Locus 1176

Sequence ID	2L_DroMel_CAF1
Location	3,218,071 – 3,218,182
Length	111
Max. P	0.615304

overview

Window 7

Location	3,218,071 – 3,218,182
Length	111
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	75.37
Mean single sequence MFE	-31.58
Consensus MFE	-14.50
Energy contribution	-15.17
Covariance contribution	0.67
Combinations/Pair	1.35
Mean z-score	-1.89
Structure conservation index	0.46
SVM decision value	0.17
SVM RNA-class probability	0.615304
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3218071 111 + 22407834
CUUGUUUGCGCAUUAUGGCAUUACAAUGGCGCGGAUGCAAGAUGCAAGUGGGCAAUUUGCAUAAUGCAUGCGAUAAGC-------UGACUUACCCAUUGACAGGCGAAUAAUGUGCAU
......((((((((((.((....((((((..((.(((((..((((((((.....))))))))..))))).)).((((.-------...)))).))))))....))..)))))))))). ( -41.60)
>DroSec_CAF1 52160 118 + 1
CUUGUUUGCGCAUUAUGGCAUUACAAUGGCACGGAUACAAGAUGCAAGUGGGUAAUUUGCAUAAUGCAUGCGAUAAGCUUAUCGCUGACUUACCCAUUGACAGGCGAACAAUGUGCAU
.(((((((((((((.((.(((....))).)).(....)..))))).(((((((((..(((.....))).((((((....))))))....))))))))).....))))))))....... ( -36.20)
>DroSim_CAF1 50640 111 + 1
CUUGUUUGCGCAUUAUGGCAUUACAAUGGCGCGGAUACAAGAUGCAAGUGGGUAAUUUGCAUAAUGCAUGCGAUAAGC-------UGACUUACCCAUUGACAGGCGAACAAUGUGCAU
......((((((((.(.((....((((((((((....((..((((((((.....))))))))..))..)))).((((.-------...)))).))))))....)).)..)))))))). ( -32.70)
>DroEre_CAF1 48769 102 + 1
CUUGUUUACGCAUUAUGGCAUUACAACGGCGCGGAUGCAAGAC---AGUGGGUAAUUUGCAUAAUGCAUGCGAUAAGC-------UGACUUGCCCAUUGACAGGCGAACAAU------
.(((((..((((((...((.........))...)))))....(---(((((((((..(((.....))).((.....))-------....))))))))))....)..))))).------ ( -28.60)
>DroYak_CAF1 47393 98 + 1
AAUGUUUACGCAUUAUGGCAUUACAACGG----GUUGCAAGAC---AGUGGGUAAUUUGCAUAAUGCAUGCGAAAAGC-------CGACUUGCUUAUUGACAAGCGAACAAU------
..((((..(((((((((..(((((.((..----(((....)))---.))..)))))...)))))))).(((((.((((-------......)))).))).)).)..))))..------ ( -24.90)
>DroPer_CAF1 62016 104 + 1
GGUGUUUUCGUAU---GGUAGAAUAAUAGCA------UAAGAC--CGGGGGCUCAUUUGCAAAAUGCUGGGGAUACGCUGAUAGGAGAACUA-CCAAUGACAGGAGCACAAUGUAC--
.((((((..((.(---(((((..((.((((.------((...(--(((.(((......))....).))))...)).)))).))......)))-)))...))..)))))).......-- ( -25.50)
>consensus
CUUGUUUGCGCAUUAUGGCAUUACAAUGGCGCGGAUGCAAGAC__AAGUGGGUAAUUUGCAUAAUGCAUGCGAUAAGC_______UGACUUACCCAUUGACAGGCGAACAAUGUGC__
..(((((((((......))...........................(((((((((..(((.....))).((.....))...........))))))))).....)))))))........ (-14.50 = -15.17 +   0.67)

alignment

secondary structure

dotplot

Window 8

Location	3,218,071 – 3,218,182
Length	111
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	75.37
Mean single sequence MFE	-27.47
Consensus MFE	-11.73
Energy contribution	-13.60
Covariance contribution	1.87
Combinations/Pair	1.17
Mean z-score	-1.95
Structure conservation index	0.43
SVM decision value	0.06
SVM RNA-class probability	0.566134
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3218071 111 - 22407834
AUGCACAUUAUUCGCCUGUCAAUGGGUAAGUCA-------GCUUAUCGCAUGCAUUAUGCAAAUUGCCCACUUGCAUCUUGCAUCCGCGCCAUUGUAAUGCCAUAAUGCGCAAACAAG
.(((.((((((..((....(((((((((((...-------.)))))((((((((..((((((.........))))))..)))))..)))))))))....)).)))))).)))...... ( -34.80)
>DroSec_CAF1 52160 118 - 1
AUGCACAUUGUUCGCCUGUCAAUGGGUAAGUCAGCGAUAAGCUUAUCGCAUGCAUUAUGCAAAUUACCCACUUGCAUCUUGUAUCCGUGCCAUUGUAAUGCCAUAAUGCGCAAACAAG
.(((.((((((..((....((((((........((((((....))))))(((((..((((((.........))))))..))))).....))))))....)).)))))).)))...... ( -34.60)
>DroSim_CAF1 50640 111 - 1
AUGCACAUUGUUCGCCUGUCAAUGGGUAAGUCA-------GCUUAUCGCAUGCAUUAUGCAAAUUACCCACUUGCAUCUUGUAUCCGCGCCAUUGUAAUGCCAUAAUGCGCAAACAAG
.(((.((((((..((....(((((((((((...-------.)))))((((((((..((((((.........))))))..)))))..)))))))))....)).)))))).)))...... ( -32.80)
>DroEre_CAF1 48769 102 - 1
------AUUGUUCGCCUGUCAAUGGGCAAGUCA-------GCUUAUCGCAUGCAUUAUGCAAAUUACCCACU---GUCUUGCAUCCGCGCCGUUGUAAUGCCAUAAUGCGUAAACAAG
------.(((((.((((......))))......-------((.....))((((((((((...(((((..((.---((...((....)))).)).)))))..)))))))))).))))). ( -24.60)
>DroYak_CAF1 47393 98 - 1
------AUUGUUCGCUUGUCAAUAAGCAAGUCG-------GCUUUUCGCAUGCAUUAUGCAAAUUACCCACU---GUCUUGCAAC----CCGUUGUAAUGCCAUAAUGCGUAAACAUU
------...((..((((((......))))))..-------)).......((((((((((.............---((.((((((.----...)))))).))))))))))))....... ( -21.81)
>DroPer_CAF1 62016 104 - 1
--GUACAUUGUGCUCCUGUCAUUGG-UAGUUCUCCUAUCAGCGUAUCCCCAGCAUUUUGCAAAUGAGCCCCCG--GUCUUA------UGCUAUUAUUCUACC---AUACGAAAACACC
--.......(((....(((...(((-(((......((..((((((...((.((.....))....(......))--)...))------))))..))..)))))---).)))....))). ( -16.20)
>consensus
__GCACAUUGUUCGCCUGUCAAUGGGUAAGUCA_______GCUUAUCGCAUGCAUUAUGCAAAUUACCCACUU__AUCUUGCAUCCGCGCCAUUGUAAUGCCAUAAUGCGCAAACAAG
.......(((((.((......((((((((((.........))))))).)))((((((((...(((((...........................)))))..)))))))))).))))). (-11.73 = -13.60 +   1.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:32 2006