Locus 6318

Sequence ID	2L_DroMel_CAF1
Location	17,616,272 – 17,616,412
Length	140
Max. P	0.999967

overview

Window 8

Location	17,616,272 – 17,616,372
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	96.20
Mean single sequence MFE	-32.00
Consensus MFE	-28.24
Energy contribution	-28.20
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-3.24
Structure conservation index	0.88
SVM decision value	3.91
SVM RNA-class probability	0.999699
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17616272 100 + 22407834
CCACUAUCGCUGGCCGUAUCUUGCUGCCAAAUUCGCUGAUUCACGUAAUUUGCCGCGACUGCAGCAGCGACAACGGCCAAAAGCCACGGCCAACAACCAA
........(.(((((((...(((((((((((((((........)).))))))..((....)).)))))))....(((.....)))))))))).)...... ( -31.80)
>DroSec_CAF1 11598 100 + 1
CCACUAUCGCUGGCCGUAUCUUUCUGCCAAAUUCGCUGAUUCACGUAAUUUGCCGCGACUGCAGCAGCGACAACGGCCAAAAGCCACGGCCAAAAACCAA
..........(((((((..((((..(((....((((((...(((((........)))..))...))))))....)))..))))..)))))))........ ( -31.10)
>DroSim_CAF1 1840 100 + 1
CCACUAUCGCUGGCCGUAUCUUGCUGCCAAAUUCGCUGAUUCACGUAAUUUGCCGCGACUGCAGCAGCGACAACGGCCAAAAGCCACGGCCAACAACCAA
........(.(((((((...(((((((((((((((........)).))))))..((....)).)))))))....(((.....)))))))))).)...... ( -31.80)
>DroEre_CAF1 80 100 + 1
CCUCUAUCGUUGGCCGUAUCUUGCUGCCAAAUUCGCUGAUUCACGUAAUUUCCCGCGACUGCAGCAGCGACAACGGCCAAAAGCCAUGGCCAACAACCAA
........(((((((((...(((((((.....((((.((...........))..)))).....)))))))....(((.....))))))))))))...... ( -33.50)
>DroYak_CAF1 11547 100 + 1
CCACUAUCGUUGGCCGUAUCUUGCUGCCAAAUUCGCUGAUUCACGUAAUUUCCCGCGACUGCAGCACCGACAACGGCCAAAAGCCAUGGCCAGCAACCAA
........(((((((((....((((((.....((((.((...........))..))))..))))))........(((.....))))))))))))...... ( -31.80)
>consensus
CCACUAUCGCUGGCCGUAUCUUGCUGCCAAAUUCGCUGAUUCACGUAAUUUGCCGCGACUGCAGCAGCGACAACGGCCAAAAGCCACGGCCAACAACCAA
..........(((((((..(((...(((....((((((...(((((........)))..))...))))))....)))...)))..)))))))........ (-28.24 = -28.20 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	17,616,272 – 17,616,372
Length	100
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	96.20
Mean single sequence MFE	-43.54
Consensus MFE	-41.08
Energy contribution	-41.96
Covariance contribution	0.88
Combinations/Pair	1.03
Mean z-score	-3.69
Structure conservation index	0.94
SVM decision value	4.99
SVM RNA-class probability	0.999967
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17616272 100 - 22407834
UUGGUUGUUGGCCGUGGCUUUUGGCCGUUGUCGCUGCUGCAGUCGCGGCAAAUUACGUGAAUCAGCGAAUUUGGCAGCAAGAUACGGCCAGCGAUAGUGG
...(((((((((((((.(((...((((...((((((......(((((........)))))..))))))...))))...))).)))))))))))))..... ( -46.30)
>DroSec_CAF1 11598 100 - 1
UUGGUUUUUGGCCGUGGCUUUUGGCCGUUGUCGCUGCUGCAGUCGCGGCAAAUUACGUGAAUCAGCGAAUUUGGCAGAAAGAUACGGCCAGCGAUAGUGG
...(((.(((((((((.(((((.((((...((((((......(((((........)))))..))))))...)))).))))).))))))))).)))..... ( -43.40)
>DroSim_CAF1 1840 100 - 1
UUGGUUGUUGGCCGUGGCUUUUGGCCGUUGUCGCUGCUGCAGUCGCGGCAAAUUACGUGAAUCAGCGAAUUUGGCAGCAAGAUACGGCCAGCGAUAGUGG
...(((((((((((((.(((...((((...((((((......(((((........)))))..))))))...))))...))).)))))))))))))..... ( -46.30)
>DroEre_CAF1 80 100 - 1
UUGGUUGUUGGCCAUGGCUUUUGGCCGUUGUCGCUGCUGCAGUCGCGGGAAAUUACGUGAAUCAGCGAAUUUGGCAGCAAGAUACGGCCAACGAUAGAGG
...((((((((((..(((.....)))(((((((.(((((...(((((........)))))..)))))....))))))).......))))))))))..... ( -42.40)
>DroYak_CAF1 11547 100 - 1
UUGGUUGCUGGCCAUGGCUUUUGGCCGUUGUCGGUGCUGCAGUCGCGGGAAAUUACGUGAAUCAGCGAAUUUGGCAGCAAGAUACGGCCAACGAUAGUGG
...((((.(((((..(((.....)))(((((((.(((((...(((((........)))))..)))))....))))))).......))))).))))..... ( -39.30)
>consensus
UUGGUUGUUGGCCGUGGCUUUUGGCCGUUGUCGCUGCUGCAGUCGCGGCAAAUUACGUGAAUCAGCGAAUUUGGCAGCAAGAUACGGCCAGCGAUAGUGG
...(((((((((((((.(((...((((...((((((......(((((........)))))..))))))...))))...))).)))))))))))))..... (-41.08 = -41.96 +   0.88)

alignment

secondary structure

dotplot

Window 0

Location	17,616,312 – 17,616,412
Length	100
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	81.08
Mean single sequence MFE	-42.03
Consensus MFE	-20.77
Energy contribution	-21.75
Covariance contribution	0.98
Combinations/Pair	1.24
Mean z-score	-3.02
Structure conservation index	0.49
SVM decision value	0.83
SVM RNA-class probability	0.861754
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17616312 100 - 22407834
UAGUGGCGGGAGAGACAACACAUUGGCUACGGCUUUGGCUUUGGUUGUUGGCCGUGG-----CUUUUGGCCGUUGUCGCUG------CUGCAGUCGCGGCAAAUUACGUGA
.....((((.((.((((((.((..((((((((((.((((....))))..))))))))-----))..))...)))))).)).------))))..(((((........))))) ( -44.70)
>DroPse_CAF1 3281 103 - 1
UAAUGGGG-CAGUGGCAUGACAUUG-------CUUUGGCUUUGGGCCUGGACCAUGAUGUCGGUUGUCGGUGCCGUCGCUGUUGUGCCUGCAGUCGCGGCAAAUUACGUGA
..(((.((-((.((((((((((((.-------((..(((.....))).)).....)))))))..))))).))))(((((..((((....))))..)))))......))).. ( -36.40)
>DroSec_CAF1 11638 100 - 1
UAGUGGCGGGUGAGACAACACAUUGGCUACGGCUUUGGCUUUGGUUUUUGGCCGUGG-----CUUUUGGCCGUUGUCGCUG------CUGCAGUCGCGGCAAAUUACGUGA
..(..((((....((((((.((..((((((((((..(((....)))...))))))))-----))..))...)))))).)))------)..)..(((((........))))) ( -44.60)
>DroSim_CAF1 1880 100 - 1
UAGUGGCGGGUGAGACAACACAUUGGCUACGGCUUUGGCUUUGGUUGUUGGCCGUGG-----CUUUUGGCCGUUGUCGCUG------CUGCAGUCGCGGCAAAUUACGUGA
..(..((((....((((((.((..((((((((((.((((....))))..))))))))-----))..))...)))))).)))------)..)..(((((........))))) ( -43.90)
>DroEre_CAF1 120 99 - 1
UAAUGGCCGGA-CGACAAGCCAUUGGCUAUGGUAUUGGCUUUGGUUGUUGGCCAUGG-----CUUUUGGCCGUUGUCGCUG------CUGCAGUCGCGGGAAAUUACGUGA
....(((.(((-((((..((((..(((((((((..((((....))))...)))))))-----))..)))).)))))).).)------))....(((((........))))) ( -40.00)
>DroYak_CAF1 11587 99 - 1
UAUUUGCGGGA-CGACAACACAUUGGCUAUGGUAUUGGCUUUGGUUGCUGGCCAUGG-----CUUUUGGCCGUUGUCGGUG------CUGCAGUCGCGGGAAAUUACGUGA
...((((((.(-(((((((.((..(((((((((...(((.......))).)))))))-----))..))...)))))).)).------))))))(((((........))))) ( -42.60)
>consensus
UAGUGGCGGGAGAGACAACACAUUGGCUACGGCUUUGGCUUUGGUUGUUGGCCAUGG_____CUUUUGGCCGUUGUCGCUG______CUGCAGUCGCGGCAAAUUACGUGA
.............((((((.....(((((.(((....))).)))))...(((((..(......)..)))))))))))................(((((........))))) (-20.77 = -21.75 +   0.98)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:11 2006