Locus 5018

Sequence ID	2L_DroMel_CAF1
Location	14,402,491 – 14,402,601
Length	110
Max. P	0.999890

overview

Window 6

Location	14,402,491 – 14,402,601
Length	110
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	87.38
Mean single sequence MFE	-34.90
Consensus MFE	-30.94
Energy contribution	-30.46
Covariance contribution	-0.48
Combinations/Pair	1.21
Mean z-score	-3.77
Structure conservation index	0.89
SVM decision value	4.40
SVM RNA-class probability	0.999890
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14402491 110 + 22407834
GCCUGGGAAAAUUCCAAGAGGCGUGAGAUGUGCAUCGCAUUGUUCUGUAACAGCUCGAUGCACUUCCUACCCUUUUUUUU----CCAGUUUUUUCCACUCCCUUCAAAGUCCAU
..(((((((((.....(((((.(((.((.((((((((..(((((....)))))..)))))))).)).)))))))))))))----)))).......................... ( -33.30)
>DroSec_CAF1 23637 105 + 1
GCCUGGGAAAAUUGCAAGAGGCGUGAGAUGUGCAUUGCAUUGUUCUGUAACAGCUCGAUGCACUUCCUACCCUUU---UU----ACAGUUUUUCCCCCU--CUUCAAAGUCCAU
....((((((((((.((((((.(((.((.((((((((..(((((....)))))..)))))))).)).))))))))---).----.))))))))))....--............. ( -33.60)
>DroSim_CAF1 22541 105 + 1
GCCUGGGAAAAUUGCAAGAGGCGUGAGAUGUGCAUCGCAUUGUUCUGUAACAGCUCGAUGCACUUCCUACCCUUU---UU----CCAGUUUUUCCCCCU--CUUCAAAGUCCAU
....((((((((((.((((((.(((.((.((((((((..(((((....)))))..)))))))).)).))))))))---).----.))))))))))....--............. ( -36.30)
>DroEre_CAF1 23633 96 + 1
GCCUGGGAAAACUGCAAGAGGCGUGAGAUGUGCAGCGCAUUGUUCUGUAACAGCUCGAUACACUUCCUACCCGCU---UU----CCAGUUUUCCC-----------AAGUCCAU
((.(((((((((((.(((.((.(((.((.(((...((..(((((....)))))..))...))).)).))))).))---).----.))))))))))-----------).)).... ( -32.10)
>DroYak_CAF1 23627 109 + 1
GCCUGGGAAAACUGCAGGAGGCGUGAGAUGUGCAUCGCAUUGUUCUGUAACAACUCGAUGCACUUCCUACCCUUU---CUCUACCCAGUUUUCCCCCCC--CUGCAAAGUCCAU
....((((((((((.((((((.(((.((.((((((((..(((((....)))))..)))))))).)).))).))))---)).....))))))))))....--............. ( -39.20)
>consensus
GCCUGGGAAAAUUGCAAGAGGCGUGAGAUGUGCAUCGCAUUGUUCUGUAACAGCUCGAUGCACUUCCUACCCUUU___UU____CCAGUUUUUCCCCCU__CUUCAAAGUCCAU
....((((((((((..(((((.(((.((.((((((((..(((((....)))))..)))))))).)).))))))))..........))))))))))................... (-30.94 = -30.46 +  -0.48)

alignment

secondary structure

dotplot

Window 7

Location	14,402,491 – 14,402,601
Length	110
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	87.38
Mean single sequence MFE	-35.50
Consensus MFE	-24.14
Energy contribution	-24.78
Covariance contribution	0.64
Combinations/Pair	1.11
Mean z-score	-2.72
Structure conservation index	0.68
SVM decision value	0.89
SVM RNA-class probability	0.874905
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14402491 110 - 22407834
AUGGACUUUGAAGGGAGUGGAAAAAACUGG----AAAAAAAAGGGUAGGAAGUGCAUCGAGCUGUUACAGAACAAUGCGAUGCACAUCUCACGCCUCUUGGAAUUUUCCCAGGC
....((((......))))........((((----((((..((((((.(((.((((((((...((((....))))...)))))))).)))...))).)))....)))).)))).. ( -30.60)
>DroSec_CAF1 23637 105 - 1
AUGGACUUUGAAG--AGGGGGAAAAACUGU----AA---AAAGGGUAGGAAGUGCAUCGAGCUGUUACAGAACAAUGCAAUGCACAUCUCACGCCUCUUGCAAUUUUCCCAGGC
.....(((....)--)).(((((((..(((----((---..(((((..((.((((((.(...((((....))))...).)))))).))..)).))).))))).))))))).... ( -30.10)
>DroSim_CAF1 22541 105 - 1
AUGGACUUUGAAG--AGGGGGAAAAACUGG----AA---AAAGGGUAGGAAGUGCAUCGAGCUGUUACAGAACAAUGCGAUGCACAUCUCACGCCUCUUGCAAUUUUCCCAGGC
.....(((....)--)).(((((((..((.----((---..(((((..((.((((((((...((((....))))...)))))))).))..)).))).)).)).))))))).... ( -33.50)
>DroEre_CAF1 23633 96 - 1
AUGGACUU-----------GGGAAAACUGG----AA---AGCGGGUAGGAAGUGUAUCGAGCUGUUACAGAACAAUGCGCUGCACAUCUCACGCCUCUUGCAGUUUUCCCAGGC
.....(((-----------((((((((((.----.(---((.((((..((.(((((.((...((((....))))...)).))))).))..)).)).))).))))))))))))). ( -39.90)
>DroYak_CAF1 23627 109 - 1
AUGGACUUUGCAG--GGGGGGGAAAACUGGGUAGAG---AAAGGGUAGGAAGUGCAUCGAGUUGUUACAGAACAAUGCGAUGCACAUCUCACGCCUCCUGCAGUUUUCCCAGGC
..(((..((((((--((((((.....))........---.....((..((.((((((((.((((((....)))))).)))))))).))..)).))))))))))...)))..... ( -43.40)
>consensus
AUGGACUUUGAAG__AGGGGGAAAAACUGG____AA___AAAGGGUAGGAAGUGCAUCGAGCUGUUACAGAACAAUGCGAUGCACAUCUCACGCCUCUUGCAAUUUUCCCAGGC
..................(((((((...((...........(((((..((.((((((((...((((....))))...)))))))).))..)).))))).....))))))).... (-24.14 = -24.78 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:37 2006