Locus 4199

Sequence ID	3R_DroMel_CAF1
Location	11,349,608 – 11,349,827
Length	219
Max. P	0.680595

overview

Window 0

Location	11,349,608 – 11,349,716
Length	108
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	92.90
Mean single sequence MFE	-39.00
Consensus MFE	-33.67
Energy contribution	-33.90
Covariance contribution	0.23
Combinations/Pair	1.06
Mean z-score	-2.05
Structure conservation index	0.86
SVM decision value	0.30
SVM RNA-class probability	0.680595
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349608 108 - 27905053
CGUCUGGUGGGCGCGGCGACGUCUGGUUCUGGCCACCAUGGCCAUCAUCAUCGUCAUCGCCACCAUGUAGAUUACCGCUUGCAAAGGCAUUGUCGCAACUCCAUCAUU
....(((((((.(((((((((..((((..(((((.....)))))..)))).))))...(((....(((((........)))))..)))...)))))...))))))).. ( -39.00)
>DroSec_CAF1 91864 102 - 1
CGUCUGGUGGGCGCGGCGAUGUCUGGUUCUGGCCACCAUGGUCAU------CGUCAUCGCCACCAUGGAGAUUAUCGUUUGCAAAGGCAUUGUCGCAACUCCAUCAUU
....(((((((.(((((((((((((((....))).(((((((...------((....))..)))))))................))))))))))))...))))))).. ( -39.90)
>DroSim_CAF1 87040 108 - 1
CGUCUGGUGGGCGCGGCGAUGUCUGGUUCUGGCCACCAUGGUCAUCAUCGUCGUCAUCGCCACCAUGGAGAUUAUCGUUUGCAAAGGCAUUGUCGCAACUCCAUCAUU
....(((((((.(((((((((((((((..(((((.....)))))..)))((((..(((.((.....)).)))...))...))..))))))))))))...))))))).. ( -38.10)
>consensus
CGUCUGGUGGGCGCGGCGAUGUCUGGUUCUGGCCACCAUGGUCAUCAUC_UCGUCAUCGCCACCAUGGAGAUUAUCGUUUGCAAAGGCAUUGUCGCAACUCCAUCAUU
....(((((((.((((((((((((.....(((((.....)))))........((.(((.((.....)).))).)).........))))))))))))...))))))).. (-33.67 = -33.90 +   0.23)

alignment

secondary structure

dotplot

Window 1

Location	11,349,716 – 11,349,827
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.62
Mean single sequence MFE	-43.20
Consensus MFE	-30.66
Energy contribution	-30.78
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-2.71
Structure conservation index	0.71
SVM decision value	0.06
SVM RNA-class probability	0.565178
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11349716 111 - 27905053
AAUCUGCAAAUUGUGCAUUUUUAAUGCAUUUCGUGUCUGCUGUUGCUG---CU------GCGUCCGCCCCCUUUAUUUUUCAUGGCCAAAGGGGGGGCGUGGCCCCAGGAGCAAUCAUGG
............((((((.....))))))..((((..((((.(((..(---(.------.((.((.((((((((.............))))))))))))..))..))).))))..)))). ( -42.62)
>DroSec_CAF1 91966 110 - 1
AAUCUGCAAAUUGUGCAUUUUUAAUGCAUUUCGUGUCUGCUGCUGCUG---CU------GCGUCCGACCCCUUUAUU-UUCAUGGCCAAAGGGGGGGCGUGGCCCCAGGAGCAAUCAUGG
............((((((.....))))))..((((..((((.(((..(---(.------.(((((..(((((((...-.........))))))))))))..))..))).))))..)))). ( -43.60)
>DroSim_CAF1 87148 117 - 1
AAUCUGCAAAUUGUGCAUUUUUAAUGCAUUUCGUGUCUGCUGCUGCUG---CUGCUGCAGCGUCCGCCCCCUUUAUUUUUCAUGGCCAAAGGGGGGGCGUGGCCCCAGGAGCAAUCAUGG
............((((((.....))))))..((((..((((.((((((---(....)))))(((((((((((((...............)))))))))).)))...)).))))..)))). ( -45.96)
>DroYak_CAF1 87135 119 - 1
AAUCUGCAAAUUGUGCAUUUUUAAUGCAUUUCGUGUCUGCUGCUGCUGAUGCUGCUGCUACGUCCGCC-CCUUUAUUUUUCAUGGCCAAAGGGAGGGCGUGGCCCCAGGAGCAAUCAUGG
.....(((....((((((.....))))))...(((((.((....)).)))))))).(((((((((..(-(((((.............)))))).))))))))).(((.((....)).))) ( -40.62)
>consensus
AAUCUGCAAAUUGUGCAUUUUUAAUGCAUUUCGUGUCUGCUGCUGCUG___CU______GCGUCCGCCCCCUUUAUUUUUCAUGGCCAAAGGGGGGGCGUGGCCCCAGGAGCAAUCAUGG
............((((((.....))))))..((((..((((.(((..............((((((..(((((((.............))))))))))))).....))).))))..)))). (-30.66 = -30.78 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:25 2006