Locus 363

Sequence ID	3R_DroMel_CAF1
Location	1,398,975 – 1,399,168
Length	193
Max. P	0.878901

overview

Window 5

Location	1,398,975 – 1,399,094
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-43.12
Consensus MFE	-38.01
Energy contribution	-38.70
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-1.91
Structure conservation index	0.88
SVM decision value	0.91
SVM RNA-class probability	0.878901
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1398975 119 - 27905053
CUCGUCACACACUCUUCCACAUUGGAUCGGAUGUGGCACCAGUGCGGUGGCUA-CAGAACGGCAUUGACGCCAAGUUCGAAUUGUGCCACACGGGCACUUUGGCGAACUGGGAAAAGAGA
(((((((((..(...(((.....)))..)..))))))..((((((.((.....-....)).))))))...((.((((((....(((((.....))))).....)))))).))....))). ( -43.40)
>DroSec_CAF1 3804 119 - 1
CUCGUCACACACUCUCCCACAUCGAAUCGGAUGUGGCACCAGUGCGGUGGCUA-CAGAACGGCAUUGACGCCAAGUUCGAAUUGUGCCACACGGGCACUUUGGCGAACUGGGAAAAGAGA
...........((((((((((((......)))))(((..((((((.((.....-....)).))))))..))).((((((....(((((.....))))).....))))))))))...))). ( -44.30)
>DroSim_CAF1 3739 119 - 1
CUCGUCACACACUCUCCCACAUCGGAUCGGAUGUGGCACCAGUGCGGUGGCUA-CAGAACGGCAUUGACGCCAAGUUCGAAUUGUGCCACACGGGCACUUUGGCGAACUGGGAAAAGAGA
...........((((((((((((......)))))(((..((((((.((.....-....)).))))))..))).((((((....(((((.....))))).....))))))))))...))). ( -44.30)
>DroYak_CAF1 4043 117 - 1
CUCGUCACCCACACUCUCACAC---AUCGGAUGUGGCACCACUGCGGUGGCUCCCAGAACGGCAUUGACGCCAAGUUCGAAUUGUGCCACACGGGCACUUUAGCAAACGGGGAAAAGAGA
(((((((((((((.(((.....---...)))))))(((....)))))))))((((.(((((((......)))..)))).....(((((.....)))))...........))))...))). ( -40.50)
>consensus
CUCGUCACACACUCUCCCACAUCGGAUCGGAUGUGGCACCAGUGCGGUGGCUA_CAGAACGGCAUUGACGCCAAGUUCGAAUUGUGCCACACGGGCACUUUGGCGAACUGGGAAAAGAGA
(((((((.........(((((((......)))))))((((.....))))(((........)))..)))).((.((((((....(((((.....))))).....)))))).))....))). (-38.01 = -38.70 +   0.69)

alignment

secondary structure

dotplot

Window 6

Location	1,399,054 – 1,399,168
Length	114
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	94.15
Mean single sequence MFE	-39.00
Consensus MFE	-34.27
Energy contribution	-35.17
Covariance contribution	0.89
Combinations/Pair	1.06
Mean z-score	-1.93
Structure conservation index	0.88
SVM decision value	0.19
SVM RNA-class probability	0.628342
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1399054 114 + 27905053
GGUGCCACAUCCGAUCCAAUGUGGAAGAGUGUGUGACGAGGGCGCAGUACGUCACUUCGCCACAUCGCAACUCGGCACCAACAUCAACAGCAAGUACGCAAUACAUAAUGCUUG
((((((........(((.....))).((((.(((((.(..((((.(((.....))).)))).).)))))))))))))))...........((((((............)))))) ( -37.00)
>DroSec_CAF1 3883 114 + 1
GGUGCCACAUCCGAUUCGAUGUGGGAGAGUGUGUGACGAGGGCGCAGUACGUCACUUCGUCACUUCUCCACUUGGCCCCAACAUCAACAGCAAGUACGCAAUACAUAAUGCUUG
((.((((((((......))))).((((((...(((((((((..((.....))..)))))))))))))))....))).))...........((((((............)))))) ( -36.80)
>DroSim_CAF1 3818 114 + 1
GGUGCCACAUCCGAUCCGAUGUGGGAGAGUGUGUGACGAGGGCGCAGUACGUCACCUCGUCACUUCGCCACUCGGCACCAACAUCAACAGCAAGUACGCAAUACAUAAUGCUUG
(((((((((((......)))))....(((((.(((((((((..((.....))..))))))))).....)))))))))))...........((((((............)))))) ( -43.20)
>consensus
GGUGCCACAUCCGAUCCGAUGUGGGAGAGUGUGUGACGAGGGCGCAGUACGUCACUUCGUCACUUCGCCACUCGGCACCAACAUCAACAGCAAGUACGCAAUACAUAAUGCUUG
(((((((((((......)))))....(((((.(((((((((..((.....))..))))))))).....)))))))))))...........((((((............)))))) (-34.27 = -35.17 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:26 2006