Locus 7480

Sequence ID	X_DroMel_CAF1
Location	18,665,590 – 18,665,750
Length	160
Max. P	0.748149

overview

Window 8

Location	18,665,590 – 18,665,710
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.18
Mean single sequence MFE	-44.38
Consensus MFE	-28.94
Energy contribution	-28.46
Covariance contribution	-0.48
Combinations/Pair	1.24
Mean z-score	-2.22
Structure conservation index	0.65
SVM decision value	0.47
SVM RNA-class probability	0.748149
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18665590 120 + 22224390
AAGAGAUUCACCCAGCGGUGCCACCUCACCGAUCACAUAAAGACGGAUCGCGGCCAUGGACACGGCACUUACACCUGUGAAUUCUGCGUGCGGCCCUUCUUCCGGGCCAUCGAUCUCGAA
..(((((((((.((((.((((((...(..(((((.(........))))))..)...))).))).))..((((....))))....)).))).(((((.......)))))...))))))... ( -38.20)
>DroSec_CAF1 10640 114 + 1
AAGAGAUUCACCCAGCGGUGCCACCUCACCGAUCACAUGGGGACGGAUCGCUGCC------ACGGUAAUUACACCUGUGAAUUCUGCGUGCGGCCCUUCUUUCGGGCCAUCGAUCUCGAA
..(((((((((.(((((((.((.(((((.........)))))..))))))))).(------(((((......))).)))........))).(((((.......)))))...))))))... ( -39.30)
>DroSim_CAF1 8747 114 + 1
AAGAGAUUCACCCAGCGGUGCCACCUCACCGAUCACAUGGAGACGGGUCGCUGCC------ACGGUAAUUACACCUGUGAAUUAUGCGUGCGGCCCUUCUCUCGGGCCAUCGAUCUCGAA
..((((((..(((..(((((......))))).......(((((.(((((((((((------(((((......))).)))......))).))))))).))))).))).....))))))... ( -43.30)
>DroEre_CAF1 10950 120 + 1
AAGAGAUUCGCCCAGCGGUGCCACCUCAUCCAGCACUUGGCCACGGAUCGCGGCCAUGGGCACGGCAAGUACGUCUGCCAACUCUGCCUGUGGCCCUUCUUUCGGGCCAUCGAUCUCGAA
..(((((((((...)))((((...........)))).(((((.((((....(((((((((((.((((........)))).....))))))))))).....)))))))))..))))))... ( -48.20)
>DroYak_CAF1 10860 120 + 1
AAGAGAUUCGCCCAGCGGUGCCACCUCACCCAGCACAUGGCCACGGAUCGCGGCCAUGGGCAAGGCAACUUCGUCUGCCAACUCUGCCUGUGGCCCUUCUUCCGGGCCAUCGAUCUCGAA
..(((((.((....((((((......))))..))..((((((.((((....(((((((((((.((((........)))).....))))))))))).....)))))))))))))))))... ( -52.90)
>consensus
AAGAGAUUCACCCAGCGGUGCCACCUCACCGAUCACAUGGAGACGGAUCGCGGCCAUGG_CACGGCAAUUACACCUGUGAAUUCUGCGUGCGGCCCUUCUUUCGGGCCAUCGAUCUCGAA
..(((...((((....))))....)))................(((((((((((.....(((.(((......)))))).......))).))(((((.......)))))...)))).)).. (-28.94 = -28.46 +  -0.48)

alignment

secondary structure

dotplot

Window 9

Location	18,665,630 – 18,665,750
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.00
Mean single sequence MFE	-44.86
Consensus MFE	-31.56
Energy contribution	-32.52
Covariance contribution	0.96
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	0.70
SVM decision value	-0.02
SVM RNA-class probability	0.521433
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18665630 120 + 22224390
AGACGGAUCGCGGCCAUGGACACGGCACUUACACCUGUGAAUUCUGCGUGCGGCCCUUCUUCCGGGCCAUCGAUCUCGAACGGCAUGUGUGUGAGGAACAUCCGUAGGGCAGUCAACCUA
..((((((....(((........))).(((((((...........(((((((((((.......))))).(((....)))...)))))))))))))....))))))(((........))). ( -42.00)
>DroSec_CAF1 10680 114 + 1
GGACGGAUCGCUGCC------ACGGUAAUUACACCUGUGAAUUCUGCGUGCGGCCCUUCUUUCGGGCCAUCGAUCUCGAACGGCAUGUGAGUGAGGCACAUCCGUAGGGCAGUCAUCCUA
....((((.((((((------..(((......)))((((.((((.(((((((((((.......))))).(((....)))...))))))))))....)))).......)))))).)))).. ( -46.40)
>DroSim_CAF1 8787 114 + 1
AGACGGGUCGCUGCC------ACGGUAAUUACACCUGUGAAUUAUGCGUGCGGCCCUUCUCUCGGGCCAUCGAUCUCGAACGGCAUGUGAGUGAGGAACAUCCGUAGGGCAGUCAUCCUA
....((((.((((((------((((...((((....)))).(((((((((((((((.......))))).(((....)))...))))))..)))).......))))..)))))).)))).. ( -42.50)
>DroEre_CAF1 10990 120 + 1
CCACGGAUCGCGGCCAUGGGCACGGCAAGUACGUCUGCCAACUCUGCCUGUGGCCCUUCUUUCGGGCCAUCGAUCUCGAACGCCAUGUGAUUAAGAAGCAUCCGUAGGGCAGUCAUCCUA
((((((((.(((((((((((((.((((........)))).....))))))))))).(((((((.(((..(((....)))..)))....))..))))))))))))).))............ ( -45.80)
>DroYak_CAF1 10900 120 + 1
CCACGGAUCGCGGCCAUGGGCAAGGCAACUUCGUCUGCCAACUCUGCCUGUGGCCCUUCUUCCGGGCCAUCGAUCUCGAACGGCAUGUGUGUAAGAAGCAUCCGUGAGGCAGUCAUCCUA
.(((((((.(((((((((((((.((((........)))).....))))))))))).((((((((.(((.(((....)))..)))...)).).))))))))))))))(((.......))). ( -47.60)
>consensus
AGACGGAUCGCGGCCAUGG_CACGGCAAUUACACCUGUGAAUUCUGCGUGCGGCCCUUCUUUCGGGCCAUCGAUCUCGAACGGCAUGUGAGUGAGGAACAUCCGUAGGGCAGUCAUCCUA
....((((.((.(((......((((........(((....((((.(((((((((((.......))))).(((....)))...)))))))))).))).....))))..))).)).)))).. (-31.56 = -32.52 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:58 2006