Locus 1047

Sequence ID	3R_DroMel_CAF1
Location	3,247,923 – 3,248,043
Length	120
Max. P	0.984452

overview

Window 4

Location	3,247,923 – 3,248,043
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.33
Mean single sequence MFE	-35.50
Consensus MFE	-22.64
Energy contribution	-22.58
Covariance contribution	-0.05
Combinations/Pair	1.22
Mean z-score	-3.48
Structure conservation index	0.64
SVM decision value	1.97
SVM RNA-class probability	0.984452
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3247923 120 + 27905053
CAAGACGAAUCGCGUAAUGCCGUGGAAAUUUGAAUUCACUAAUGAGGUCUACAACUACUUGGGUUUAGCUCGCAUUAAUGAAUACAAAAUUCCCAGCAAUAUGACUGUCUUGCAGGGCAA
(((((((.....((((.(((.(.((((.((((.(((((.(((((.(..(((.((((.....)))))))..).))))).))))).)))).))))).))).))))..)))))))........ ( -34.40)
>DroVir_CAF1 686 120 + 1
CAAGACGCACCGCAUUAUGCCUUGGAAAUUUGAAUUCAUUAAUGAGGUCUACAACUACUUGGGUUUGGCCCGCAUUAAUGAAUACAAAAUUUCAAGCGCCCUAAAAACAUUAUCGGGACG
.....((..(((......(((((((((.((((.(((((((((((.((.(((.((((.....))))))).)).))))))))))).)))).))))))).))..(((.....))).)))..)) ( -33.30)
>DroGri_CAF1 692 120 + 1
UAAAACAAAUCGCAUUAUGCCUUGGAAAUUUGAAUUCAUUAAUGAGGUCUACAACUAUUUGGGCUUGGCCCGCAUUAAUGAAUACAAAUUUUCAGGCAGCAUGAAAACGUUAACUGGGAG
.........((.((((((((((((((((((((.(((((((((((((........))....((((...)))).))))))))))).))))))))))))..))))))..........)).)). ( -36.40)
>DroWil_CAF1 109751 120 + 1
CAAGACAAAUCGUGUUAUGCCAUGGAAAUUUGAAUUCAUUAAUGAGGUCUAUAACUAUUUGGGUUUGGCCCGCAUUAAUGAAUACAAAAUUCCCAGCGAUAUGAAAGUCUUGCAGGGUAA
((((((...(((((((..((...((((.((((.(((((((((((.((((...((((.....)))).))))..))))))))))).)))).))))..)))))))))..))))))........ ( -39.30)
>DroMoj_CAF1 581 117 + 1
CAAGACGCACCGCGUUAUGCCUUGGAAAUUUGAAUUCAUUAAUGAGGUCAUCAAUUACUUGGGUUUGGCCCGCAUUAAUGAAUACAAAAUUUCAAACA---UAUACAAAUCGAUGGGGCG
.....(((.(((((.((((..((((((.((((.(((((((((((.(((((((((....))))...)))))..))))))))))).)))).)))))).))---)).......)).))).))) ( -33.60)
>DroAna_CAF1 10155 120 + 1
AAAGACGCAUCGAGUCAUGCCGUGGAAAUUUGAAUUCAUUAAUGAGGUCUAUAACUACCUAGGUUUAGCCCGCCUUAAUGAGUUCAAAAUUCCCACCAACAUGUCGAUCUUGCAAGGCAA
......(((((((..((((..((((((.((((((((((((((.(.((.(((.((((.....))))))).)).).)))))))))))))).)).))))...))))))))...)))....... ( -36.00)
>consensus
CAAGACGAAUCGCGUUAUGCCUUGGAAAUUUGAAUUCAUUAAUGAGGUCUACAACUACUUGGGUUUGGCCCGCAUUAAUGAAUACAAAAUUCCAAGCAACAUGAAAAUCUUGCAGGGCAA
.................(((.(.((((.((((.(((((((((((.((.(((.((((.....))))))).)).))))))))))).)))).))))).)))...................... (-22.64 = -22.58 +  -0.05)

alignment

secondary structure

dotplot

Window 5

Location	3,247,923 – 3,248,043
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.33
Mean single sequence MFE	-33.47
Consensus MFE	-20.08
Energy contribution	-19.58
Covariance contribution	-0.50
Combinations/Pair	1.25
Mean z-score	-2.81
Structure conservation index	0.60
SVM decision value	1.60
SVM RNA-class probability	0.966935
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3247923 120 - 27905053
UUGCCCUGCAAGACAGUCAUAUUGCUGGGAAUUUUGUAUUCAUUAAUGCGAGCUAAACCCAAGUAGUUGUAGACCUCAUUAGUGAAUUCAAAUUUCCACGGCAUUACGCGAUUCGUCUUG
........((((((((((.((.(((((((((.((((.(((((((((((.(..((((((.......))).)))..).))))))))))).)))).)))).))))).))...)))).)))))) ( -38.80)
>DroVir_CAF1 686 120 - 1
CGUCCCGAUAAUGUUUUUAGGGCGCUUGAAAUUUUGUAUUCAUUAAUGCGGGCCAAACCCAAGUAGUUGUAGACCUCAUUAAUGAAUUCAAAUUUCCAAGGCAUAAUGCGGUGCGUCUUG
(((((..(........)..)))))((((.((.((((.(((((((((((.((....(((.......))).....)).))))))))))).)))).)).))))((((......))))...... ( -32.30)
>DroGri_CAF1 692 120 - 1
CUCCCAGUUAACGUUUUCAUGCUGCCUGAAAAUUUGUAUUCAUUAAUGCGGGCCAAGCCCAAAUAGUUGUAGACCUCAUUAAUGAAUUCAAAUUUCCAAGGCAUAAUGCGAUUUGUUUUA
.........((((..(((((..(((((..(((((((.(((((((((((.((((...)))).....(((...)))..))))))))))).)))))))...)))))..))).))..))))... ( -31.90)
>DroWil_CAF1 109751 120 - 1
UUACCCUGCAAGACUUUCAUAUCGCUGGGAAUUUUGUAUUCAUUAAUGCGGGCCAAACCCAAAUAGUUAUAGACCUCAUUAAUGAAUUCAAAUUUCCAUGGCAUAACACGAUUUGUCUUG
........((((((..((.(((.((((((((.((((.(((((((((((.((....(((.......))).....)).))))))))))).)))).)))).)))))))....))...)))))) ( -32.00)
>DroMoj_CAF1 581 117 - 1
CGCCCCAUCGAUUUGUAUA---UGUUUGAAAUUUUGUAUUCAUUAAUGCGGGCCAAACCCAAGUAAUUGAUGACCUCAUUAAUGAAUUCAAAUUUCCAAGGCAUAACGCGGUGCGUCUUG
.....(((((....((.((---((((((((((((.(.(((((((((((.(((.((....(((....))).)).)))))))))))))).))))))))..))))))))).)))))....... ( -29.00)
>DroAna_CAF1 10155 120 - 1
UUGCCUUGCAAGAUCGACAUGUUGGUGGGAAUUUUGAACUCAUUAAGGCGGGCUAAACCUAGGUAGUUAUAGACCUCAUUAAUGAAUUCAAAUUUCCACGGCAUGACUCGAUGCGUCUUU
.......(((...(((((((((((...((((.((((((.(((((((...(((((((((.......))).))).)))..))))))).)))))).)))).)))))))..)))))))...... ( -36.80)
>consensus
CUCCCCUGCAAGAUUUUCAUGUUGCUGGAAAUUUUGUAUUCAUUAAUGCGGGCCAAACCCAAGUAGUUGUAGACCUCAUUAAUGAAUUCAAAUUUCCAAGGCAUAACGCGAUGCGUCUUG
.......................((((((((.((((.(((((((((((.((....(((.......))).....)).))))))))))).))))))))..)))).................. (-20.08 = -19.58 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:14 2006