Locus 2460

Sequence ID	X_DroMel_CAF1
Location	6,574,380 – 6,574,582
Length	202
Max. P	0.904197

overview

Window 7

Location	6,574,380 – 6,574,475
Length	95
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	96.48
Mean single sequence MFE	-29.55
Consensus MFE	-23.54
Energy contribution	-24.14
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.80
SVM decision value	1.03
SVM RNA-class probability	0.904197
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6574380 95 - 22224390
AUGCGGAUCGGAAAGAUGUCGAAAGA----UACUCGACUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGCACAGCGCACGCAGUUUGAU
.((((..((((((...((((....))----)).((((.(((((..............))))).)))).....))))))((.....)).))))....... ( -27.34)
>DroSec_CAF1 19177 95 - 1
AUGCGGAUCGGAAAGAUGUCGAAAGA----UACUCGCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGCACAGCGCACGCAGUUUGAU
...((((((((.....((((....))----))(((((....)))))............))))))))........((((((...((....)).)))))). ( -29.60)
>DroSim_CAF1 30956 95 - 1
AUGCGGAUCGGAAAGAUGUCGAAAGA----UACUCGCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGCACAGCGCACGCAGUUUGAU
...((((((((.....((((....))----))(((((....)))))............))))))))........((((((...((....)).)))))). ( -29.60)
>DroEre_CAF1 18841 95 - 1
AUACGGAUCGGAAAGAUGUCGAAAGA----UACUCUCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGCACAGCGCACGCAGUUUGAU
...((((((((...((((((....))----)).))(((((....))))).........))))))))........((((((...((....)).)))))). ( -29.80)
>DroYak_CAF1 28942 99 - 1
AUGCGGAUCGGAAAGAUGUCGAAAGAUAUAUACUCUCCUUGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGCACAGCGCACGCAGUUUGAU
...((((((((....(((((....)))))....((((((....)))))).........))))))))........((((((...((....)).)))))). ( -31.40)
>consensus
AUGCGGAUCGGAAAGAUGUCGAAAGA____UACUCGCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGCACAGCGCACGCAGUUUGAU
...((((((((.......((....))......(((((....)))))............))))))))........((((((...((....)).)))))). (-23.54 = -24.14 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	6,574,399 – 6,574,512
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.57
Mean single sequence MFE	-34.46
Consensus MFE	-24.46
Energy contribution	-24.78
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-2.32
Structure conservation index	0.71
SVM decision value	0.07
SVM RNA-class probability	0.567869
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6574399 113 - 22224390
GCAAGAAGCGCACAAAU---GCUGCUACGUUCAAUUGAAGAUGCGGAUCGGAAAGAUGUCGAAAGA----UACUCGACUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGC
((..(((((((((....---).)))..(((((....(......)(((((((.....((((....))----))(((.((...)).)))...........)))))))))))).)))))..)) ( -31.50)
>DroSec_CAF1 19196 113 - 1
GCAAGGAGCGCACAAAU---GCUGCUAUGCUCAAUUGAAGAUGCGGAUCGGAAAGAUGUCGAAAGA----UACUCGCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGC
(((((.((((......)---))).)).)))....((((((...((((((((.....((((....))----))(((((....)))))............))))))))......)))))).. ( -36.00)
>DroSim_CAF1 30975 113 - 1
GCAAGGAGCGCACAAAU---GCUGCUAUGCUCAAUUGAAGAUGCGGAUCGGAAAGAUGUCGAAAGA----UACUCGCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGC
(((((.((((......)---))).)).)))....((((((...((((((((.....((((....))----))(((((....)))))............))))))))......)))))).. ( -36.00)
>DroEre_CAF1 18860 113 - 1
GCAAGAAGCGCACAAAU---GCUGGCCUGUUCAAUUGAAGAUACGGAUCGGAAAGAUGUCGAAAGA----UACUCUCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGC
((..((((((((....)---)).....(((((....(......)(((((((...((((((....))----)).))(((((....))))).........)))))))))))).)))))..)) ( -32.60)
>DroYak_CAF1 28961 120 - 1
GCAAGAAGCGCACAAAUGAUGCUGGUCUCUUUAAUUGAAGAUGCGGAUCGGAAAGAUGUCGAAAGAUAUAUACUCUCCUUGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGC
((..(((((((((....).)))..((.(((((....))))).))(((((((....(((((....)))))....((((((....)))))).........)))))))......)))))..)) ( -36.20)
>consensus
GCAAGAAGCGCACAAAU___GCUGCUAUGUUCAAUUGAAGAUGCGGAUCGGAAAGAUGUCGAAAGA____UACUCGCCUCGGUGGGGGAAAUAAAAAACCGAUUCGAACGAGUUUCGAGC
((..(((((.(.(((.....((......))....)))......((((((((.......((....))......(((((....)))))............))))))))...).)))))..)) (-24.46 = -24.78 +   0.32)

alignment

secondary structure

dotplot

Window 9

Location	6,574,475 – 6,574,582
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.70
Mean single sequence MFE	-32.26
Consensus MFE	-20.68
Energy contribution	-21.60
Covariance contribution	0.92
Combinations/Pair	1.10
Mean z-score	-2.48
Structure conservation index	0.64
SVM decision value	0.37
SVM RNA-class probability	0.709168
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6574475 107 - 22224390
UUAUUUCCCACAU------UCGCACAUCAUCUUCAAUUGAAAGUGGUCAAUUAAUUGAAAUGUUUGUGCAGCGAUC----GCAAGAAGCGCACAAAU---GCUGCUACGUUCAAUUGAAG
.............------...........(((((((((((.((((((((....))))...((((((((.((..((----....)).))))))))))---....)))).))))))))))) ( -32.50)
>DroSec_CAF1 19272 107 - 1
UCGUUGACCACAU------UCGCACAUCGUCUUCAAUUGAAAGUGGUCAAUUAAUUGAAAUGUUUGUGCAGCGAUC----GCAAGGAGCGCACAAAU---GCUGCUAUGCUCAAUUGAAG
...((((((((.(------(((...............)))).))))))))((((((((...((((((((.((..((----....)).))))))))))---((......)))))))))).. ( -34.36)
>DroSim_CAF1 31051 107 - 1
UCGUUGACCACAU------UCGCACAUCGUCUUCAAUUGAAAGUGGUCAAUUAAUUGAAAUGUUUGUGCAGCGAUC----GCAAGGAGCGCACAAAU---GCUGCUAUGCUCAAUUGAAG
...((((((((.(------(((...............)))).))))))))((((((((...((((((((.((..((----....)).))))))))))---((......)))))))))).. ( -34.36)
>DroEre_CAF1 18936 106 - 1
UCGUUUCGCACAUCG-------CACAUUGUCUUCAAUUGAAAGUGGUCAAUUAAUUGAAAUGUUUGUGAAGCGAUC----GCAAGAAGCGCACAAAU---GCUGGCCUGUUCAAUUGAAG
.......((.....)-------).......(((((((((((...((((((((......)))(((((((..((..((----....)).)).)))))))---..)))))..))))))))))) ( -30.70)
>DroYak_CAF1 29041 120 - 1
UCGUUUCGCACAUCGCGCAUCGCACGUCGUCUUCAAUUGAAAGUGGUCAAUUAAUUGAAAUGUUUGUGCAGCGAUCAGCAGCAAGAAGCGCACAAAUGAUGCUGGUCUCUUUAAUUGAAG
.((...(((.....)))...))........(((((((((((.(.(..((....(((.....((((((((.((.....)).((.....)))))))))))))..))..).)))))))))))) ( -29.40)
>consensus
UCGUUUCCCACAU______UCGCACAUCGUCUUCAAUUGAAAGUGGUCAAUUAAUUGAAAUGUUUGUGCAGCGAUC____GCAAGAAGCGCACAAAU___GCUGCUAUGUUCAAUUGAAG
..............................(((((((((((.((((((((....))))...((((((((.((...............)))))))))).......)))).))))))))))) (-20.68 = -21.60 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:17 2006