Locus 4484

Sequence ID	X_DroMel_CAF1
Location	11,868,323 – 11,868,436
Length	113
Max. P	0.722337

overview

Window 0

Location	11,868,323 – 11,868,436
Length	113
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	81.18
Mean single sequence MFE	-37.10
Consensus MFE	-27.08
Energy contribution	-27.58
Covariance contribution	0.50
Combinations/Pair	1.17
Mean z-score	-1.57
Structure conservation index	0.73
SVM decision value	0.40
SVM RNA-class probability	0.722337
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11868323 113 + 22224390
UUUUAUAUUUUACUGCAAUUU----CCAGUCCUUUGAGACGGUAUCCAAUAGCAUAAUGCUGGCCCUGCUCUGCUUGGCCACCAACAAGGGUGAUUGCCAGCGACGUUUGCUGGCGG
...........((((......----.))))((((((....(((.......(((.....)))((((..((...))..)))))))..))))))....(((((((((...))))))))). ( -32.80)
>DroSec_CAF1 1704 105 + 1
U--------UUACCCCCGUUU----CCAGUCCUUUGAGACGGUGUCCAAUAGCAUAAUGCUGGCCCUGCUCUGCUUGGCCACCAACAAGGGCGACUGCCAGCGACGUUUGCUGGCGG
.--------......((((((----(.........)))))))(((((...(((.....)))((((..((...))..))))........))))).((((((((((...)))))))))) ( -39.80)
>DroSim_CAF1 1650 105 + 1
U--------UUACUCCCGUUU----CCAGUCCUUUGAGACGGUGUCCAAUAGCAUAAUGCUGGCCCUGCUCUGCUUGGCCACCAACAAGGGCGACUGCCAGCGACGCUUGCUGGCGG
.--------......((((((----(.........)))))))(((((...(((.....)))((((..((...))..))))........))))).((((((((((...)))))))))) ( -39.80)
>DroEre_CAF1 3365 100 + 1
-----------------AUUUCCUGCCAGUCCUUUGAGACGGUGUCCAAUAGCAUAAUGCUGGCCCUGCUCUGCCUGGCCACCAACAAGAGCGACUGCCAGCAACGAUUGCUGGCGG
-----------------.....((((((((...(((.....((((......))))..(((((((..((((((...(((...)))...))))))...))))))).)))..)))))))) ( -38.10)
>DroYak_CAF1 1609 96 + 1
-----------------AUUU----GCAGUCCUUCGAGACGGUGUCCAAUAGCAUAAUGCUGGCCCUCCUCUGCUUGGCCACCAACAAGGGCGUCUGCCAGCGUCGCUUGCUGGCGG
-----------------....----...((((((...(..((((.((((((((.....))))((........)))))).))))..)))))))..(((((((((.....))))))))) ( -34.90)
>DroMoj_CAF1 12890 97 + 1
----------------UCCUU----GCAGUCCUUUGAGACCGUCUCGAAUAGCAUUAUGAUCGCGCUGCUCUGCCUGGCCACGCACAAGGGCGACUGCCAGCAGCGCCUGCGCGCGG
----------------....(----((.((..((((((.....))))))..)).........((((.((.((((.((((..(((......)))...)))))))).))..))))))). ( -37.20)
>consensus
_________________AUUU____CCAGUCCUUUGAGACGGUGUCCAAUAGCAUAAUGCUGGCCCUGCUCUGCUUGGCCACCAACAAGGGCGACUGCCAGCGACGCUUGCUGGCGG
............................((((((...(..((((.(((.((((.....))))((........)).))).))))..)))))))..((((((((((...)))))))))) (-27.08 = -27.58 +   0.50)

alignment

secondary structure

dotplot

Window 1

Location	11,868,323 – 11,868,436
Length	113
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	81.18
Mean single sequence MFE	-37.70
Consensus MFE	-26.53
Energy contribution	-26.65
Covariance contribution	0.12
Combinations/Pair	1.20
Mean z-score	-1.44
Structure conservation index	0.70
SVM decision value	0.20
SVM RNA-class probability	0.629725
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11868323 113 - 22224390
CCGCCAGCAAACGUCGCUGGCAAUCACCCUUGUUGGUGGCCAAGCAGAGCAGGGCCAGCAUUAUGCUAUUGGAUACCGUCUCAAAGGACUGG----AAAUUGCAGUAAAAUAUAAAA
..((((((.......)))))).....((.(((.((((((((..((...))..))))(((.....))).......))))...))).))((((.----......))))........... ( -33.20)
>DroSec_CAF1 1704 105 - 1
CCGCCAGCAAACGUCGCUGGCAGUCGCCCUUGUUGGUGGCCAAGCAGAGCAGGGCCAGCAUUAUGCUAUUGGACACCGUCUCAAAGGACUGG----AAACGGGGGUAA--------A
..((((((.......))))))....(((((((((((((.((((....((((..(....)....)))).)))).))))((((....))))...----.)))))))))..--------. ( -42.90)
>DroSim_CAF1 1650 105 - 1
CCGCCAGCAAGCGUCGCUGGCAGUCGCCCUUGUUGGUGGCCAAGCAGAGCAGGGCCAGCAUUAUGCUAUUGGACACCGUCUCAAAGGACUGG----AAACGGGAGUAA--------A
..((((((.......))))))(.((.((.(((.(((((.((((....((((..(....)....)))).)))).)))))...))).)).(((.----...))))).)..--------. ( -37.20)
>DroEre_CAF1 3365 100 - 1
CCGCCAGCAAUCGUUGCUGGCAGUCGCUCUUGUUGGUGGCCAGGCAGAGCAGGGCCAGCAUUAUGCUAUUGGACACCGUCUCAAAGGACUGGCAGGAAAU-----------------
..(((((((.....)))))))......(((((((((((.((((((........)))(((.....)))..))).))))((((....)))).)))))))...----------------- ( -39.10)
>DroYak_CAF1 1609 96 - 1
CCGCCAGCAAGCGACGCUGGCAGACGCCCUUGUUGGUGGCCAAGCAGAGGAGGGCCAGCAUUAUGCUAUUGGACACCGUCUCGAAGGACUGC----AAAU-----------------
(((((((((((.......(((....))))))))))))))....((((.(..((.(((((.....))...)))...))..)((....))))))----....----------------- ( -33.51)
>DroMoj_CAF1 12890 97 - 1
CCGCGCGCAGGCGCUGCUGGCAGUCGCCCUUGUGCGUGGCCAGGCAGAGCAGCGCGAUCAUAAUGCUAUUCGAGACGGUCUCAAAGGACUGC----AAGGA----------------
((((((((((((((((....))).))))..)))))))))((..((((((((............))))....(((.....)))......))))----..)).---------------- ( -40.30)
>consensus
CCGCCAGCAAGCGUCGCUGGCAGUCGCCCUUGUUGGUGGCCAAGCAGAGCAGGGCCAGCAUUAUGCUAUUGGACACCGUCUCAAAGGACUGG____AAAU_________________
..((((((.......)))))).....((.(((.(((((.((((....((((..(....)....)))).)))).)))))...))).)).............................. (-26.53 = -26.65 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:14 2006