Locus 6158

Sequence ID	2L_DroMel_CAF1
Location	17,154,179 – 17,154,373
Length	194
Max. P	0.972208

overview

Window 2

Location	17,154,179 – 17,154,299
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.25
Mean single sequence MFE	-38.77
Consensus MFE	-34.62
Energy contribution	-34.75
Covariance contribution	0.12
Combinations/Pair	1.05
Mean z-score	-1.65
Structure conservation index	0.89
SVM decision value	0.14
SVM RNA-class probability	0.601820
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17154179 120 + 22407834
CCCGGGAUCUAGUAGCCGGAGUCCAGCAGGGCAAGUACAAAUUCAUAUGAGAGGGCUGCAAAAGGUUUUUUGUGUUUGCCUUCUGGCCAUUUUGGUGGAAAAAUAUGGCCAGCUGGAAUC
.((((..........))))..(((((((((((((((((((((((....))).(((((......))))))))))))))))))).(((((((.((........)).)))))))))))))... ( -42.40)
>DroSec_CAF1 115041 120 + 1
CCCGGGAUCUAGUAGCCGGAGUCCAGCAGGACAAGUACAAAUUCAUAUGACAGGGCUGCAAAAGGUUUUUUGUGUUUGCCUUCUGGCCAUUUUGGUUGAAAAAUAUGGCCAGCUGGAAUC
.((((......((((((...((((....))))..((.((........))))..))))))..(((((...........)))))((((((((.((........)).)))))))))))).... ( -37.20)
>DroSim_CAF1 127229 120 + 1
CCCGGGAUCUAGUAGCCGGAGUCCAGCAGGACAAGUACAAAUUCAUAUGACAGGGCUGCAAAAGGUUUUUUGUGUUUGCCUUCUGGCCAUUUUGGUGGAAAAAUAUGGCCAGCUGGAAUC
.((((......((((((...((((....))))..((.((........))))..))))))..(((((...........)))))((((((((.((........)).)))))))))))).... ( -37.20)
>DroYak_CAF1 115079 120 + 1
CCCGGGAUCUAGUAGCCAGAGUCCAGCAGGACAAGUACAAAUUCAUGUGACAGGACCGCAAAAGGUUUUUUGUGUUUGGCUUCUGGCCAUUUUGGUGGGAAAAUAUGGCCAGCUGGAAUC
.((((........(((((((((((....))))...((((((.((....))..(((((......)))))))))))))))))).((((((((.((........)).)))))))))))).... ( -38.30)
>consensus
CCCGGGAUCUAGUAGCCGGAGUCCAGCAGGACAAGUACAAAUUCAUAUGACAGGGCUGCAAAAGGUUUUUUGUGUUUGCCUUCUGGCCAUUUUGGUGGAAAAAUAUGGCCAGCUGGAAUC
.((((..........))))..(((((((((.((((((((((.((....))..(((((......))))))))))))))))))..(((((((.((........)).)))))))))))))... (-34.62 = -34.75 +   0.12)

alignment

secondary structure

dotplot

Window 3

Location	17,154,219 – 17,154,339
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-24.95
Consensus MFE	-22.02
Energy contribution	-23.02
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	0.88
SVM decision value	1.69
SVM RNA-class probability	0.972208
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17154219 120 - 22407834
AUUCGUAUGCCCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCCACCAAAAUGGCCAGAAGGCAAACACAAAAAACCUUUUGCAGCCCUCUCAUAUGAAU
(((((((((.............(((((..........)))))......((((((((.((........)).))))))))..(((.....(((((....)))))..)))....))))))))) ( -24.60)
>DroSec_CAF1 115081 120 - 1
AUUCGUAUGUCCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCAACCAAAAUGGCCAGAAGGCAAACACAAAAAACCUUUUGCAGCCCUGUCAUAUGAAU
(((((((((.............(((((..........)))))...(((((((((((.((........)).))))))))..(((.....(((((....)))))..)))))).))))))))) ( -26.40)
>DroSim_CAF1 127269 120 - 1
AUUCGUAUGCUCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCCACCAAAAUGGCCAGAAGGCAAACACAAAAAACCUUUUGCAGCCCUGUCAUAUGAAU
(((((((((.............(((((..........)))))...(((((((((((.((........)).))))))))..(((.....(((((....)))))..)))))).))))))))) ( -26.20)
>DroYak_CAF1 115119 120 - 1
AUUCGAAUGCCCUAGCCCGCUUUCAUAUUUCAAUUGUUAUGAUUCCAGCUGGCCAUAUUUUCCCACCAAAAUGGCCAGAAGCCAAACACAAAAAACCUUUUGCGGUCCUGUCACAUGAAU
(((((..((...(((.((((..(((((..........)))))......((((((((.((........)).)))))))).......................))))..))).))..))))) ( -22.60)
>consensus
AUUCGUAUGCCCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCCACCAAAAUGGCCAGAAGGCAAACACAAAAAACCUUUUGCAGCCCUGUCAUAUGAAU
(((((((((.............(((((..........)))))...(((((((((((.((........)).))))))))..(((.....(((((....)))))..)))))).))))))))) (-22.02 = -23.02 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	17,154,259 – 17,154,373
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.31
Mean single sequence MFE	-19.27
Consensus MFE	-15.48
Energy contribution	-15.79
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.82
Structure conservation index	0.80
SVM decision value	0.39
SVM RNA-class probability	0.717191
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17154259 114 - 22407834
UCUCAACUGCAAGUGC------ACCAAAGUUAUCCCCUUAAUUCGUAUGCCCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCCACCAAAAUGGCCAGAA
......(((..((.((------(....(((((......)))))....))).)).........(((((..........)))))...)))((((((((.((........)).)))))))).. ( -19.20)
>DroSec_CAF1 115121 114 - 1
UCUCAACUGCAAGUGC------ACCAAAGUUAUCCCCUUAAUUCGUAUGUCCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCAACCAAAAUGGCCAGAA
......(((..((..(------(....(((((......)))))....))..)).........(((((..........)))))...)))((((((((.((........)).)))))))).. ( -18.20)
>DroSim_CAF1 127309 114 - 1
UCUCAACUGCAAGUGC------ACCAAAGUUAUCCCCUUAAUUCGUAUGCUCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCCACCAAAAUGGCCAGAA
......(((..((.((------(....(((((......)))))....))).)).........(((((..........)))))...)))((((((((.((........)).)))))))).. ( -20.00)
>DroYak_CAF1 115159 120 - 1
UCUAAACUGCACUUGCACUUACACAAAAGUUAUCCCCUUAAUUCGAAUGCCCUAGCCCGCUUUCAUAUUUCAAUUGUUAUGAUUCCAGCUGGCCAUAUUUUCCCACCAAAAUGGCCAGAA
.......(((....)))...........(..(((....(((((.(((((....((....))....))))).)))))....)))..)..((((((((.((........)).)))))))).. ( -19.70)
>consensus
UCUCAACUGCAAGUGC______ACCAAAGUUAUCCCCUUAAUUCGUAUGCCCUAACCCACUUUCAUAUUUCAACUGUUAUGAUUCCAGCUGGCCAUAUUUUUCCACCAAAAUGGCCAGAA
......(((.(((((............(((((......)))))..............)))))(((((..........)))))...)))((((((((.((........)).)))))))).. (-15.48 = -15.79 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:00 2006