Locus 5360

Sequence ID	X_DroMel_CAF1
Location	13,954,658 – 13,954,767
Length	109
Max. P	0.849850

overview

Window 7

Location	13,954,658 – 13,954,767
Length	109
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	86.59
Mean single sequence MFE	-41.10
Consensus MFE	-30.99
Energy contribution	-31.17
Covariance contribution	0.19
Combinations/Pair	1.19
Mean z-score	-2.00
Structure conservation index	0.75
SVM decision value	0.78
SVM RNA-class probability	0.849850
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13954658 109 + 22224390
G--GGGGGGGUGGUGCUAGGUGAGGAGCCGGCGAAUGGAAUUGCCAACU-------GACAACGUGGGCGGCAACAUCUCGCACAGUUGGCAACAUUCUAUUUUCCAAUUCUUCCGAAG
(--((((((.(((.(((.(((.....))))))(((((((((((((((((-------(.....(((((.(....)..))))).)))))))))..))))))))).))).))))))).... ( -42.40)
>DroSec_CAF1 6101 110 + 1
GU-UGGGGGGAGGGGUGAGGCGUGGAGCCGGCGAAUGGAAUUGCCAACU-------GACAACGUGGGCGGCAACAUCUCGCACAGUUGGCAACAUUCUAUUUUCCAAUUCUUUCGAAG
.(-((..((((.......(((.....)))((.(((((((((((((((((-------(.....(((((.(....)..))))).)))))))))..))))))))).))..))))..))).. ( -42.80)
>DroSim_CAF1 6503 111 + 1
GUUUGGGGGGAGGGGUGAGGCGUGGAGCCGGCGAAUGGAAUUGCCAACU-------GACAACGUGGGCGGCAACAUCUCGCACAGUUGGCAACAUUCUAUUUUCCAAUUCUUUCGAAG
.((((..((((.......(((.....)))((.(((((((((((((((((-------(.....(((((.(....)..))))).)))))))))..))))))))).))..))))..)))). ( -43.70)
>DroYak_CAF1 6539 118 + 1
GGAUGGCAAAGGGGGGGAUACGGGGAGCUGGCAAAUGAAAUUGCCAACUGACAACUGACAACGUGGGCGGCAACAUCUUGCACAGUUGGCAACAUUCUAUUUUCCAAUUCUUCCGAAG
...........((((((((...(((((.(((..((((...((((((((((...........((....))((((....)))).))))))))))))))))).))))).)))))))).... ( -35.50)
>consensus
GU_UGGGGGGAGGGGUGAGGCGUGGAGCCGGCGAAUGGAAUUGCCAACU_______GACAACGUGGGCGGCAACAUCUCGCACAGUUGGCAACAUUCUAUUUUCCAAUUCUUCCGAAG
....(((((((.......(((.....)))((.(((((((((((((((((.......(....)(((((.(....)..)))))..))))))))..))))))))).))..))))))).... (-30.99 = -31.17 +   0.19)

alignment

secondary structure

dotplot

Window 8

Location	13,954,658 – 13,954,767
Length	109
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	86.59
Mean single sequence MFE	-31.77
Consensus MFE	-23.23
Energy contribution	-22.85
Covariance contribution	-0.38
Combinations/Pair	1.08
Mean z-score	-1.49
Structure conservation index	0.73
SVM decision value	0.07
SVM RNA-class probability	0.570180
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13954658 109 - 22224390
CUUCGGAAGAAUUGGAAAAUAGAAUGUUGCCAACUGUGCGAGAUGUUGCCGCCCACGUUGUC-------AGUUGGCAAUUCCAUUCGCCGGCUCCUCACCUAGCACCACCCCCCC--C
.(((....))).(((......(((((((((((((((.((((..((........))..)))))-------)))))))))...)))))((..(........)..)).))).......--. ( -30.10)
>DroSec_CAF1 6101 110 - 1
CUUCGAAAGAAUUGGAAAAUAGAAUGUUGCCAACUGUGCGAGAUGUUGCCGCCCACGUUGUC-------AGUUGGCAAUUCCAUUCGCCGGCUCCACGCCUCACCCCUCCCCCCA-AC
.(((....)))((((......(((((((((((((((.((((..((........))..)))))-------)))))))))...)))))...(((.....)))............)))-). ( -32.90)
>DroSim_CAF1 6503 111 - 1
CUUCGAAAGAAUUGGAAAAUAGAAUGUUGCCAACUGUGCGAGAUGUUGCCGCCCACGUUGUC-------AGUUGGCAAUUCCAUUCGCCGGCUCCACGCCUCACCCCUCCCCCCAAAC
.(((....)))((((......(((((((((((((((.((((..((........))..)))))-------)))))))))...)))))...(((.....)))............)))).. ( -33.20)
>DroYak_CAF1 6539 118 - 1
CUUCGGAAGAAUUGGAAAAUAGAAUGUUGCCAACUGUGCAAGAUGUUGCCGCCCACGUUGUCAGUUGUCAGUUGGCAAUUUCAUUUGCCAGCUCCCCGUAUCCCCCCCUUUGCCAUCC
...(((..((.((((.((((.(((.(((((((((((.((((..((.(..((....))..).)).)))))))))))))))))))))).)))).)).))).................... ( -30.90)
>consensus
CUUCGAAAGAAUUGGAAAAUAGAAUGUUGCCAACUGUGCGAGAUGUUGCCGCCCACGUUGUC_______AGUUGGCAAUUCCAUUCGCCGGCUCCACGCCUCACCCCUCCCCCCA_AC
.(((....)))..(((.....((((((((((((((..((((....))))((....))............)))))))))...)))))......)))....................... (-23.23 = -22.85 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:05 2006