Locus 5554

Sequence ID	3L_DroMel_CAF1
Location	15,241,436 – 15,241,585
Length	149
Max. P	0.991978

overview

Window 7

Location	15,241,436 – 15,241,545
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	96.61
Mean single sequence MFE	-26.28
Consensus MFE	-23.42
Energy contribution	-23.94
Covariance contribution	0.52
Combinations/Pair	1.06
Mean z-score	-2.02
Structure conservation index	0.89
SVM decision value	2.30
SVM RNA-class probability	0.991978
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15241436 109 + 23771897
CGACGGGAAUGAAAUGAAAGCAAGUGCCUUAAGGAGGCUCUGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUAAUAGGAAUUUUAAGCAUUUCCUUCGGGA
(((.(((((((...(((..((.((.(((((...))))).))......((.....)).....))....)))((((((((......))))))))...))))))).)))... ( -26.30)
>DroSec_CAF1 130738 109 + 1
CGACGGGAAUGAAAUGAAAGCAAGUGCCUUAAGGAGGCUCUGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUGAUAGGAAUUUUAAGCAUUUCCUUAGGGA
..........................(((((((((.(((.(((((..((((((.((((.....(....).....)))).))))))...))))))))...))))))))). ( -26.40)
>DroSim_CAF1 138542 109 + 1
CGACGGGAAUGAAAUGAAAGCAAGUGCCUUAAGGAGGCUCUGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUAAUAGGAAUUUUAAGCAUUUCCUUCGGGA
(((.(((((((...(((..((.((.(((((...))))).))......((.....)).....))....)))((((((((......))))))))...))))))).)))... ( -26.30)
>DroEre_CAF1 130832 109 + 1
CGACGGGAAUGAAAUGAAAGCAAGUGCCUCAAGGAGGCUGUGAAAAACUAUCAAAGGAAAGGCGAAGUCAAAAGUUCUCUAAUAUGAAUUUUAAGCAUUUCCUUCGGGA
(((.(((((((...(((..((....(((((...))))).........((.((....)).))))....)))(((((((........)))))))...))))))).)))... ( -27.10)
>DroYak_CAF1 136699 109 + 1
CGACGGGAAUGAAAUGAAAGCAAGUGCCUUAAGGAGGCUCUGAAAAACUAUCAAAGGAAAGGCGAAGUCAAAAGUUCUCUAAUAAGAAUUUUGAGCAUUUCCUCCGGGA
((..(((((((...(((..((.((.(((((...))))).))......((.((....)).))))....)))((((((((......))))))))...)))))))..))... ( -25.30)
>consensus
CGACGGGAAUGAAAUGAAAGCAAGUGCCUUAAGGAGGCUCUGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUAAUAGGAAUUUUAAGCAUUUCCUUCGGGA
(((.(((((((...(((..((.((.(((((...))))).))......((.....)).....))....)))((((((((......))))))))...))))))).)))... (-23.42 = -23.94 +   0.52)

alignment

secondary structure

dotplot

Window 8

Location	15,241,436 – 15,241,545
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	96.61
Mean single sequence MFE	-21.24
Consensus MFE	-19.48
Energy contribution	-19.36
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-1.45
Structure conservation index	0.92
SVM decision value	1.05
SVM RNA-class probability	0.906137
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15241436 109 - 23771897
UCCCGAAGGAAAUGCUUAAAAUUCCUAUUAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCAGAGCCUCCUUAAGGCACUUGCUUUCAUUUCAUUCCCGUCG
...(((((((((.((((((((((((.....).))).))))))....)).))))))))).............((((.....))))......................... ( -19.30)
>DroSec_CAF1 130738 109 - 1
UCCCUAAGGAAAUGCUUAAAAUUCCUAUCAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCAGAGCCUCCUUAAGGCACUUGCUUUCAUUUCAUUCCCGUCG
.((.((((((...((((..((...(((((((((......((....))......)))))))))...))..)))).)))))).)).......................... ( -20.20)
>DroSim_CAF1 138542 109 - 1
UCCCGAAGGAAAUGCUUAAAAUUCCUAUUAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCAGAGCCUCCUUAAGGCACUUGCUUUCAUUUCAUUCCCGUCG
...(((((((((.((((((((((((.....).))).))))))....)).))))))))).............((((.....))))......................... ( -19.30)
>DroEre_CAF1 130832 109 - 1
UCCCGAAGGAAAUGCUUAAAAUUCAUAUUAGAGAACUUUUGACUUCGCCUUUCCUUUGAUAGUUUUUCACAGCCUCCUUGAGGCACUUGCUUUCAUUUCAUUCCCGUCG
...(((((((((.(((((((((((........))).))))))....)).))))))))).............(((((...)))))......................... ( -21.70)
>DroYak_CAF1 136699 109 - 1
UCCCGGAGGAAAUGCUCAAAAUUCUUAUUAGAGAACUUUUGACUUCGCCUUUCCUUUGAUAGUUUUUCAGAGCCUCCUUAAGGCACUUGCUUUCAUUUCAUUCCCGUCG
....((((((((((.(((((((((((....))))).))))))....(((((..((((((.......)))))).......))))).........)))))).))))..... ( -25.70)
>consensus
UCCCGAAGGAAAUGCUUAAAAUUCCUAUUAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCAGAGCCUCCUUAAGGCACUUGCUUUCAUUUCAUUCCCGUCG
...(((((((((.(((((((((((........))).))))))....)).))))))))).............((((.....))))......................... (-19.48 = -19.36 +  -0.12)

alignment

secondary structure

dotplot

Window 9

Location	15,241,476 – 15,241,585
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	93.12
Mean single sequence MFE	-22.04
Consensus MFE	-17.50
Energy contribution	-17.30
Covariance contribution	-0.20
Combinations/Pair	1.15
Mean z-score	-1.67
Structure conservation index	0.79
SVM decision value	0.47
SVM RNA-class probability	0.748630
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15241476 109 + 23771897
UGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUAAUAGGAAUUUUAAGCAUUUCCUUCGGGACAUAAAAUGUUUCAAAAAAAUGCAUUAGGAUGCUUCUAAG
.............(((((((.(((....).((((((((......))))))))..)).))))))).(..((((...))))..)........((((....))))....... ( -20.40)
>DroSec_CAF1 130778 109 + 1
UGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUGAUAGGAAUUUUAAGCAUUUCCUUAGGGACAUAAAAUGUUUCAAAAAAAUGCAUUAGGAUGCUUCUAAG
.(((...((((((.((((.....(....).....)))).))))))..(((((((((((((..((.(..((((...))))..)))..)))))).)))))))..))).... ( -21.30)
>DroSim_CAF1 138582 109 + 1
UGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUAAUAGGAAUUUUAAGCAUUUCCUUCGGGACAUAAAAUGUUUCGAAAAAAUGCAUUAGGAUGCUUCUAAG
.......................(((((..((((((((......))))))))..((((((..((((..((((...))))..)))).))))))........))))).... ( -24.60)
>DroEre_CAF1 130872 109 + 1
UGAAAAACUAUCAAAGGAAAGGCGAAGUCAAAAGUUCUCUAAUAUGAAUUUUAAGCAUUUCCUUCGGGACAUAGAAGGUUUCAAAAAAAUGCAUUAGAAGGCUUCUAGG
.......((.((....)).))..((((((.(((((((........)))))))..(((((((((((........)))))........)))))).......)))))).... ( -23.00)
>DroYak_CAF1 136739 108 + 1
UGAAAAACUAUCAAAGGAAAGGCGAAGUCAAAAGUUCUCUAAUAAGAAUUUUGAGCAUUUCCUCCGGGACUUAGAAUGUUUCAAA-AAAUGUGUUAGGGUGCUUCUAAG
(((....((.((....)).))......))).((((.((((((((....((((((((((((((....))).....)))).))))))-)....)))))))).))))..... ( -20.90)
>consensus
UGAAAAACUAUCAAAGGAAAAGCGAAGUCAAAAGUUCUCUAAUAGGAAUUUUAAGCAUUUCCUUCGGGACAUAAAAUGUUUCAAAAAAAUGCAUUAGGAUGCUUCUAAG
.............(((((((.(((....).((((((((......))))))))..)).))))))).(..((.......))..)...........((((((...)))))). (-17.50 = -17.30 +  -0.20)

alignment

secondary structure

dotplot

Window 0

Location	15,241,476 – 15,241,585
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	93.12
Mean single sequence MFE	-19.76
Consensus MFE	-15.40
Energy contribution	-16.08
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.78
SVM decision value	0.09
SVM RNA-class probability	0.579560
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15241476 109 - 23771897
CUUAGAAGCAUCCUAAUGCAUUUUUUUGAAACAUUUUAUGUCCCGAAGGAAAUGCUUAAAAUUCCUAUUAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCA
....(((((((....))))........................(((((((((.((((((((((((.....).))).))))))....)).))))))))).......))). ( -18.20)
>DroSec_CAF1 130778 109 - 1
CUUAGAAGCAUCCUAAUGCAUUUUUUUGAAACAUUUUAUGUCCCUAAGGAAAUGCUUAAAAUUCCUAUCAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCA
....((((.........(((((((((((..((((...))))...))))))))))).........(((((((((......((....))......)))))))))..)))). ( -19.20)
>DroSim_CAF1 138582 109 - 1
CUUAGAAGCAUCCUAAUGCAUUUUUUCGAAACAUUUUAUGUCCCGAAGGAAAUGCUUAAAAUUCCUAUUAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCA
....((((.........(((((((((((..((((...))))..)))).))))))).........(((((((((......((....))......)))))))))..)))). ( -18.80)
>DroEre_CAF1 130872 109 - 1
CCUAGAAGCCUUCUAAUGCAUUUUUUUGAAACCUUCUAUGUCCCGAAGGAAAUGCUUAAAAUUCAUAUUAGAGAACUUUUGACUUCGCCUUUCCUUUGAUAGUUUUUCA
..((((((..(((.((........)).)))..)))))).....(((((((((.(((((((((((........))).))))))....)).)))))))))........... ( -20.20)
>DroYak_CAF1 136739 108 - 1
CUUAGAAGCACCCUAACACAUUU-UUUGAAACAUUCUAAGUCCCGGAGGAAAUGCUCAAAAUUCUUAUUAGAGAACUUUUGACUUCGCCUUUCCUUUGAUAGUUUUUCA
(((((((................-.........)))))))...(((((((((.(((((((((((((....))))).))))))....)).)))))))))........... ( -22.41)
>consensus
CUUAGAAGCAUCCUAAUGCAUUUUUUUGAAACAUUUUAUGUCCCGAAGGAAAUGCUUAAAAUUCCUAUUAGAGAACUUUUGACUUCGCUUUUCCUUUGAUAGUUUUUCA
....(((((((....))))........................(((((((((.(((((((((((........))).))))))....)).))))))))).......))). (-15.40 = -16.08 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:10 2006