Locus 744

Sequence ID	2R_DroMel_CAF1
Location	3,643,835 – 3,643,954
Length	119
Max. P	0.841091

overview

Window 1

Location	3,643,835 – 3,643,926
Length	91
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	75.31
Mean single sequence MFE	-24.62
Consensus MFE	-14.86
Energy contribution	-15.53
Covariance contribution	0.67
Combinations/Pair	1.29
Mean z-score	-1.64
Structure conservation index	0.60
SVM decision value	0.75
SVM RNA-class probability	0.841091
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3643835 91 + 20766785
---------AAUCC-------AAA-------GCAAUGGCCGAUGAAGAUAUCACAUUGAACGAGGAUCAGCUCCUGGAGUCAUUGGAGGAGACGAACGGGGAGCAAGAGACUGA
---------.((((-------...-------.(((((...((((....)))).))))).....))))..((((((.(.(((.........)))...).)))))).......... ( -22.50)
>DroVir_CAF1 4407 109 + 1
UCAAACGACAAAUCAA-----UAAAAGCAAUAUAAUGGCCGAUGAAGAUAUUACUUUAAACGAGGAUCAGCUCUUGGAGUCGCUGGAGGAGACAAACGGCGAACAGGAGACUGA
................-----.................((..(((((......))))).....)).((((((((((...((((((..(....)...)))))).)))))).)))) ( -26.70)
>DroWil_CAF1 5283 91 + 1
---------AAUCA-------CAC-------ACAAUGGCCGAUGAAGAUAUUACUUUGAAUGAGGAUCAGCUGUUGGAGUCGCUGGAGGAGACAAACGGCGAGCAGGAGACUGA
---------.....-------...-------.(((((((.(((((((......))))........))).)))))))...((((((..(....)...)))))).(((....))). ( -24.90)
>DroMoj_CAF1 4712 103 + 1
--------UAAAUCAAUA---UAAAAUAAUUAUAAUGGCUGAUGAAGAUAUUACUUUAAACGAGGAUCAGCUUCUGGAGUCGCUGGAAGAGACAAACGGCGAACAGGAGACUGG
--------....(((.((---(((.....))))).)))....(((((......))))).........(((((((((...((((((...........)))))).)))))).))). ( -23.70)
>DroAna_CAF1 4120 91 + 1
---------AAUCC-------GCA-------AUAAUGGCCGAUGAAGAUAUUACACUGAAUGAGGAUCAGCUCUUGGAGUCGCUGGAGGAGACAAAUGGCGAGCAGGAGGCCGA
---------.....-------...-------....(((((...............((((.......)))).(((((...((((((..(....)...)))))).)))))))))). ( -23.30)
>DroPer_CAF1 7122 105 + 1
---------AAAACCACUCACAAAAAUUAGCAAAAUGGCUGAUGAAGAUAUCUCAUUGAACGAGGACCAGCUCUUGGAGUCGAUGGAAGAGACCAAUGGCGAGCAGGAGACUGA
---------.......(((......((((((......)))))).......((.....))..)))...(((((((((..((((.(((......))).))))...)))))).))). ( -26.60)
>consensus
_________AAACC_______AAA_______AUAAUGGCCGAUGAAGAUAUUACAUUGAACGAGGAUCAGCUCUUGGAGUCGCUGGAGGAGACAAACGGCGAGCAGGAGACUGA
..................................................................((((((((((...((((((..(....)...)))))).)))))).)))) (-14.86 = -15.53 +   0.67)

alignment

secondary structure

dotplot

Window 2

Location	3,643,846 – 3,643,954
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	81.59
Mean single sequence MFE	-28.62
Consensus MFE	-20.89
Energy contribution	-20.98
Covariance contribution	0.09
Combinations/Pair	1.36
Mean z-score	-1.38
Structure conservation index	0.73
SVM decision value	0.14
SVM RNA-class probability	0.602120
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3643846 108 + 20766785
AUGGCCGAUGAAGAUAUCACAUUGAACGAGGAUCAGCUCCUGGAGUCAUUGGAGGAGACGAACGGGGAGCAAGAGACUGAGAUCGCCACAGAGGU---CGAGGUGAGUUGG
.((..(((((.........)))))..)).......((((((.(.(((.........)))...).))))))....((((.(..(((((.....)).---)))..).)))).. ( -27.00)
>DroVir_CAF1 4436 108 + 1
AUGGCCGAUGAAGAUAUUACUUUAAACGAGGAUCAGCUCUUGGAGUCGCUGGAGGAGACAAACGGCGAACAGGAGACUGAAAUUGUGACUGA---AACAGAGGUAAGUGUG
...(((..(((((......))))).((((...((((((((((...((((((..(....)...)))))).)))))).))))..))))......---......)))....... ( -32.70)
>DroGri_CAF1 4524 108 + 1
AUGGCAGAUGAAGAUAUUACUUUAAACGAAGACCAGCUCUUGGAGUCGCUGGAUGAGACAAACGGUGAACAGGAGGCUGAAAUUGUGACUGA---AACAGAGGUGAGUGUU
.((.(((.(((((......))))).((((....(((((((((...((((((..((...))..)))))).))))).))))...))))..))).---..))............ ( -25.00)
>DroWil_CAF1 5294 108 + 1
AUGGCCGAUGAAGAUAUUACUUUGAAUGAGGAUCAGCUGUUGGAGUCGCUGGAGGAGACAAACGGCGAGCAGGAGACUGAAAUUACCAAUGA---AGUCGAGGUAAGAUAC
................(((((((((.((.....))...(((((..((((((..(....)...)))))).(((....)))......)))))..---..)))))))))..... ( -29.10)
>DroMoj_CAF1 4735 108 + 1
AUGGCUGAUGAAGAUAUUACUUUAAACGAGGAUCAGCUUCUGGAGUCGCUGGAAGAGACAAACGGCGAACAGGAGACUGGGAUUGCGACUGA---AGCAGAGGUAAGCGUA
...(((..(((((......))))).((.....((((((((((...((((((...........)))))).)))))).))))..((((......---.))))..)).)))... ( -28.80)
>DroAna_CAF1 4131 107 + 1
AUGGCCGAUGAAGAUAUUACACUGAAUGAGGAUCAGCUCUUGGAGUCGCUGGAGGAGACAAAUGGCGAGCAGGAGGCCGAGAUCACCACAGA---GACCGAGGUGAGUUG-
.(((((...............((((.......)))).(((((...((((((..(....)...)))))).))))))))))...(((((.(...---....).)))))....- ( -29.10)
>consensus
AUGGCCGAUGAAGAUAUUACUUUAAACGAGGAUCAGCUCUUGGAGUCGCUGGAGGAGACAAACGGCGAACAGGAGACUGAAAUUGCCACUGA___AACAGAGGUAAGUGUG
...(((..(((((......)))))..(((...((((((((((...((((((..(....)...)))))).)))))).))))..)))................)))....... (-20.89 = -20.98 +   0.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:06 2006