Locus 2901

Sequence ID	X_DroMel_CAF1
Location	7,768,198 – 7,768,489
Length	291
Max. P	0.958138

overview

Window 0

Location	7,768,198 – 7,768,316
Length	118
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	98.87
Mean single sequence MFE	-19.53
Consensus MFE	-18.55
Energy contribution	-18.67
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.54
Structure conservation index	0.95
SVM decision value	0.03
SVM RNA-class probability	0.546569
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7768198 118 - 22224390
CAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCCAUUGUGAUAACAGCUGCGUAAACGAAACACGUUAGAACCU
.(((((.((((((((((...(((.....)))...))))))))...........((((((....(((....)))....)))))).......))))))).((((.....))))....... ( -20.30)
>DroSec_CAF1 2309 118 - 1
CAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCCAUUGUGAUAACAUCUGCAUAAACGAAACACGUUAGAACCU
.(((((...((((((((...(((.....)))...))))))))...........((((((....(((....)))....)))))).........))))).((((.....))))....... ( -18.00)
>DroSim_CAF1 2331 118 - 1
CAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCCAUUGUGAUAACAGCUGCGUAAACGAAACACGUUAGAACCU
.(((((.((((((((((...(((.....)))...))))))))...........((((((....(((....)))....)))))).......))))))).((((.....))))....... ( -20.30)
>consensus
CAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCCAUUGUGAUAACAGCUGCGUAAACGAAACACGUUAGAACCU
.(((((.((((((((((...(((.....)))...))))))))...........((((((....(((....)))....)))))).......))))))).((((.....))))....... (-18.55 = -18.67 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	7,768,238 – 7,768,356
Length	118
Sequences	3
Columns	118
Reading direction	reverse
Mean pairwise identity	94.35
Mean single sequence MFE	-22.22
Consensus MFE	-19.71
Energy contribution	-19.82
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.19
Structure conservation index	0.89
SVM decision value	0.61
SVM RNA-class probability	0.797917
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7768238 118 - 22224390
UAAACACUAGAAUCGUGGGGCAAAUAACAUUUAGCUGCUGCAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCC
...............((((((((......(((((((((.....)).))))))).))))).(((.....)))......................................)))...... ( -21.50)
>DroSec_CAF1 2349 111 - 1
UAAACACCAGAAUCGUGGGGCAAAUAA-------CUGCUCCAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCC
..(((........(((((((((.....-------.))))))))).....((((((((...(((.....)))...))))))))....................)))............. ( -23.50)
>DroSim_CAF1 2371 118 - 1
UAAACACCAGAAUUGUGGGGCAAAUAACAUUUAGCUGCUCCAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCC
............(((((((((((......(((((((((.....)).))))))).))))).)).))))..((...((((((....................))))))...))....... ( -21.65)
>consensus
UAAACACCAGAAUCGUGGGGCAAAUAACAUUUAGCUGCUCCAUGUAAGCUAAAGUUGCCACCGGCAAACGGAACUAACUUUAAAAUAAUAAAAAUAAUGCAAGUUGAAACCAAAACCC
..(((........(((((((((.............))))))))).....((((((((...(((.....)))...))))))))....................)))............. (-19.71 = -19.82 +   0.11)

alignment

secondary structure

dotplot

Window 2

Location	7,768,278 – 7,768,396
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.94
Mean single sequence MFE	-28.24
Consensus MFE	-21.06
Energy contribution	-21.00
Covariance contribution	-0.06
Combinations/Pair	1.13
Mean z-score	-1.44
Structure conservation index	0.75
SVM decision value	-0.02
SVM RNA-class probability	0.522391
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7768278 118 - 22224390
GCGGCUUUUGAGGGUUCUGAAAACAAAAUAUGGAAACCAUUAAACACUAGAAUCGUGGGGCAAAUAACAUUUAGCUGCUGCAUGUAAGCUAAAG--UUGCCACCGGCAAACGGAACUAAC
............(((((((............(....).................(((((((((......(((((((((.....)).))))))).--))))).)).))...)))))))... ( -26.80)
>DroSec_CAF1 2389 111 - 1
GCGGCUUUUGAGGGUUCUGAAAACAAAAUAUGGAAACUAUUAAACACCAGAAUCGUGGGGCAAAUAA-------CUGCUCCAUGUAAGCUAAAG--UUGCCACCGGCAAACGGAACUAAC
((((((((.(..(((((((.......((((.(....)))))......)))))))((((((((.....-------.)))))))).....).))))--))))..(((.....)))....... ( -33.22)
>DroSim_CAF1 2411 118 - 1
GCGGCUUUUGAGGGUUCUGAAAACAAAAUAUGGAAACCAUUAAACACCAGAAUUGUGGGGCAAAUAACAUUUAGCUGCUCCAUGUAAGCUAAAG--UUGCCACCGGCAAACGGAACUAAC
((((((((.(..(((((((..........((((...)))).......)))))))((((((((..((.....))..)))))))).....).))))--))))..(((.....)))....... ( -29.33)
>DroYak_CAF1 2482 120 - 1
GCGUCUUUUGAGGGUUCUAAAAACAAAAUAAGAAAACCAUUAAACACCAGACUUGUUGGGCAAUUAACAUUUAACUGCUGGAUGUAGGCUAAAUUUUUGCCAUCGGCAGACGGAACUAAC
.(((((.((((((.((((............))))..)).....(((((((...((((((....))))))........)))).))).(((.........))).)))).)))))........ ( -23.60)
>consensus
GCGGCUUUUGAGGGUUCUGAAAACAAAAUAUGGAAACCAUUAAACACCAGAAUCGUGGGGCAAAUAACAUUUAGCUGCUCCAUGUAAGCUAAAG__UUGCCACCGGCAAACGGAACUAAC
............(((((((.............................((...(((((((((.............)))))))))....))......(((((...))))).)))))))... (-21.06 = -21.00 +  -0.06)

alignment

secondary structure

dotplot

Window 3

Location	7,768,396 – 7,768,489
Length	93
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	83.75
Mean single sequence MFE	-28.74
Consensus MFE	-24.47
Energy contribution	-25.78
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-2.42
Structure conservation index	0.85
SVM decision value	1.49
SVM RNA-class probability	0.958138
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7768396 93 - 22224390
AUGAUACAAACACAAGCGAACACAUUACAUGUACAUGUGUACA--------------------------UGCACGCAAGACCUGCAAAACAAGCAUACUUUUAAGCGCCAAAGUUAGGA
......(.(((....(((.........(((((((....)))))--------------------------))...(((.....)))....................)))....))).).. ( -14.50)
>DroSec_CAF1 2500 119 - 1
AUGAUACAAACACAAGCGAACACAUUACAUGUACAUGUGUACGGUGGGCACAUCCUGUGCUGCCCACUGUGCACGCAUGACCUGCAAAACAAGCAUACUUUUAAGCGCCAAAGUUAGGA
......(.(((....(((.........(((((....(((((((((((((((((...))).)))))))))))))))))))...(((.......)))..........)))....))).).. ( -36.20)
>DroSim_CAF1 2529 119 - 1
AUGAUACAAAAACAAGCGAACACAUUACAUGUACAUGUGUACAGUGGGCACAUCCUGUGCUGCCCACUGUGCACGCAAGACCUGCAAAACAAGCAUACUUUUAAGCGCCAAAGUUAGGA
...............(((..........((((....(((((((((((((((((...))).))))))))))))))(((.....))).......)))).........)))........... ( -35.51)
>consensus
AUGAUACAAACACAAGCGAACACAUUACAUGUACAUGUGUACAGUGGGCACAUCCUGUGCUGCCCACUGUGCACGCAAGACCUGCAAAACAAGCAUACUUUUAAGCGCCAAAGUUAGGA
...............(((..........((((....((((((((((((((((.....)).))))))))))))))(((.....))).......)))).........)))........... (-24.47 = -25.78 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:12 2006