Locus 2071

Sequence ID	2L_DroMel_CAF1
Location	5,577,253 – 5,577,435
Length	182
Max. P	0.999955

overview

Window 6

Location	5,577,253 – 5,577,362
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.95
Mean single sequence MFE	-30.42
Consensus MFE	-20.26
Energy contribution	-21.26
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.91
Structure conservation index	0.67
SVM decision value	0.12
SVM RNA-class probability	0.591905
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5577253 109 - 22407834
ACCUGUAUUAUUAGCCUGCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGCGGCGC--ACUCGCAGAACAGAUG---------CUUUGACC
....(((((......((((.(((.......))).(((((.(((((.((((((((..((....))..))))))))..)))))..))--))).))))....))))---------)....... ( -29.80)
>DroSec_CAF1 21288 111 - 1
ACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGCGGCGCACACUCGCAGAGCAGAUG---------CUCUGACC
....(((((((..........))))))).......((((.(((((.((((((((..((....))..))))))))..)))))..)))).....((((((....)---------)))))... ( -35.50)
>DroSim_CAF1 22936 111 - 1
ACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGCGGCGCACACUUGCAGAGCAGAUG---------CUCUGACC
....(((((((..........)))))))..((((.((((.(((((.((((((((..((....))..))))))))..)))))..))))..))))(((((....)---------)))).... ( -36.10)
>DroEre_CAF1 21233 118 - 1
ACGUGUAUUAUUAGCGUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUCACUUUGCCGCAUACGUUUCAAAGUCAUUAGGCGGCGC--ACUCGCAGAGCAGAUGCUAGCCCAACUCUGACC
..........((((((((..((.....(((((..(((((.(((((...((((((..((....))..))))))....)))))..))--))).)).)))))))))))))............. ( -28.30)
>DroYak_CAF1 21140 101 - 1
ACCUGUAUUAUUAGCUUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGCG-------------------AUGCUAACCCAACUCUGACC
....(((((((..........))))))).........((((((((.((((((((..((....))..))))))))..)))).-------------------))))................ ( -22.40)
>consensus
ACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGCGGCGC__ACUCGCAGAGCAGAUG_________CUCUGACC
....(((((((..........))))))).......((((.(((((.((((((((..((....))..))))))))..)))))))))................................... (-20.26 = -21.26 +   1.00)

alignment

secondary structure

dotplot

Window 7

Location	5,577,282 – 5,577,402
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.42
Mean single sequence MFE	-33.60
Consensus MFE	-30.44
Energy contribution	-31.04
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.69
Structure conservation index	0.91
SVM decision value	3.52
SVM RNA-class probability	0.999331
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5577282 120 + 22407834
GCCUAAUGACUUUGAAACGUAUGCGGCAAAGUCAAAAGCAUGCACUUUGCGAGUAUUACAUGCAGGCUAAUAAUACAGGUGAGCAUAAUAGCGACCUGCAACGCAAUAUGAAUGCUAAAU
......((((((((...((....)).))))))))..(((((.((..(((((.((((((...(....)...))))))((((..((......)).))))....)))))..)).))))).... ( -35.90)
>DroSec_CAF1 21319 120 + 1
GCCUAAUGACUUUGAAACGUAUGCGGCAAAGUCAAAAGCAUGCACUUUGCGAGUAUUACAUGGAGGCUAAUAAUACAGGUGAGCAUAAUAGCGAGCUGCAACGCAAUAUGAAUGCUAAAU
......((((((((...((....)).))))))))..(((((.((..(((((.((((((..(((...))).)))))).(((..((......))..)))....)))))..)).))))).... ( -33.50)
>DroSim_CAF1 22967 120 + 1
GCCUAAUGACUUUGAAACGUAUGCGGCAAAGUCAAAAGCAUGCACUUUGCGAGUAUUACAUGGAGGCUAAUAAUACAGGUGAGCAUAAUAGCGAGCUGCAACGCAAUAUGAAUGCUAAAU
......((((((((...((....)).))))))))..(((((.((..(((((.((((((..(((...))).)))))).(((..((......))..)))....)))))..)).))))).... ( -33.50)
>DroEre_CAF1 21271 120 + 1
GCCUAAUGACUUUGAAACGUAUGCGGCAAAGUGAAAAGCAUGCACUUUGCGAGUAUUACAUGGACGCUAAUAAUACACGUGGGCAUAAUAGCGAGCUGCAACGCAAUAUGAAUGCUAAAU
......(.((((((...((....)).)))))).)..(((((.((..(((((.((((((..(((...))).))))))..((..((......))..)).....)))))..)).))))).... ( -27.60)
>DroYak_CAF1 21161 120 + 1
GCCUAAUGACUUUGAAACGUAUGCGGCAAAGUCAAAAGCAUGCACUUUGCGAGUAUUACAUGGAAGCUAAUAAUACAGGUGAGCAUAAUAGCGAGCUGCAACGCAAUGUGAAUGCUAAAU
......((((((((...((....)).))))))))..(((((.(((.(((((.((((((...(....)...)))))).(((..((......))..)))....))))).))).))))).... ( -37.50)
>consensus
GCCUAAUGACUUUGAAACGUAUGCGGCAAAGUCAAAAGCAUGCACUUUGCGAGUAUUACAUGGAGGCUAAUAAUACAGGUGAGCAUAAUAGCGAGCUGCAACGCAAUAUGAAUGCUAAAU
......((((((((...((....)).))))))))..(((((.((..(((((.((((((...(....)...)))))).(((..((......))..)))....)))))..)).))))).... (-30.44 = -31.04 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	5,577,282 – 5,577,402
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.42
Mean single sequence MFE	-33.20
Consensus MFE	-32.20
Energy contribution	-32.24
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-3.14
Structure conservation index	0.97
SVM decision value	4.84
SVM RNA-class probability	0.999955
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5577282 120 - 22407834
AUUUAGCAUUCAUAUUGCGUUGCAGGUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUGCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGC
....(((((.(((.(((((.(((((((....((.((((......)))).))..))))))).........))))).))).)))))..((((((((..((....))..))))))))...... ( -35.00)
>DroSec_CAF1 21319 120 - 1
AUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGC
....(((((.(((.((((((((((....((((..((((......))))...)))).....)))))....))))).))).)))))..((((((((..((....))..))))))))...... ( -33.10)
>DroSim_CAF1 22967 120 - 1
AUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGC
....(((((.(((.((((((((((....((((..((((......))))...)))).....)))))....))))).))).)))))..((((((((..((....))..))))))))...... ( -33.10)
>DroEre_CAF1 21271 120 - 1
AUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCCCACGUGUAUUAUUAGCGUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUCACUUUGCCGCAUACGUUUCAAAGUCAUUAGGC
....(((((.(((.((((((((((...(((((..((((......))))...)))))....)))))....))))).))).)))))....((((((..((....))..))))))........ ( -30.30)
>DroYak_CAF1 21161 120 - 1
AUUUAGCAUUCACAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCUUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGC
....(((((.(((.((((((((((....((((..((((......))))...)))).....)))))....))))).))).)))))..((((((((..((....))..))))))))...... ( -34.50)
>consensus
AUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCAUGCUUUUGACUUUGCCGCAUACGUUUCAAAGUCAUUAGGC
....(((((.(((.((((((((((....((((..((((......))))...)))).....)))))....))))).))).)))))..((((((((..((....))..))))))))...... (-32.20 = -32.24 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	5,577,322 – 5,577,435
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.84
Mean single sequence MFE	-27.90
Consensus MFE	-21.14
Energy contribution	-20.90
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.27
Structure conservation index	0.76
SVM decision value	0.86
SVM RNA-class probability	0.868136
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5577322 113 - 22407834
AUAGGCAAGAUCUUCG-----AUUUUCCCACCGCA--CAUAUUUAGCAUUCAUAUUGCGUUGCAGGUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUGCAUGUAAUACUCGCAAAGUGCA
...((.((((((...)-----))))).))...(((--(...(((.((.....((((((((.((((((....((.((((......)))).))..))))))))))))))...))))))))). ( -28.30)
>DroSec_CAF1 21359 118 - 1
AUAGGCAAAAUCUUCGAUUCGAUUUUCCCACCGCA--CAUAUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCA
...((.((((((........)))))).))...(((--(.......(((.......)))((((((....((((..((((......))))...)))).....)))))).........)))). ( -27.30)
>DroSim_CAF1 23007 118 - 1
AUAGGCAAAAUCUUCGAUUCGAUUUUCCCACCGCA--CAUAUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCA
...((.((((((........)))))).))...(((--(.......(((.......)))((((((....((((..((((......))))...)))).....)))))).........)))). ( -27.30)
>DroEre_CAF1 21311 113 - 1
UGAGGCAAGAUCUUCG-----AUUUUCCCACCGCA--CAUAUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCCCACGUGUAUUAUUAGCGUCCAUGUAAUACUCGCAAAGUGCA
...((.((((((...)-----))))).))...(((--(.......(((.......)))((((((...(((((..((((......))))...)))))....)))))).........)))). ( -28.00)
>DroYak_CAF1 21201 115 - 1
GGAGGCAAGAUCUUCG-----AUUUUCCCACCGCACACAUAUUUAGCAUUCACAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCUUCCAUGUAAUACUCGCAAAGUGCA
((.((.((((((...)-----))))).)).))((((.........(((.......)))((((((....((((..((((......))))...)))).....)))))).........)))). ( -28.60)
>consensus
AUAGGCAAGAUCUUCG_____AUUUUCCCACCGCA__CAUAUUUAGCAUUCAUAUUGCGUUGCAGCUCGCUAUUAUGCUCACCUGUAUUAUUAGCCUCCAUGUAAUACUCGCAAAGUGCA
...((.(((((..........))))).))................(((((....((((((((((....((((..((((......))))...)))).....)))))....)))))))))). (-21.14 = -20.90 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:51 2006