Locus 9323

Sequence ID	3R_DroMel_CAF1
Location	24,786,546 – 24,786,696
Length	150
Max. P	0.636039

overview

Window 1

Location	24,786,546 – 24,786,656
Length	110
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.32
Mean single sequence MFE	-34.13
Consensus MFE	-26.49
Energy contribution	-26.93
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.14
Structure conservation index	0.78
SVM decision value	0.21
SVM RNA-class probability	0.636039
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24786546 110 + 27905053
AAUGACAAUCAAUCAUUCAGUUAGUUGCAGCAGCAAACUUCAGCAAUUUGGGGAC---------CCCCCUCGAAAACACCGCCCCUUUUUUUGGAGAGGGGGUCAUUAGGCC-CCCGCCC
((((((.............(((.((((.((.......)).))))..(((((((..---------...))))))))))....((((((((....)))))))))))))).(((.-...))). ( -31.90)
>DroEre_CAF1 26724 109 + 1
AAUGACAAUCAAUCAUUCAGUUAGUUGCAGCAGCAAACUUCAGCAAUUUGGGGAU--------CCCCCCUCAAAAACACCGCCCA--UUUCGGGUGAGGGGGUCAUUAGGCC-CCCGCCC
(((((.......))))).((((.((((...)))).))))...((..(((((((..--------....))))))).....(((((.--....))))).(((((((....))))-))))).. ( -35.50)
>DroYak_CAF1 18626 120 + 1
AAUGACAAUCAAUCAUUCAGUUAGUUGCAGCAGCAAACUUCAGCAAUUUGGGGACUCCCCCCCCCCCCCUUAAAAACCCCGCCCACUUUUUGGGUGAGGGGGUCAUUAGGCCCCCCGCCC
..((.((((.(((......))).))))))((.((........)).....((((......)))).................)).........(((((.(((((((....)))))))))))) ( -35.00)
>consensus
AAUGACAAUCAAUCAUUCAGUUAGUUGCAGCAGCAAACUUCAGCAAUUUGGGGAC________CCCCCCUCAAAAACACCGCCCA_UUUUUGGGUGAGGGGGUCAUUAGGCC_CCCGCCC
((((((..................((((....)))).((((((....))))))............((((((.........((((.......)))))))))))))))).(((.....))). (-26.49 = -26.93 +   0.45)

alignment

secondary structure

dotplot

Window 2

Location	24,786,586 – 24,786,696
Length	110
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.32
Mean single sequence MFE	-37.50
Consensus MFE	-29.82
Energy contribution	-30.27
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-2.01
Structure conservation index	0.80
SVM decision value	0.14
SVM RNA-class probability	0.604062
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24786586 110 + 27905053
CAGCAAUUUGGGGAC---------CCCCCUCGAAAACACCGCCCCUUUUUUUGGAGAGGGGGUCAUUAGGCC-CCCGCCCUCGAGCAUUUUGCCAGCCGCAAUUCUGGUCUGUUUCACUC
..(((((((((((((---------(((((((.((((............)))).))).)))))))....(((.-...)))))))))....))))((((((......))).)))........ ( -34.60)
>DroEre_CAF1 26764 109 + 1
CAGCAAUUUGGGGAU--------CCCCCCUCAAAAACACCGCCCA--UUUCGGGUGAGGGGGUCAUUAGGCC-CCCGCCCUCGAGCAUUUUGCCAGCCGCAAUUCUGGUCUGUUUCACUC
..((((..(((((..--------..)))(((........(((((.--....))))).(((((((....))))-)))......)))))..))))((((((......))).)))........ ( -38.70)
>DroYak_CAF1 18666 120 + 1
CAGCAAUUUGGGGACUCCCCCCCCCCCCCUUAAAAACCCCGCCCACUUUUUGGGUGAGGGGGUCAUUAGGCCCCCCGCCCUCGAGCAUUUUGCCAGCCGCAAUUCUGGUCUGUUUCACUC
..((((...((((......))))......................(((...(((((.(((((((....))))))))))))..)))....))))((((((......))).)))........ ( -39.20)
>consensus
CAGCAAUUUGGGGAC________CCCCCCUCAAAAACACCGCCCA_UUUUUGGGUGAGGGGGUCAUUAGGCC_CCCGCCCUCGAGCAUUUUGCCAGCCGCAAUUCUGGUCUGUUUCACUC
..((((...((((...........))))(((........(((((.......))))).(((((((....)))).)))......)))....))))((((((......))).)))........ (-29.82 = -30.27 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:41 2006