Locus 7209

Sequence ID	3R_DroMel_CAF1
Location	18,974,152 – 18,974,375
Length	223
Max. P	0.949769

overview

Window 4

Location	18,974,152 – 18,974,264
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.47
Mean single sequence MFE	-35.23
Consensus MFE	-31.70
Energy contribution	-31.57
Covariance contribution	-0.14
Combinations/Pair	1.14
Mean z-score	-1.38
Structure conservation index	0.90
SVM decision value	0.42
SVM RNA-class probability	0.730224
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18974152 112 + 27905053
GCAGGAGAACAAGUUUCGAGUGGAAAUGCGUGUAGCGUGCAGCGUGCGAAACACUGCAGAACAUGGACACGAAUCGAGAUCGAGGCGAAAGCCUGA-CGCUGAUGCAGAUCUC-------
(((((....)..((((((.((....((((.....))))...))...)))))).))))..................((((((.((((....))))..-.((....)).))))))------- ( -36.10)
>DroSec_CAF1 85207 112 + 1
GCAGGAGAACAAGUUUCGAGUGGAAAUGCGUGUAGCGUGCAGCGUGCGAAACACUGCAGAACAUGGACACGAAUCGGGAUCGAGGCGAAAGCCUGA-CGCUGAUGCAGAUCUC-------
....((((....((((((.((....((((.....))))...))...)))))).((((......((....)).(((((..((.((((....))))))-..))))))))).))))------- ( -36.70)
>DroSim_CAF1 87000 112 + 1
GCAGGAGAACAAGUUUCGAGUGGAAAUGCGUGUAGCGUGCAGCGUGCGAAACACUGCAGAACAUGGACACGAAUCGGGAUCGAGGCGAAAGCCUGA-CGCUGAUGCAGAUCUC-------
....((((....((((((.((....((((.....))))...))...)))))).((((......((....)).(((((..((.((((....))))))-..))))))))).))))------- ( -36.70)
>DroEre_CAF1 85804 112 + 1
GCAAGAGAACAAGUUUCGAGUGGAAAUGCGUGUAGCGUGCAGCGUGCGAAACACUGCAGAACAUGGACACGAAUCGAGAUCGAGGCGAAAGCCUGA-CGCUGAUGCAGAUCUC-------
......((....((.((..(((....(((((((..((..(...)..))..)))).)))...))).)).))...))((((((.((((....))))..-.((....)).))))))------- ( -35.90)
>DroYak_CAF1 88369 110 + 1
--CAGAGAACAAGUUUCGAGUGGAAAUGCGUGUAGCGUGCAGCGUGCGAAACACUGCAGAACAUGGACACGAAUCGAGAUCGAGGCGAAAGCCUGA-CGCUGAUGCAGAUCUC-------
--....((....((.((..(((....(((((((..((..(...)..))..)))).)))...))).)).))...))((((((.((((....))))..-.((....)).))))))------- ( -35.90)
>DroAna_CAF1 87849 116 + 1
GUACAAGAACAAGUUUCAAGUGGAAAUGCGUGUAGCGUGCAGCGUGCGAAACACUGCAGAACAUGAACACAA----GAACCGAGGCGAAAGUCUGAGCUCUGGCGAGGAUCCCUGAUCCC
((...(((.(..((((((.((.....(((((((..((..(...)..))..)))).)))..)).)))).))..----......((((....))))..).))).))..(((((...))))). ( -30.10)
>consensus
GCAGGAGAACAAGUUUCGAGUGGAAAUGCGUGUAGCGUGCAGCGUGCGAAACACUGCAGAACAUGGACACGAAUCGAGAUCGAGGCGAAAGCCUGA_CGCUGAUGCAGAUCUC_______
............((.((..(((....(((((((..((..(...)..))..)))).)))...))).)).)).....((((((.((((....))))....((....)).))))))....... (-31.70 = -31.57 +  -0.14)

alignment

secondary structure

dotplot

Window 5

Location	18,974,232 – 18,974,337
Length	105
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	88.85
Mean single sequence MFE	-47.26
Consensus MFE	-33.44
Energy contribution	-34.72
Covariance contribution	1.28
Combinations/Pair	1.17
Mean z-score	-3.13
Structure conservation index	0.71
SVM decision value	1.39
SVM RNA-class probability	0.949769
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18974232 105 + 27905053
CGAGGCGAAAGCCUGACGCUGAUGCAGAUCUCCUCC----CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-GGCCAUGAUGAUGGUGGCGCGGGUCGGAGG
..((((....))))...((....))....((((..(----((((((..((.(..(....((((..(((....)))...)-)))....)..).))..)))))))..)))). ( -48.20)
>DroSec_CAF1 85287 105 + 1
CGAGGCGAAAGCCUGACGCUGAUGCAGAUCUCCUCC----CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-GGCAAUGGUGGUGGUGGCGCGGGUCGGAGG
..((((....))))...((....))....((((..(----((((((..((.(..(...(((((..(((....)))...)-))))...)..).))..)))))))..)))). ( -49.90)
>DroSim_CAF1 87080 105 + 1
CGAGGCGAAAGCCUGACGCUGAUGCAGAUCUCCUCC----CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-GGCAAUGGUGGUGGCGGCGCGGGUCGGGGG
..((((....))))...((....))....((((..(----((((((((((.(..(...(((((..(((....)))...)-))))...)..).)))))))))))..)))). ( -51.50)
>DroEre_CAF1 85884 101 + 1
CGAGGCGAAAGCCUGACGCUGAUGCAGAUCUCCUCC----CCGGGCCGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGGGUGGAAUGGUGG---CGGCGGGU--CGGUGG
..((((....))))..(((((((.(......((...----..))((((((((........(((((((((......)))))))))..)).))---))))).))--))))). ( -44.50)
>DroYak_CAF1 88447 106 + 1
CGAGGCGAAAGCCUGACGCUGAUGCAGAUCUCCUCCUCCGCCGGGCCGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-UUUAAUGGUGG---CGGCGGGUUUUGGAGG
..((((....))))...((....))......(((((((((((..((((((....((((...(((.(((....))).)))-))))..)))))---)))))))....))))) ( -42.20)
>consensus
CGAGGCGAAAGCCUGACGCUGAUGCAGAUCUCCUCC____CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG_GGCAAUGGUGGUGGCGGCGCGGGUCGGAGG
..((((....))))...((....))......(((((....((((((((((.(..(......(((.(((....))).)))........)..).))))))))))...))))) (-33.44 = -34.72 +   1.28)

alignment

secondary structure

dotplot

Window 6

Location	18,974,264 – 18,974,375
Length	111
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	88.42
Mean single sequence MFE	-40.50
Consensus MFE	-29.60
Energy contribution	-30.88
Covariance contribution	1.28
Combinations/Pair	1.16
Mean z-score	-2.11
Structure conservation index	0.73
SVM decision value	0.65
SVM RNA-class probability	0.812159
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18974264 111 + 27905053
CUCC----CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-GGCCAUGAUGAUGGUGGCGCGGGUCGGAGGCAUGAAU-UUGCCAGCAUGAAAAAUGGCAACACUUUUGC
((((----((((((..((.(..(....((((..(((....)))...)-)))....)..).))..))))))...))))(((.....-((((((..........))))))......))) ( -39.10)
>DroSec_CAF1 85319 111 + 1
CUCC----CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-GGCAAUGGUGGUGGUGGCGCGGGUCGGAGGCAUGGAU-UUGCCAGCAUGAAAAAUGGCAACACUUUUGC
((((----((((((..((.(..(...(((((..(((....)))...)-))))...)..).))..))))))...))))(((.((..-((((((..........))))))..))..))) ( -41.60)
>DroSim_CAF1 87112 111 + 1
CUCC----CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-GGCAAUGGUGGUGGCGGCGCGGGUCGGGGGCAUGGAU-UUGCCAGCAUGAAAAAUGGCAACACUUUUGC
((((----((((((((((.(..(...(((((..(((....)))...)-))))...)..).)))))))))))..)))((((.....-.))))......((((.((....)).)))).. ( -43.90)
>DroEre_CAF1 85916 107 + 1
CUCC----CCGGGCCGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGGGUGGAAUGGUGG---CGGCGGGU--CGGUGGCAUGGAU-UUGCCAGCAUGAAAAAUGGCAACACUUUUGC
....----((((.(((((.(..(.....(((((((((......)))))))))...)..)---.))))).)--)))(((((.....-.))))).....((((.((....)).)))).. ( -40.10)
>DroYak_CAF1 88479 113 + 1
CUCCUCCGCCGGGCCGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG-UUUAAUGGUGG---CGGCGGGUUUUGGAGGCAUAGAUUUUGCCAGCAUGAAAAAUGGCAACACUUUUGC
((((((((((..((((((....((((...(((.(((....))).)))-))))..)))))---)))))))....))))(((......((((((..........))))))......))) ( -37.80)
>consensus
CUCC____CCGUGCUGCCCUUGUAAAUGUCCAUCUAAAAAUAGUUGG_GGCAAUGGUGGUGGCGGCGCGGGUCGGAGGCAUGGAU_UUGCCAGCAUGAAAAAUGGCAACACUUUUGC
((((....((((((((((.(..(......(((.(((....))).)))........)..).))))))))))...))))(((......((((((..........))))))......))) (-29.60 = -30.88 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:13 2006