Locus 2579

Sequence ID	X_DroMel_CAF1
Location	6,912,837 – 6,913,027
Length	190
Max. P	0.893216

overview

Window 1

Location	6,912,837 – 6,912,947
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.65
Mean single sequence MFE	-22.97
Consensus MFE	-19.62
Energy contribution	-20.75
Covariance contribution	1.12
Combinations/Pair	1.05
Mean z-score	-1.42
Structure conservation index	0.85
SVM decision value	0.06
SVM RNA-class probability	0.565937
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6912837 110 + 22224390
CAGACAAACUCACGUUUUCGUUCUUACUGUUUUAUCAGCCGUCUGGCAUGGCAUUUACAUAU----------AAUCGAACGAUUCAGUGUGUUUGGGUUUUUUUUUUAUAUAUAUUGUUU
....(((((.(((....((((((....((......))(((((.....)))))..........----------....))))))....))).)))))......................... ( -23.00)
>DroSec_CAF1 37200 105 + 1
CAGACAAACUCACGUUUUCGUUCUUACUGUUUUAUCAGCCGUCUGGCAAGGCAUUUACAUAU----------AAUCGAACGAUUCAGUGUGUUUGUGCUUUUUUU-----UAUAUGGUUU
...((((((.(((....((((((...(((......)))..((((....))))..........----------....))))))....))).)))))).........-----.......... ( -24.60)
>DroSim_CAF1 21350 105 + 1
CAGACAAACUCACGUUUUCGUUCUUACUGUUUUAUCAGCAGUCUGGCAAGGCAUUUACAUAU----------AAUCGAACGAUUCAGUGUGUUUGGGUUUUUUUU-----UAUAUUGUUU
....(((((.(((....((((((...(((......)))..((((....))))..........----------....))))))....))).)))))..........-----.......... ( -23.50)
>DroYak_CAF1 41112 117 + 1
CAGGCAAUCUCACGUUUUCGUUGUUACUGUUUUAUCAGCCGUCUGGCAAGGCAUUUACAUAUACAUAUAUACAAUCGAACGAUUUAGUGUGUUUGCGUCUUGUUUUCGU---UAUUUUUG
...((((.(.(((....(((((((...((((((..(((....)))..))))))...))((((....)))).......)))))....))).).)))).............---........ ( -20.80)
>consensus
CAGACAAACUCACGUUUUCGUUCUUACUGUUUUAUCAGCCGUCUGGCAAGGCAUUUACAUAU__________AAUCGAACGAUUCAGUGUGUUUGGGUUUUUUUU_____UAUAUUGUUU
...((((((.(((....((((((...(((......)))..((((....))))........................))))))....))).))))))........................ (-19.62 = -20.75 +   1.12)

alignment

secondary structure

dotplot

Window 2

Location	6,912,837 – 6,912,947
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.65
Mean single sequence MFE	-19.68
Consensus MFE	-15.60
Energy contribution	-16.73
Covariance contribution	1.12
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.79
SVM decision value	0.25
SVM RNA-class probability	0.652804
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6912837 110 - 22224390
AAACAAUAUAUAUAAAAAAAAAACCCAAACACACUGAAUCGUUCGAUU----------AUAUGUAAAUGCCAUGCCAGACGGCUGAUAAAACAGUAAGAACGAAAACGUGAGUUUGUCUG
.........................(((((.(((....((((((....----------...(((...((.((.(((....))))).))..)))....))))))....))).))))).... ( -19.10)
>DroSec_CAF1 37200 105 - 1
AAACCAUAUA-----AAAAAAAGCACAAACACACUGAAUCGUUCGAUU----------AUAUGUAAAUGCCUUGCCAGACGGCUGAUAAAACAGUAAGAACGAAAACGUGAGUUUGUCUG
..........-----......((.((((((.(((....((((((....----------....((((.....))))......((((......))))..))))))....))).)))))))). ( -21.10)
>DroSim_CAF1 21350 105 - 1
AAACAAUAUA-----AAAAAAAACCCAAACACACUGAAUCGUUCGAUU----------AUAUGUAAAUGCCUUGCCAGACUGCUGAUAAAACAGUAAGAACGAAAACGUGAGUUUGUCUG
..........-----..........(((((.(((....((((((....----------....((((.....)))).....(((((......))))).))))))....))).))))).... ( -19.40)
>DroYak_CAF1 41112 117 - 1
CAAAAAUA---ACGAAAACAAGACGCAAACACACUAAAUCGUUCGAUUGUAUAUAUGUAUAUGUAAAUGCCUUGCCAGACGGCUGAUAAAACAGUAACAACGAAAACGUGAGAUUGCCUG
........---.............((((.(.(((....(((((..(((((......((((......))))...(((....))).......)))))...)))))....))).).))))... ( -19.10)
>consensus
AAACAAUAUA_____AAAAAAAACCCAAACACACUGAAUCGUUCGAUU__________AUAUGUAAAUGCCUUGCCAGACGGCUGAUAAAACAGUAAGAACGAAAACGUGAGUUUGUCUG
........................((((((.(((....((((((..................((((.....))))......((((......))))..))))))....))).))))))... (-15.60 = -16.73 +   1.12)

alignment

secondary structure

dotplot

Window 3

Location	6,912,877 – 6,912,987
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.70
Mean single sequence MFE	-25.18
Consensus MFE	-18.27
Energy contribution	-18.77
Covariance contribution	0.50
Combinations/Pair	1.14
Mean z-score	-2.01
Structure conservation index	0.73
SVM decision value	0.98
SVM RNA-class probability	0.893216
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6912877 110 + 22224390
GUCUGGCAUGGCAUUUACAUAU----------AAUCGAACGAUUCAGUGUGUUUGGGUUUUUUUUUUAUAUAUAUUGUUUUAGAUUCUUUUUUCGUUUUGGCUUUUGCCGAGACACGGGA
((((((((.(((....((((((----------((..(((.(((((((.....))))))).)))..))))))...........((........))))....)))..)))).))))...... ( -24.40)
>DroSec_CAF1 37240 105 + 1
GUCUGGCAAGGCAUUUACAUAU----------AAUCGAACGAUUCAGUGUGUUUGUGCUUUUUUU-----UAUAUGGUUUUUGAUUAUUUUUUCGUUUUGGCAUUUGCCGAGACACCGGA
.(((((.(((((((..((((((----------((((....))))..))))))..)))))))....-----........................((((((((....)))))))).))))) ( -31.30)
>DroSim_CAF1 21390 105 + 1
GUCUGGCAAGGCAUUUACAUAU----------AAUCGAACGAUUCAGUGUGUUUGGGUUUUUUUU-----UAUAUUGUUUUUGAUUUUUUUUUCGUUUUGGCAUUUGCCGAGACACCGGA
.(((((.(((((....((((((----------((((....))))..))))))....)))))....-----........................((((((((....)))))))).))))) ( -25.20)
>DroYak_CAF1 41152 117 + 1
GUCUGGCAAGGCAUUUACAUAUACAUAUAUACAAUCGAACGAUUUAGUGUGUUUGCGUCUUGUUUUCGU---UAUUUUUGUUUCUUUUUUUUUUAUUUCGACUUUUGCCGAGACAUCGGC
(((.((((((((((......)).((.((((((((((....))))..)))))).)).))))))))...(.---.((....))..)...............)))....(((((....))))) ( -19.80)
>consensus
GUCUGGCAAGGCAUUUACAUAU__________AAUCGAACGAUUCAGUGUGUUUGGGUUUUUUUU_____UAUAUUGUUUUUGAUUUUUUUUUCGUUUUGGCAUUUGCCGAGACACCGGA
.(((((.(((((....((((((..........((((....))))..))))))....))))).................................((((((((....)))))))).))))) (-18.27 = -18.77 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	6,912,907 – 6,913,027
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.71
Mean single sequence MFE	-27.60
Consensus MFE	-19.86
Energy contribution	-20.80
Covariance contribution	0.94
Combinations/Pair	1.11
Mean z-score	-2.13
Structure conservation index	0.72
SVM decision value	0.94
SVM RNA-class probability	0.886858
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6912907 120 + 22224390
GAUUCAGUGUGUUUGGGUUUUUUUUUUAUAUAUAUUGUUUUAGAUUCUUUUUUCGUUUUGGCUUUUGCCGAGACACGGGAGAGUAAUUAAUACAGAAUUACAAGCUGAAACUGAUUGAUU
...(((((..((((.(((((.........................(((((..(.((((((((....)))))))))..)))))((((((.......))))))))))).))))..))))).. ( -28.40)
>DroSec_CAF1 37270 115 + 1
GAUUCAGUGUGUUUGUGCUUUUUUU-----UAUAUGGUUUUUGAUUAUUUUUUCGUUUUGGCAUUUGCCGAGACACCGGAGAGUAAUUAAUACAGAAUUACAAGCUGAAACUGAUUGAUU
...(((((..(((((((.((((...-----......((..(((((((((((((.((((((((....))))))))...))))))))))))).)))))).)))))))....)))))...... ( -30.30)
>DroSim_CAF1 21420 115 + 1
GAUUCAGUGUGUUUGGGUUUUUUUU-----UAUAUUGUUUUUGAUUUUUUUUUCGUUUUGGCAUUUGCCGAGACACCGGAGAGUAAUGCAAACAGAAUUACAAGCUGAAACUGAUUGAUG
...(((((..(((((...((((.((-----(.((((((((((((........))((((((((....))))))))....)))))))))).))).))))...)))))....)))))...... ( -27.40)
>DroYak_CAF1 41192 117 + 1
GAUUUAGUGUGUUUGCGUCUUGUUUUCGU---UAUUUUUGUUUCUUUUUUUUUUAUUUCGACUUUUGCCGAGACAUCGGCGAGUAAUUGAUGCAGAAUUACAAGCUGAAACUGAUUGAUU
..((((((.((((((((((......(((.---.((...................))..)))..((((((((....)))))))).....)))))))....))).))))))........... ( -24.31)
>consensus
GAUUCAGUGUGUUUGGGUUUUUUUU_____UAUAUUGUUUUUGAUUUUUUUUUCGUUUUGGCAUUUGCCGAGACACCGGAGAGUAAUUAAUACAGAAUUACAAGCUGAAACUGAUUGAUU
...(((((..((((.(((((..................................((((((((....))))))))........((((((.......))))))))))).))))..))))).. (-19.86 = -20.80 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:13 2006