Locus 4125

Sequence ID 3R_DroMel_CAF1
Location 11,244,094 – 11,244,184
Length 90
Max. P 0.998012
window6611 window6612

overview

Window 1

Location 11,244,094 – 11,244,184
Length 90
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 80.58
Mean single sequence MFE -28.81
Consensus MFE -19.62
Energy contribution -20.25
Covariance contribution 0.62
Combinations/Pair 1.05
Mean z-score -2.90
Structure conservation index 0.68
SVM decision value 2.66
SVM RNA-class probability 0.996174
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11244094 90 + 27905053
UUCGUUGCAUGUUGCAUACAUA----UGUA--UAUA----UGUAUGUGUAUGCAUCGCAGGAUAUGCCUGCCUAUGUGCUAGUGCAUUUUCAUAAGUGUG
......((((((((((((((((----((..--....----..))))))))))))..(((((.....)))))..))))))....((((((....)))))). ( -29.10)
>DroSim_CAF1 3283 96 + 1
UUCGUUGCAUGUUGCAUACAUACAUAUGUAUGUGUA----UGUAUGUGUAUGCAUCGCAGGAUGUGCCUGCCUAUGUGCUAGUGCAUUUGCAUAAGUGUG
...(.(((((...(((((((((((((....))))))----)))))))..))))).)(((((.....)))))....(..((.((((....)))).))..). ( -36.20)
>DroEre_CAF1 3302 86 + 1
UUCGUUGCAUGUUGCAUACAUACAUACAGA--GAUAUGUGCACAUGUGUAUGCAUCGCAGGAUGUGCC------------AGUGCAUUUGCAUAAGUGUG
......(((((.((((((((((..((((..--....))))....)))))))))).)((((.(((((..------------..)))))))))....)))). ( -23.20)
>DroYak_CAF1 3278 94 + 1
UUCGUUGCAUGUUGCAUACAUAUUUACACA--CAUA----CAUAUGUGUAUGCAUCGCAGGAUGUGCCUGUCUAUGUGCUAGUGCAUUUGCAUGAGUGUG
......(((((.(((((((((((.......--....----...)))))))))))..(((((.....))))).)))))(((.((((....)))).)))... ( -26.74)
>consensus
UUCGUUGCAUGUUGCAUACAUACAUACAUA__UAUA____CAUAUGUGUAUGCAUCGCAGGAUGUGCCUGCCUAUGUGCUAGUGCAUUUGCAUAAGUGUG
.....((((((.((((((((((......................)))))))))).)(((((.....)))))..........))))).............. (-19.62 = -20.25 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 11,244,094 – 11,244,184
Length 90
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 80.58
Mean single sequence MFE -24.48
Consensus MFE -14.38
Energy contribution -16.57
Covariance contribution 2.19
Combinations/Pair 1.13
Mean z-score -3.85
Structure conservation index 0.59
SVM decision value 2.98
SVM RNA-class probability 0.998012
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11244094 90 - 27905053
CACACUUAUGAAAAUGCACUAGCACAUAGGCAGGCAUAUCCUGCGAUGCAUACACAUACA----UAUA--UACA----UAUGUAUGCAACAUGCAACGAA
.....(((((....(((....))))))))(((((.....)))))(.(((((...((((((----(((.--...)----))))))))....))))).)... ( -23.50)
>DroSim_CAF1 3283 96 - 1
CACACUUAUGCAAAUGCACUAGCACAUAGGCAGGCACAUCCUGCGAUGCAUACACAUACA----UACACAUACAUAUGUAUGUAUGCAACAUGCAACGAA
........((((.((((((((.....)))(((((.....)))))..)))))...((((((----((((........)))))))))).....))))..... ( -28.20)
>DroEre_CAF1 3302 86 - 1
CACACUUAUGCAAAUGCACU------------GGCACAUCCUGCGAUGCAUACACAUGUGCACAUAUC--UCUGUAUGUAUGUAUGCAACAUGCAACGAA
..............((((.(------------((((.....)))..((((((((.(((((((......--..))))))).)))))))).))))))..... ( -22.50)
>DroYak_CAF1 3278 94 - 1
CACACUCAUGCAAAUGCACUAGCACAUAGACAGGCACAUCCUGCGAUGCAUACACAUAUG----UAUG--UGUGUAAAUAUGUAUGCAACAUGCAACGAA
.((((.((((((.(((.....(((....(.((((.....)))))..))).....))).))----))))--.)))).....((((((...))))))..... ( -23.70)
>consensus
CACACUUAUGCAAAUGCACUAGCACAUAGGCAGGCACAUCCUGCGAUGCAUACACAUACA____UAUA__UACAUAUGUAUGUAUGCAACAUGCAACGAA
..............((((...........(((((.....)))))(.((((((((.(((((..............))))).)))))))).).))))..... (-14.38 = -16.57 +   2.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:52 2006