Locus 4599

Sequence ID	2R_DroMel_CAF1
Location	14,987,996 – 14,988,129
Length	133
Max. P	0.926087

overview

Window 2

Location	14,987,996 – 14,988,099
Length	103
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	87.74
Mean single sequence MFE	-28.82
Consensus MFE	-24.46
Energy contribution	-25.02
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-1.55
Structure conservation index	0.85
SVM decision value	0.01
SVM RNA-class probability	0.540244
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14987996 103 + 20766785
AGCACGAAGCCAAGUCGCCGAGCCUCGUCUGGUGCGGAAACUUUGCGUAAGUCCCACUUUGGGGCUAACGAUUCAUCUAUAUUUAAUCAAGAGU-AAAAACUUU
.....(((((.((((..(((.(((......))).)))..)))).))((.((((((.....)))))).))..)))...............(((((-....))))) ( -29.70)
>DroSec_CAF1 5909 103 + 1
AGCACGAAGCCAAGUCGCCGAGCCUCGUCUGGUGCGGAAACUUUGCGUAAGUCCCACUUUGGGGCUAACGGUUCAUCUAUAUUUAAUAAAAAGU-AAAAACUUU
.....(((((.((((..(((.(((......))).)))..)))).))((.((((((.....)))))).))..)))...............(((((-....))))) ( -29.50)
>DroSim_CAF1 2539 103 + 1
AGCACGAAGCCAAGUCGCCGAGCCUCGUCUGGUGCGGAAACUUUGCGUAAGUCCCAUUUUGGGGCUAACGGUUCAUCUAUAUUUAAUCAAGAGU-AAAAACUUU
.....(((((.((((..(((.(((......))).)))..)))).))((.((((((.....)))))).))..)))...............(((((-....))))) ( -29.60)
>DroEre_CAF1 2595 103 + 1
AGCACGAAGCCAAGUCGCCGAGCCUCGUCUGGUGCGGAAACUUUGCGUAAGUCCCAUUUUGGGGCUAACGGUUCAUCUAUAAUUAAUCGAGAGU-AAAAACUUU
....(((.((.((((..(((.(((......))).)))..)))).))((.((((((.....)))))).)).................)))(((((-....))))) ( -30.90)
>DroYak_CAF1 5964 103 + 1
AGCACGAAGCCAAGUCGCCGAGCCUCGUCUGGUGCGGAAACUUUGCGUAAGUCCCACUUUGGGGCUAACGGUUCAACUUUAAUUAAUCAAUAGU-AACAACUUU
.....(((((.((((..(((.(((......))).)))..)))).))((.((((((.....)))))).))..)))....................-......... ( -28.70)
>DroMoj_CAF1 13524 97 + 1
AGUACCAAGCCAAGUCGUCGAGCUUCGUCCGGUGCGGAAACGUUACGUAAGUCCCAUAAUGGGGCUGCA-AUUUA------CUGAAUGAAUAAUGAAUAACAUU
.(((((..((.((((......)))).))..)))))(....)((((.(((.(((((.....)))))))).-(((((------.....)))))......))))... ( -24.50)
>consensus
AGCACGAAGCCAAGUCGCCGAGCCUCGUCUGGUGCGGAAACUUUGCGUAAGUCCCACUUUGGGGCUAACGGUUCAUCUAUAUUUAAUCAAGAGU_AAAAACUUU
.....(((((.((((..(((.(((......))).)))..)))).))((.((((((.....)))))).))..))).............................. (-24.46 = -25.02 +   0.56)

alignment

secondary structure

dotplot

Window 3

Location	14,988,036 – 14,988,129
Length	93
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	76.96
Mean single sequence MFE	-23.63
Consensus MFE	-14.08
Energy contribution	-13.92
Covariance contribution	-0.17
Combinations/Pair	1.21
Mean z-score	-2.01
Structure conservation index	0.60
SVM decision value	1.17
SVM RNA-class probability	0.926087
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14988036 93 + 20766785
CUUUGCGUAAGUCCCACUUUGGGGCUAACGAUUCAU-------CUAUAUUUAAUCAAGAGUAAAAACUUUCU---------UGGUCGAAC-UACAGGAUUAGGAAACCGA
.....(((.((((((.....)))))).))).....(-------((.((((..((((((((........))))---------))))..)).-)).)))....(....)... ( -22.90)
>DroSec_CAF1 5949 94 + 1
CUUUGCGUAAGUCCCACUUUGGGGCUAACGGUUCAU-------CUAUAUUUAAUAAAAAGUAAAAACUUUCU---------UGGUCGAACAUGCAGAGUUAGGAAACCCA
((((((((.((((((.....)))))).)).((((..-------(((..........(((((....)))))..---------)))..))))..))))))...((....)). ( -24.60)
>DroSim_CAF1 2579 94 + 1
CUUUGCGUAAGUCCCAUUUUGGGGCUAACGGUUCAU-------CUAUAUUUAAUCAAGAGUAAAAACUUUCU---------UGGUCGAACAUGCAGAGCUAGGAAACCCA
((((((((.((((((.....)))))).)).......-------.....((..((((((((........))))---------))))..))...))))))...((....)). ( -27.70)
>DroEre_CAF1 2635 94 + 1
CUUUGCGUAAGUCCCAUUUUGGGGCUAACGGUUCAU-------CUAUAAUUAAUCGAGAGUAAAAACUUUCU---------UGGUCGAACAUUCAGGAUUAGGAAACCGA
......((.((((((.....)))))).))((((..(-------((.....(((((((((((....))))))(---------(((........)))))))))))))))).. ( -23.40)
>DroYak_CAF1 6004 94 + 1
CUUUGCGUAAGUCCCACUUUGGGGCUAACGGUUCAA-------CUUUAAUUAAUCAAUAGUAACAACUUUCU---------UGUUCGGACAUUCAAGAUUAGUAAACCCA
.....(((.((((((.....)))))).)))......-------.....(((((((....(.(((((.....)---------))))).(.....)..)))))))....... ( -18.20)
>DroAna_CAF1 17334 109 + 1
CAUUGCGUAAGUCCCACUAAGGGGCUAACGACUUACUAACACUUUAUUUUUCUUUAAAGGCAAAAGCUCUCGCAGCUCGCUUAGUCUUAC-UAUCGAAUGUGUCACCUAA
..((((((.((((((.....)))))).))............(((((........))))))))).((....((((..(((..(((.....)-)).))).))))....)).. ( -25.00)
>consensus
CUUUGCGUAAGUCCCACUUUGGGGCUAACGGUUCAU_______CUAUAUUUAAUCAAGAGUAAAAACUUUCU_________UGGUCGAACAUACAGAAUUAGGAAACCCA
.....(((.((((((.....)))))).)))..........................(((((....)))))........................................ (-14.08 = -13.92 +  -0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:25 2006