Locus 995

Sequence ID	3L_DroMel_CAF1
Location	2,963,817 – 2,964,078
Length	261
Max. P	0.997693

overview

Window 8

Location	2,963,817 – 2,963,919
Length	102
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	93.80
Mean single sequence MFE	-35.22
Consensus MFE	-27.50
Energy contribution	-28.26
Covariance contribution	0.76
Combinations/Pair	1.10
Mean z-score	-2.78
Structure conservation index	0.78
SVM decision value	1.77
SVM RNA-class probability	0.976644
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963817 102 + 23771897
CAAUUCCUCAAAUUAAGUAAAGUGAGUAGGGGAAUCCCCUUUUCCAUUUAAAUUUGCAUAAGAGGCAUCGGCGAAAGC------GGAUGAGGAUGCGGAUGGGUUGCA
((((((...........((((..(((.(((((...))))).)))..)))).((((((((......((((.((....))------.))))...)))))))))))))).. ( -31.40)
>DroSec_CAF1 192460 108 + 1
CAAUUCCUCAAAUUAAGUAAAGUGAGUAGGGGAAUCCCCUUUUCCAUUUAAAUUUGCAUAAGAGGCAUCGGCGAAUGCGGAUGCGGAUGAGGAUGCGGAUGGGUUGCA
....((((((......(((((..(((.(((((...))))).)))........))))).......(((((.((....)).)))))...))))))(((((.....))))) ( -31.20)
>DroSim_CAF1 178569 108 + 1
CAAUUCCUCAAAUUAAGUAAAGUGAGUAGGGGAAUCCCCUUUUCCAUUUAAAUUUGCAUAAGAGGCAUCGGCGAAUGCGGAUGCGGAUGAGGAUGCGGAUGGGUUGCA
....((((((......(((((..(((.(((((...))))).)))........))))).......(((((.((....)).)))))...))))))(((((.....))))) ( -31.20)
>DroEre_CAF1 200551 108 + 1
CAAUUCCUCAAAUUAAGCAAAGUGGAUAGGGGAAUCCCCUUUUCCAUUUAAAUUUGCAUAAGAGGCAUCGGCGAAGGCGGAUGCCGUUGAGGAUGCGGAUGGGUUGCA
....(((((((.....((((((((((.(((((....))))).))))).....)))))......((((((.((....)).)))))).)))))))(((((.....))))) ( -45.90)
>DroYak_CAF1 204769 108 + 1
CAAUACCUCAAAUUAAGUAAAGUGGAUAGGGGAAUCCCCUUUUCCAUUUAAAUUUGCAUAAGAGGCAUCGACGGAUGCGGAUGCGGAUGAGGAUGCGGAUGGGUUGCA
.....((((..........(((((((.(((((....))))).)))))))..((((((((.....(((((....)))))..)))))))))))).(((((.....))))) ( -36.40)
>consensus
CAAUUCCUCAAAUUAAGUAAAGUGAGUAGGGGAAUCCCCUUUUCCAUUUAAAUUUGCAUAAGAGGCAUCGGCGAAUGCGGAUGCGGAUGAGGAUGCGGAUGGGUUGCA
....((((((......(((((..(((.(((((...))))).)))........))))).......(((((.((....)).)))))...))))))(((((.....))))) (-27.50 = -28.26 +   0.76)

alignment

secondary structure

dotplot

Window 9

Location	2,963,817 – 2,963,919
Length	102
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	93.80
Mean single sequence MFE	-27.04
Consensus MFE	-21.96
Energy contribution	-22.60
Covariance contribution	0.64
Combinations/Pair	1.11
Mean z-score	-2.54
Structure conservation index	0.81
SVM decision value	2.18
SVM RNA-class probability	0.989831
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963817 102 - 23771897
UGCAACCCAUCCGCAUCCUCAUCC------GCUUUCGCCGAUGCCUCUUAUGCAAAUUUAAAUGGAAAAGGGGAUUCCCCUACUCACUUUACUUAAUUUGAGGAAUUG
(((.........)))(((((((((------((....))...(((.......))).........)))..(((((...))))).................)))))).... ( -20.80)
>DroSec_CAF1 192460 108 - 1
UGCAACCCAUCCGCAUCCUCAUCCGCAUCCGCAUUCGCCGAUGCCUCUUAUGCAAAUUUAAAUGGAAAAGGGGAUUCCCCUACUCACUUUACUUAAUUUGAGGAAUUG
(((.........)))((((((((((((((.((....)).)))))...(((........)))..)))..(((((...))))).................)))))).... ( -26.60)
>DroSim_CAF1 178569 108 - 1
UGCAACCCAUCCGCAUCCUCAUCCGCAUCCGCAUUCGCCGAUGCCUCUUAUGCAAAUUUAAAUGGAAAAGGGGAUUCCCCUACUCACUUUACUUAAUUUGAGGAAUUG
(((.........)))((((((((((((((.((....)).)))))...(((........)))..)))..(((((...))))).................)))))).... ( -26.60)
>DroEre_CAF1 200551 108 - 1
UGCAACCCAUCCGCAUCCUCAACGGCAUCCGCCUUCGCCGAUGCCUCUUAUGCAAAUUUAAAUGGAAAAGGGGAUUCCCCUAUCCACUUUGCUUAAUUUGAGGAAUUG
(((.........)))(((((((.((((((.((....)).))))))..(((.(((((......((((..(((((...))))).)))).))))).))).))))))).... ( -34.90)
>DroYak_CAF1 204769 108 - 1
UGCAACCCAUCCGCAUCCUCAUCCGCAUCCGCAUCCGUCGAUGCCUCUUAUGCAAAUUUAAAUGGAAAAGGGGAUUCCCCUAUCCACUUUACUUAAUUUGAGGUAUUG
(((.........))).(((((...((((..(((((....))))).....)))).....((((((((..(((((...))))).)))).)))).......)))))..... ( -26.30)
>consensus
UGCAACCCAUCCGCAUCCUCAUCCGCAUCCGCAUUCGCCGAUGCCUCUUAUGCAAAUUUAAAUGGAAAAGGGGAUUCCCCUACUCACUUUACUUAAUUUGAGGAAUUG
(((.........)))((((((...(((((.((....)).)))))..............(((((((...(((((...)))))..))).)))).......)))))).... (-21.96 = -22.60 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	2,963,919 – 2,964,039
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.83
Mean single sequence MFE	-31.10
Consensus MFE	-28.86
Energy contribution	-28.86
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.93
SVM decision value	1.69
SVM RNA-class probability	0.972038
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963919 120 + 23771897
GUGUAAUUGGGCGAAGUGAAAUUGCGUUAAUAUUUAACAAGCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUAGUCCUUCGGGGCAAAGUGCGAA
.(((..((((((...((......))((((.....))))..))).((....)).)))..)))...((((((................((((....))))((((....))))..)))))).. ( -32.40)
>DroSec_CAF1 192568 120 + 1
GUGUAAUUGGGCGAAGUGAAAUUGCGUUAAUAUUUAACAAGCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAA
.(((..((((((...((......))((((.....))))..))).((....)).)))..)))...((((((...(((.....(((((((((....))).))))))....))).)))))).. ( -31.00)
>DroSim_CAF1 178677 120 + 1
GUGUAAUUGGGCGAAGUGAAAUUGCGUUAAUAUUUAACAAGCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAA
.(((..((((((...((......))((((.....))))..))).((....)).)))..)))...((((((...(((.....(((((((((....))).))))))....))).)))))).. ( -31.00)
>DroEre_CAF1 200659 120 + 1
GUGUAAUUGGGCGAAGUGAAAUUGCGUUAAUAUUUAACAAGCCGGCGAAAGUGCAAAAGCGAAGCGCAUCAAAUGGGGAAAAGGGAUACGGAAGCGUCGUCCUUCGGGGCAAAGUGCGAA
......(((.((((.(((...((((((((.....))))..((..((....))))....))))..))).))..............((..(....)..))((((....))))...)).))). ( -30.30)
>DroYak_CAF1 204877 120 + 1
GUGUAAUUGGGCGAAGUGAAAUUGCGUUAAUAUUUAACAAGCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGGGCAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAA
......(((.((...(((...((((((((.....))))..((..((....))))....))))..))).........((...(((((((((....))).))))))....))...)).))). ( -30.80)
>consensus
GUGUAAUUGGGCGAAGUGAAAUUGCGUUAAUAUUUAACAAGCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAA
......(((.((.............((((.....))))..(((.(((....(((....)))...)))..............(((((((((....))).))))))...)))...)).))). (-28.86 = -28.86 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	2,963,959 – 2,964,078
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.40
Mean single sequence MFE	-39.94
Consensus MFE	-34.44
Energy contribution	-34.60
Covariance contribution	0.16
Combinations/Pair	1.09
Mean z-score	-2.39
Structure conservation index	0.86
SVM decision value	2.91
SVM RNA-class probability	0.997693
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2963959 119 + 23771897
GCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUAGUCCUUCGGGGCAAAGUGCGAAAUUAUGCGGAGUUCAGGGAGAUCCGCA-AGCCCUUUCCUU
((..((....))((....))...))((((...))))(((((.(((.((((....))))((((....))))..............((((((.(((...))).))))))-..)))))))).. ( -42.20)
>DroSec_CAF1 192608 119 + 1
GCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAAAUUAUGCGGAAUUCAGGGAGAUCCGCA-AACCCCUUGCUU
((..((....))))..((((....(((((...)))))...(((((..(((....))).((((....))))..............((((((.(((...))).))))))-...))))))))) ( -40.50)
>DroSim_CAF1 178717 119 + 1
GCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAAAUUAUGCGGAAUUCAGGGAGAUCCGCA-AACCCUUUGCUU
((..((....))))..((((((((((((((...(((.....(((((((((....))).))))))....))).))))))......((((((.(((...))).))))))-....)))))))) ( -42.10)
>DroEre_CAF1 200699 120 + 1
GCCGGCGAAAGUGCAAAAGCGAAGCGCAUCAAAUGGGGAAAAGGGAUACGGAAGCGUCGUCCUUCGGGGCAAAGUGCGAAAUUAUGCGGAAUUCAGGGAAAUCCGCAGAACCCUUUCCUU
....(((....(((....)))...))).......(((((((.(((..(((....))).((((....))))..............((((((.(((...))).))))))...)))))))))) ( -38.60)
>DroYak_CAF1 204917 120 + 1
GCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGGGCAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAAUUUAUGCGGAAUUCAGGGCGAUCUGCAAAACCCUUUCCUU
(((.((....))......(((...)))........))).((((((..(((....))).((((....))))..............((((((..((.....))))))))...)))))).... ( -36.30)
>consensus
GCCAGCGAAAGUGCAAAAGCGAAGCGCAUUAAAUGCGGAAAAGGGAUACGGAAACGUCGUCCUUCGGGGCAAAGUGCGAAAUUAUGCGGAAUUCAGGGAGAUCCGCA_AACCCUUUCCUU
....(((....(((....)))...))).......(((((..(((((((((....))).)))))).(((((.....)).......((((((.(((...))).))))))...)))))))).. (-34.44 = -34.60 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:26 2006