Locus 6223

Sequence ID	X_DroMel_CAF1
Location	15,820,887 – 15,821,047
Length	160
Max. P	0.845652

overview

Window 2

Location	15,820,887 – 15,820,977
Length	90
Sequences	3
Columns	92
Reading direction	forward
Mean pairwise identity	88.93
Mean single sequence MFE	-20.07
Consensus MFE	-15.91
Energy contribution	-16.13
Covariance contribution	0.23
Combinations/Pair	1.07
Mean z-score	-2.53
Structure conservation index	0.79
SVM decision value	0.64
SVM RNA-class probability	0.809943
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15820887 90 + 22224390
UCAACUUGCUUGAAGGUCAUAGCUUAAGCUGACCAAAAGGCAAGUAAAAAAGUAGUUAUUAAUGUUUUUGUUUGCUUUAUUUUGUAAUAU--
...((((((((...(((((..((....)))))))...))))))))...(((((((....(((.....))).)))))))............-- ( -21.10)
>DroSec_CAF1 3923 89 + 1
UCAUGUUACUUGAAGGUCAUAGCUAAAGCUGACCAAAAUGCAAGUAAAAAAGUAGUA---AAUAUUUUUUUUUGCUUUAUUUUGUAUUAUGU
.((((.(((.....(((((..((....)))))))((((((.(((((((((((.....---......)))))))))))))))))))).)))). ( -20.30)
>DroSim_CAF1 4032 87 + 1
UCAACUUACUUGAAGGUCAUAGCUAAAGCUGACCAAAAGGCAAGUAAAAAAGUAGUA---AAUAUUUUUUGUUGCUUUAUUUUGUAUUAU--
......(((..((.(((((..((....)))))))..(((((((...((((((((...---..)))))))).))))))).))..)))....-- ( -18.80)
>consensus
UCAACUUACUUGAAGGUCAUAGCUAAAGCUGACCAAAAGGCAAGUAAAAAAGUAGUA___AAUAUUUUUUUUUGCUUUAUUUUGUAUUAU__
......(((..((.(((((..((....)))))))..((((((((...(((((((........))))))).)))))))).))..)))...... (-15.91 = -16.13 +   0.23)

alignment

secondary structure

dotplot

Window 3

Location	15,820,887 – 15,820,977
Length	90
Sequences	3
Columns	92
Reading direction	reverse
Mean pairwise identity	88.93
Mean single sequence MFE	-14.10
Consensus MFE	-11.59
Energy contribution	-12.03
Covariance contribution	0.45
Combinations/Pair	1.08
Mean z-score	-1.96
Structure conservation index	0.82
SVM decision value	0.17
SVM RNA-class probability	0.617876
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15820887 90 - 22224390
--AUAUUACAAAAUAAAGCAAACAAAAACAUUAAUAACUACUUUUUUACUUGCCUUUUGGUCAGCUUAAGCUAUGACCUUCAAGCAAGUUGA
--.............................................((((((.....(((((((....))..))))).....))))))... ( -14.90)
>DroSec_CAF1 3923 89 - 1
ACAUAAUACAAAAUAAAGCAAAAAAAAAUAUU---UACUACUUUUUUACUUGCAUUUUGGUCAGCUUUAGCUAUGACCUUCAAGUAACAUGA
.(((..(((........((((..(((((....---.......)))))..)))).....(((((((....))..))))).....)))..))). ( -14.00)
>DroSim_CAF1 4032 87 - 1
--AUAAUACAAAAUAAAGCAACAAAAAAUAUU---UACUACUUUUUUACUUGCCUUUUGGUCAGCUUUAGCUAUGACCUUCAAGUAAGUUGA
--................((((.(((....))---).........(((((((......(((((((....))..)))))..))))))))))). ( -13.40)
>consensus
__AUAAUACAAAAUAAAGCAAAAAAAAAUAUU___UACUACUUUUUUACUUGCCUUUUGGUCAGCUUUAGCUAUGACCUUCAAGUAAGUUGA
...............................................((((((.....(((((((....))..))))).....))))))... (-11.59 = -12.03 +   0.45)

alignment

secondary structure

dotplot

Window 4

Location	15,820,942 – 15,821,047
Length	105
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	81.10
Mean single sequence MFE	-24.00
Consensus MFE	-18.57
Energy contribution	-18.12
Covariance contribution	-0.44
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.77
SVM decision value	0.77
SVM RNA-class probability	0.845652
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15820942 105 + 22224390
-UUAUUAAUGUUUUUGUUUGCUUUAUUUUGUAAUAU----GUUGGUGUAAU----------UCUAUUGUUACAGCGGCUUGGGAAAUGUUAUGCAAACAAUUGAAUGGUAGUAAAGCGAC
-((((((..((((((((((((..((((((.(((...----((((.((((((----------......)))))).))))))).))))))....))))))))..))))..))))))...... ( -26.50)
>DroSim_CAF1 4087 102 + 1
-UA---AAUAUUUUUUGUUGCUUUAUUUUGUAUUAU----GUUGGUGUAAU----------UGUAUUGUUACAGCGGCUUGGGAAAUGUUAUGCAAACAAUUGAAUGGUAGUAAAGCGAC
-..---..........(((((((((((...((((..----((((.((((((----------......)))))).))))........((((.....))))....))))..))))))))))) ( -22.10)
>DroYak_CAF1 2799 117 + 1
CUUAU---UCAUUUUUUUUGCUUUAUUUUGUAAUAUAUGUGUUGGUGUAAUUUAGUUGUUUUCUAUUGUUACAGCGGCGUGGGAAAUGUAAUGCUUACAAUUGAAUGGUAGUAAAGCGAU
.....---.........(((((((((((..(.........((((.((((((.(((.......)))..)))))).))))(((((..........)))))......)..).)))))))))). ( -23.40)
>consensus
_UUAU_AAUAUUUUUUUUUGCUUUAUUUUGUAAUAU____GUUGGUGUAAU__________UCUAUUGUUACAGCGGCUUGGGAAAUGUUAUGCAAACAAUUGAAUGGUAGUAAAGCGAC
.................(((((((((((..(.........((((.((((((................)))))).))))........((((.....)))).....)..).)))))))))). (-18.57 = -18.12 +  -0.44)

alignment

secondary structure

dotplot

Window 5

Location	15,820,942 – 15,821,047
Length	105
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	81.10
Mean single sequence MFE	-10.07
Consensus MFE	-7.78
Energy contribution	-7.34
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.41
Structure conservation index	0.77
SVM decision value	0.00
SVM RNA-class probability	0.536074
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15820942 105 - 22224390
GUCGCUUUACUACCAUUCAAUUGUUUGCAUAACAUUUCCCAAGCCGCUGUAACAAUAGA----------AUUACACCAAC----AUAUUACAAAAUAAAGCAAACAAAAACAUUAAUAA-
....................((((((((.................(.(((((.......----------.))))).)...----.((((....))))..))))))))............- ( -11.10)
>DroSim_CAF1 4087 102 - 1
GUCGCUUUACUACCAUUCAAUUGUUUGCAUAACAUUUCCCAAGCCGCUGUAACAAUACA----------AUUACACCAAC----AUAAUACAAAAUAAAGCAACAAAAAAUAUU---UA-
((.((((((.............(((((............))))).(.(((((.......----------.))))).)...----...........)))))).))..........---..- (  -9.90)
>DroYak_CAF1 2799 117 - 1
AUCGCUUUACUACCAUUCAAUUGUAAGCAUUACAUUUCCCACGCCGCUGUAACAAUAGAAAACAACUAAAUUACACCAACACAUAUAUUACAAAAUAAAGCAAAAAAAAUGA---AUAAG
...((((((............((((.....))))...........(.(((((...(((.......)))..))))).)..................))))))...........---..... (  -9.20)
>consensus
GUCGCUUUACUACCAUUCAAUUGUUUGCAUAACAUUUCCCAAGCCGCUGUAACAAUAGA__________AUUACACCAAC____AUAUUACAAAAUAAAGCAAAAAAAAACAUU_AUAA_
...((((((............((((.....))))...........(.(((((..................))))).)..................))))))................... ( -7.78 =  -7.34 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:36 2006