Locus 5755

Sequence ID	2L_DroMel_CAF1
Location	16,379,889 – 16,380,159
Length	270
Max. P	0.999882

overview

Window 5

Location	16,379,889 – 16,379,999
Length	110
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	65.43
Mean single sequence MFE	-20.67
Consensus MFE	-11.92
Energy contribution	-12.90
Covariance contribution	0.98
Combinations/Pair	1.20
Mean z-score	-1.28
Structure conservation index	0.58
SVM decision value	0.31
SVM RNA-class probability	0.684097
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16379889 110 - 22407834
UUCUUAUUUAACCAAUCCCGGCUGGAAAGUUCUGAAUUUUCUUAAGCCGGC----------UUUAUUCGGAUUUUCAUAUUAUUUUACUCACAUCGAAUGCUAAAUUCAGUGUUUAAUUU
...........(((((.(((((((((((((.....)))))))..)))))).----------...))).))....................((((.((((.....)))).))))....... ( -19.60)
>DroSec_CAF1 3573 101 - 1
UUCUUAUUUAACCAAUCCGGGCUGGAAAGUUCAGAGUUUUCUUAAGCCGGAGUUUUCUUUUCUUAUUAGGAUUUUCGAAU-------------------GCUAAAUUCAGUGUUAAAUAU
....(((((((((((((((((((....)))))((((..((((......))))..))))..........)))))...((((-------------------.....)))).).)))))))). ( -22.90)
>DroYak_CAF1 3934 98 - 1
UUCUCAUUUAACCAAUCCCGGCUGGAAAGUUCCGAGUUUUCUUGAGCCGGC----------UUUAUUUGGAUUUUGCUAUUAUUGUACCCACACCGAAUGU--------GCAUUUG----
...........((((..(((((((((....)))(((....))).)))))).----------.....))))....(((((((..(((....)))...)))).--------)))....---- ( -19.50)
>consensus
UUCUUAUUUAACCAAUCCCGGCUGGAAAGUUCAGAGUUUUCUUAAGCCGGC__________UUUAUUAGGAUUUUCAUAUUAUU_UAC_CACA_CGAAUGCUAAAUUCAGUGUUUAAU_U
.................(((((((((((((.....)))))))..)))))).............................................(((((((......)))))))..... (-11.92 = -12.90 +   0.98)

alignment

secondary structure

dotplot

Window 6

Location	16,379,999 – 16,380,119
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.33
Mean single sequence MFE	-32.90
Consensus MFE	-29.38
Energy contribution	-29.54
Covariance contribution	0.16
Combinations/Pair	1.09
Mean z-score	-2.67
Structure conservation index	0.89
SVM decision value	3.58
SVM RNA-class probability	0.999410
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16379999 120 - 22407834
CAUUCCCUGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAAUUAUGAUGCCAUGCCGUGACACAAGGUGUAACAGUAUACC
..(((((.((((((....))).((((((....))))))..((((.....))))......))))))))...(((((......((((....)))).))))).....((((((....)))))) ( -31.10)
>DroSec_CAF1 3674 120 - 1
CAUUCCCCGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAAUUAUGAUGCCAUGGCGUGACACAAGGUGUAACAGUAUACC
.....(((((((((....))).((((((....))))))..((((.....))))......)))))).....(((((.....(((((....)))))))))).....((((((....)))))) ( -33.80)
>DroSim_CAF1 1697 120 - 1
CAUUCCCCGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAAUUAUGAUGCCAUGGCGUGACACAAGGUGUAACAGUAUACC
.....(((((((((....))).((((((....))))))..((((.....))))......)))))).....(((((.....(((((....)))))))))).....((((((....)))))) ( -33.80)
>DroEre_CAF1 1931 120 - 1
CAUUCCCCGUCGGCACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCUCGGAAAAUUAUGAUGGCUUGGCGUGACACAAGGUGUAACAGUGUACC
(((.((((((((((((((....((((((....)))))))))))))..........((((((.(......)))))))........)))))...)).)))((((...........))))... ( -33.50)
>DroYak_CAF1 4032 120 - 1
CAUUCCCUGUCGGCACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAGCUCACGAAAAAUUAUGAUGCCAUGGCGUAACACAAGGUGUAACAGUAUACC
..(((((.((((((((((....((((((....)))))))))))))...((.....))..))))))))..................((((....)))).......((((((....)))))) ( -32.30)
>consensus
CAUUCCCCGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAAUUAUGAUGCCAUGGCGUGACACAAGGUGUAACAGUAUACC
.....(((((((((....))).((((((....))))))..((((.....))))......)))))).....(((((.....(((((....)))))))))).....((((((....)))))) (-29.38 = -29.54 +   0.16)

alignment

secondary structure

dotplot

Window 7

Location	16,380,039 – 16,380,159
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-37.40
Consensus MFE	-35.36
Energy contribution	-34.96
Covariance contribution	-0.40
Combinations/Pair	1.11
Mean z-score	-2.55
Structure conservation index	0.95
SVM decision value	3.85
SVM RNA-class probability	0.999661
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16380039 120 + 22407834
UUUUUCGUGAGUUUUCCCGUCUCAGUUGUGCUUUUGGCACUUCAUUCAUUUGUGAAUGUGACAAGUGUCGACAGGGAAUGAGAAUUGUUGCUGACGACGCUCAACUUUAUGUUGAUUACC
....((((.(((.......(((((....(.((.(((((((((((((((....))))))....))))))))).)).)..)))))......))).))))...(((((.....)))))..... ( -35.22)
>DroSec_CAF1 3714 120 + 1
UUUUUCGUGAGUUUUCCCGUCUCAGUUGUGCUUUUGGCACUUCAUUCAUUUGUGAAUGUGACAAGUGUCGACGGGGAAUGAGAAUUGUUGCUGACGACGCUCAACUUUAUGUUGAUUACC
....((((.((((((((((((......((((.....))))..((((((....)))))).(((....))))))))))))...........))).))))...(((((.....)))))..... ( -36.10)
>DroSim_CAF1 1737 120 + 1
UUUUUCGUGAGUUUUCCCGUCUCAGUUGUGCUUUUGGCACUUCAUUCAUUUGUGAAUGUGACAAGUGUCGACGGGGAAUGAGAAUUGUUGCUGACGACGCUCAACUUUAUGUUGAUUACC
....((((.((((((((((((......((((.....))))..((((((....)))))).(((....))))))))))))...........))).))))...(((((.....)))))..... ( -36.10)
>DroEre_CAF1 1971 120 + 1
UUUUCCGAGAGUUUUCCCGUCUCAGUUGUGCUUUUGGCACUUCAUUCAUUUGUGAAUGUGACAAGUGCCGACGGGGAAUGAGAAUUGUUGCUGACGACGCUCAACUUUAUGUUGAUUACC
.......((((((((((((((..((.....))...(((((((((((((....))))))....))))))))))))))))((((..(((((...)))))..)))))))))............ ( -37.10)
>DroYak_CAF1 4072 120 + 1
UUUUUCGUGAGCUUUCCCGUCUCAGUUGUGCUUUUGGCACUUCAUUCAUUUGUGAAUGUGACAAGUGCCGACAGGGAAUGGGAAUUGUUGCUGACGACGCUCAACUUUAUGUUGAUUACC
....((((.(((.((((((((((.((((.((.((((.((((((((......))))).))).)))).)))))).))).))))))).....))).))))...(((((.....)))))..... ( -42.50)
>consensus
UUUUUCGUGAGUUUUCCCGUCUCAGUUGUGCUUUUGGCACUUCAUUCAUUUGUGAAUGUGACAAGUGUCGACGGGGAAUGAGAAUUGUUGCUGACGACGCUCAACUUUAUGUUGAUUACC
....((((.(((.......(((((....(.((.(((((((((((((((....))))))....))))))))).)).)..)))))......))).))))...(((((.....)))))..... (-35.36 = -34.96 +  -0.40)

alignment

secondary structure

dotplot

Window 8

Location	16,380,039 – 16,380,159
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-30.54
Consensus MFE	-29.46
Energy contribution	-28.98
Covariance contribution	-0.48
Combinations/Pair	1.08
Mean z-score	-2.76
Structure conservation index	0.96
SVM decision value	4.37
SVM RNA-class probability	0.999882
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16380039 120 - 22407834
GGUAAUCAACAUAAAGUUGAGCGUCGUCAGCAACAAUUCUCAUUCCCUGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAA
.....(((((.....)))))..((((.(((................))).)))).((((((.((((((....))))))..((((.....))))......))))))............... ( -28.89)
>DroSec_CAF1 3714 120 - 1
GGUAAUCAACAUAAAGUUGAGCGUCGUCAGCAACAAUUCUCAUUCCCCGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAA
.....(((((.....)))))((.......))..............(((((((((....))).((((((....))))))..((((.....))))......))))))............... ( -30.10)
>DroSim_CAF1 1737 120 - 1
GGUAAUCAACAUAAAGUUGAGCGUCGUCAGCAACAAUUCUCAUUCCCCGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAA
.....(((((.....)))))((.......))..............(((((((((....))).((((((....))))))..((((.....))))......))))))............... ( -30.10)
>DroEre_CAF1 1971 120 - 1
GGUAAUCAACAUAAAGUUGAGCGUCGUCAGCAACAAUUCUCAUUCCCCGUCGGCACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCUCGGAAAA
.....(((((.....)))))((.......))..............(((((((((((((....((((((....)))))))))))))...((.....))..))))))............... ( -31.10)
>DroYak_CAF1 4072 120 - 1
GGUAAUCAACAUAAAGUUGAGCGUCGUCAGCAACAAUUCCCAUUCCCUGUCGGCACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAGCUCACGAAAAA
.....(((((.....)))))...((((.(((...........(((((.((((((((((....((((((....)))))))))))))...((.....))..)))))))).))).)))).... ( -32.50)
>consensus
GGUAAUCAACAUAAAGUUGAGCGUCGUCAGCAACAAUUCUCAUUCCCCGUCGACACUUGUCACAUUCACAAAUGAAUGAAGUGCCAAAAGCACAACUGAGACGGGAAAACUCACGAAAAA
.....(((((.....)))))((.......))..............(((((((((....))).((((((....))))))..((((.....))))......))))))............... (-29.46 = -28.98 +  -0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:56 2006