Locus 7700

Sequence ID	2L_DroMel_CAF1
Location	21,774,688 – 21,774,782
Length	94
Max. P	0.995848

overview

Window 8

Location	21,774,688 – 21,774,782
Length	94
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	75.88
Mean single sequence MFE	-25.32
Consensus MFE	-13.46
Energy contribution	-14.82
Covariance contribution	1.36
Combinations/Pair	1.20
Mean z-score	-2.61
Structure conservation index	0.53
SVM decision value	2.62
SVM RNA-class probability	0.995848
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21774688 94 + 22407834
AUUUCGCUGGGGGCAGACUGAAAGAAAUCAGUUUGAGCUGUCAGCAAAAUAGA--------UUUUCGAAUUGGGGCUAUGGUAGGCUUCGCAGAAAGAUAUA
.....(((((.((((((((((......)))))))..))).)))))........--------(((((....(((((((......)))))))..)))))..... ( -28.20)
>DroSec_CAF1 16435 94 + 1
AUUUCGCUGAGGGCAGACUGAAAGAAAUCAGUCUAAGCGGUCAGCCAAAUAGA--------UUUUUAAAUUGGGGCUAUGGUAGGCAUCGAAGAAAGAUAUG
((((.(((((..(((((((((......)))))))..))..))))).))))..(--------(((((...(((..(((......)))..)))..))))))... ( -25.90)
>DroSim_CAF1 9213 94 + 1
AUUUCGCUGAGGGCAGACUGAAAGAAAUCAGUCUAAGCGGUCAGCCAAAUAGA--------UUUUAUAAUUGGGGCUAUGGUAGGCAUCGAAGAAAGAUAUA
.(((((((((..(((((((((......)))))))..))..)))))........--------........(((..(((......)))..))).))))...... ( -24.90)
>DroEre_CAF1 19323 96 + 1
AUUUCGCUGAGAGCAGACUGAGAGAAAUUAGGUUGGGG-GUCAGCAAUAUAGAUACAUACAUAUAUAAAUUGGUGUUAUG-----CUAGGCACCAAGAUAUA
.....(((((.....((((..((....)).))))....-.)))))................(((((...((((((((...-----...)))))))).))))) ( -22.50)
>DroYak_CAF1 6584 87 + 1
AUUUCGCUGAGGGCAGACUGAGAGAAAUCAGUUUGAAC-GGAAGCAAUAU----------AUAUAUAAAUUGGUGCCAUG----GCUUUCCAGGAAGUUAUA
((((((((..(..((((((((......))))))))..)-...))).....----------.........((((.((....----))...))))))))).... ( -25.10)
>consensus
AUUUCGCUGAGGGCAGACUGAAAGAAAUCAGUUUGAGC_GUCAGCAAAAUAGA________UUUUUAAAUUGGGGCUAUGGUAGGCUUCGCAGAAAGAUAUA
.(((((((((...((((((((......)))))))).....))))).............................(((......)))......))))...... (-13.46 = -14.82 +   1.36)

alignment

secondary structure

dotplot

Window 9

Location	21,774,688 – 21,774,782
Length	94
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	75.88
Mean single sequence MFE	-17.56
Consensus MFE	-9.50
Energy contribution	-11.34
Covariance contribution	1.84
Combinations/Pair	1.06
Mean z-score	-2.17
Structure conservation index	0.54
SVM decision value	1.45
SVM RNA-class probability	0.954742
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21774688 94 - 22407834
UAUAUCUUUCUGCGAAGCCUACCAUAGCCCCAAUUCGAAAA--------UCUAUUUUGCUGACAGCUCAAACUGAUUUCUUUCAGUCUGCCCCCAGCGAAAU
............((((((........)).....))))....--------...(((((((((...((....(((((......)))))..))...))))))))) ( -17.10)
>DroSec_CAF1 16435 94 - 1
CAUAUCUUUCUUCGAUGCCUACCAUAGCCCCAAUUUAAAAA--------UCUAUUUGGCUGACCGCUUAGACUGAUUUCUUUCAGUCUGCCCUCAGCGAAAU
..((((.......))))........................--------...((((.(((((..((..(((((((......)))))))))..))))).)))) ( -21.10)
>DroSim_CAF1 9213 94 - 1
UAUAUCUUUCUUCGAUGCCUACCAUAGCCCCAAUUAUAAAA--------UCUAUUUGGCUGACCGCUUAGACUGAUUUCUUUCAGUCUGCCCUCAGCGAAAU
..((((.......))))........................--------...((((.(((((..((..(((((((......)))))))))..))))).)))) ( -21.10)
>DroEre_CAF1 19323 96 - 1
UAUAUCUUGGUGCCUAG-----CAUAACACCAAUUUAUAUAUGUAUGUAUCUAUAUUGCUGAC-CCCCAACCUAAUUUCUCUCAGUCUGCUCUCAGCGAAAU
((((..((((((.....-----.....))))))..))))................(((((((.-...((..((..........))..))...)))))))... ( -14.80)
>DroYak_CAF1 6584 87 - 1
UAUAACUUCCUGGAAAGC----CAUGGCACCAAUUUAUAUAU----------AUAUUGCUUCC-GUUCAAACUGAUUUCUCUCAGUCUGCCCUCAGCGAAAU
..........(((...((----....)).)))..........----------...(((((...-(..((.(((((......))))).))..)..)))))... ( -13.70)
>consensus
UAUAUCUUUCUGCGAAGCCUACCAUAGCCCCAAUUUAAAAA________UCUAUUUUGCUGAC_GCUCAAACUGAUUUCUUUCAGUCUGCCCUCAGCGAAAU
....................................................((((((((((..((....(((((......)))))..))..)))))))))) ( -9.50 = -11.34 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:05 2006