Locus 1443

Sequence ID	3R_DroMel_CAF1
Location	4,163,524 – 4,163,657
Length	133
Max. P	0.654786

overview

Window 4

Location	4,163,524 – 4,163,620
Length	96
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	83.09
Mean single sequence MFE	-34.32
Consensus MFE	-25.69
Energy contribution	-26.05
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.61
Structure conservation index	0.75
SVM decision value	0.12
SVM RNA-class probability	0.594924
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4163524 96 + 27905053
CGGCGGAGC------------GGGGGCAUUGAAGUUGGGGACGCAAAUCGAGUUGGAGACGAAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCA
.........------------.(((((.((.((((.(....)((((..((((((((((.((((.((....))...))))))))).))))))))))))).)).))))). ( -33.80)
>DroSec_CAF1 7485 108 + 1
CGUCGGAGAGGGAGAGGGGGGGGGGGCACUGAAGUUGGGGACGCAAAUCGAGUUGGAGACGAAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCA
....((((.(...(((..(.((.(((((.((((((.(((..(((...(((..(((....)))...)))..)))..)))))))))))))).)).).)))...).)))). ( -35.00)
>DroSim_CAF1 13697 104 + 1
CGUCGGAGAGGGGAAGG----GGGGGCAUUGAAGUUGGGGACGCAAAUCGAGUUGGAGACGAAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCA
(.((.....)).)....----.(((((.((.((((.(....)((((..((((((((((.((((.((....))...))))))))).))))))))))))).)).))))). ( -34.00)
>DroEre_CAF1 1000 94 + 1
AGGGGAA--------------GGGGACGUUGAAGUUGGGGACGCAAAUCGAGUUGGAGACGAAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCA
.......--------------((((.((((.((((.(....)((((..((((((((((.((((.((....))...))))))))).))))))))))))).)))))))). ( -35.90)
>DroYak_CAF1 13541 94 + 1
CGGAGGA--------------GGGGGCGUUGAAGUUGGGGACGCAAAUCGAGUUGGAGACGAAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCA
.......--------------.((((((((.((((.(....)((((..((((((((((.((((.((....))...))))))))).))))))))))))).)))))))). ( -39.50)
>DroAna_CAF1 7810 76 + 1
------A--------------GGAGACGAUGAAGCUGGGGACG------------GAGACGAAAGCGGCAGCGAGUUUGCUUCAUGCUCGUUGCACUUGAACGCUUCA
------.--------------(....)..((((((......((------------....)).(((..(((((((((.((...)).))))))))).)))....)))))) ( -27.70)
>consensus
CGGCGGA______________GGGGGCAUUGAAGUUGGGGACGCAAAUCGAGUUGGAGACGAAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCA
.............................((((((.(....).........(((.(((.(....)..(((((((((.........))))))))).))).))))))))) (-25.69 = -26.05 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	4,163,552 – 4,163,657
Length	105
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	79.65
Mean single sequence MFE	-35.58
Consensus MFE	-22.83
Energy contribution	-23.33
Covariance contribution	0.50
Combinations/Pair	1.16
Mean z-score	-1.52
Structure conservation index	0.64
SVM decision value	0.25
SVM RNA-class probability	0.654786
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4163552 105 + 27905053
ACGCAAAUCGAGUUGGAGACG----AAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCAACGGCAUUCUGAUUUGUGGCUGCGGCUGCUGUGCUGU
.(((((((((.(((((((.((----.(((..(((((((((.........))))))))).)))...))))))))).......)))))))))...(((((......))))) ( -38.90)
>DroVir_CAF1 4545 100 + 1
------ACGUAGCCGGAGACUGGCAGCCGCAGCAGCGAAUUCGCUUCACGCCGGUUGCACUUGAAUGCUUCAACGACAUUCUGAUUUGUGGCUGCGGCUGCUGCCA---
------.....((.(....).((((((((((((((((....)))).(((((.....))....((((((......).)))))......)))))))))))))))))..--- ( -40.20)
>DroPse_CAF1 14586 92 + 1
GG-------AAGUUGGAGACG----ACGAAGGCAGCGAGUUCUCUUCAUGCUCGUUGCACUUGAACGCUUCAACGGCAUUCUGAUUUGUGGCUGCGGCUGCUA------
.(-------..(((((((.((----...((((((((((((.........))))))))).)))...)))))))))..)..........(..((....))..)..------ ( -31.70)
>DroSim_CAF1 13733 105 + 1
ACGCAAAUCGAGUUGGAGACG----AAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCAACGGCAUUCUGAUUUGUGGCUGCGGCUGCUGUGCUGC
.(((((((((.(((((((.((----.(((..(((((((((.........))))))))).)))...))))))))).......)))))))))...(((((......))))) ( -40.10)
>DroAna_CAF1 7830 89 + 1
ACG------------GAGACG----AAAGCGGCAGCGAGUUUGCUUCAUGCUCGUUGCACUUGAACGCUUCAACGGCAUUCUGAUUUGUGGCUGCGGCUGCUGU----U
.((------------....))----..(((((((((((((.((...)).))))((..((...(((.(((.....))).))).....))..))....))))))))----) ( -30.90)
>DroPer_CAF1 14481 92 + 1
GG-------AAGUUGGAGACG----ACGAAGGCAGCGAGUUCUCUUCAUGCUCGUUGCACUUGAACGCUUCAACGGCAUUCUGAUUUGUGGCUGCGGCUGCUA------
.(-------..(((((((.((----...((((((((((((.........))))))))).)))...)))))))))..)..........(..((....))..)..------ ( -31.70)
>consensus
AC_______AAGUUGGAGACG____AAAGCGGCAGCGAGUUCGCUUCAUGCUCGUUGCACUUGAACGCUUCAACGGCAUUCUGAUUUGUGGCUGCGGCUGCUGU_____
..............(....)........(((((((((((.....))).(((..((..((...(((.(((.....))).))).....))..)).)))))))))))..... (-22.83 = -23.33 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:43 2006