Locus 1588

Sequence ID	3L_DroMel_CAF1
Location	4,647,584 – 4,647,732
Length	148
Max. P	0.937710

overview

Window 2

Location	4,647,584 – 4,647,692
Length	108
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	82.58
Mean single sequence MFE	-41.16
Consensus MFE	-29.31
Energy contribution	-28.23
Covariance contribution	-1.07
Combinations/Pair	1.43
Mean z-score	-2.36
Structure conservation index	0.71
SVM decision value	0.65
SVM RNA-class probability	0.810744
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4647584 108 + 23771897
UCCUGGCUCAAGCGAUCUGCCAGCUCACGGAUUUUAUUCCGAUUCGACUGAAGG--GCGGGAAAAUGGCGAUUGAAGCUAUCCACACCCCCCUUUAGUCGAUUGGUCUUG
..(((((...........)))))....((((......))))..(((((((((((--(.(((...(((((.......))))).....)))))))))))))))......... ( -42.10)
>DroSec_CAF1 20010 108 + 1
UCCUGGCUCAAGCGGUCUGCCAGCUCACGGAUCUUGUUCCGAUUCGACUGAAGG--GCGGGAAAAUGGCGAUUGAAGCUAUCCACACCUCCCUUUAGUCGAUUGGUCUUG
..(((((...........)))))....((((......))))..(((((((((((--(.((....(((((.......))))).....)).))))))))))))......... ( -40.80)
>DroSim_CAF1 20585 108 + 1
UCCUGGCUCAAGCGGUCUGCCAGCUCACGGAUCUUGUUCCGAUUCGACUGAAGG--GCGGGAAAAUGGCGAUUGAAGCUAUCCACACCUCCCUUUAGUCGAUUGGUCUUG
..(((((...........)))))....((((......))))..(((((((((((--(.((....(((((.......))))).....)).))))))))))))......... ( -40.80)
>DroEre_CAF1 20232 108 + 1
UCCUGGCUCAGGCGGUCUGCCAGUUCGCGGAUCUUGUUCCGAUUCGACUGAAGG--GCGGGAAAAUGGCGGUUGAAGCUAUCCACGCCCCCCUUCAGUCGAUUGGUCUUG
.((((...)))).(((((((......))))))).....(((((.((((((((((--(.(((...(((((.......))))).....)))))))))))))))))))..... ( -48.20)
>DroYak_CAF1 23487 108 + 1
UCCUGGCUCAAACGGUCUGCCAGCUCACGGAUCUUGUUCCGAUUCGACUGAAGG--GCGGGAAAAUUGCGAUUAAAGCUAUCCACGCCCCCCUUCAGUCGAUUGGUCUUG
..(((((...........)))))....((((......))))..(((((((((((--(.(((......((.......))........)))))))))))))))......... ( -42.04)
>DroPer_CAF1 25237 108 + 1
UCCCGACUCAAGCGCUCCGCCUGCUUCAGUUUACUGUGCCUAAGCGA-UGAGUAUCUCUGAAACGUUGU-GUUGAAGCAGUCGACUGCGCCGUGCAGCCGUUGGGUCCUA
....(((((((..(((.(((..((..(((((.(((((..(...((((-((.............))))))-...)..))))).))))).)).))).)))..)))))))... ( -33.02)
>consensus
UCCUGGCUCAAGCGGUCUGCCAGCUCACGGAUCUUGUUCCGAUUCGACUGAAGG__GCGGGAAAAUGGCGAUUGAAGCUAUCCACACCCCCCUUCAGUCGAUUGGUCUUG
..(((((...........)))))....((((......))))..(((((((((((....(((...(((((.......))))).....))).)))))))))))......... (-29.31 = -28.23 +  -1.07)

alignment

secondary structure

dotplot

Window 3

Location	4,647,624 – 4,647,732
Length	108
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	80.12
Mean single sequence MFE	-37.06
Consensus MFE	-25.07
Energy contribution	-25.99
Covariance contribution	0.92
Combinations/Pair	1.29
Mean z-score	-2.48
Structure conservation index	0.68
SVM decision value	1.26
SVM RNA-class probability	0.937710
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4647624 108 + 23771897
GAUUCGACUGAAGGGCGGGA-----AAAUGGCGAUUGAAGCUAUCCACACCCCCCUUUAGUCGAUUGGUCUUGUUAAUCCGUCCAAGGAGUUCCAUAUUUUUUCGGAAAAUCU
(((((((((((((((.(((.-----..(((((.......))))).....)))))))))))))))...))).......((((...(((((((.....)))))))))))...... ( -35.70)
>DroVir_CAF1 35010 112 + 1
GAGGUGACUCUGGAUCGGUAAUUGCAA-GCGCUGUUGUAGCAGUCAACGCGACCCUGCACUCGCUGGAUCUCGUUCAUGCGACGCAGCAGCAACAUAUUCUCGCGCAAAAUAU
(((....)))...........((((..-..((((((((.(((...((((.((.((.((....)).)).)).))))..)))...))))))))..(........).))))..... ( -33.60)
>DroSec_CAF1 20050 108 + 1
GAUUCGACUGAAGGGCGGGA-----AAAUGGCGAUUGAAGCUAUCCACACCUCCCUUUAGUCGAUUGGUCUUGUUAAUCCGUCCAAGGAGUUCCAUGUUCUGUCGGAAAAUCU
(((((((((((((((.((..-----..(((((.......))))).....)).))))))))))))...))).......((((.(((.((....)).))....).))))...... ( -35.50)
>DroSim_CAF1 20625 108 + 1
GAUUCGACUGAAGGGCGGGA-----AAAUGGCGAUUGAAGCUAUCCACACCUCCCUUUAGUCGAUUGGUCUUGUUAAUCCGUCCAAGGAGUUCCAUAUUCUGUCGGAAAAUCU
(((((((((((((((.((..-----..(((((.......))))).....)).))))))))))))...))).......((((.....(((((.....)))))..))))...... ( -36.70)
>DroEre_CAF1 20272 108 + 1
GAUUCGACUGAAGGGCGGGA-----AAAUGGCGGUUGAAGCUAUCCACGCCCCCCUUCAGUCGAUUGGUCUUGCUGAUCCUUCCCAGAAGUCCCAGAUUUUGUCGAAAAAUCU
...((((((((((((.(((.-----..(((((.......))))).....)))))))))))))))..((.(((.(((........)))))).)).(((((((.....))))))) ( -43.40)
>DroYak_CAF1 23527 108 + 1
GAUUCGACUGAAGGGCGGGA-----AAAUUGCGAUUAAAGCUAUCCACGCCCCCCUUCAGUCGAUUGGUCUUGCUGAUCCGUCCAAGAAGUCCCAGAUUUUGUCGAAAAAUCG
...((((((((((((.(((.-----.....((.......))........))))))))))))))).((((((((..((....)))))))....)))((((((.....)))))). ( -37.44)
>consensus
GAUUCGACUGAAGGGCGGGA_____AAAUGGCGAUUGAAGCUAUCCACACCCCCCUUCAGUCGAUUGGUCUUGUUAAUCCGUCCAAGGAGUUCCAUAUUCUGUCGGAAAAUCU
(((((((((((((((.(((........(((((.......))))).....)))))))))))))))...))).......((((....((((........))))..))))...... (-25.07 = -25.99 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:21 2006