Locus 3317

Sequence ID	X_DroMel_CAF1
Location	8,865,379 – 8,865,494
Length	115
Max. P	0.991069

overview

Window 4

Location	8,865,379 – 8,865,494
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.77
Mean single sequence MFE	-27.48
Consensus MFE	-17.88
Energy contribution	-18.68
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.79
Structure conservation index	0.65
SVM decision value	2.16
SVM RNA-class probability	0.989383
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8865379 115 + 22224390
AAAUUUUACAUU-UUGGUUUUGCCAACCGUGCGUAUGAGCAAUAUUAUUGCGAAUCGUAAAAAUUACUCAUACGCCGCGUUAGCCACAUAAUCUACUGAAAGCCUAAACUAU----CGAG
............-..((((((((.(((((.(((((((((....(((.(((((...))))).)))..))))))))))).))).))..((........))))))))........----.... ( -26.80)
>DroSec_CAF1 772 106 + 1
AAAUUUUAAAUUUUUGGUUCUGCCAACUGUGCGUAUGAGCAAUAUUAUUUCGAAUCGUAAAAAAUACUCAUACGCCGCGUUGGCCACAACAACUCGUGAAUGCCUA--------------
...............(((...((((((((.(((((((((...((((.(((((...)).))).))))))))))))))).))))))(((........)))...)))..-------------- ( -27.70)
>DroSim_CAF1 571 103 + 1
AAAUUUUACAUUUUUGGUUCUGCCAACCGUGCGUAUGAGCAAUAUUAUUUCGAAUCGUAAAAAAUACUCAUACGCCGCGUUGGCCAC---AACUCGUGAAAGCCUA--------------
...............((((..((((((((.(((((((((...((((.(((((...)).))).))))))))))))))).))))))(((---.....)))..))))..-------------- ( -30.60)
>DroEre_CAF1 898 117 + 1
AAAUUUG--AUUUUUGGUUCUGCCAACCGUGCGUAUGAGCAAUAUUAUUACGAAUCGUAA-AAAUACUCAUACGCCCUGUUAGCCACAACAACUACUGAAAGCUUAAAGUCAAUGCAGAC
....(((--(((((.((((..((.(((.(.(((((((((...((((.(((((...)))))-.))))))))))))).).))).)).....((.....))..)))).))))))))....... ( -28.20)
>DroYak_CAF1 844 115 + 1
AAAUUUA-CAAUUUCGGUUCUGCCAACCAUGCGUAUGAGCAAUAUUAUUUCGAAUUGCAAAAAAUACGCAUACGCCUCGUUGGCCACAACAACUACUGAAAGCUUCAAUUCU----UGAG
.......-...(((((((...((((((...(((((((.(((((..........)))))..........)))))))...))))))..........)))))))...........----.... ( -24.12)
>consensus
AAAUUUUACAUUUUUGGUUCUGCCAACCGUGCGUAUGAGCAAUAUUAUUUCGAAUCGUAAAAAAUACUCAUACGCCGCGUUGGCCACAACAACUACUGAAAGCCUAAA_U_______GA_
.....................((((((...(((((((((.....((((........))))......)))))))))...)))))).................................... (-17.88 = -18.68 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	8,865,379 – 8,865,494
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.77
Mean single sequence MFE	-31.48
Consensus MFE	-25.50
Energy contribution	-25.46
Covariance contribution	-0.04
Combinations/Pair	1.05
Mean z-score	-2.57
Structure conservation index	0.81
SVM decision value	2.25
SVM RNA-class probability	0.991069
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8865379 115 - 22224390
CUCG----AUAGUUUAGGCUUUCAGUAGAUUAUGUGGCUAACGCGGCGUAUGAGUAAUUUUUACGAUUCGCAAUAAUAUUGCUCAUACGCACGGUUGGCAAAACCAA-AAUGUAAAAUUU
...(----(.(((....))).))..((.(((..((.((((((.(((((((((((((((...................))))))))))))).))))))))...))...-))).))...... ( -31.81)
>DroSec_CAF1 772 106 - 1
--------------UAGGCAUUCACGAGUUGUUGUGGCCAACGCGGCGUAUGAGUAUUUUUUACGAUUCGAAAUAAUAUUGCUCAUACGCACAGUUGGCAGAACCAAAAAUUUAAAAUUU
--------------..((....(((((....)))))((((((...(((((((((((.......................)))))))))))...))))))....))............... ( -32.50)
>DroSim_CAF1 571 103 - 1
--------------UAGGCUUUCACGAGUU---GUGGCCAACGCGGCGUAUGAGUAUUUUUUACGAUUCGAAAUAAUAUUGCUCAUACGCACGGUUGGCAGAACCAAAAAUGUAAAAUUU
--------------..((....(((.....---)))((((((.(((((((((((((.......................))))))))))).))))))))....))............... ( -31.90)
>DroEre_CAF1 898 117 - 1
GUCUGCAUUGACUUUAAGCUUUCAGUAGUUGUUGUGGCUAACAGGGCGUAUGAGUAUUU-UUACGAUUCGUAAUAAUAUUGCUCAUACGCACGGUUGGCAGAACCAAAAAU--CAAAUUU
(((......)))....((((......))))(((.((.(((((...(((((((((((...-(((((...)))))......)))))))))))...))))))).))).......--....... ( -33.60)
>DroYak_CAF1 844 115 - 1
CUCA----AGAAUUGAAGCUUUCAGUAGUUGUUGUGGCCAACGAGGCGUAUGCGUAUUUUUUGCAAUUCGAAAUAAUAUUGCUCAUACGCAUGGUUGGCAGAACCGAAAUUG-UAAAUUU
(.((----(.(((((..(....)..))))).))).)((((((.(.(((((((.(((..(((((.....)))))......))).))))))).).)))))).............-....... ( -27.60)
>consensus
_UC_______A_UUUAGGCUUUCAGUAGUUGUUGUGGCCAACGCGGCGUAUGAGUAUUUUUUACGAUUCGAAAUAAUAUUGCUCAUACGCACGGUUGGCAGAACCAAAAAUGUAAAAUUU
.................................((.((((((...(((((((((((.......................)))))))))))...))))))...))................ (-25.50 = -25.46 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:16 2006