Locus 4293

Sequence ID	3L_DroMel_CAF1
Location	12,597,878 – 12,597,977
Length	99
Max. P	0.925545

overview

Window 1

Location	12,597,878 – 12,597,977
Length	99
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	79.07
Mean single sequence MFE	-33.10
Consensus MFE	-21.74
Energy contribution	-20.77
Covariance contribution	-0.97
Combinations/Pair	1.27
Mean z-score	-2.13
Structure conservation index	0.66
SVM decision value	1.17
SVM RNA-class probability	0.925545
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12597878 99 + 23771897
UUUUAUGGCUGCGCCGUGGCAAUAAAAUCGCCAACAAGGCCAAUAACUCAUUCUAGAGCGCUG------GCGCUGCAGUUGGUAGUUUGCUAGUUGG-UAGUUGGA
((((((.((..(...)..)).))))))...(((((...((((....(((......))).((((------(((((((.....)))))..)))))))))-).))))). ( -30.60)
>DroPse_CAF1 87807 84 + 1
UUUUAUGGCUGCGCUGUGGCAAUAAAAUCGCCAACAAGCUCUAUAACUCAUUCUAGAGCGCUGG--CUGGCGCUGCAG--GGCGGCCG------------------
......((((((.(((..((.........((((.((.((((((..........))))))..)).--.))))))..)))--.)))))).------------------ ( -37.40)
>DroEre_CAF1 89078 99 + 1
UUUUAUGGCUGCGCCGUGGCAAUAAAAUCGCCAACAAGACCAAUAACUCAUUCUAGAGCGCUG------GCGCUGCAGUUGGUAGUUGGCUAGUUGG-UAGUUGGA
..(((((((...)))))))......(((..(((((.((.(((((.((.((..((..((((...------.))))..)).)))).))))))).)))))-..)))... ( -31.40)
>DroYak_CAF1 88898 106 + 1
UUUUAUGGCUGCGCCGUGGCAAUAAAAUCGCCAACAAGGCCAAUAACUCAUUCUACAGCGCUGGCGCUGGCGCUGCAGUUGGUAGUUGUCCAGUUGCCCAGUUGGU
((((((.((..(...)..)).))))))..((((((..(((..(((((((...((.(((((((......))))))).))...).))))))......)))..)))))) ( -35.30)
>DroAna_CAF1 82351 80 + 1
UUUUAUGGCUGCGCCGUGGCAAUAAAAUCGCCAACAAGGCCAAUAACUCAUUCUAGAGCGCUG------GCGCUGCAG--GGCGGCUG------------------
......(((((((((.((((.........))))....)))...........(((..((((...------.))))..))--))))))).------------------ ( -26.50)
>DroPer_CAF1 89777 84 + 1
UUUUAUGGCUGCGCUGUGGCAAUAAAAUCGCCAACAAGCUCUAUAACUCAUUCUAGAGCGCUGG--CUGGCGCUGCAG--GGCGGCCG------------------
......((((((.(((..((.........((((.((.((((((..........))))))..)).--.))))))..)))--.)))))).------------------ ( -37.40)
>consensus
UUUUAUGGCUGCGCCGUGGCAAUAAAAUCGCCAACAAGGCCAAUAACUCAUUCUAGAGCGCUG______GCGCUGCAG__GGCAGCUG__________________
......((((((....((((.........)))).......................(((((........))))).......))))))................... (-21.74 = -20.77 +  -0.97)

alignment

secondary structure

dotplot

Window 2

Location	12,597,878 – 12,597,977
Length	99
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	79.07
Mean single sequence MFE	-28.57
Consensus MFE	-19.43
Energy contribution	-19.43
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.68
SVM decision value	0.72
SVM RNA-class probability	0.833474
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12597878 99 - 23771897
UCCAACUA-CCAACUAGCAAACUACCAACUGCAGCGC------CAGCGCUCUAGAAUGAGUUAUUGGCCUUGUUGGCGAUUUUAUUGCCACGGCGCAGCCAUAAAA
........-...................((((.((((------(((.((((......))))..)))))..(((.((((((...)))))))))))))))........ ( -24.40)
>DroPse_CAF1 87807 84 - 1
------------------CGGCCGCC--CUGCAGCGCCAG--CCAGCGCUCUAGAAUGAGUUAUAGAGCUUGUUGGCGAUUUUAUUGCCACAGCGCAGCCAUAAAA
------------------.(((.((.--(((..(((...(--(((((((((((..........))))))..))))))........)))..))).)).)))...... ( -29.50)
>DroEre_CAF1 89078 99 - 1
UCCAACUA-CCAACUAGCCAACUACCAACUGCAGCGC------CAGCGCUCUAGAAUGAGUUAUUGGUCUUGUUGGCGAUUUUAUUGCCACGGCGCAGCCAUAAAA
........-..(((.((((((..((((.(((.((((.------...)))).)))..)).))..)))).)).)))((((((...))))))..(((...)))...... ( -24.50)
>DroYak_CAF1 88898 106 - 1
ACCAACUGGGCAACUGGACAACUACCAACUGCAGCGCCAGCGCCAGCGCUGUAGAAUGAGUUAUUGGCCUUGUUGGCGAUUUUAUUGCCACGGCGCAGCCAUAAAA
.....(..(....)..)..((((.....(((((((((........)))))))))....))))..((((..((((((((((...)))))))..)))..))))..... ( -36.70)
>DroAna_CAF1 82351 80 - 1
------------------CAGCCGCC--CUGCAGCGC------CAGCGCUCUAGAAUGAGUUAUUGGCCUUGUUGGCGAUUUUAUUGCCACGGCGCAGCCAUAAAA
------------------..((((..--..((((.((------(((.((((......))))..))))).))))(((((((...)))))))))))............ ( -26.80)
>DroPer_CAF1 89777 84 - 1
------------------CGGCCGCC--CUGCAGCGCCAG--CCAGCGCUCUAGAAUGAGUUAUAGAGCUUGUUGGCGAUUUUAUUGCCACAGCGCAGCCAUAAAA
------------------.(((.((.--(((..(((...(--(((((((((((..........))))))..))))))........)))..))).)).)))...... ( -29.50)
>consensus
__________________CAACCACC__CUGCAGCGC______CAGCGCUCUAGAAUGAGUUAUUGGCCUUGUUGGCGAUUUUAUUGCCACGGCGCAGCCAUAAAA
............................(((((((((........)))))....((..((........))..))((((((...)))))).....))))........ (-19.43 = -19.43 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:48 2006