Locus 6879

Sequence ID	3R_DroMel_CAF1
Location	18,187,321 – 18,187,481
Length	160
Max. P	0.696254

overview

Window 7

Location	18,187,321 – 18,187,441
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.56
Mean single sequence MFE	-43.17
Consensus MFE	-31.84
Energy contribution	-31.15
Covariance contribution	-0.69
Combinations/Pair	1.47
Mean z-score	-1.44
Structure conservation index	0.74
SVM decision value	0.21
SVM RNA-class probability	0.636488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18187321 120 - 27905053
AUUGAUCCACUGGGCACUAGUGCCUGGAACACGCUGAUCCGCGGCCACAAGCGCUGGUGCCUGUUCCCCACCCAAACGCCCAAGGAGCUGCUCAAGGUCACCAGUGCCAUGGGUGGCAAG
.(((.......((((((((((((.(((....(((......))).)))...)))))))))))).....(((((((...(((....).)).......((.((....)))).)))))))))). ( -46.50)
>DroVir_CAF1 589 120 - 1
AUUGAUCCAUUGGGUACCAGUGCCUGGAAUACGUUAAUACGUGGUCACAAGCGGUGGUGCUUAUUUCCCACGCACACGCCCAAGGACCUGCUGAAGGUCACCAGCGCUAUGGGCGGCAAG
..........(((((((((.(((.((((.(((((....))))).)).)).))).)))))))))........((...((((((.((....((((........)))).)).))))))))... ( -42.80)
>DroGri_CAF1 620 120 - 1
AUAGAUCCGUUGGGUACCAGUGCCUGGAAUACGUUGAUACGCGGCCACAAACGCUGGUGCUUGUUUCCCACGCACACGCCUAAGGAUCUGUUGAAGGUGACAAGCGCAAUGGGCGGGAAG
((((((((.((((((..(((((..(((....(((......))).)))....)))))((((.((.....)).))))..))))))))))))))....(....)...(((.....)))..... ( -37.80)
>DroWil_CAF1 12855 120 - 1
AUCGAUCCGCUGGGUACCAGCGCCUGGAAUACACUGAUACAUGGCCACAAACGUUGGUGCCUUUUUCCCACCCAGACGCCUAAGGAUCUUCUUAAGGUCACGAGCGCUAUGGGUGGCAAA
...........(((((((((((..(((....((........)).)))....))))))))))).....(((((((...((((...(((((.....)))))...)).))..))))))).... ( -40.70)
>DroMoj_CAF1 593 120 - 1
AUAGAUCCGCUGGGCACCAGCGCAUGGAAUACCCUAGUUCGUGGCCACAAGCGCUGGUGCUUGUUUCCCACGCACACGCCCAAGGAUCUGCUCAAGGUUACUAGUGCUAUGGGAGGCAAG
.(((((((..(((((.(((.....))).........((.(((((..(((((((....)))))))...))))).))..))))).)))))))((((.(((.......))).))))....... ( -46.00)
>DroAna_CAF1 608 120 - 1
AUCGAUCCGCUAGGCACCAGUGCUUGGAACACUCUAAUCCGCGGUCACAAGCGGUGGUGCCUAUUCCCCACCCAAACACCGAAGGACUUGCUGAAAGUGACCAGUGCCAUGGGUGGAAAG
..........(((((((((.((((((..((.(.(......).)))..)))))).)))))))))....(((((((..((((....)((((.....)))).....)))...))))))).... ( -45.20)
>consensus
AUAGAUCCGCUGGGCACCAGUGCCUGGAAUACGCUAAUACGCGGCCACAAGCGCUGGUGCCUGUUUCCCACCCACACGCCCAAGGAUCUGCUGAAGGUCACCAGCGCUAUGGGUGGCAAG
......((..(((((((((((((.((.....(((......)))....)).)))))))))))))...((((......(((.....(((((.....)))))....)))...)))).)).... (-31.84 = -31.15 +  -0.69)

alignment

secondary structure

dotplot

Window 8

Location	18,187,361 – 18,187,481
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.33
Mean single sequence MFE	-44.98
Consensus MFE	-31.63
Energy contribution	-31.13
Covariance contribution	-0.50
Combinations/Pair	1.41
Mean z-score	-1.86
Structure conservation index	0.70
SVM decision value	0.34
SVM RNA-class probability	0.696254
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18187361 120 - 27905053
GUUUGUCAUGGGACCGGCUCGCUCCGGCACCGGCAUCCACAUUGAUCCACUGGGCACUAGUGCCUGGAACACGCUGAUCCGCGGCCACAAGCGCUGGUGCCUGUUCCCCACCCAAACGCC
(((((...((((.((((......))))....((.(((......)))))...((((((((((((.(((....(((......))).)))...))))))))))))....))))..)))))... ( -46.40)
>DroVir_CAF1 629 120 - 1
GUUUGUAAUGGGUCCAGCUCGCUCCGGCACUGGUAUUCAUAUUGAUCCAUUGGGUACCAGUGCCUGGAAUACGUUAAUACGUGGUCACAAGCGGUGGUGCUUAUUUCCCACGCACACGCC
((((((...(((.....)))..(((((((((((((((((...........)))))))))))))).))).(((((....)))))...))))))((((((((...........)))).)))) ( -47.20)
>DroGri_CAF1 660 120 - 1
GUUUGUAAUGGGCCCGGCACGUUCUGGCACCGGUAUUCACAUAGAUCCGUUGGGUACCAGUGCCUGGAAUACGUUGAUACGCGGCCACAAACGCUGGUGCUUGUUUCCCACGCACACGCC
((((((....((((((.(((((((((((((.(((((((((........).)))))))).))))).)))..))).))...)).))))))))))((..((((.((.....)).))))..)). ( -45.20)
>DroWil_CAF1 12895 120 - 1
GUUUGUUAUGGGACCCGGACGCUCUGGCACGGGCAUACAUAUCGAUCCGCUGGGUACCAGCGCCUGGAAUACACUGAUACAUGGCCACAAACGUUGGUGCCUUUUUCCCACCCAGACGCC
(((((...(((((((((...((....)).))))..................(((((((((((..(((....((........)).)))....)))))))))))...)))))..)))))... ( -38.50)
>DroMoj_CAF1 633 120 - 1
GUUUGUCAUGGGCCCGGCUCGUUCCGGCACCGGCAUUCAUAUAGAUCCGCUGGGCACCAGCGCAUGGAAUACCCUAGUUCGUGGCCACAAGCGCUGGUGCUUGUUUCCCACGCACACGCC
((.((((.((((.((((......))))..(((((..((.....))...)))))((((((((((...((((......))))((....))..))))))))))......)))).).))).)). ( -44.60)
>DroAna_CAF1 648 120 - 1
GUUUGUUAUGGGGCCUGCUCGGUCCGGCACCGGUAUCCACAUCGAUCCGCUAGGCACCAGUGCUUGGAACACUCUAAUCCGCGGUCACAAGCGGUGGUGCCUAUUCCCCACCCAAACACC
(((((...(((((.......((.(((....)))...))............(((((((((.((((((..((.(.(......).)))..)))))).)))))))))..)))))..)))))... ( -48.00)
>consensus
GUUUGUAAUGGGACCGGCUCGCUCCGGCACCGGCAUUCACAUAGAUCCGCUGGGCACCAGUGCCUGGAAUACGCUAAUACGCGGCCACAAGCGCUGGUGCCUGUUUCCCACCCACACGCC
((.((...((((.((((...((....)).)))).................(((((((((((((.((.....(((......)))....)).)))))))))))))...))))..)).))... (-31.63 = -31.13 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:17 2006