Locus 3

Sequence ID	4_DroMel_CAF1
Location	86,865 – 87,021
Length	156
Max. P	0.868040

overview

Window 3

Location	86,865 – 86,981
Length	116
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	93.48
Mean single sequence MFE	-31.25
Consensus MFE	-27.85
Energy contribution	-28.85
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.89
SVM decision value	0.20
SVM RNA-class probability	0.628570
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 86865 116 + 1281640
AAUACAUAAAA---AAAUAUGCAUUUCAUAUUUAAUUUAAACAGCUUCCUGUACUGGGGGCUCAUAACCUUCAGGGCGGUCGAUUACGGCUCCCUCGGAUGAAACAACGGCUUCCACGG
....((((...---...))))..((((((.............(((((((......))))))).....((...((((.(((((....))))))))).))))))))...((.......)). ( -26.00)
>DroSec_CAF1 29164 116 + 1
AAUACAUUAAA---AAAUAUGCAUUUCAUAUUUAAUUUAAACAGCUUCCUGUACUGGGGGCUCAUAACCUUCAGGGCGGUCGAUUACGGCUCCCUCGGAGGAAACAACGGCUUCCACGG
......(((((---(((((((.....)))))))..)))))((((....))))..((((((((.....(((((((((.(((((....))))))))).))))).......))))))))... ( -32.70)
>DroEre_CAF1 46379 118 + 1
AAUACAUUUAAAAAAAAUACGCAUUUCAUAUUCAAU-UAAACAGCUUCCUGUACGGGGGGCUCAUAACCUUCGGGACGGUCGAUUACGGCUCCCUCGGAGGAAACAACGGCUUCCACGG
....................................-...((((....)))).(((((((((.....((((((((..(((((....)))))..)))))))).......))))))).)). ( -30.60)
>DroYak_CAF1 52556 116 + 1
AAUACAUUGCA---AAAUAUGCAUUUCAUAUUCAAUUUAAACAGCUUCCUGUACUGGGGGCUCAUAACCUUCGGGGCGGUCGAUCACGGCUCCCUCGGAGGAAACAACGGCUUCCACGG
.......((((---.....)))).................((((....))))..((((((((.....(((((((((.(((((....))))).))))))))).......))))))))... ( -35.70)
>consensus
AAUACAUUAAA___AAAUAUGCAUUUCAUAUUCAAUUUAAACAGCUUCCUGUACUGGGGGCUCAUAACCUUCAGGGCGGUCGAUUACGGCUCCCUCGGAGGAAACAACGGCUUCCACGG
....................((....................(((((((......))))))).....(((((((((.(((((....))))).)))))))))........))........ (-27.85 = -28.85 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	86,901 – 87,021
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.69
Mean single sequence MFE	-42.49
Consensus MFE	-39.53
Energy contribution	-40.04
Covariance contribution	0.50
Combinations/Pair	1.05
Mean z-score	-1.87
Structure conservation index	0.93
SVM decision value	0.86
SVM RNA-class probability	0.868040
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 86901 120 + 1281640
AACAGCUUCCUGUACUGGGGGCUCAUAACCUUCAGGGCGGUCGAUUACGGCUCCCUCGGAUGAAACAACGGCUUCCACGGAUUUGCCACCGCCAUCGCCAUGCAAUUCCAGAAGCUUUGA
....((((((......))))))((((..((...((((.(((((....))))))))).))))))..(((.((((((...(((.((((....((....))...)))).))).))))))))). ( -38.30)
>DroSec_CAF1 29200 120 + 1
AACAGCUUCCUGUACUGGGGGCUCAUAACCUUCAGGGCGGUCGAUUACGGCUCCCUCGGAGGAAACAACGGCUUCCACGGAUUUGCCACCGCCAUCGCCAUGCAAUUCCAGAAGCUUUGA
...(((((((......))))))).....(((((((((.(((((....))))))))).)))))...(((.((((((...(((.((((....((....))...)))).))).))))))))). ( -44.40)
>DroEre_CAF1 46417 120 + 1
AACAGCUUCCUGUACGGGGGGCUCAUAACCUUCGGGACGGUCGAUUACGGCUCCCUCGGAGGAAACAACGGCUUCCACGGAUUUGCCACCACCAUCGCCAUGUAGUUCCAGAAGCUUUGA
...((((((((....))(((((((((..((((((((..(((((....)))))..)))))))).......(((.((....))...)))............))).)))))).)))))).... ( -40.20)
>DroYak_CAF1 52592 120 + 1
AACAGCUUCCUGUACUGGGGGCUCAUAACCUUCGGGGCGGUCGAUCACGGCUCCCUCGGAGGAAACAACGGCUUCCACGGAUUUGCCACCACCAUCGCCAUGUAGAUCCAGAAGCUUUGA
...(((((((......))))))).....(((((((((.(((((....))))).)))))))))...(((.((((((...((((((((...............)))))))).))))))))). ( -47.06)
>consensus
AACAGCUUCCUGUACUGGGGGCUCAUAACCUUCAGGGCGGUCGAUUACGGCUCCCUCGGAGGAAACAACGGCUUCCACGGAUUUGCCACCACCAUCGCCAUGCAAUUCCAGAAGCUUUGA
...(((((((......))))))).....(((((((((.(((((....))))).)))))))))...(((.((((((...(((.((((...............)))).))).))))))))). (-39.53 = -40.04 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:49 2006