Locus 5753

Sequence ID	2L_DroMel_CAF1
Location	16,378,365 – 16,378,634
Length	269
Max. P	0.923095

overview

Window 0

Location	16,378,365 – 16,378,474
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.20
Mean single sequence MFE	-25.49
Consensus MFE	-17.56
Energy contribution	-19.00
Covariance contribution	1.44
Combinations/Pair	1.05
Mean z-score	-1.96
Structure conservation index	0.69
SVM decision value	0.87
SVM RNA-class probability	0.870848
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16378365 109 - 22407834
AGUGCCAACUGCCAAAUGGCCAAGGCACCAUCCGCACCCACCAUCCGCCCACCUUUCGCCCACCUUACGGCCACCUUUCGCC-----------CACCACUCCCCUUCUGGCCACGUGUGC
.(((((....(((....)))...)))))....(((((.........((.........)).........(((((.........-----------..............)))))..))))). ( -23.50)
>DroSec_CAF1 2034 109 - 1
AGUGCCAACUGCCAAAUGGCCAAGGCACCACCCGCACCCACCAUCCGCCCACCUUUCGUCCACCUUACAGCCACCUUUCGCC-----------CACCACCCCCCUUCUGGCCACGUGGGC
.(((((....(((....)))...)))))..................((((((.....((.......)).((((.........-----------..............))))...)))))) ( -24.20)
>DroSim_CAF1 75 120 - 1
AGUGCCAACUGCCAAAUGGCCAAGGCACCACCCGCACCCACCAUCCGCCCACCUUUCGUCCACCUUUCGACCACCUUUCGACCACCUUUCGUACACCACCCCCCUUCUGGCCACGUGGGC
.(((((....(((....)))...)))))..................((((((..............((((.......)))).....................((....))....)))))) ( -25.40)
>DroEre_CAF1 216 113 - 1
AGUGCCAACUGCCAAAUGGCCAAGGCAGC------GCCCACCUUUCGGCCAGCUUUCCCCCACCUUUGGGCCAGCUUUCCCCCACCCUUCGCCCACCACCCUCUG-CUGACCACGUGGUA
..(((((...(((....)))...((((((------(((........))).((((..(((........)))..))))............................)-))).))...))))) ( -28.20)
>DroYak_CAF1 2235 110 - 1
AGUGCCAACUGCCAAAUGGCCAAGGCACCAC---CACCCACCUUUCGACCACCAUCCACCCACCUUUCGGCCACCUUUCGCCCACC-------CACCAACCCCCGUUUGGCCACGUGGGA
.(((((....(((....)))...)))))...---..(((((.....((......))............(((((.............-------..............)))))..))))). ( -26.13)
>consensus
AGUGCCAACUGCCAAAUGGCCAAGGCACCACCCGCACCCACCAUCCGCCCACCUUUCGCCCACCUUUCGGCCACCUUUCGCCCACC_______CACCACCCCCCUUCUGGCCACGUGGGC
.(((((....(((....)))...))))).............................((((((.....(((((..................................)))))..)))))) (-17.56 = -19.00 +   1.44)

alignment

secondary structure

dotplot

Window 1

Location	16,378,474 – 16,378,594
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-25.54
Consensus MFE	-23.68
Energy contribution	-24.48
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.93
SVM decision value	1.15
SVM RNA-class probability	0.923095
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16378474 120 + 22407834
CGAAUGCAAUUUCAGUAAUUAAAAUAAACAACACACGAUGACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACA
.(((......))).......................((((((((.((((((.....))))))((((.(((....).))..)))).........))))))))................... ( -28.00)
>DroSec_CAF1 2143 120 + 1
CGAAUGCAAUUUCAGUAAUUAAAAUAAACAACACACGAUGACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACA
.(((......))).......................((((((((.((((((.....))))))((((.(((....).))..)))).........))))))))................... ( -28.00)
>DroSim_CAF1 195 120 + 1
CGAAUGCAAUUUCAGUAAUUAAAAUAAACAACACACGAUGACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACA
.(((......))).......................((((((((.((((((.....))))))((((.(((....).))..)))).........))))))))................... ( -28.00)
>DroEre_CAF1 329 117 + 1
CGAAUGCAAUUUCAGUAAUUAAAAUAAACAACACACGACGACGACGUGCAGUUUGACUGCAGCGACGGGCUUUUGACCAGAUCG---ACAACAUCGUCAUCAACAUAUCAUUAUCAGACA
.(((......))).......................((.(((((.((((((.....)))).((((..(((....).))...)))---.).)).))))).))................... ( -20.00)
>DroYak_CAF1 2345 120 + 1
CGAAUGCAAUUUCAGUAAUUAAAAUAAACAACACACGAUGACGAAGUGGAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACA
.(((......))).......................((((((((.(((.((.....)).)))((((.(((....).))..)))).........))))))))................... ( -23.70)
>consensus
CGAAUGCAAUUUCAGUAAUUAAAAUAAACAACACACGAUGACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACA
.(((......))).......................((((((((.((((((.....))))))((((((........)))..))).........))))))))................... (-23.68 = -24.48 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	16,378,514 – 16,378,634
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-30.84
Consensus MFE	-25.14
Energy contribution	-26.74
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.82
SVM decision value	0.41
SVM RNA-class probability	0.723972
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16378514 120 + 22407834
ACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACAAUCCUGGCAUCCAUUUGGGCCAAUUGCUUUGUCAAAAUAA
..(((((((((.....))))))....((((..(((.((((((.(((((.....)))))...............((((......)))).....))))))..)))..)))).)))....... ( -32.80)
>DroSec_CAF1 2183 120 + 1
ACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACAAUCCUGGCAUCCAUUUGGGCCAAUUGCUUUGUCAAAAUAA
..(((((((((.....))))))....((((..(((.((((((.(((((.....)))))...............((((......)))).....))))))..)))..)))).)))....... ( -32.80)
>DroSim_CAF1 235 120 + 1
ACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACAAUCCUGGCAUCCAUUUGGGCCAAUUGCUUUGUCAAAAUAA
..(((((((((.....))))))....((((..(((.((((((.(((((.....)))))...............((((......)))).....))))))..)))..)))).)))....... ( -32.80)
>DroEre_CAF1 369 117 + 1
ACGACGUGCAGUUUGACUGCAGCGACGGGCUUUUGACCAGAUCG---ACAACAUCGUCAUCAACAUAUCAUUAUCAGACAAUCCUUGCAUCCAUUUGGGCCAAUUGCUUUGUCAAAAUAA
..(((((((((.....)))))((((..(((.........(((.(---((......)))))).............................((....)))))..))))..))))....... ( -25.50)
>DroYak_CAF1 2385 120 + 1
ACGAAGUGGAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACAAUCCUUGCGUCCAUUUGGGCCAAUUGCUUUGUCAAAAUAA
((((((((((((((((.........(((........)))(((.(((((.....))))))))............))))))..)))(((.((((....)))))))..)))))))........ ( -30.30)
>consensus
ACGACGUGCAGUUUGACUGCACCGAUGGGCUUUUGACCAGAUCGACGACAACAUCGUCAUCAACAUAUCAUUAUCAGACAAUCCUGGCAUCCAUUUGGGCCAAUUGCUUUGUCAAAAUAA
..(((((((((.....))))))....((((..(((.((((((.(((((.....)))))...............((((......)))).....))))))..)))..)))).)))....... (-25.14 = -26.74 +   1.60)

alignment

secondary structure

dotplot

Window 3

Location	16,378,514 – 16,378,634
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.83
Mean single sequence MFE	-34.34
Consensus MFE	-31.38
Energy contribution	-32.86
Covariance contribution	1.48
Combinations/Pair	1.03
Mean z-score	-1.38
Structure conservation index	0.91
SVM decision value	0.72
SVM RNA-class probability	0.833025
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16378514 120 - 22407834
UUAUUUUGACAAAGCAAUUGGCCCAAAUGGAUGCCAGGAUUGUCUGAUAAUGAUAUGUUGAUGACGAUGUUGUCGUCGAUCUGGUCAAAAGCCCAUCGGUGCAGUCAAACUGCACGUCGU
.......(((...((..((((((...((.((((.(((.((((((...((((.....))))..)))))).))).)))).))..))))))..))......((((((.....))))))))).. ( -37.80)
>DroSec_CAF1 2183 120 - 1
UUAUUUUGACAAAGCAAUUGGCCCAAAUGGAUGCCAGGAUUGUCUGAUAAUGAUAUGUUGAUGACGAUGUUGUCGUCGAUCUGGUCAAAAGCCCAUCGGUGCAGUCAAACUGCACGUCGU
.......(((...((..((((((...((.((((.(((.((((((...((((.....))))..)))))).))).)))).))..))))))..))......((((((.....))))))))).. ( -37.80)
>DroSim_CAF1 235 120 - 1
UUAUUUUGACAAAGCAAUUGGCCCAAAUGGAUGCCAGGAUUGUCUGAUAAUGAUAUGUUGAUGACGAUGUUGUCGUCGAUCUGGUCAAAAGCCCAUCGGUGCAGUCAAACUGCACGUCGU
.......(((...((..((((((...((.((((.(((.((((((...((((.....))))..)))))).))).)))).))..))))))..))......((((((.....))))))))).. ( -37.80)
>DroEre_CAF1 369 117 - 1
UUAUUUUGACAAAGCAAUUGGCCCAAAUGGAUGCAAGGAUUGUCUGAUAAUGAUAUGUUGAUGACGAUGUUGU---CGAUCUGGUCAAAAGCCCGUCGCUGCAGUCAAACUGCACGUCGU
...(((((((...((((((.((((....))..))...))))))..........((.(((((..((...))..)---)))).)))))))))...((.((.(((((.....))))))).)). ( -28.90)
>DroYak_CAF1 2385 120 - 1
UUAUUUUGACAAAGCAAUUGGCCCAAAUGGACGCAAGGAUUGUCUGAUAAUGAUAUGUUGAUGACGAUGUUGUCGUCGAUCUGGUCAAAAGCCCAUCGGUGCAGUCAAACUCCACUUCGU
....((((((.......((((((...((.(((((((.(.(((((...((((.....))))..)))))).))).)))).))..))))))..((((...)).)).))))))........... ( -29.40)
>consensus
UUAUUUUGACAAAGCAAUUGGCCCAAAUGGAUGCCAGGAUUGUCUGAUAAUGAUAUGUUGAUGACGAUGUUGUCGUCGAUCUGGUCAAAAGCCCAUCGGUGCAGUCAAACUGCACGUCGU
.......(((...((..((((((...((.((((.(((.((((((...((((.....))))..)))))).))).)))).))..))))))..))......((((((.....))))))))).. (-31.38 = -32.86 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:51 2006