Locus 6379

Sequence ID	2R_DroMel_CAF1
Location	19,962,703 – 19,962,795
Length	92
Max. P	0.898935

overview

Window 4

Location	19,962,703 – 19,962,795
Length	92
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-33.48
Consensus MFE	-16.46
Energy contribution	-17.21
Covariance contribution	0.75
Combinations/Pair	1.12
Mean z-score	-2.21
Structure conservation index	0.49
SVM decision value	-0.01
SVM RNA-class probability	0.527660
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19962703 92 + 20766785
UUGCAUACGCACCGUGGGCAUGCGCAAAACGGGUUCCGAUUCCGCAGCAUUC------------CG-AAACAUCGCCCCAUUCAUAAAGCCCGGCGAUGUUUCUU--
.(((....)))((((..((....))...))))(((.((....)).)))....------------.(-((((((((((...............)))))))))))..-- ( -28.36)
>DroVir_CAF1 31628 105 + 1
UUGCAUACAUGCGGAGCGCAUGCGCCAAACGUGUUCCAAUGCCACAGCGUUUCGCCUGGCCGUUAG-AAACAUCGCGCCAUUCAUAAAACCGGGCGAUGUUCUUGC-
..(((....)))(((((((...........)))))))...((((..(((...))).)))).((.((-((.((((((.((............)))))))))))).))- ( -32.10)
>DroSec_CAF1 3861 93 + 1
UUGCAUACGCCCCGUGGGCAUGCGCAGAUCGGGUUCCGAUUCCGCAGCGUUCC-----------CG-AAACAUCGCCCCAUUCAUAAAGCGCGGCGAUGUUUCUU--
..((....((((...)))).((((..((((((...)))))).)))))).....-----------.(-((((((((((.(...........).)))))))))))..-- ( -36.00)
>DroSim_CAF1 3863 93 + 1
UUGCAUACGCCCCGUGGGCAUGCGCAGAUCGGGUUCCGAUUCCGCAGCGUUCC-----------CA-AAACAUCGCCCCAUUCAUAAAGCGCGGCGAUGUUUCUU--
..((....((((...)))).((((..((((((...)))))).)))))).....-----------..-((((((((((.(...........).))))))))))...-- ( -32.00)
>DroYak_CAF1 3828 95 + 1
UUGCAUACGCCCCGUGGGCAUGCGCGGAUCGGGUUCCGAUUCCAUGGCAUUCC-----------CG-AAACAUCGCCCCAUUCAUAAAGUGCGGCGAUGUUUCUUCC
..((((..((((...))))))))(((((((((...)))))))....)).....-----------.(-((((((((((.((((.....)))).))))))))))).... ( -38.20)
>DroAna_CAF1 3665 94 + 1
UUUCAUACGCCCUGUGGGCAUGCGCGGUCGGUGUUCCGUUUCCGAUGCAUUCC-----------AGAAAACAUCGCACCAUUCAUAAAGUGCGGCGAUGUUUCUU--
........((((...))))((((((((.(((....)))...))).)))))...-----------(((((.((((((..((((.....))))..))))))))))).-- ( -34.20)
>consensus
UUGCAUACGCCCCGUGGGCAUGCGCAGAUCGGGUUCCGAUUCCGCAGCAUUCC___________CG_AAACAUCGCCCCAUUCAUAAAGCGCGGCGAUGUUUCUU__
..((((..((((...))))))))((.....((((....))))....))...................((((((((((...............))))))))))..... (-16.46 = -17.21 +   0.75)

alignment

secondary structure

dotplot

Window 5

Location	19,962,703 – 19,962,795
Length	92
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.46
Mean single sequence MFE	-37.29
Consensus MFE	-22.52
Energy contribution	-22.75
Covariance contribution	0.23
Combinations/Pair	1.31
Mean z-score	-2.51
Structure conservation index	0.60
SVM decision value	1.01
SVM RNA-class probability	0.898935
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19962703 92 - 20766785
--AAGAAACAUCGCCGGGCUUUAUGAAUGGGGCGAUGUUU-CG------------GAAUGCUGCGGAAUCGGAACCCGUUUUGCGCAUGCCCACGGUGCGUAUGCAA
--..(((((((((((...............))))))))))-)(------------(.((((.((((((.(((...)))))))))))))..))....(((....))). ( -34.16)
>DroVir_CAF1 31628 105 - 1
-GCAAGAACAUCGCCCGGUUUUAUGAAUGGCGCGAUGUUU-CUAACGGCCAGGCGAAACGCUGUGGCAUUGGAACACGUUUGGCGCAUGCGCUCCGCAUGUAUGCAA
-(((.((((((((((((.((....)).))).)))))))))-......((((((((.....(((......)))....))))))))(((((((...))))))).))).. ( -38.10)
>DroSec_CAF1 3861 93 - 1
--AAGAAACAUCGCCGCGCUUUAUGAAUGGGGCGAUGUUU-CG-----------GGAACGCUGCGGAAUCGGAACCCGAUCUGCGCAUGCCCACGGGGCGUAUGCAA
--..(((((((((((.((.........)).))))))))))-)(-----------....)...(((((.((((...)))))))))((((((((....)).)))))).. ( -41.50)
>DroSim_CAF1 3863 93 - 1
--AAGAAACAUCGCCGCGCUUUAUGAAUGGGGCGAUGUUU-UG-----------GGAACGCUGCGGAAUCGGAACCCGAUCUGCGCAUGCCCACGGGGCGUAUGCAA
--..(((((((((((.((.........)).))))))))))-).-----------........(((((.((((...)))))))))((((((((....)).)))))).. ( -38.70)
>DroYak_CAF1 3828 95 - 1
GGAAGAAACAUCGCCGCACUUUAUGAAUGGGGCGAUGUUU-CG-----------GGAAUGCCAUGGAAUCGGAACCCGAUCCGCGCAUGCCCACGGGGCGUAUGCAA
(((.(((((((((((.((.........)).))))))))))-)(-----------((....((........))..)))..)))(((.((((((...)))))).))).. ( -42.00)
>DroAna_CAF1 3665 94 - 1
--AAGAAACAUCGCCGCACUUUAUGAAUGGUGCGAUGUUUUCU-----------GGAAUGCAUCGGAAACGGAACACCGACCGCGCAUGCCCACAGGGCGUAUGAAA
--......((((((((((((........))))).........(-----------((.((((..(((...(((....))).))).))))..)))...)))).)))... ( -29.30)
>consensus
__AAGAAACAUCGCCGCGCUUUAUGAAUGGGGCGAUGUUU_CG___________GGAACGCUGCGGAAUCGGAACCCGAUCUGCGCAUGCCCACGGGGCGUAUGCAA
.....((((((((((.((.........)).))))))))))...................((.((((...((.....))..))))))((((((...))))))...... (-22.52 = -22.75 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:35 2006