Locus 6434

Sequence ID	2L_DroMel_CAF1
Location	18,084,229 – 18,084,389
Length	160
Max. P	0.837044

overview

Window 9

Location	18,084,229 – 18,084,349
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-30.30
Consensus MFE	-24.70
Energy contribution	-25.32
Covariance contribution	0.62
Combinations/Pair	1.09
Mean z-score	-1.86
Structure conservation index	0.82
SVM decision value	0.39
SVM RNA-class probability	0.715627
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18084229 120 + 22407834
UUGUCAUUGUUGACAGUCUCUCUCUGCUCAAGGACGUGUUCUGUGCCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUUAAAAUGUCUGCGUUUUGAGCCG
((((((....)))))).........(((((((.((((....(((((.((........))))))).(((((((..((((((.......)))))).)))))))......))))))))))).. ( -30.00)
>DroSec_CAF1 291585 120 + 1
UUGUCAUUGUUGACAGUCUCUCUCGGCUCAAGGACGUGUUCUGUGGCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUGAAAAUGUCUGUGUUUUGAGCCG
((((((....)))))).......((((((((((((((.(((....((((........))))((((...(((((((......))))))).....))))))).)))))).....)))))))) ( -35.10)
>DroSim_CAF1 293608 120 + 1
UUGUCAUUGUUGACAGUCUCUCUCGGCUCAAGGACGUGUUCUGUGGCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUGAAAAUGUCUGUGUUUUGAGCCG
((((((....)))))).......((((((((((((((.(((....((((........))))((((...(((((((......))))))).....))))))).)))))).....)))))))) ( -35.10)
>DroYak_CAF1 309003 118 + 1
UUUUCAUUGUUGACAGUCUCCCUCGGCUCAAGGACGUGUUCUGUGUCG-UUCGUUUUUCGCACAAUUUAAUUUUACUUAAUCGGCAUUUAAGUUUGUGUAAAUGCUUGCGUUUU-AGCAG
.......((((((..........((((...((((....))))..))))-.........((((..(((((.....((((((.......)))))).....)))))...))))..))-)))). ( -21.00)
>consensus
UUGUCAUUGUUGACAGUCUCUCUCGGCUCAAGGACGUGUUCUGUGGCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUGAAAAUGUCUGCGUUUUGAGCCG
((((((....)))))).......(((((((((.((((....((((.(((........)))))))..................(((((((..........))))))).))))))))))))) (-24.70 = -25.32 +   0.62)

alignment

secondary structure

dotplot

Window 0

Location	18,084,229 – 18,084,349
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-24.17
Consensus MFE	-20.02
Energy contribution	-21.27
Covariance contribution	1.25
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.83
SVM decision value	0.74
SVM RNA-class probability	0.837044
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18084229 120 - 22407834
CGGCUCAAAACGCAGACAUUUUAACAAACUUAAAUGCCAAUUAAGUAACAUUAAAUUGUGCGAAAAAUGAAUCGGCACAGAACACGUCCUUGAGCAGAGAGAGACUGUCAACAAUGACAA
..((((((.(((...............((((((.......)))))).........((((((((........)).))))))....)))..))))))..........(((((....))))). ( -23.20)
>DroSec_CAF1 291585 120 - 1
CGGCUCAAAACACAGACAUUUUCACAAACUUAAAUGCCAAUUAAGUAACAUUAAAUUGUGCGAAAAAUGAAUCGCCACAGAACACGUCCUUGAGCCGAGAGAGACUGUCAACAAUGACAA
((((((((......(((..........((((((.......)))))).........((((((((........))).))))).....))).))))))))........(((((....))))). ( -27.20)
>DroSim_CAF1 293608 120 - 1
CGGCUCAAAACACAGACAUUUUCACAAACUUAAAUGCCAAUUAAGUAACAUUAAAUUGUGCGAAAAAUGAAUCGCCACAGAACACGUCCUUGAGCCGAGAGAGACUGUCAACAAUGACAA
((((((((......(((..........((((((.......)))))).........((((((((........))).))))).....))).))))))))........(((((....))))). ( -27.20)
>DroYak_CAF1 309003 118 - 1
CUGCU-AAAACGCAAGCAUUUACACAAACUUAAAUGCCGAUUAAGUAAAAUUAAAUUGUGCGAAAAACGAA-CGACACAGAACACGUCCUUGAGCCGAGGGAGACUGUCAACAAUGAAAA
.(((.-.....))).(((((((........))))))).(((..(((.........(((((((.........-)).)))))....(..(((((...)))))..)))))))........... ( -19.10)
>consensus
CGGCUCAAAACACAGACAUUUUCACAAACUUAAAUGCCAAUUAAGUAACAUUAAAUUGUGCGAAAAAUGAAUCGCCACAGAACACGUCCUUGAGCCGAGAGAGACUGUCAACAAUGACAA
((((((((.((................((((((.......)))))).........((((((((........))).))))).....))..))))))))........(((((....))))). (-20.02 = -21.27 +   1.25)

alignment

secondary structure

dotplot

Window 1

Location	18,084,269 – 18,084,389
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.43
Mean single sequence MFE	-26.95
Consensus MFE	-20.91
Energy contribution	-20.85
Covariance contribution	-0.06
Combinations/Pair	1.13
Mean z-score	-1.62
Structure conservation index	0.78
SVM decision value	0.25
SVM RNA-class probability	0.652317
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18084269 120 + 22407834
CUGUGCCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUUAAAAUGUCUGCGUUUUGAGCCGCGAUAAGGCAGACAUUAAAUUAAUGUUUGAACCUACUUUA
..((((.((........))))))(((((((((((((((((.......))))))...((((((((....))))))))(((.......))).)))))))))))................... ( -26.80)
>DroSec_CAF1 291625 119 + 1
CUGUGGCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUGAAAAUGUCUGUGUUUUGAGCCGCGAUAAGGCAGACAUUAAAUUAAUGUUUGAACC-AUUUUA
.((((((.......((((((((.((((((((((((......))))).)))))))))))))))..((........))))))))....(((((((((((...)))))))))..))-...... ( -29.50)
>DroSim_CAF1 293648 119 + 1
CUGUGGCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUGAAAAUGUCUGUGUUUUGAGCCGCGAUAAGGCAGACAUUAAAAUAAUGAUUGAAGC-AUUUUA
.(((..((((.((((.((((((.((((((((((((......))))).)))))))))))))(((((((((.(((((.....))).)).))))))))).....))))))))..))-)..... ( -30.60)
>DroYak_CAF1 309043 118 + 1
CUGUGUCG-UUCGUUUUUCGCACAAUUUAAUUUUACUUAAUCGGCAUUUAAGUUUGUGUAAAUGCUUGCGUUUU-AGCAGCGAUGAGGCAAACAUUAAAUUAAUAUUUUACCCUAUUUAG
..(((.((-.........)))))(((((((((((.(((.(((((((((((........)))))))((((.....-.)))))))).))).))).))))))))................... ( -20.90)
>consensus
CUGUGGCGAUUCAUUUUUCGCACAAUUUAAUGUUACUUAAUUGGCAUUUAAGUUUGUGAAAAUGUCUGCGUUUUGAGCCGCGAUAAGGCAGACAUUAAAUUAAUGUUUGAACC_AUUUUA
..(((.(((........))))))(((((((((((((((((.......)))))).........(((((.(((........)))...))))))))))))))))................... (-20.91 = -20.85 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:02 2006