Locus 1301

Sequence ID	2R_DroMel_CAF1
Location	5,062,594 – 5,062,697
Length	103
Max. P	0.910223

overview

Window 2

Location	5,062,594 – 5,062,697
Length	103
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	86.67
Mean single sequence MFE	-30.77
Consensus MFE	-21.52
Energy contribution	-22.15
Covariance contribution	0.63
Combinations/Pair	1.04
Mean z-score	-2.51
Structure conservation index	0.70
SVM decision value	1.07
SVM RNA-class probability	0.910223
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5062594 103 + 20766785
CGUCCAUCGACAUCGCCUCAUACCC-CGACCAAAUCGCAUUUGUUUAAAGUCCAACUUUGGACCAGAUG--------ACCAGAUGGCGAUGUGUCGGGGCAGCUACCAUUAA
.(((....)))...........(((-((((...((((((((((.(((..(((((....)))))....))--------).))))).)))))..)))))))............. ( -32.70)
>DroSec_CAF1 5460 108 + 1
CGUCCAUCGACAUCGCCUCAUACCC-CGACCAAAUCGCAUUUGUUUAAAGUCCAACUUUGGACCAGAUGACCAGAUGACCAGAUGUCGAUGUGUCGGGG---CUACCAUUAA
((.(((((((((((...((((....-(((.....)))(((((((((((((.....))))))).)))))).....))))...)))))))))).).))((.---...))..... ( -33.80)
>DroSim_CAF1 5556 103 + 1
CGUCCAUCGACAUCGCCUCAUACCC-CGACCAAACCGCAUUUGUUUAAAGUCCAACUUUGGACCAGAUG--------ACCAGAUGCCGCUGUGUCGGGGCAGCUACCAUUAA
.(((....)))...........(((-((((((....(((((((.(((..(((((....)))))....))--------).)))))))...)).)))))))............. ( -30.70)
>DroEre_CAF1 5779 96 + 1
CGUCCAUAGACAUCGCCUCAUACCCCCAACCAAAUCGCAAUUGUUUAAAGUCCAACUUUGGACCA----------------GAUGCCGAUGUGUUGGGGCAGCUACCAUUAG
.(((....)))............(((((((...((((((.((((((((((.....))))))).))----------------).)).))))..)))))))............. ( -25.90)
>consensus
CGUCCAUCGACAUCGCCUCAUACCC_CGACCAAAUCGCAUUUGUUUAAAGUCCAACUUUGGACCAGAUG________ACCAGAUGCCGAUGUGUCGGGGCAGCUACCAUUAA
.(((....)))...........(((.((((...((((((((((......(((((....)))))................)))))).))))..)))))))............. (-21.52 = -22.15 +   0.63)

alignment

secondary structure

dotplot

Window 3

Location	5,062,594 – 5,062,697
Length	103
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	86.67
Mean single sequence MFE	-34.90
Consensus MFE	-25.23
Energy contribution	-26.35
Covariance contribution	1.12
Combinations/Pair	1.03
Mean z-score	-1.72
Structure conservation index	0.72
SVM decision value	0.33
SVM RNA-class probability	0.692896
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5062594 103 - 20766785
UUAAUGGUAGCUGCCCCGACACAUCGCCAUCUGGU--------CAUCUGGUCCAAAGUUGGACUUUAAACAAAUGCGAUUUGGUCG-GGGUAUGAGGCGAUGUCGAUGGACG
...((.((..((((((((((..(((((.((.((..--------.....((((((....)))))).....)).)))))))...))))-))))).)..)).))(((....))). ( -37.80)
>DroSec_CAF1 5460 108 - 1
UUAAUGGUAG---CCCCGACACAUCGACAUCUGGUCAUCUGGUCAUCUGGUCCAAAGUUGGACUUUAAACAAAUGCGAUUUGGUCG-GGGUAUGAGGCGAUGUCGAUGGACG
...((.((.(---(((((((..((((.(((.((..(....)..))...((((((....))))))........)))))))...))))-)))).....)).))(((....))). ( -33.80)
>DroSim_CAF1 5556 103 - 1
UUAAUGGUAGCUGCCCCGACACAGCGGCAUCUGGU--------CAUCUGGUCCAAAGUUGGACUUUAAACAAAUGCGGUUUGGUCG-GGGUAUGAGGCGAUGUCGAUGGACG
...((.((..((((((((((..(((.((((.((..--------.....((((((....)))))).....)).)))).)))..))))-))))).)..)).))(((....))). ( -40.10)
>DroEre_CAF1 5779 96 - 1
CUAAUGGUAGCUGCCCCAACACAUCGGCAUC----------------UGGUCCAAAGUUGGACUUUAAACAAUUGCGAUUUGGUUGGGGGUAUGAGGCGAUGUCUAUGGACG
...((.((..(((((((..((.((((.((..----------------.((((((....)))))).........)))))).))....)))))).)..)).))(((....))). ( -27.90)
>consensus
UUAAUGGUAGCUGCCCCGACACAUCGGCAUCUGGU________CAUCUGGUCCAAAGUUGGACUUUAAACAAAUGCGAUUUGGUCG_GGGUAUGAGGCGAUGUCGAUGGACG
...((.((...(((((((((..((((.(((.((...............((((((....)))))).....)).)))))))...)))).)))))....)).))(((....))). (-25.23 = -26.35 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:41 2006