Locus 5541

Sequence ID	X_DroMel_CAF1
Location	14,337,999 – 14,338,129
Length	130
Max. P	0.988730

overview

Window 4

Location	14,337,999 – 14,338,090
Length	91
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	95.38
Mean single sequence MFE	-26.98
Consensus MFE	-23.58
Energy contribution	-24.22
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.97
Structure conservation index	0.87
SVM decision value	2.13
SVM RNA-class probability	0.988730
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14337999 91 - 22224390
CAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAAAAUUUUGGGCAUGCAUCAGUCAACCGGGCGGAGAAAGAGA
........(((((.(((((...)))))(((((..((((((.(((((......))))).))).))).)))))......)))))......... ( -30.10)
>DroSec_CAF1 50009 91 - 1
CAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAAAAUUUUGGGCAUGCAUCAGUCAACCGGACGGAGAAAGAGA
........(((((.(((((...)))))(((((..((((((.(((((......))))).))).))).))))).....)).)))......... ( -26.60)
>DroSim_CAF1 48033 91 - 1
CAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAAAAUUUUGGGCAUGCAUCAGUCAACCGGACGGAGAAAGAGA
........(((((.(((((...)))))(((((..((((((.(((((......))))).))).))).))))).....)).)))......... ( -26.60)
>DroEre_CAF1 49013 91 - 1
CAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAGUUCGAAAAUGCUGGGCAUGCAUCAGUCAACCGGACGGAGAAAGAGA
........(((((.(((((...)))))(((((..((((((...(((........))).))).))).))))).....)).)))......... ( -23.30)
>DroYak_CAF1 52511 90 - 1
CAUCAUAACUGCCGAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAAAAUGUUG-GCAUGCAUCAGUCCGCCGGACGGCGAAAGAGA
.........(((((((((......((.((((....))))))...((((.((....)).-))))))))).((((...))))))))....... ( -28.30)
>consensus
CAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAAAAUUUUGGGCAUGCAUCAGUCAACCGGACGGAGAAAGAGA
........(((((.(((((...)))))(((((..((((((.(((((......))))).))).))).))))).....)).)))......... (-23.58 = -24.22 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	14,338,039 – 14,338,129
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	81.44
Mean single sequence MFE	-24.20
Consensus MFE	-17.69
Energy contribution	-18.44
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.73
SVM decision value	0.80
SVM RNA-class probability	0.853864
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14338039 90 + 22224390
UUCGCAUUUUCGGCUGCCUUCAGCACGCGUUUCGCAUUGGCAGUUAUGAUGCGGUUGCCUUGGCUUCCUCCGUUCUCGCAUCAUUUGCAA
...(((.....(((((((....((.........))...)))))))(((((((((..((...((...))...))..))))))))).))).. ( -27.20)
>DroSec_CAF1 50049 90 + 1
UUCGCAUUUUCGGCUGCCUUCAGCACGCGUUUCGCAUUGGCAGUUAUGAUGCGGUUGCCUUGGCUUCCUUCGUUCUCGCAUCAUUUGCAA
...(((.....(((((((....((.........))...)))))))(((((((((..((...((...))...))..))))))))).))).. ( -27.20)
>DroSim_CAF1 48073 90 + 1
UUCGCAUUUUCGGCUGCCUUCAGCACGCGUUUCGCAUUGGCAGUUAUGAUGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...(((((...(((((((....((.........))...)))))))..)))))...................................... ( -15.60)
>DroEre_CAF1 49053 90 + 1
UUCGAACUUUCGGCUGCCUUCAGCACGCGUUUCGCAUUGGCAGUUAUGAUGCGGUUGCCUUGGCUUCCUUCGUUCUCGCAUCAUUUGCAA
...((((....((..(((..((((.((((((.(((....)).)....))))))))))....)))..))...))))..(((.....))).. ( -24.50)
>DroYak_CAF1 52550 90 + 1
UUCGCAUUUUCGGCUGCCUUCAGCACGCGUUUCGCAUCGGCAGUUAUGAUGCGGUUGCCUUGGCUUCCUUCGUUCUCGCAUCAUUUGCAA
...(((.....(((((((....((.........))...)))))))(((((((((..((...((...))...))..))))))))).))).. ( -26.50)
>consensus
UUCGCAUUUUCGGCUGCCUUCAGCACGCGUUUCGCAUUGGCAGUUAUGAUGCGGUUGCCUUGGCUUCCUUCGUUCUCGCAUCAUUUGCAA
...(((((...(((((((....((.........))...)))))))..)))))((..((....))..)).........(((.....))).. (-17.69 = -18.44 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	14,338,039 – 14,338,129
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	81.44
Mean single sequence MFE	-25.72
Consensus MFE	-16.58
Energy contribution	-19.38
Covariance contribution	2.80
Combinations/Pair	1.00
Mean z-score	-2.83
Structure conservation index	0.64
SVM decision value	2.05
SVM RNA-class probability	0.986587
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14338039 90 - 22224390
UUGCAAAUGAUGCGAGAACGGAGGAAGCCAAGGCAACCGCAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAA
(((((.((((((((.....((......))..(....)))))))))..(((((.(((((...)))))......))))).......))))). ( -28.30)
>DroSec_CAF1 50049 90 - 1
UUGCAAAUGAUGCGAGAACGAAGGAAGCCAAGGCAACCGCAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAA
(((((.((((((((....(....)..((....))...))))))))..(((((.(((((...)))))......))))).......))))). ( -29.50)
>DroSim_CAF1 48073 90 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAA
......................................((((.....(((((.(((((...)))))......)))))......))))... ( -14.00)
>DroEre_CAF1 49053 90 - 1
UUGCAAAUGAUGCGAGAACGAAGGAAGCCAAGGCAACCGCAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAGUUCGAA
..(((.((((((((....(....)..((....))...))))))))...))).....((((...((.((((....))))))....)))).. ( -27.30)
>DroYak_CAF1 52550 90 - 1
UUGCAAAUGAUGCGAGAACGAAGGAAGCCAAGGCAACCGCAUCAUAACUGCCGAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAA
(((((.((((((((....(....)..((....))...))))))))..(((((.(((((...)))))......))))).......))))). ( -29.50)
>consensus
UUGCAAAUGAUGCGAGAACGAAGGAAGCCAAGGCAACCGCAUCAUAACUGCCAAUGCGAAACGCGUGCUGAAGGCAGCCGAAAAUGCGAA
(((((.((((((((....(....)..((....))...))))))))..(((((.(((((...)))))......))))).......))))). (-16.58 = -19.38 +   2.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:50:31 2006