCGGCAGGCACAGGUGCUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUUUAGUUGUUUAA
.....(((((((....)))))))(((......)))(((((((((((....(((.....((((((.....))))))))).))))))))))). (-19.76 = -19.84 +   0.08)

alignment

secondary structure

dotplot

Window 6

Location	27,860,770 – 27,860,866
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	93.23
Mean single sequence MFE	-23.46
Consensus MFE	-20.90
Energy contribution	-21.06
Covariance contribution	0.16
Combinations/Pair	1.15
Mean z-score	-1.96
Structure conservation index	0.89
SVM decision value	2.52
SVM RNA-class probability	0.994882
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27860770 96 + 27905053
AAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUAAAAGCACCUGUGCCUGCCGUAGCAGAAUUGCAAAACAU
.....((((((.....))))))((((((....((((((..........)))))).......(((....)))((((....))))..))))))..... ( -24.00)
>DroSec_CAF1 169994 96 + 1
AAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAGCACCUGUGCCAGCCACAGCAGAAUUACAAAACAU
...((((((((.....)))))((((((.....((((((..........))))))..)))))))))(((((.....)))))................ ( -22.30)
>DroSim_CAF1 172219 96 + 1
AAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAGCACCUGUGCCAGCCACAGCAGAAUUACAAAACAU
...((((((((.....)))))((((((.....((((((..........))))))..)))))))))(((((.....)))))................ ( -22.30)
>DroEre_CAF1 200060 96 + 1
AAAGUGUCACAAUUGUUGUGACUUGUAACCAGGACCAAUUGUUUAACUUUGGUUAGCACAAACACCUGUGCCUGCUGAAGCAGAACUACAAAACAU
.....((((((.....))))))(((((.....((((((..........)))))).(((((......)))))((((....))))...)))))..... ( -25.20)
>DroYak_CAF1 173792 96 + 1
AAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAACACCUGUGCCUUUCGGAGCAGAACUACAAAACAU
..(((((((((.....))))))(((((.....((((((..........))))))..)))))....((((.((....)).)))).)))......... ( -23.50)
>consensus
AAAGUGUCACAAUUGUUGUGACUUGUAACUAGGACCAAUUGUUUAACUUUGGUCAGUACAAGCACCUGUGCCUGCCGCAGCAGAAUUACAAAACAU
.....((((((.....))))))(((((.....((((((..........)))))).(((((......)))))((((....))))...)))))..... (-20.90 = -21.06 +   0.16)

alignment

secondary structure

dotplot

Window 7

Location	27,860,770 – 27,860,866
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	93.23
Mean single sequence MFE	-25.22
Consensus MFE	-21.00
Energy contribution	-20.44
Covariance contribution	-0.56
Combinations/Pair	1.17
Mean z-score	-2.05
Structure conservation index	0.83
SVM decision value	1.82
SVM RNA-class probability	0.978551
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27860770 96 - 27905053
AUGUUUUGCAAUUCUGCUACGGCAGGCACAGGUGCUUUUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUU
.(((...((....((((....))))(((....))).......((((((..........))))))...)).))).((((((.....))))))..... ( -25.00)
>DroSec_CAF1 169994 96 - 1
AUGUUUUGUAAUUCUGCUGUGGCUGGCACAGGUGCUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUU
..((.(..(((((...(((((.....)))))(((((((((((((((((..........))))))..)).)))))).)))...)))))..).))... ( -25.30)
>DroSim_CAF1 172219 96 - 1
AUGUUUUGUAAUUCUGCUGUGGCUGGCACAGGUGCUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUU
..((.(..(((((...(((((.....)))))(((((((((((((((((..........))))))..)).)))))).)))...)))))..).))... ( -25.30)
>DroEre_CAF1 200060 96 - 1
AUGUUUUGUAGUUCUGCUUCAGCAGGCACAGGUGUUUGUGCUAACCAAAGUUAAACAAUUGGUCCUGGUUACAAGUCACAACAAUUGUGACACUUU
.....((((((.(((((....)))))..((((...((((..((((....)))).)))).....)))).))))))((((((.....))))))..... ( -25.90)
>DroYak_CAF1 173792 96 - 1
AUGUUUUGUAGUUCUGCUCCGAAAGGCACAGGUGUUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUU
..((.(..((((((((..((....))..)))(((((((((((((((((..........))))))..)).)))))).)))...)))))..).))... ( -24.60)
>consensus
AUGUUUUGUAAUUCUGCUGCGGCAGGCACAGGUGCUUGUACUGACCAAAGUUAAACAAUUGGUCCUAGUUACAAGUCACAACAAUUGUGACACUUU
..((.(..(((((.((((......))))...(((((((((((((((((..........))))))..)).)))))).)))...)))))..).))... (-21.00 = -20.44 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:54:34 2006