Locus 7337

Sequence ID	2L_DroMel_CAF1
Location	20,479,664 – 20,479,818
Length	154
Max. P	0.988824

overview

Window 0

Location	20,479,664 – 20,479,778
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.85
Mean single sequence MFE	-31.30
Consensus MFE	-27.50
Energy contribution	-27.78
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-1.40
Structure conservation index	0.88
SVM decision value	0.68
SVM RNA-class probability	0.819510
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20479664 114 - 22407834
GAGUGUGCGUGUGGGC------ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAAUUAAGAGGAAACACUGUGCUGCGUAAUCAUGCCACAAUAU
((((((((((((((..------..).))).))))))))))...(.(((((.(((...(((((......((.((.((((........)))).)))).)))))..))).))))))....... ( -31.00)
>DroSec_CAF1 32599 114 - 1
GAGUGUGCGUGUGAGC------ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAAUUAAGAGGAAACACUGUGCUGCGUAAUCAUGCCACAAUAU
..(((.(((((...((------(.((((.((.......(((((.....((((......)))).......)))))((((........)))).)).)))).))).....))))))))..... ( -29.90)
>DroSim_CAF1 36418 114 - 1
GAGUGUGCGUGUGGGC------ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAAUUAAGAGGAAACACUGUGCUGCGUAAUCAUGCCACAAUAU
((((((((((((((..------..).))).))))))))))...(.(((((.(((...(((((......((.((.((((........)))).)))).)))))..))).))))))....... ( -31.00)
>DroEre_CAF1 34650 112 - 1
GAGUGUGCAUGUGGG--------CCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAAUUAGGAGGAAACACUGCGCUGCGUAAUCACGGCACAAUAU
...(((((.(((((.--------..((.(.(((((...(((((.....((((......)))).......))))).(((.....)))(....)..))))).).))..)))))))))).... ( -30.50)
>DroYak_CAF1 32116 120 - 1
GAGUGUGCAUGUGGGCACCGGCACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAAUUAAGAGGAAACACUGUGCUGCGUAAUCAUGGCACAAUAU
.(((((((((((((((....)).))))).)))......(((((.....((((......)))).......)))))((((........)))))))))(((((..(....)..)))))..... ( -34.10)
>consensus
GAGUGUGCGUGUGGGC______ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAAUUAAGAGGAAACACUGUGCUGCGUAAUCAUGCCACAAUAU
((((((((((((((.........))))))...))))))))..((((((..((((((.(((.(((((.....)))))))))))))).(....)....)))).))................. (-27.50 = -27.78 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	20,479,704 – 20,479,818
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.02
Mean single sequence MFE	-27.70
Consensus MFE	-23.30
Energy contribution	-23.10
Covariance contribution	-0.20
Combinations/Pair	1.08
Mean z-score	-1.39
Structure conservation index	0.84
SVM decision value	0.21
SVM RNA-class probability	0.634936
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20479704 114 + 22407834
UUGGAAUCAUCUUUUAAUUGCCAUAUUAAGCACGCUCGAUAAGUAUACGCAGUGUGGU------GCCCACACGCACACUCCUCGCUCGCAUCCUGCACACACACUAGCACAAUGGCAAGC
.................(((((((((..((....))..))).......((((((((((------((......))))...........((.....))...)))))).))....)))))).. ( -28.70)
>DroSec_CAF1 32639 114 + 1
UUGGAAUCAUCUUUUAAUUGCCAUAUUAAGCACGCUCGAUAAGUAUACGCAGUGUGGU------GCUCACACGCACACUCCUCGCUCGCAUCCUGCACACACACUAGCACAAUGGCAAGC
.................(((((((((..((....))..))).......((((((((((------((......))))...........((.....))...)))))).))....)))))).. ( -29.20)
>DroSim_CAF1 36458 114 + 1
UUGGAAUCAUCUUUUAAUUGCCAUAUUAAGCACGCUCGAUAAGUAUACGCAGUGUGGU------GCCCACACGCACACUCCUCGCUCGCAUCCUGCACACACACUAGCACAAUGGCAAGC
.................(((((((((..((....))..))).......((((((((((------((......))))...........((.....))...)))))).))....)))))).. ( -28.70)
>DroEre_CAF1 34690 112 + 1
UUGGAAUCAUCUUUUAAUUGCCAUAUUAAGCACGCUCGAUAAGUAUACGCAGUGUGG--------CCCACAUGCACACUCUUCGCUCGCAUCCUGCACACACACAAGCACAAUGGCACGC
..................((((((((..((....))..))).......((.((((((--------(....((((.............))))...)).)))))....))....)))))... ( -20.82)
>DroYak_CAF1 32156 120 + 1
UUGGAAUCAUCUUUUAAUUGCCAUAUUAAGCACGCUCGAUAAGUAUACGCAGUGUGGUGCCGGUGCCCACAUGCACACUCUUCGCUCGCAUCCUGCACACACACAAGCACAAUGGCAAGC
.................(((((((((..((....))..))).......((.(((((((((.(((((......((.........))..))).)).)))).)))))..))....)))))).. ( -31.10)
>consensus
UUGGAAUCAUCUUUUAAUUGCCAUAUUAAGCACGCUCGAUAAGUAUACGCAGUGUGGU______GCCCACACGCACACUCCUCGCUCGCAUCCUGCACACACACUAGCACAAUGGCAAGC
.................(((((((.....((..(..(((..(((....((.((((((.........))))))))..)))..)))..)((.....))..........))...))))))).. (-23.30 = -23.10 +  -0.20)

alignment

secondary structure

dotplot

Window 2

Location	20,479,704 – 20,479,818
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.02
Mean single sequence MFE	-37.82
Consensus MFE	-35.92
Energy contribution	-36.72
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.95
SVM decision value	2.14
SVM RNA-class probability	0.988824
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20479704 114 - 22407834
GCUUGCCAUUGUGCUAGUGUGUGUGCAGGAUGCGAGCGAGGAGUGUGCGUGUGGGC------ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAA
((((((.(((.(((..........))).)))))))))..(((((((((((((((..------..).))).))))))))(((((.....((((......)))).......))))).))).. ( -38.80)
>DroSec_CAF1 32639 114 - 1
GCUUGCCAUUGUGCUAGUGUGUGUGCAGGAUGCGAGCGAGGAGUGUGCGUGUGAGC------ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAA
((((((.(((.(((..........))).)))))))))..((((((((((((((...------....))).))))))))(((((.....((((......)))).......))))).))).. ( -37.20)
>DroSim_CAF1 36458 114 - 1
GCUUGCCAUUGUGCUAGUGUGUGUGCAGGAUGCGAGCGAGGAGUGUGCGUGUGGGC------ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAA
((((((.(((.(((..........))).)))))))))..(((((((((((((((..------..).))).))))))))(((((.....((((......)))).......))))).))).. ( -38.80)
>DroEre_CAF1 34690 112 - 1
GCGUGCCAUUGUGCUUGUGUGUGUGCAGGAUGCGAGCGAAGAGUGUGCAUGUGGG--------CCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAA
(((..((((.......))).)..))).(((.(((..(((.((((((((..(((..--------...)))...)))))))).)))..)))(((......)))..............))).. ( -34.50)
>DroYak_CAF1 32156 120 - 1
GCUUGCCAUUGUGCUUGUGUGUGUGCAGGAUGCGAGCGAAGAGUGUGCAUGUGGGCACCGGCACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAA
..(((((((.(((((((.((((((((((.(((((.((.....)).)))))((((((....)).)))).))))))))))....)))))..)).....)))))))................. ( -39.80)
>consensus
GCUUGCCAUUGUGCUAGUGUGUGUGCAGGAUGCGAGCGAGGAGUGUGCGUGUGGGC______ACCACACUGCGUAUACUUAUCGAGCGUGCUUAAUAUGGCAAUUAAAAGAUGAUUCCAA
..(((((((((..(........)..))(.((((...(((.((((((((((((((.........))))))...)))))))).))).)))).).....)))))))................. (-35.92 = -36.72 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:34:04 2006