Locus 4216

Sequence ID	3L_DroMel_CAF1
Location	12,346,573 – 12,346,673
Length	100
Max. P	0.868618

overview

Window 3

Location	12,346,573 – 12,346,673
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.81
Mean single sequence MFE	-31.47
Consensus MFE	-20.58
Energy contribution	-20.12
Covariance contribution	-0.47
Combinations/Pair	1.50
Mean z-score	-1.25
Structure conservation index	0.65
SVM decision value	0.11
SVM RNA-class probability	0.589817
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12346573 100 + 23771897
-------------UG-------CUCACCUUAAAGGUCGGUCGCCAGCCCACUGGCUUGGCCAGACUGGCAUGGAAGGUACUGAAGUUGAUCAACAUGUAGGCGGCCAGGAAGAAGUUCGA
-------------.(-------((((((((....((((((((((((((....))).))))..)))))))....))))).(((..((((.((........)))))))))...).))).... ( -30.50)
>DroVir_CAF1 32600 100 + 1
-------------UG-------CUUACCUUGAACGUGGGCCGCCAGCCCACAGGCUUGGCCAGGCUAGCAUGGAAUGUGCUAAAGUUGAUUAACAUAUAUGCGGCCAGGAAGAAAUUCGA
-------------..-------......(((((.((((((.....))))))...(((((((....((((((.....))))))..(((....)))........)))))))......))))) ( -31.90)
>DroGri_CAF1 34398 107 + 1
-------------UAAUUGUAACCCACCUUAAAAGUUGGUCGCCAGCCAACUGGCUUGGCCAGGCUAGCAUGGAAUGUGCUAAAAUUGAUUAACAUAUAGGCGGCUAAGAAGAAAUUCGA
-------------..........((.(((.....((((((((((((((....))).)))).....((((((.....)))))).....)))))))....))).))....(((....))).. ( -32.00)
>DroWil_CAF1 60029 100 + 1
-------------AA-------CAAACCUUAAAAGUUGGACGCCAGCCGACUGGUUUGGCCAAACUGGCAUGGAAUGUACUAAAGUUAAUCAACAUGUAGGCGGCCAAAAAGAAAUUUGA
-------------..-------((((.......((((((.(....)))))))..(((((((...(((.((((......((....)).......)))))))..)))))))......)))). ( -24.62)
>DroMoj_CAF1 33639 100 + 1
-------------UU-------CUCACCUUGAAUGUUGGCCGCCAGCCGACGGGCUUGGCCAGACUGGCAUGGAAUGUGCUGAAAUUGAUUAACAUAUAUGCAGCCAGGAAGAAGUUAGA
-------------((-------(((..........(((((((..((((....))))))))))).(((((.((.((((((.(((......))).))))).).)))))))).))))...... ( -29.90)
>DroPer_CAF1 35021 113 + 1
CGGUGCGAGUGUGGG-------AUUACCUUGAAGGUUGGACGCCAGCCCACCGGCUUGGCCAGACUGGCGUGGAAGGUGCUGAAGUUGAUCAGCAUGUAAGCGGCCAGGAAGAAGUUCGA
(((((((((.(((..-------..)))))))..((((((...))))))))))).(((((((...((........))(((((((......)))))))......)))))))........... ( -39.90)
>consensus
_____________UG_______CUCACCUUAAAAGUUGGACGCCAGCCCACUGGCUUGGCCAGACUGGCAUGGAAUGUGCUAAAGUUGAUCAACAUAUAGGCGGCCAGGAAGAAAUUCGA
...........................(((...(((((((.....)))))))..(((((((....((((((.....))))))..(((....)))........))))))))))........ (-20.58 = -20.12 +  -0.47)

alignment

secondary structure

dotplot

Window 4

Location	12,346,573 – 12,346,673
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.81
Mean single sequence MFE	-28.46
Consensus MFE	-21.64
Energy contribution	-20.67
Covariance contribution	-0.97
Combinations/Pair	1.48
Mean z-score	-1.40
Structure conservation index	0.76
SVM decision value	0.86
SVM RNA-class probability	0.868618
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12346573 100 - 23771897
UCGAACUUCUUCCUGGCCGCCUACAUGUUGAUCAACUUCAGUACCUUCCAUGCCAGUCUGGCCAAGCCAGUGGGCUGGCGACCGACCUUUAAGGUGAG-------CA-------------
...............(((((((....((((.((.((....)).........(((((((((((...)))))...)))))))).)))).....))))).)-------).------------- ( -29.30)
>DroVir_CAF1 32600 100 - 1
UCGAAUUUCUUCCUGGCCGCAUAUAUGUUAAUCAACUUUAGCACAUUCCAUGCUAGCCUGGCCAAGCCUGUGGGCUGGCGGCCCACGUUCAAGGUAAG-------CA-------------
........((((((((((.......((((((......))))))........(((((((((((...)))...))))))))))))........))).)))-------..------------- ( -29.50)
>DroGri_CAF1 34398 107 - 1
UCGAAUUUCUUCUUAGCCGCCUAUAUGUUAAUCAAUUUUAGCACAUUCCAUGCUAGCCUGGCCAAGCCAGUUGGCUGGCGACCAACUUUUAAGGUGGGUUACAAUUA-------------
................((((((...((((((......)))))).......((((((((((((...))))...))))))))...........))))))..........------------- ( -30.10)
>DroWil_CAF1 60029 100 - 1
UCAAAUUUCUUUUUGGCCGCCUACAUGUUGAUUAACUUUAGUACAUUCCAUGCCAGUUUGGCCAAACCAGUCGGCUGGCGUCCAACUUUUAAGGUUUG-------UU-------------
.(((((((....((((.((((.....(((((((.((....)).........(((.....)))......))))))).)))).))))......)))))))-------..------------- ( -21.80)
>DroMoj_CAF1 33639 100 - 1
UCUAACUUCUUCCUGGCUGCAUAUAUGUUAAUCAAUUUCAGCACAUUCCAUGCCAGUCUGGCCAAGCCCGUCGGCUGGCGGCCAACAUUCAAGGUGAG-------AA-------------
.......(((((((((((((((..((((..............))))...))).)))))(((((.((((....))))...))))).......))).)))-------).------------- ( -27.44)
>DroPer_CAF1 35021 113 - 1
UCGAACUUCUUCCUGGCCGCUUACAUGCUGAUCAACUUCAGCACCUUCCACGCCAGUCUGGCCAAGCCGGUGGGCUGGCGUCCAACCUUCAAGGUAAU-------CCCACACUCGCACCG
..............((..((.....((((((......))))))......(((((((.((.(((.....))).)))))))))...(((.....)))...-------.........)).)). ( -32.60)
>consensus
UCGAACUUCUUCCUGGCCGCCUACAUGUUAAUCAACUUCAGCACAUUCCAUGCCAGUCUGGCCAAGCCAGUGGGCUGGCGACCAACCUUCAAGGUGAG_______CA_____________
...............(((.......((((((......)))))).......((((((((((((...))))...))))))))............)))......................... (-21.64 = -20.67 +  -0.97)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:03 2006