Locus 4905

Sequence ID	2L_DroMel_CAF1
Location	14,039,889 – 14,040,023
Length	134
Max. P	0.999919

overview

Window 9

Location	14,039,889 – 14,039,986
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	95.15
Mean single sequence MFE	-37.02
Consensus MFE	-37.14
Energy contribution	-36.66
Covariance contribution	-0.48
Combinations/Pair	1.12
Mean z-score	-2.26
Structure conservation index	1.00
SVM decision value	4.55
SVM RNA-class probability	0.999919
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14039889 97 + 22407834
GACACACACACACUCGCACAUAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCC
..............((((((((..........(((((....).))))((((((((((((..(.....)..)))))))))))).....)))))))).. ( -37.30)
>DroSec_CAF1 128836 97 + 1
GAGACCCACACACUCGCAUAUAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCC
(((.........)))(((((((..........(((((....).))))((((((((((((..(.....)..)))))))))))).....)))))))... ( -35.40)
>DroSim_CAF1 132033 97 + 1
GAGACCCACACACUCGCACAUAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCC
(((.........)))(((((((..........(((((....).))))((((((((((((..(.....)..)))))))))))).....)))))))... ( -37.30)
>DroEre_CAF1 130486 97 + 1
GAGUCCAGCACACUCGCACAUAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCC
((((.......))))(((((((..........(((((....).))))((((((((((((..(.....)..)))))))))))).....)))))))... ( -39.00)
>DroYak_CAF1 138191 97 + 1
GAGUCGAACACACUUGCACAUAGCCAGCACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUGUGUGCGCC
...............(((((((..........(((((....).))))((((((((((((..(.....)..)))))))))))).....)))))))... ( -36.10)
>consensus
GAGACCCACACACUCGCACAUAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCC
..............((((((((..........(((((....).))))((((((((((((..(.....)..)))))))))))).....)))))))).. (-37.14 = -36.66 +  -0.48)

alignment

secondary structure

dotplot

Window 0

Location	14,039,889 – 14,039,986
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	95.15
Mean single sequence MFE	-41.08
Consensus MFE	-37.18
Energy contribution	-36.74
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-2.67
Structure conservation index	0.91
SVM decision value	4.06
SVM RNA-class probability	0.999781
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14039889 97 - 22407834
GGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUAUGUGCGAGUGUGUGUGUGUC
(((((((((((......((((((((((.((.....)).))))))))))((((((((((((((....)).))))....)))).))))))))))))))) ( -45.40)
>DroSec_CAF1 128836 97 - 1
GGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUAUAUGCGAGUGUGUGGGUCUC
(((.(((((........((((((((((.((.....)).))))))))))((((....((((((....)).))))((.....))))))))))).))).. ( -40.90)
>DroSim_CAF1 132033 97 - 1
GGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUAUGUGCGAGUGUGUGGGUCUC
(((.(((((........((((((((((.((.....)).))))))))))((((((((((((((....)).))))....)))).))))))))).))).. ( -42.00)
>DroEre_CAF1 130486 97 - 1
GGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUAUGUGCGAGUGUGCUGGACUC
(((((((.((((((.((((((((((((.((.....)).))))))))))........((((((....)).))))))))))))...)))))))...... ( -39.30)
>DroYak_CAF1 138191 97 - 1
GGCGCACACAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGCUGGCUAUGUGCAAGUGUGUUCGACUC
(((((((.((((((.((((((((((((.((.....)).)))))))))..........(((((....)).))))))))))))...)))))))...... ( -37.80)
>consensus
GGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUAUGUGCGAGUGUGUGGGUCUC
.((((((.((((((.((((((((((((.((.....)).))))))))))........((((((....)).))))))))))))...))))))....... (-37.18 = -36.74 +  -0.44)

alignment

secondary structure

dotplot

Window 1

Location	14,039,909 – 14,040,023
Length	114
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	85.20
Mean single sequence MFE	-41.48
Consensus MFE	-33.84
Energy contribution	-35.87
Covariance contribution	2.03
Combinations/Pair	1.03
Mean z-score	-2.19
Structure conservation index	0.82
SVM decision value	0.61
SVM RNA-class probability	0.797672
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14039909 114 + 22407834
UAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCCUAGGUACAUGUUCCAGCCUUCAAAUCGGCAGCGCAUC
..(((((((....((((((.(((((..((((((((((((..(.....)..)))))))))))).....)))).).)))).))....)))))..(((........)))...))... ( -44.30)
>DroSec_CAF1 128856 114 + 1
UAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCCUAGGUACAUGUUCCAGCCUUCACAUCGGCAGCGCAUC
..(((((((....((((((.(((((..((((((((((((..(.....)..)))))))))))).....)))).).)))).))....)))))..(((........)))...))... ( -44.30)
>DroSim_CAF1 132053 114 + 1
UAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCCUAGGUACAUGUUCCAGCCUUCACAUCGGCAGCGCAUC
..(((((((....((((((.(((((..((((((((((((..(.....)..)))))))))))).....)))).).)))).))....)))))..(((........)))...))... ( -44.30)
>DroEre_CAF1 130506 114 + 1
UAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCCUAGGUACAUGUUCCAGCCUUCACAUCGGCAGCGCAUC
..(((((((....((((((.(((((..((((((((((((..(.....)..)))))))))))).....)))).).)))).))....)))))..(((........)))...))... ( -44.30)
>DroYak_CAF1 138211 114 + 1
UAGCCAGCACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUGUGUGCGCCUAGGUACAUGUUCCAGCCUUCACAUCGGCAGCGCAUC
......((((..(((((....).))))((((((((((((..(.....)..))))))))))))......))))((((...((........)).(((........))).))))... ( -42.90)
>DroPer_CAF1 171546 86 + 1
-----------UUCCAGGCACA--GGAGUCACGAGUCCUGACGACUCGCUAGGACUCGUG-------UAU--------GGUCACAUCUUCCAGCCUUGGCUCUAGCAAAAAAUC
-----------..(((((((((--.(((((.((((((.....))))))....))))).))-------).(--------((.........)))))).)))............... ( -28.80)
>consensus
UAGCGAACACUUUCCAGGCUCCGUGGAGUCACGAGUCCUGACGGCUGGCAAGGACUCGUGGCAUAUAUAUGUGCGCCUAGGUACAUGUUCCAGCCUUCACAUCGGCAGCGCAUC
..(((..........(((((....(((((((((((((((..(.....)..))))))))))))....((((((((......))))))))))))))))............)))... (-33.84 = -35.87 +   2.03)

alignment

secondary structure

dotplot

Window 2

Location	14,039,909 – 14,040,023
Length	114
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	85.20
Mean single sequence MFE	-41.43
Consensus MFE	-33.65
Energy contribution	-35.83
Covariance contribution	2.18
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.81
SVM decision value	0.29
SVM RNA-class probability	0.672292
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14039909 114 - 22407834
GAUGCGCUGCCGAUUUGAAGGCUGGAACAUGUACCUAGGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUA
...((...(((........)))..((((((....(((((((((........)))((((((((((.((.....)).))))))))))..........))))))...)))))))).. ( -43.90)
>DroSec_CAF1 128856 114 - 1
GAUGCGCUGCCGAUGUGAAGGCUGGAACAUGUACCUAGGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUA
...((...(((........)))..((((((....(((((((((........)))((((((((((.((.....)).))))))))))..........))))))...)))))))).. ( -43.90)
>DroSim_CAF1 132053 114 - 1
GAUGCGCUGCCGAUGUGAAGGCUGGAACAUGUACCUAGGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUA
...((...(((........)))..((((((....(((((((((........)))((((((((((.((.....)).))))))))))..........))))))...)))))))).. ( -43.90)
>DroEre_CAF1 130506 114 - 1
GAUGCGCUGCCGAUGUGAAGGCUGGAACAUGUACCUAGGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUA
...((...(((........)))..((((((....(((((((((........)))((((((((((.((.....)).))))))))))..........))))))...)))))))).. ( -43.90)
>DroYak_CAF1 138211 114 - 1
GAUGCGCUGCCGAUGUGAAGGCUGGAACAUGUACCUAGGCGCACACAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGCUGGCUA
...((((((((........)))............(((((((((........)))((((((((((.((.....)).))))))))))..........))))))..)))))...... ( -41.40)
>DroPer_CAF1 171546 86 - 1
GAUUUUUUGCUAGAGCCAAGGCUGGAAGAUGUGACC--------AUA-------CACGAGUCCUAGCGAGUCGUCAGGACUCGUGACUCC--UGUGCCUGGAA-----------
...............(((.(((.(((..(((....)--------)).-------((((((((((..((...))..))))))))))..)))--...))))))..----------- ( -31.60)
>consensus
GAUGCGCUGCCGAUGUGAAGGCUGGAACAUGUACCUAGGCGCACAUAUAUAUGCCACGAGUCCUUGCCAGCCGUCAGGACUCGUGACUCCACGGAGCCUGGAAAGUGUUCGCUA
...((...(((........)))..((((((....(((((((((........)))((((((((((.((.....)).))))))))))..........))))))...)))))))).. (-33.65 = -35.83 +   2.18)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:41 2006