Locus 3810

Sequence ID	3L_DroMel_CAF1
Location	10,991,636 – 10,991,782
Length	146
Max. P	0.998852

overview

Window 5

Location	10,991,636 – 10,991,743
Length	107
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	93.76
Mean single sequence MFE	-18.62
Consensus MFE	-15.88
Energy contribution	-16.60
Covariance contribution	0.72
Combinations/Pair	1.07
Mean z-score	-2.69
Structure conservation index	0.85
SVM decision value	3.25
SVM RNA-class probability	0.998852
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10991636 107 + 23771897
UUUCUGCAACUCCACCUACUGAUCUUUUUACCUUUCUUCCGAAACUUUUUCAGCGUCUAGUCAAUGGUCGAUUAAUUUU-CGUUUUUUAUUAAUCUUUGCAGGACCAU
.((((((((..(((...((((((((.......((((....)))).......)).))).)))...)))..(((((((...-........))))))).)))))))).... ( -17.24)
>DroSec_CAF1 123667 107 + 1
UUUCUGCAACUCCACCUACUGAUCUUUUUACCUUUCUUCCGAAACUUUUUCAGCGUCUAGUCGUUGGUCGAUUAAUUUU-CGUUUUUUAUUAAUCUUUGCAGGACCAU
.((((((((...........(((.........((((....))))......(((((......))))))))(((((((...-........))))))).)))))))).... ( -18.70)
>DroSim_CAF1 122270 106 + 1
UUUCUGCAACUCCACCUACUGAUCUUUUUACCUUUCUACCGAAACUUUUUCAGCGUCUAG-CGCUGGUCGAUUAAUUUU-CGUUUUUUAUUAAUCUUUGCAGGACCAU
.((((((((...........(((.........((((....))))......(((((.....-))))))))(((((((...-........))))))).)))))))).... ( -21.60)
>DroEre_CAF1 124462 106 + 1
UUUCUGCAACUCCACCUACUGAUCUUUUUACCUUUCUUCCGAAACUUUUUCAGCGUCUAGUCGUUGGUCGAUUAGUUUC-CUUUUUUUAAUAAUCUCUGCAGGACCA-
.(((((((.........(((((((........((((....)))).....((((((......))))))..)))))))...-.................)))))))...- ( -17.95)
>DroYak_CAF1 128236 108 + 1
UUUCUGCAACUCCACCUACUGAUCUUUUUACCUUUCCUCCGAAACUUUUUCAGCGUCUAGUCGUUGCUCGAUUAAUUUCCCUUUUUUUAUUAAUCUUUGCAGAAGCAU
(((((((((.........................................(((((......)))))...(((((((............))))))).)))))))))... ( -17.60)
>consensus
UUUCUGCAACUCCACCUACUGAUCUUUUUACCUUUCUUCCGAAACUUUUUCAGCGUCUAGUCGUUGGUCGAUUAAUUUU_CGUUUUUUAUUAAUCUUUGCAGGACCAU
.((((((((...........(((.........((((....))))......(((((......))))))))(((((((............))))))).)))))))).... (-15.88 = -16.60 +   0.72)

alignment

secondary structure

dotplot

Window 6

Location	10,991,636 – 10,991,743
Length	107
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	93.76
Mean single sequence MFE	-22.20
Consensus MFE	-18.00
Energy contribution	-18.28
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-2.57
Structure conservation index	0.81
SVM decision value	2.21
SVM RNA-class probability	0.990286
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10991636 107 - 23771897
AUGGUCCUGCAAAGAUUAAUAAAAAACG-AAAAUUAAUCGACCAUUGACUAGACGCUGAAAAAGUUUCGGAAGAAAGGUAAAAAGAUCAGUAGGUGGAGUUGCAGAAA
......((((((.(((((((........-...)))))))..((((..(((.((..((.......((((....)))).......)).)))))..))))..))))))... ( -24.44)
>DroSec_CAF1 123667 107 - 1
AUGGUCCUGCAAAGAUUAAUAAAAAACG-AAAAUUAAUCGACCAACGACUAGACGCUGAAAAAGUUUCGGAAGAAAGGUAAAAAGAUCAGUAGGUGGAGUUGCAGAAA
......((((((.(((((((........-...)))))))..(((...(((.((..((.......((((....)))).......)).)))))...)))..))))))... ( -22.54)
>DroSim_CAF1 122270 106 - 1
AUGGUCCUGCAAAGAUUAAUAAAAAACG-AAAAUUAAUCGACCAGCG-CUAGACGCUGAAAAAGUUUCGGUAGAAAGGUAAAAAGAUCAGUAGGUGGAGUUGCAGAAA
......((((((.(((((((........-...)))))))..(((.((-((....((((((.....)))))).....(((......)))))).).)))..))))))... ( -22.00)
>DroEre_CAF1 124462 106 - 1
-UGGUCCUGCAGAGAUUAUUAAAAAAAG-GAAACUAAUCGACCAACGACUAGACGCUGAAAAAGUUUCGGAAGAAAGGUAAAAAGAUCAGUAGGUGGAGUUGCAGAAA
-.....((((((..............((-....))..((.(((.((..................((((....))))(((......))).)).))).)).))))))... ( -22.20)
>DroYak_CAF1 128236 108 - 1
AUGCUUCUGCAAAGAUUAAUAAAAAAAGGGAAAUUAAUCGAGCAACGACUAGACGCUGAAAAAGUUUCGGAGGAAAGGUAAAAAGAUCAGUAGGUGGAGUUGCAGAAA
....((((((((.(((((((............)))))))......(.(((...(.(((((.....))))).)....(((......)))....))).)..)))))))). ( -19.80)
>consensus
AUGGUCCUGCAAAGAUUAAUAAAAAACG_AAAAUUAAUCGACCAACGACUAGACGCUGAAAAAGUUUCGGAAGAAAGGUAAAAAGAUCAGUAGGUGGAGUUGCAGAAA
......((((((.(((((((............)))))))..(((.(.(((.((..((.......((((....)))).......)).))))).).)))..))))))... (-18.00 = -18.28 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	10,991,675 – 10,991,782
Length	107
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	87.62
Mean single sequence MFE	-23.84
Consensus MFE	-17.50
Energy contribution	-18.54
Covariance contribution	1.04
Combinations/Pair	1.14
Mean z-score	-2.14
Structure conservation index	0.73
SVM decision value	0.77
SVM RNA-class probability	0.846258
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10991675 107 + 23771897
CGAAACUUUUUCAGCGUCUAGUCAAUGGUCGAUUAAUUUU-CGUUUUUUAUUAAUCUUUGCAGGACCAUCCUGCAUAUGACCGUUUAAUAGGUACUUCAGUUUUUAUG
.((((((.....((..((((...((((((((((((((...-........)))))))..((((((.....))))))...)))))))...))))..))..)))))).... ( -29.30)
>DroSec_CAF1 123706 107 + 1
CGAAACUUUUUCAGCGUCUAGUCGUUGGUCGAUUAAUUUU-CGUUUUUUAUUAAUCUUUGCAGGACCAUCCUGCAUAUGACUGUUUAAUAGGUACUUCAGUUUUUAUG
.((((((.....((..((((.....((((((((((((...-........)))))))..((((((.....))))))...))))).....))))..))..)))))).... ( -24.30)
>DroSim_CAF1 122309 106 + 1
CGAAACUUUUUCAGCGUCUAG-CGCUGGUCGAUUAAUUUU-CGUUUUUUAUUAAUCUUUGCAGGACCAUCCUGCAUAUGACUUUUUAAUAGGUACUUCAGUUUUUAUG
.((((((....(((((.....-)))))((((((((((...-........)))))))..((((((.....))))))...))).................)))))).... ( -26.70)
>DroEre_CAF1 124501 98 + 1
CGAAACUUUUUCAGCGUCUAGUCGUUGGUCGAUUAGUUUC-CUUUUUUUAAUAAUCUCUGCAGGACCA---------UGAGUGUUUAAUGGGUACUCAAGUUUUUAUG
.((((((...((((((......))))))......))))))-....................(((((..---------((((((..(...)..)))))).))))).... ( -17.20)
>DroYak_CAF1 128275 108 + 1
CGAAACUUUUUCAGCGUCUAGUCGUUGCUCGAUUAAUUUCCCUUUUUUUAUUAAUCUUUGCAGAAGCAUCCUGCUUAUGAGUAUUUAAUGGGUACUCAAGUUUUUACG
.((((((.....((((....((..((((..(((((((............)))))))...))))..))....))))..((((((((.....)))))))))))))).... ( -21.70)
>consensus
CGAAACUUUUUCAGCGUCUAGUCGUUGGUCGAUUAAUUUU_CGUUUUUUAUUAAUCUUUGCAGGACCAUCCUGCAUAUGACUGUUUAAUAGGUACUUCAGUUUUUAUG
.((((((.....((..((((.....((((((((((((............)))))))...(((((.....)))))....))))).....))))..))..)))))).... (-17.50 = -18.54 +   1.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:10 2006