Locus 5845

Sequence ID	2R_DroMel_CAF1
Location	18,498,024 – 18,498,224
Length	200
Max. P	0.987430

overview

Window 9

Location	18,498,024 – 18,498,144
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-44.13
Consensus MFE	-43.30
Energy contribution	-43.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.98
SVM decision value	0.41
SVM RNA-class probability	0.724111
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18498024 120 - 20766785
GGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCUACGGUCGAUGGUCGAUGGGCCUGUCUAGGAAAGGCCUGCU
.(((((((((.((.((.....)).))))))))).))...(((...((..(((((((((...(((((((.....)))))))..))))(((((((....)))).))).)))))..)).))). ( -44.80)
>DroSec_CAF1 16683 120 - 1
GGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCUACGGUCGAUGGUCGAUGGGCCUGUCUAGCAAAGGCCUGCU
((((((((((.((.((.....)).)))))))).((((((((....)))))....((((...(((((((.....)))))))...((((.....)))).))))......)))..)))).... ( -43.80)
>DroSim_CAF1 5820 120 - 1
GGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCUACGGUCGAUGGUCGAUGGGCCUGUCUAGCAAAGGCCUGCU
((((((((((.((.((.....)).)))))))).((((((((....)))))....((((...(((((((.....)))))))...((((.....)))).))))......)))..)))).... ( -43.80)
>consensus
GGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCUACGGUCGAUGGUCGAUGGGCCUGUCUAGCAAAGGCCUGCU
...(((((((.((.((.....)).))))))))).(((((((....)))))...(((((((.(((((((.....))))))).(....))))))))..((((((.........)))))))). (-43.30 = -43.30 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	18,498,064 – 18,498,184
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-38.60
Consensus MFE	-38.60
Energy contribution	-38.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.44
Structure conservation index	1.00
SVM decision value	1.60
SVM RNA-class probability	0.966781
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18498064 120 + 20766785
AGACCAUUGGAUAUGGCCUUAUGGCCAGGAAUUGCAAAUGCAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGC
...((........(((((....)))))((..((((....)))).((((((((((((.((.....)).)).)))))).....(((((.....))))).....))))........))))... ( -38.60)
>DroSec_CAF1 16723 120 + 1
AGACCAUUGGAUAUGGCCUUAUGGCCAGGAAUUGCAAAUGCAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGC
...((........(((((....)))))((..((((....)))).((((((((((((.((.....)).)).)))))).....(((((.....))))).....))))........))))... ( -38.60)
>DroSim_CAF1 5860 120 + 1
AGACCAUUGGAUAUGGCCUUAUGGCCAGGAAUUGCAAAUGCAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGC
...((........(((((....)))))((..((((....)))).((((((((((((.((.....)).)).)))))).....(((((.....))))).....))))........))))... ( -38.60)
>consensus
AGACCAUUGGAUAUGGCCUUAUGGCCAGGAAUUGCAAAUGCAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGC
...((........(((((....)))))((..((((....)))).((((((((((((.((.....)).)).)))))).....(((((.....))))).....))))........))))... (-38.60 = -38.60 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	18,498,064 – 18,498,184
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	100.00
Mean single sequence MFE	-40.60
Consensus MFE	-40.60
Energy contribution	-40.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.01
Structure conservation index	1.00
SVM decision value	2.08
SVM RNA-class probability	0.987430
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18498064 120 - 20766785
GCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCU
...((((.((((((((((...((((((((.....)))).....(((((((.((.((.....)).))))))))))))).)))))))).))..))(((((....)))))........))... ( -40.60)
>DroSec_CAF1 16723 120 - 1
GCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCU
...((((.((((((((((...((((((((.....)))).....(((((((.((.((.....)).))))))))))))).)))))))).))..))(((((....)))))........))... ( -40.60)
>DroSim_CAF1 5860 120 - 1
GCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCU
...((((.((((((((((...((((((((.....)))).....(((((((.((.((.....)).))))))))))))).)))))))).))..))(((((....)))))........))... ( -40.60)
>consensus
GCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUGCAUUUGCAAUUCCUGGCCAUAAGGCCAUAUCCAAUGGUCU
...((((.((((((((((...((((((((.....)))).....(((((((.((.((.....)).))))))))))))).)))))))).))..))(((((....)))))........))... (-40.60 = -40.60 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	18,498,104 – 18,498,224
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-42.07
Consensus MFE	-41.60
Energy contribution	-41.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.73
Structure conservation index	0.99
SVM decision value	1.97
SVM RNA-class probability	0.984356
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18498104 120 + 20766785
CAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGCCAGCUGGCCAACAGCUGACGAAGCUGGACAAAACCGGCCG
....((.(((((((((.((.....)).)).))))))).((.(((((.....))))).((((.....)))).....)).))((((((.....)))))).....(((((......))))).. ( -41.60)
>DroSec_CAF1 16763 120 + 1
CAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGCCAGCUGGCCAACAGCUGACGUAGCUGGCUAAAACCGGCCU
....((((((((((((.((.....)).)).)))))).....(((((.....))))).....))))........((((((((((((((.((.....)).).)))))))))....))))... ( -42.30)
>DroSim_CAF1 5900 120 + 1
CAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGCCAGCUGGCCAACAGCUGACGUAGCUGGCUAAAACCGGCCU
....((((((((((((.((.....)).)).)))))).....(((((.....))))).....))))........((((((((((((((.((.....)).).)))))))))....))))... ( -42.30)
>consensus
CAACGCAUGCUGCAGUGGCGAGUUGCAACUUGCAGCAACCAACAUGAUUAUCAUGUACGAAAUGCAUUCGAAACCGGAGCCAGCUGGCCAACAGCUGACGUAGCUGGCUAAAACCGGCCU
....((.(((((((((.((.....)).)).))))))).((.(((((.....))))).((((.....)))).....)).))((((((.....)))))).....(((((......))))).. (-41.60 = -41.60 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	18,498,104 – 18,498,224
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-47.37
Consensus MFE	-46.45
Energy contribution	-46.57
Covariance contribution	0.11
Combinations/Pair	1.02
Mean z-score	-2.90
Structure conservation index	0.98
SVM decision value	2.04
SVM RNA-class probability	0.986447
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18498104 120 - 20766785
CGGCCGGUUUUGUCCAGCUUCGUCAGCUGUUGGCCAGCUGGCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUG
.((((((....(.((((((..(((((...))))).))))))).))))))...((((((..(((.(((((.....)))))))).(((((((.((.((.....)).))))))))))))))). ( -44.90)
>DroSec_CAF1 16763 120 - 1
AGGCCGGUUUUAGCCAGCUACGUCAGCUGUUGGCCAGCUGGCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUG
(((((((....((((((((..(((((...))))).)))))))))))))))..((((((..(((.(((((.....)))))))).(((((((.((.((.....)).))))))))))))))). ( -48.60)
>DroSim_CAF1 5900 120 - 1
AGGCCGGUUUUAGCCAGCUACGUCAGCUGUUGGCCAGCUGGCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUG
(((((((....((((((((..(((((...))))).)))))))))))))))..((((((..(((.(((((.....)))))))).(((((((.((.((.....)).))))))))))))))). ( -48.60)
>consensus
AGGCCGGUUUUAGCCAGCUACGUCAGCUGUUGGCCAGCUGGCUCCGGUUUCGAAUGCAUUUCGUACAUGAUAAUCAUGUUGGUUGCUGCAAGUUGCAACUCGCCACUGCAGCAUGCGUUG
.((((((....((((((((..(((((...))))).))))))))))))))...((((((..(((.(((((.....)))))))).(((((((.((.((.....)).))))))))))))))). (-46.45 = -46.57 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:13 2006