Locus 3836

Sequence ID	2L_DroMel_CAF1
Location	11,209,296 – 11,209,426
Length	130
Max. P	0.999870

overview

Window 3

Location	11,209,296 – 11,209,386
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-28.08
Consensus MFE	-24.38
Energy contribution	-24.82
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.69
Structure conservation index	0.87
SVM decision value	0.87
SVM RNA-class probability	0.870084
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11209296 90 + 22407834
UCGCUCCAAUGGAAGCGCUUGACGUGCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCACCAACUUGCGCUCCCUUUUUGGGA
....(((((.((.(((((.((.(((((.((.(((((((.....))))))).....)).))))).)).......))))).))...))))). ( -27.70)
>DroSec_CAF1 45166 90 + 1
UCGCUCCAAUGGAAGCGCUUGACGUGCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUGGGA
....(((((.((.(((((..(....((((..(((((((.....))))))))))).((.(....).))...)..))))).))...))))). ( -27.50)
>DroSim_CAF1 47056 90 + 1
UCGCUCCAAUGGAAGCGCUUGACGUGCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUGGGA
....(((((.((.(((((..(....((((..(((((((.....))))))))))).((.(....).))...)..))))).))...))))). ( -27.50)
>DroEre_CAF1 45692 89 + 1
UCGCUCCAAUGGAAGCGCUUGACGCGCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUU-UUUGGA
....(((((.((.(((((..(..((((((..(((((((.....))))))))))).)).((.....))...)..))))).))..-.))))) ( -30.00)
>DroYak_CAF1 47200 90 + 1
UCGCUCCAAUGGAAGCGCUUGACGUGCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUUGGA
....(((((.((.(((((..(....((((..(((((((.....))))))))))).((.(....).))...)..))))).))....))))) ( -27.70)
>consensus
UCGCUCCAAUGGAAGCGCUUGACGUGCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUGGGA
....(((((.((.(((((..(..((((((..(((((((.....))))))))))).)).((.....))...)..))))).))...))))). (-24.38 = -24.82 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	11,209,296 – 11,209,386
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-35.12
Consensus MFE	-32.74
Energy contribution	-32.58
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-3.56
Structure conservation index	0.93
SVM decision value	4.32
SVM RNA-class probability	0.999870
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11209296 90 - 22407834
UCCCAAAAAGGGAGCGCAAGUUGGUGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGA
..((((...((((((((.(((((.((.....)).)))))..((((((.....)))))).(((.....)))..)))))))).))))..... ( -32.60)
>DroSec_CAF1 45166 90 - 1
UCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGA
..((((...((((((((.(((((.((.....)).)))))..((((((.....)))))).(((.....)))..)))))))).))))..... ( -35.80)
>DroSim_CAF1 47056 90 - 1
UCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGA
..((((...((((((((.(((((.((.....)).)))))..((((((.....)))))).(((.....)))..)))))))).))))..... ( -35.80)
>DroEre_CAF1 45692 89 - 1
UCCAAA-AAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCGCGUCAAGCGCUUCCAUUGGAGCGA
(((((.-..((((((((.(((((.((.....)).)))))..((((((.....)))))).(((.....)))..)))))))).))))).... ( -36.00)
>DroYak_CAF1 47200 90 - 1
UCCAAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGA
(((((....((((((((.(((((.((.....)).)))))..((((((.....)))))).(((.....)))..)))))))).))))).... ( -35.40)
>consensus
UCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGA
(((.((...((((((((.(((((.((.....)).)))))..((((((.....)))))).(((.....)))..)))))))).))))).... (-32.74 = -32.58 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	11,209,306 – 11,209,426
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.38
Mean single sequence MFE	-38.63
Consensus MFE	-33.01
Energy contribution	-33.98
Covariance contribution	0.97
Combinations/Pair	1.12
Mean z-score	-1.85
Structure conservation index	0.85
SVM decision value	0.52
SVM RNA-class probability	0.767988
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11209306 120 - 22407834
AGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAAAAGGGAGCGCAAGUUGGUGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCC
........(((.((....((((((((((((((((((....((((.....))))((....))..)))))..((....))...))))))).))))))....(((.....)))....)).))) ( -37.80)
>DroSec_CAF1 45176 120 - 1
AAAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCC
........(((.((....(((((((((((((......((((((......))))))...(((((.((.....)).)))))..))))))).))))))....(((.....)))....)).))) ( -38.70)
>DroSim_CAF1 47066 120 - 1
AGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCC
........(((.((....(((((((((((((......((((((......))))))...(((((.((.....)).)))))..))))))).))))))....(((.....)))....)).))) ( -38.70)
>DroEre_CAF1 45702 112 - 1
-------CGGAUGCAGCGAUCUGUGGAUGCAGCCGCAGCUUCCAAA-AAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCGCGUCAAGCGCUUCC
-------.(((...((((..((...(((((.((((((((((((...-..))))))((......))....)))))).(((..((((((.....))))))....)))))))).))))))))) ( -45.30)
>DroYak_CAF1 47210 120 - 1
AGAGUUUCGGUUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCAAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCC
.(((((..(((((((.(........).)))))))..)))))........((((((((.(((((.((.....)).)))))..((((((.....)))))).(((.....)))..)))))))) ( -42.50)
>DroAna_CAF1 41544 100 - 1
---------GAUGCAACGAUCUGAAGAUGCAGUAUCU-----------GGGGAUCUCUAGCCAGCGGCAUGCGGUAGCUAAUGUAUCUAAUAGAUACACGACAGCAUGUCAAACGCUUCC
---------((.((...(((((..(((((...)))))-----------..)))))..........(((((((.((......((((((.....))))))..)).)))))))....)).)). ( -28.80)
>consensus
AGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCC
........(((.((....(((((((((((((......((((((......))))))...(((((.((.....)).)))))..))))))).))))))....(((.....)))....)).))) (-33.01 = -33.98 +   0.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:37 2006