Locus 3938

Sequence ID	2L_DroMel_CAF1
Location	11,485,244 – 11,485,364
Length	120
Max. P	0.980452

overview

Window 7

Location	11,485,244 – 11,485,364
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-38.23
Consensus MFE	-31.30
Energy contribution	-32.17
Covariance contribution	0.88
Combinations/Pair	1.08
Mean z-score	-2.94
Structure conservation index	0.82
SVM decision value	1.86
SVM RNA-class probability	0.980452
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11485244 120 + 22407834
CAUCACCCACACGGAGGUCCACCUCCCCCUCGUCACCAUCAUCACCAUCGUGGCAGACAUGGUGCUGGUGGACGCUGUGGACACGGACACCAGCACCAGCCUUUUCCACCACCGCCUCAU
............(((((....))))).......................((((.(((..(((((((((((..((.((....))))..)))))))))))...))).))))........... ( -42.10)
>DroSec_CAF1 49066 120 + 1
CAUCACCCACACGGAGGUCCGCCACCCCCUCGUCACCAUCACCACCAUCGUGGCAGACAUGGUGGUGGUAGACACUGUGGACACGGACCCCAGCACCAGCCUUUUCCACCACCCCCUCAU
............((.((((((((((......(((......((((((((((((.....)))))))))))).)))...))))...)))))))).((....)).................... ( -38.20)
>DroSim_CAF1 52848 120 + 1
CAUCACCCACACGGAGGUCCGCCUCCCCCUCGUCACCAUCACCACCAUCGUGGCAGACAUGGUGGUGGUAGACACUGUGGACACGGACCCCAGCACCAGCCUUUUCCACCACCCCAUCAU
......(((((.(((((....))))).....(((......((((((((((((.....)))))))))))).)))..)))))....(((.....((....))....)))............. ( -39.80)
>DroYak_CAF1 54726 114 + 1
CACCACCCGCCUGGAGGUCCGCCUCCCCCUCGCCAUCACCACCACCAUCGUGGCAGACAUGGUAGUGGUAGACACUGUGGACACGGAC------ACCAGCGUUUUCCACCACCCCAUCAU
.......(((.(((..(((((..(((....((...(((((((.(((((.((.....))))))).))))).))...)).)))..)))))------.))))))................... ( -32.80)
>consensus
CAUCACCCACACGGAGGUCCGCCUCCCCCUCGUCACCAUCACCACCAUCGUGGCAGACAUGGUGGUGGUAGACACUGUGGACACGGACCCCAGCACCAGCCUUUUCCACCACCCCAUCAU
......((((..(((((....)))))..............((((((((((((.....)))))))))))).......))))....(((.....((....))....)))............. (-31.30 = -32.17 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	11,485,244 – 11,485,364
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.00
Mean single sequence MFE	-50.65
Consensus MFE	-41.09
Energy contribution	-41.52
Covariance contribution	0.44
Combinations/Pair	1.21
Mean z-score	-2.05
Structure conservation index	0.81
SVM decision value	0.95
SVM RNA-class probability	0.888245
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11485244 120 - 22407834
AUGAGGCGGUGGUGGAAAAGGCUGGUGCUGGUGUCCGUGUCCACAGCGUCCACCAGCACCAUGUCUGCCACGAUGGUGAUGAUGGUGACGAGGGGGAGGUGGACCUCCGUGUGGGUGAUG
.....((.((.((((...(((((((((((((((..(((.......)))..))))))))))).)))).)))).)).))...........(.(.(.(((((....))))).).).)...... ( -54.60)
>DroSec_CAF1 49066 120 - 1
AUGAGGGGGUGGUGGAAAAGGCUGGUGCUGGGGUCCGUGUCCACAGUGUCUACCACCACCAUGUCUGCCACGAUGGUGGUGAUGGUGACGAGGGGGUGGCGGACCUCCGUGUGGGUGAUG
....................(((.(..(.(((((((((..((.(..((((.((((.(((((((((......))).)))))).))))))))..).))..))))))))).)..).))).... ( -47.60)
>DroSim_CAF1 52848 120 - 1
AUGAUGGGGUGGUGGAAAAGGCUGGUGCUGGGGUCCGUGUCCACAGUGUCUACCACCACCAUGUCUGCCACGAUGGUGGUGAUGGUGACGAGGGGGAGGCGGACCUCCGUGUGGGUGAUG
....................(((.(..(.(((((((((.(((.(..((((.((((.(((((((((......))).)))))).))))))))..).))).))))))))).)..).))).... ( -51.90)
>DroYak_CAF1 54726 114 - 1
AUGAUGGGGUGGUGGAAAACGCUGGU------GUCCGUGUCCACAGUGUCUACCACUACCAUGUCUGCCACGAUGGUGGUGGUGAUGGCGAGGGGGAGGCGGACCUCCAGGCGGGUGGUG
...................((((((.------((((((.(((.(..((((((((((((((((((.....)).))))))))))))..))))..).))).))))))..))).)))....... ( -48.50)
>consensus
AUGAGGGGGUGGUGGAAAAGGCUGGUGCUGGGGUCCGUGUCCACAGUGUCUACCACCACCAUGUCUGCCACGAUGGUGGUGAUGGUGACGAGGGGGAGGCGGACCUCCGUGUGGGUGAUG
....................(((.(..(.(((((((((.(((.(..(((((..(((((((((((.....)).)))))))))...).))))..).))).))))))))).)..).))).... (-41.09 = -41.52 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:13 2006