Locus 6558

Sequence ID	3R_DroMel_CAF1
Location	17,267,472 – 17,267,570
Length	98
Max. P	0.896499

overview

Window 6

Location	17,267,472 – 17,267,570
Length	98
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	79.13
Mean single sequence MFE	-37.47
Consensus MFE	-23.45
Energy contribution	-23.83
Covariance contribution	0.38
Combinations/Pair	1.24
Mean z-score	-2.08
Structure conservation index	0.63
SVM decision value	0.99
SVM RNA-class probability	0.896499
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17267472 98 + 27905053
CCCUUGCCCUCUGCGUCGUGGCCAUGGAAGAUGUUAAGGAUGUCCUGGAUCUUCCUUUGGCC---GUCGAAUGCCUGGUGAAAAUGAAUUGGGCGAAA--AGA
...((((((...((((((((((((.(((((((....(((....)))..)))))))..)))))---).)).)))).(.((....)).)...))))))..--... ( -38.20)
>DroSec_CAF1 164 98 + 1
CCCUUGCCCUCUGCGUCGUGGCCACGGAAGAUGUUAAGGAUGUCCUGGAUCUUCCUUUGGCC---GUCGAAUGUCUACAGGAAAUGCGUUGGGCGAAA--AUA
...((((((..(((((((((((((.(((((((....(((....)))..)))))))..)))))---).)))...((.....))..))))..))))))..--... ( -38.60)
>DroSim_CAF1 164 98 + 1
CCCUUGCCCUCUGCGUCGUGGGCACGGAAGAUGUUAAGGAUGUCCUGGAUCUUCCUUUGGCC---GUCGAAUGCCUUCAGGAAAUGCGUUGGGCGAAA--AUA
...((((((..((((((((((.((.(((((((....(((....)))..)))))))..)).))---).)))...((....))...))))..))))))..--... ( -35.60)
>DroEre_CAF1 1516 98 + 1
CCCUUGCCCUCUGCGUUGUGGCCUCGGAAGCUGUUAAGGAUGUCCUGCAUCUUCCUUUGGCC---GGCGAAUGUCUGGGGGAAAUGGGUUGGGCGAAA--AGA
(((...(((((.(((((((((((..(((((.(((..(((....)))))).)))))...))))---.)).)))))..)))))....)))..........--... ( -37.70)
>DroYak_CAF1 209 97 + 1
CCCUUGCCCUCUGCGUUGUGGCCUCGGAAGCUGUUCAGGAUGUCCUGCAUCUUCCU-UGGCC---GUCGAAUGCCUGGGGGAAAUGCGUUGGGCGAAA--AGA
...((((((..((((((((((((..(((((.((..((((....)))))).))))).-.))))---).).....((....)).))))))..))))))..--... ( -39.60)
>DroPer_CAF1 34900 91 + 1
CCUUUGCCCUCUUUAU--UGGCCUCGGAAGAACUUCAGGAUGUCCUUGUGCUUCCCGGGGCCUAAGCCCAGUGC----------UGGGUCGGGGAACUCUUCU
(((..((((.......--.(((((((((((.((...(((....))).)).))).))))))))..(((.....))----------)))))..)))......... ( -35.10)
>consensus
CCCUUGCCCUCUGCGUCGUGGCCACGGAAGAUGUUAAGGAUGUCCUGGAUCUUCCUUUGGCC___GUCGAAUGCCUGGAGGAAAUGCGUUGGGCGAAA__AGA
...((((((..(((((...((((..(((((......(((....)))....)))))...))))...........((....))..)))))..))))))....... (-23.45 = -23.83 +   0.38)

alignment

secondary structure

dotplot

Window 7

Location	17,267,472 – 17,267,570
Length	98
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	79.13
Mean single sequence MFE	-30.37
Consensus MFE	-21.27
Energy contribution	-21.77
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.70
SVM decision value	0.51
SVM RNA-class probability	0.763520
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17267472 98 - 27905053
UCU--UUUCGCCCAAUUCAUUUUCACCAGGCAUUCGAC---GGCCAAAGGAAGAUCCAGGACAUCCUUAACAUCUUCCAUGGCCACGACGCAGAGGGCAAGGG
.((--(((.((((..........(....)((..(((..---(((((..(((((((..(((....)))....))))))).))))).))).))...))))))))) ( -30.40)
>DroSec_CAF1 164 98 - 1
UAU--UUUCGCCCAACGCAUUUCCUGUAGACAUUCGAC---GGCCAAAGGAAGAUCCAGGACAUCCUUAACAUCUUCCGUGGCCACGACGCAGAGGGCAAGGG
...--....((((...((......((....)).(((..---(((((..(((((((..(((....)))....))))))).))))).))).))...))))..... ( -31.50)
>DroSim_CAF1 164 98 - 1
UAU--UUUCGCCCAACGCAUUUCCUGAAGGCAUUCGAC---GGCCAAAGGAAGAUCCAGGACAUCCUUAACAUCUUCCGUGCCCACGACGCAGAGGGCAAGGG
...--.....(((...............(((.......---.)))...(((((((..(((....)))....))))))).(((((.(......).))))).))) ( -28.70)
>DroEre_CAF1 1516 98 - 1
UCU--UUUCGCCCAACCCAUUUCCCCCAGACAUUCGCC---GGCCAAAGGAAGAUGCAGGACAUCCUUAACAGCUUCCGAGGCCACAACGCAGAGGGCAAGGG
.((--(((.((((...............(.....)...---((((...(((((.((.(((....)))...)).)))))..))))..........))))))))) ( -27.20)
>DroYak_CAF1 209 97 - 1
UCU--UUUCGCCCAACGCAUUUCCCCCAGGCAUUCGAC---GGCCA-AGGAAGAUGCAGGACAUCCUGAACAGCUUCCGAGGCCACAACGCAGAGGGCAAGGG
.((--(((.((((...((....((....))........---((((.-.(((((...((((....)))).....)))))..)))).....))...))))))))) ( -33.80)
>DroPer_CAF1 34900 91 - 1
AGAAGAGUUCCCCGACCCA----------GCACUGGGCUUAGGCCCCGGGAAGCACAAGGACAUCCUGAAGUUCUUCCGAGGCCA--AUAAAGAGGGCAAAGG
..........((((.((((----------....)))))...((((.((((((((...(((....)))...))).))))).)))).--.......)))...... ( -30.60)
>consensus
UCU__UUUCGCCCAACGCAUUUCCCCCAGGCAUUCGAC___GGCCAAAGGAAGAUCCAGGACAUCCUUAACAUCUUCCGAGGCCACGACGCAGAGGGCAAGGG
.........((((............................((((...(((((....(((....)))......)))))..)))).(......).))))..... (-21.27 = -21.77 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:29 2006