Locus 8172

Sequence ID	3L_DroMel_CAF1
Location	21,517,540 – 21,517,780
Length	240
Max. P	0.828502

overview

Window 3

Location	21,517,540 – 21,517,660
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	99.44
Mean single sequence MFE	-25.77
Consensus MFE	-22.50
Energy contribution	-25.50
Covariance contribution	3.00
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.87
SVM decision value	0.12
SVM RNA-class probability	0.591818
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21517540 120 + 23771897
UCGACUGCAAUUGCAUUUGAAUGUUUUUCGAGGCUUCGGCCUCUUUUUGUUUAAAUAUAUAAAAGCCAUUAAAUACUAAUCUAUUCUCGAUUGCUCUUCUUCGGCUUCUUCGGGCACCUA
..((..(((((((.....(((((......(((((....)))))(((((((........)))))))................))))).)))))))...))...((..((....))..)).. ( -26.30)
>DroSec_CAF1 22778 120 + 1
UCGACUGCAAUUGCAUUUGAAUGUUUUUCGAGGCUUCGGCCUCUUUUUGUUUAAAUAUAUAAAAGCCAUUAAAUACUAAUCUAUUCUCGAUUGCUCUUCUUCGGCUACUUCGGGCACCUA
((((.(((....))).)))).........(((((....))))).((((((........))))))(((((((.....)))).......(((..(((.......)))....))))))..... ( -25.50)
>DroSim_CAF1 22891 120 + 1
UCGACUGCAAUUGCAUUUGAAUGUUUUUCGAGGCUUCGGCCUCUUUUUGUUUAAAUAUAUAAAAGCCAUUAAAUACUAAUCUAUUCUCGAUUGCUCUUCUUCGGCUACUUCGGGCACCUA
((((.(((....))).)))).........(((((....))))).((((((........))))))(((((((.....)))).......(((..(((.......)))....))))))..... ( -25.50)
>consensus
UCGACUGCAAUUGCAUUUGAAUGUUUUUCGAGGCUUCGGCCUCUUUUUGUUUAAAUAUAUAAAAGCCAUUAAAUACUAAUCUAUUCUCGAUUGCUCUUCUUCGGCUACUUCGGGCACCUA
((((.(((....))).)))).........(((((....))))).((((((........))))))(((((((.....)))).......(((..(((.......)))....))))))..... (-22.50 = -25.50 +   3.00)

alignment

secondary structure

dotplot

Window 4

Location	21,517,660 – 21,517,780
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-42.57
Consensus MFE	-40.85
Energy contribution	-40.97
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.70
Structure conservation index	0.96
SVM decision value	0.33
SVM RNA-class probability	0.690112
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21517660 120 + 23771897
AUGACGCGCGUUCAACAUUUAGGCCACCAUCGGGCCAGGGGACCAGUGGGUCCCGUCCAGUGCAAGGAGGCAGUGCCUCCUCCCUCCUAAGUAUGAUUAAUUAAUAAUGCAGGUAAGCAU
..(((................((((.......))))..((((((....)))))))))..((((.(((((((...)))))))....(((..((((.(((....))).)))))))...)))) ( -39.60)
>DroSec_CAF1 22898 120 + 1
AUGACGCGCGGCCAACAUUUAGGCCACCAUCGGGCCAGGGGACCAGUGGGUCCCGUCCAGUGCAAGGAGGCAGUGUCUCCUCCCUCCUAAGUAUGAUUAAUUAAUAAUGCAGGUAAGCAU
...((((((((((........))))......((((...((((((....)))))))))).)))).((((((.((......)).))))))..))..............((((......)))) ( -43.80)
>DroSim_CAF1 23011 120 + 1
AUGACGCGCGGCCAACAUUUAGGCCACCAUCGGGCCAGGGGACCAGUGGGUCCCGUCCAGUGCAAGGAGGCAGUGCCUCCUCCCUCCUAAGUAUGAUUAAUUAAUAAUGCAGGUAAGCAU
.....((((((((........))))......((((...((((((....)))))))))).)))).(((((((...)))))))....(((..((((.(((....))).)))))))....... ( -44.30)
>consensus
AUGACGCGCGGCCAACAUUUAGGCCACCAUCGGGCCAGGGGACCAGUGGGUCCCGUCCAGUGCAAGGAGGCAGUGCCUCCUCCCUCCUAAGUAUGAUUAAUUAAUAAUGCAGGUAAGCAU
...((((((((((........))))......((((...((((((....)))))))))).)))).((((((.((......)).))))))..))..............((((......)))) (-40.85 = -40.97 +   0.11)

alignment

secondary structure

dotplot

Window 5

Location	21,517,660 – 21,517,780
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-44.77
Consensus MFE	-42.33
Energy contribution	-43.33
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.95
SVM decision value	0.71
SVM RNA-class probability	0.828502
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21517660 120 - 23771897
AUGCUUACCUGCAUUAUUAAUUAAUCAUACUUAGGAGGGAGGAGGCACUGCCUCCUUGCACUGGACGGGACCCACUGGUCCCCUGGCCCGAUGGUGGCCUAAAUGUUGAACGCGCGUCAU
((((......)))).................(((..(.((((((((...)))))))).).)))(((((((((....))))))..(((((....).))))................))).. ( -40.00)
>DroSec_CAF1 22898 120 - 1
AUGCUUACCUGCAUUAUUAAUUAAUCAUACUUAGGAGGGAGGAGACACUGCCUCCUUGCACUGGACGGGACCCACUGGUCCCCUGGCCCGAUGGUGGCCUAAAUGUUGGCCGCGCGUCAU
..(((..(((((((((.....)))........((((((.((......)).))))))))))..))..((((((....))))))..)))..((((((((((........)))))).)))).. ( -45.40)
>DroSim_CAF1 23011 120 - 1
AUGCUUACCUGCAUUAUUAAUUAAUCAUACUUAGGAGGGAGGAGGCACUGCCUCCUUGCACUGGACGGGACCCACUGGUCCCCUGGCCCGAUGGUGGCCUAAAUGUUGGCCGCGCGUCAU
((((......))))...................((.(.((((((((...)))))))).).(..(..((((((....)))))))..).))((((((((((........)))))).)))).. ( -48.90)
>consensus
AUGCUUACCUGCAUUAUUAAUUAAUCAUACUUAGGAGGGAGGAGGCACUGCCUCCUUGCACUGGACGGGACCCACUGGUCCCCUGGCCCGAUGGUGGCCUAAAUGUUGGCCGCGCGUCAU
((((......))))...................((.(.((((((((...)))))))).).(..(..((((((....)))))))..).))((((((((((........)))))).)))).. (-42.33 = -43.33 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:26 2006