Locus 4942

Sequence ID	X_DroMel_CAF1
Location	12,896,454 – 12,896,599
Length	145
Max. P	0.934930

overview

Window 9

Location	12,896,454 – 12,896,570
Length	116
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	92.50
Mean single sequence MFE	-30.11
Consensus MFE	-24.56
Energy contribution	-24.96
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.82
SVM decision value	1.24
SVM RNA-class probability	0.934930
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12896454 116 + 22224390
--GGCUACUGCAAGGGUAUAGGAAACAUGGCCGGGAGUGAAUUUCCAUUUGGUUUUCGGUAUGAAUUUUGAGAUAGAAAUUUGAAUUUGAAGAGCGGAAACUGAAGUGGAAGCGUCAA
--(((((((.(..((.(((.(....)))).))..)))))..(((((((((((((((((.(.(((((((.((........)).)))))))...).)))))))).))))))))).))).. ( -31.40)
>DroSec_CAF1 97325 117 + 1
AUAGCUACUGCAAGGGUAUAGGAAACAUGGCCGGGAGUGAAUUUCCAUUUGGUUUUCGGUAUGAAUUUUUAGAUAGGAAUUUGA-UUUGAAGAGCGGAAACUAAAGUGGAAGCGUCAA
...(((.(..(..((.(((.(....)))).)).((((.....)))).(((((((((((.(........((((((....))))))-.......).))))))))))))..).)))..... ( -30.36)
>DroSim_CAF1 81334 117 + 1
AUGGCUACUGCAAGGGUAUAGGAAACAUGGCCGGGAGUGAAUUUCCAUUUGGUUUUCGGUAUGAAUUUUGAGAUAGGAAUUUGA-UUUGAAGAGCGGAAACUGAAGUGGAAGCGUCAA
.((((((((.(..((.(((.(....)))).))..)))))..((((((((((.(((((((...(((((((......)))))))..-.))))))).)(....)..))))))))).)))). ( -31.40)
>DroEre_CAF1 94422 117 + 1
AUAGCUACUGCAAGGGUAUGGAAAACAUGGCCGGGAGUGUAUUUCCAUUUGGUUUUCGGUUUGAUUUUUGAGAUAGAAAUUUGA-UUUGAGCAGCGGAAGCAGAAGUGGAAGCGUCAA
...((((((.(..((.((((.....)))).))..)))))...((((((((.((((..((((.((((((((...)))))))).))-)).)))).((....))..))))))))))..... ( -30.50)
>DroYak_CAF1 105997 117 + 1
AUAGCUACUGCAAGGGUAUAGGAAACAUGGCCGGGAGUGUAUUUCCAUUUGGUUUUCGGUUUGAUUUUUGGGAUAGGAAUUUGA-UUUGAAGAGCGGCAAAAGAAGUGGAAGCGUCAA
...(((.(..(.........(....)...(((.((((.....))))....(.(((((((.(..(.((((......)))).)..)-.))))))).)))).......)..).)))..... ( -26.90)
>consensus
AUAGCUACUGCAAGGGUAUAGGAAACAUGGCCGGGAGUGAAUUUCCAUUUGGUUUUCGGUAUGAAUUUUGAGAUAGGAAUUUGA_UUUGAAGAGCGGAAACUGAAGUGGAAGCGUCAA
...(((.(..(..((.(((.(....)))).)).((((.....)))).((((.(((((((..((((((((......))))))))...))))))).)))).......)..).)))..... (-24.56 = -24.96 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	12,896,492 – 12,896,599
Length	107
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	80.02
Mean single sequence MFE	-26.78
Consensus MFE	-14.65
Energy contribution	-16.32
Covariance contribution	1.67
Combinations/Pair	1.22
Mean z-score	-1.85
Structure conservation index	0.55
SVM decision value	-0.02
SVM RNA-class probability	0.524291
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12896492 107 + 22224390
AUUUCCAUUUGGUUUUCGG--UAUGAAUUUUGAGAUAGAAAUUUGAAUUUGAAGAGCGGAAACUGAAGUGGAAGCGUCAACGGAAACGG------AAACAUCGACGGAAGCGGAA
.(((((((((((((((((.--(.(((((((.((........)).)))))))...).)))))))).)))))))))((((...(....)(.------...)...))))......... ( -28.80)
>DroSec_CAF1 97365 105 + 1
AUUUCCAUUUGGUUUUCGG--UAUGAAUUUUUAGAUAGGAAUUUGA-UUUGAAGAGCGGAAACUAAAGUGGAAGCGUCAACGGAAACG-------AAACAUCGACGGAAGCGGAA
.(((((((((((((((((.--(........((((((....))))))-.......).)))))))).)))))))))......((....))-------.....(((.(....)))).. ( -26.66)
>DroSim_CAF1 81374 106 + 1
AUUUCCAUUUGGUUUUCGG--UAUGAAUUUUGAGAUAGGAAUUUGA-UUUGAAGAGCGGAAACUGAAGUGGAAGCGUCAACGGAAACGG------AAACAUCGACGGAAGCGGAA
.((((((((((.(((((((--...(((((((......)))))))..-.))))))).)(....)..)))))))))((((...(....)(.------...)...))))......... ( -27.80)
>DroEre_CAF1 94462 112 + 1
AUUUCCAUUUGGUUUUCGG--UUUGAUUUUUGAGAUAGAAAUUUGA-UUUGAGCAGCGGAAGCAGAAGUGGAAGCGUCAACGGAAACGGAAACGGAAACAUCGACGGAAGCGGAA
.(((((((((.((((..((--((.((((((((...)))))))).))-)).)))).((....))..)))))))))((((..((....)).....(....)...))))......... ( -30.40)
>DroYak_CAF1 106037 112 + 1
AUUUCCAUUUGGUUUUCGG--UUUGAUUUUUGGGAUAGGAAUUUGA-UUUGAAGAGCGGCAAAAGAAGUGGAAGCGUCAACGGAAACGGAAACUGAAACAUCAACGGAAGCGGAA
.(((((..(((((((((((--(((......................-.((((.(..(.((.......)).)...).))))((....)).))))))))).))))).)))))..... ( -22.70)
>DroAna_CAF1 108753 103 + 1
-----------AUUUUUGGAAUUUAAAUUUGAACAUUUGAGUCUGA-UUUGUAAAUCGGAAACGGAAAUGGAAACGGUAGCGGAAACGGAAACGGCAAAGUCGCCGUCAGCGGAU
-----------....(..((.(((((((......)))))))))..)-(((((...(((....)))........((((..((.....((....)).....))..))))..))))). ( -24.30)
>consensus
AUUUCCAUUUGGUUUUCGG__UAUGAAUUUUGAGAUAGGAAUUUGA_UUUGAAGAGCGGAAACUGAAGUGGAAGCGUCAACGGAAACGG______AAACAUCGACGGAAGCGGAA
.((((((((((.(((((((....((((((((......))))))))...))))))).)(....)..)))))))))......((....))............(((.(....)))).. (-14.65 = -16.32 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:37 2006