Locus 3749

Sequence ID	X_DroMel_CAF1
Location	9,958,678 – 9,958,821
Length	143
Max. P	0.685721

overview

Window 9

Location	9,958,678 – 9,958,786
Length	108
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	67.35
Mean single sequence MFE	-37.35
Consensus MFE	-12.06
Energy contribution	-13.25
Covariance contribution	1.19
Combinations/Pair	1.35
Mean z-score	-2.95
Structure conservation index	0.32
SVM decision value	0.32
SVM RNA-class probability	0.685721
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9958678 108 - 22224390
CCCAGAGCGG-------CCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCUUGGUUAUAUAGCCGCCGAUACACACACACAUAUUUACA-GAACGUA----UGUGUAUACGUAUACAGCUC
....((((((-------(((.(.(((....))).).)))))....((((..((((....))))))))((((....((((((((.....-....)))----)))))....))))...)))) ( -36.10)
>DroSec_CAF1 26656 104 - 1
CCCAGAGCGG-------CCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCAUGGCUAUAUAGCCGCCGAUACAC----ACGUAUUUACA-GUAUGUA----UGUAGANNNNNNNNNNNNNN
....((..((-------(((.(.(((....))).).))))).)).((((..((((....)))))))).((((.----((((((.....-)))))).----))))................ ( -34.10)
>DroEre_CAF1 21286 106 - 1
CCCAGAGCGGCCAGCGGCCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCCUGGCUAUUU--------AUAUUUA--UAUGUUUUUACUUGUAUAUA----UGUAUGUGUGCGUACAGCUC
....(((((((((..((((.(((((((.........)))))))...)))))))))....--------((((.((--((.((....)).)))).)))----)(((((....))))).)))) ( -33.90)
>DroYak_CAF1 21062 104 - 1
CCCAGAGCGG--------------CCAAGUGGCAAGUGGCUAUCAUGGCCUGGCUAUAUGCCCGCCGAUACACA--CGUAUUUGUACUUGUGUAUAAGUAUGUAUGUAUGUAUGCCGCUC
....((((((--------------(....((((....((((.....)))).(((.....))).))))(((((.(--(((((((((((....)))))))))))).)))))....))))))) ( -45.30)
>consensus
CCCAGAGCGG_______CCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCCUGGCUAUAUAGCCGCCGAUACACA__CACAUAUUUACA_GUAUAUA____UGUAUAUAUGUAUACAGCUC
....((((............(((((((...(((..(((.....))).))))))))))..........(((((.....((((..........)))).....)))))...........)))) (-12.06 = -13.25 +   1.19)

alignment

secondary structure

dotplot

Window 0

Location	9,958,713 – 9,958,821
Length	108
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	77.34
Mean single sequence MFE	-38.05
Consensus MFE	-24.92
Energy contribution	-26.05
Covariance contribution	1.13
Combinations/Pair	1.17
Mean z-score	-1.60
Structure conservation index	0.66
SVM decision value	0.05
SVM RNA-class probability	0.561227
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9958713 108 - 22224390
GAAUUUGGCCAGGUAAGCCAGGUAGG-----UAAGUGCAGCCCAGAGCGG-------CCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCUUGGUUAUAUAGCCGCCGAUACACACACACA
.....(((((..(((.(((.....))-----)...))).((.....))))-------)))((((((....)))..(((..((((.(((((.........)))))..))))..))).))). ( -36.70)
>DroSec_CAF1 26691 104 - 1
GAAUUUGGCCAGGUAAGCCAGGUAGG-----UAAGUGCAGCCCAGAGCGG-------CCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCAUGGCUAUAUAGCCGCCGAUACAC----ACG
..(((((((.......)))))))...-----...(((.......((..((-------(((.(.(((....))).).))))).)).((((..((((....))))))))...)))----... ( -36.30)
>DroEre_CAF1 21322 110 - 1
GAAUUUGGCCAAGAAAGCCAGGUAAGCCACGUAAGUGCAGCCCAGAGCGGCCAGCGGCCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCCUGGCUAUUU--------AUAUUUA--UAUG
...........(((.((((((((..(((((......((.(((......)))..))((((...))))..)))))..(((.....))).)))))))).)))--------.......--.... ( -39.00)
>DroYak_CAF1 21102 100 - 1
GAAUUUGGCCAGGUAAGCCAGGCAAGCCA----AGUGCAGCCCAGAGCGG--------------CCAAGUGGCAAGUGGCUAUCAUGGCCUGGCUAUAUGCCCGCCGAUACACA--CGUA
....(((((..((((((((((((.(((((----..(((.(((......))--------------)......)))..)))))......))))))))...)))).)))))......--.... ( -40.20)
>consensus
GAAUUUGGCCAGGUAAGCCAGGUAAG_____UAAGUGCAGCCCAGAGCGG_______CCAGUGGCCAAGUGGCAAGUGGCUAUCACGGCCUGGCUAUAUAGCCGCCGAUACACA__CACA
....(((((...(((((((((((...........(((.(((((.....(((.....)))....(((....)))..).))))..))).)))))))).)))....)))))............ (-24.92 = -26.05 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:30 2006