Locus 37

Sequence ID	2R_DroMel_CAF1
Location	1,255,159 – 1,255,289
Length	130
Max. P	0.795467

overview

Window 4

Location	1,255,159 – 1,255,264
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	93.14
Mean single sequence MFE	-25.02
Consensus MFE	-19.78
Energy contribution	-19.62
Covariance contribution	-0.16
Combinations/Pair	1.10
Mean z-score	-1.44
Structure conservation index	0.79
SVM decision value	-0.05
SVM RNA-class probability	0.509377
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1255159 105 + 20766785
AGCGUUAUUUCUCAUUUUUAAUCAGUUUCUGUGCACAAUCGCGCAUUGCACGCGAUUAAAACGGCAAGAGCAUGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUGC
.(((((.....((((((..........(((.(((..(((((((.......)))))))......))))))(((((..((......))..).))))))))))))))) ( -20.60)
>DroSec_CAF1 6890 105 + 1
CGCGUUAUUUCUCAUUUUUAAUCAGUUGCUGUGCACAAUCGCGCAUUGCACGCGAUUAAAACGGCAAGAGCACGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUGC
.(((((.....((((((.((.....(((((((....(((((((.......)))))))...)))))))..(((.((........)).)))..)).))))))))))) ( -25.40)
>DroSim_CAF1 12716 105 + 1
AGCGUUAUUUCUCAUUUUUAAUCAGUUGCUGUGCACAAUCGCGCAUUGCACGCGAUUAAAACGGCAAGAGCAUGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUUC
.(((((((((.((((......((..(((((((....(((((((.......)))))))...)))))))))....)))).)))))))..))................ ( -25.60)
>DroEre_CAF1 11119 105 + 1
AGCGGUAUUUCUUAUUUUUAAUCAGUUGGUGUGCACAAUCGCGCAUUGCACGCGAUUAAAACGGCGAGAGCAUGUGAAAAGUAAUUAGCAAUGUAAAUGAAAUAC
....(((((((.....(((((((.((((((((((......)))))))).))..)))))))(((((....)).))).......................))))))) ( -24.00)
>DroYak_CAF1 10403 105 + 1
AGAGUUAUUUUUUAUUUUUAAUCCGUUGGUGUGCAGAAUCGCGCAUUGCACGCGAUUAAAACGGCGAGAGCAUGUGAAGAGUAAUUAGUAAUGUAAAUGAAAUUC
..((((((((((((((((((((((((((((((((......)))))))).))).))))))))..((....))..)))))))))))))................... ( -29.50)
>consensus
AGCGUUAUUUCUCAUUUUUAAUCAGUUGCUGUGCACAAUCGCGCAUUGCACGCGAUUAAAACGGCAAGAGCAUGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUGC
.(((((((((.((((((((((((.(((..(((((......)))))..).))..))))))))..((....))..)))).)))))))..))................ (-19.78 = -19.62 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	1,255,199 – 1,255,289
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-21.42
Consensus MFE	-18.58
Energy contribution	-19.26
Covariance contribution	0.68
Combinations/Pair	1.08
Mean z-score	-1.41
Structure conservation index	0.87
SVM decision value	0.60
SVM RNA-class probability	0.795467
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1255199 90 + 20766785
GCGCAUUGCACGCGAUUAAAACGGCAAGAGCAUGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUGCUGCGCAUUCAGUGCACAGUAAGUGG
..((((((((...(((((..(((((....)).)))......)))))))))))))........(((((.((((...)))).)))))..... ( -22.20)
>DroSec_CAF1 6930 90 + 1
GCGCAUUGCACGCGAUUAAAACGGCAAGAGCACGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUGCUGCGCAUUCAGUGCAGAGUAAGUGG
..((((((((...(((((..(((((....)).)))......)))))))))))))..........((((((.....))))))......... ( -23.70)
>DroSim_CAF1 12756 90 + 1
GCGCAUUGCACGCGAUUAAAACGGCAAGAGCAUGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUUCUGCGCAUUCAAUGCAGAGUAAGUGG
..((((((((...(((((..(((((....)).)))......))))))))))))).......((((((((.......))))))))...... ( -20.90)
>DroEre_CAF1 11159 90 + 1
GCGCAUUGCACGCGAUUAAAACGGCGAGAGCAUGUGAAAAGUAAUUAGCAAUGUAAAUGAAAUACUGCGCAUUCAGUGCAGAGUAAGUGG
..(((((((....(((((..(((((....)).)))......))))).)))))))..........((((((.....))))))......... ( -22.60)
>DroYak_CAF1 10443 89 + 1
GCGCAUUGCACGCGAUUAAAACGGCGAGAGCAUGUGAAGAGUAAUUAGUAAUGUAAAUGAAAUUCUGCGCAUACAGU-CAGAGUAAGUGG
..(((((((.....(((...(((((....)).)))....))).....))))))).......((((((.((.....))-))))))...... ( -17.70)
>consensus
GCGCAUUGCACGCGAUUAAAACGGCAAGAGCAUGUGAAAAGUAAUUUGCAAUGUAAAUGAAAUGCUGCGCAUUCAGUGCAGAGUAAGUGG
..((((((((...(((((..(((((....)).)))......)))))))))))))..........((((((.....))))))......... (-18.58 = -19.26 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:24:10 2006