Locus 6048

Sequence ID 3L_DroMel_CAF1
Location 16,118,970 – 16,119,170
Length 200
Max. P 0.935682
window9683 window9684 window9685 window9686

overview

Window 3

Location 16,118,970 – 16,119,090
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 92.22
Mean single sequence MFE -32.87
Consensus MFE -28.79
Energy contribution -28.90
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.76
Structure conservation index 0.88
SVM decision value 1.25
SVM RNA-class probability 0.935682
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16118970 120 + 23771897
AGAUUUGUUCAUCAUAAUUUGCAAACGCAUUUAAUUAAUGGGAAAUCACGUGGUGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUACGUUACGUAUACGCAGCGUAUCGCA
......(((((((((....(((....))).........(((....))).)))))))))((((((((.((.....)).))))))))......((((((((.((....)).))))))..)). ( -31.50)
>DroSec_CAF1 4722 120 + 1
AGAUUUGUUCAUCAUAAUUCGCAAACGCAUUUAAUUAAUGGGAAAUCACGUGGUGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCA
.(((..(((((((((.....((....))..........(((....))).)))))))))((((((((.((.....)).))))))))......(((((((.......)))))))..)))... ( -35.10)
>DroSim_CAF1 4081 109 + 1
-----------UCAUAAUUCGCAAACGCAUUUAAUUAAUGGGAAAUCACGUGGCGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCA
-----------..............(.((((.....)))).)..........((((((((((((((.((.....)).))))))))......(((((((.......))))))))).)))). ( -32.00)
>consensus
AGAUUUGUUCAUCAUAAUUCGCAAACGCAUUUAAUUAAUGGGAAAUCACGUGGUGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCA
.........................(.((((.....)))).)..........((((((((((((((.((.....)).))))))))......(((((((.......))))))))).)))). (-28.79 = -28.90 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 16,118,970 – 16,119,090
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -29.80
Consensus MFE -29.99
Energy contribution -29.33
Covariance contribution -0.66
Combinations/Pair 1.10
Mean z-score -1.30
Structure conservation index 1.01
SVM decision value 0.38
SVM RNA-class probability 0.713337
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16118970 120 - 23771897
UGCGAUACGCUGCGUAUACGUAACGUAGCUGAAUUAUUGCGCAUACGAGGUGUUUGCACAAUGUUCACCACGUGAUUUCCCAUUAAUUAAAUGCGUUUGCAAAUUAUGAUGAACAAAUCU
(((((...(((((((.......))))))).........(((((((((.((((...((.....)).)))).)))((((.......))))..)))))))))))......(((......))). ( -29.30)
>DroSec_CAF1 4722 120 - 1
UGCGAUACGCUGCGUAUACGUAACGCAGCUGAAUUAUUGCGCAUACGAGGUGUUUGCACAAUGUUCACCACGUGAUUUCCCAUUAAUUAAAUGCGUUUGCGAAUUAUGAUGAACAAAUCU
.((((...(((((((.......))))))).........(((((((((.((((...((.....)).)))).)))((((.......))))..)))))))))).......(((......))). ( -30.60)
>DroSim_CAF1 4081 109 - 1
UGCGAUACGCUGCGUAUACGUAACGCAGCUGAAUUAUUGCGCAUACGAGGUGUUUGCACAAUGUUCGCCACGUGAUUUCCCAUUAAUUAAAUGCGUUUGCGAAUUAUGA-----------
.((((...(((((((.......))))))).........(((((((((.((((...((.....)).)))).)))((((.......))))..)))))))))).........----------- ( -29.50)
>consensus
UGCGAUACGCUGCGUAUACGUAACGCAGCUGAAUUAUUGCGCAUACGAGGUGUUUGCACAAUGUUCACCACGUGAUUUCCCAUUAAUUAAAUGCGUUUGCGAAUUAUGAUGAACAAAUCU
(((((...(((((((.......))))))).........(((((((((.((((...((.....)).)))).)))((((.......))))..)))))))))))................... (-29.99 = -29.33 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 16,119,010 – 16,119,130
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -37.03
Consensus MFE -34.73
Energy contribution -35.73
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.94
SVM decision value 0.91
SVM RNA-class probability 0.879341
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16119010 120 + 23771897
GGAAAUCACGUGGUGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUACGUUACGUAUACGCAGCGUAUCGCAUUGGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGAC
(((((....((((((((.((...((((((((((((.((((((.........))((((((.((....)).))))))..)))))))).)))))))).)))))))))).)))))......... ( -35.80)
>DroSec_CAF1 4762 120 + 1
GGAAAUCACGUGGUGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCAUUUGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGAC
(((((....((((((((.((...((((((((.(((.(((((..(((.....(((((((.......))))))).)))))))).))).)))))))).)))))))))).)))))......... ( -39.20)
>DroSim_CAF1 4110 120 + 1
GGAAAUCACGUGGCGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCAUUUGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGAC
........(((.((((((...))((((((((.(((.(((((..(((.....(((((((.......))))))).)))))))).))).))))))))................)))).))).. ( -36.10)
>consensus
GGAAAUCACGUGGUGAACAUUGUGCAAACACCUCGUAUGCGCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCAUUUGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGAC
(((((....((((((((.((...((((((((.(((.(((((..(((.....(((((((.......))))))).)))))))).))).)))))))).)))))))))).)))))......... (-34.73 = -35.73 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 16,119,050 – 16,119,170
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -34.47
Consensus MFE -33.05
Energy contribution -33.50
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.96
SVM decision value 0.70
SVM RNA-class probability 0.826754
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16119050 120 + 23771897
GCAAUAAUUCAGCUACGUUACGUAUACGCAGCGUAUCGCAUUGGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGACGACUUGAUAAUAGAGUAGGCAAAUUCUAGAUGCAUAAGGA
...........(.((((((.((....)).)))))).)(((((.((...((((((((((..((.(((....((((....))))...))).))..)))).)))))).)).)))))....... ( -28.20)
>DroSec_CAF1 4802 120 + 1
GCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCAUUUGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGACGACUUGAUAAUAGAGCAGGCAAAUUCUAGAUGCAUUAGGA
...........(((((((.......))))))).....((((((((..((((((((.....((((......((((....))))..)))).....))))))))....))))))))....... ( -37.20)
>DroSim_CAF1 4150 120 + 1
GCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCAUUUGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGACGACUUGAUAAUAGAGUAGGCAAAUUCUAGAUGCAUUGGGA
.((((......(((((((.......))))))).....((((((((...((((((((((..((.(((....((((....))))...))).))..)))).)))))).))))))))))))... ( -38.00)
>consensus
GCAAUAAUUCAGCUGCGUUACGUAUACGCAGCGUAUCGCAUUUGGUGUGUUUGCUAUUUCAUCAUCUUUCUCGUAGCGACGACUUGAUAAUAGAGUAGGCAAAUUCUAGAUGCAUUAGGA
...........(((((((.......))))))).....((((((((..((((((((.....((((......((((....))))..)))).....))))))))....))))))))....... (-33.05 = -33.50 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:01 2006