Locus 3463

Sequence ID	3R_DroMel_CAF1
Location	9,362,822 – 9,362,925
Length	103
Max. P	0.972620

overview

Window 6

Location	9,362,822 – 9,362,925
Length	103
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	76.19
Mean single sequence MFE	-24.99
Consensus MFE	-16.28
Energy contribution	-16.98
Covariance contribution	0.70
Combinations/Pair	1.05
Mean z-score	-1.30
Structure conservation index	0.65
SVM decision value	0.33
SVM RNA-class probability	0.690135
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9362822 103 + 27905053
CCAGCC--CGCCCACAUCAGGCCAUCAACCC-ACUGCCUUU-----CCCGUAAUUGGGUCACUUGUAUGCGAAAAAGCAGCGAACUGUUGCAUGCAAAGUAAAUGCAACAU--------
......--.(((.......)))........(-.((((.(((-----(.((((...((....))..)))).))))..)))).)...((((((((.........)))))))).-------- ( -23.10)
>DroSim_CAF1 141264 103 + 1
CCACCU--CGUCCACAUCAGCCCAUCAACCC-ACUGCCUUU-----CCCGUAAUUGGGUCACUUGUAUGCGAAAAAGCAGCGAACUGUUGCAUGCAAAGUACAUGCAACAU--------
.....(--(((..(((...(((((.......-.........-----........)))))....))).(((......)))))))..(((((((((.......))))))))).-------- ( -23.56)
>DroEre_CAF1 132961 96 + 1
-----C--CGCCCACAUCUGCCCACU--UCC-ACUGCCUUU-----CCCGUAAUUGGGUCACUUGUAUGCGAAAAAGCAGCGAACUGUUGCAUGCAAAGUACAUGCAACAU--------
-----.--(((..(((..((((((.(--(.(-.........-----...).)).)))).))..))).(((......))))))...(((((((((.......))))))))).-------- ( -24.60)
>DroYak_CAF1 133259 98 + 1
C-A--C--CCCCUACAUUUGCCCACU--CCC-ACUGCCUUU-----GCCGUAAUUGGGUCACUUGUAUGCGAAAAAGCAGCGAACUGUUGCAUGCAAAGUACAUGCAACAU--------
.-.--.--....((((..((((((..--...-((.((....-----)).))...)))).))..))))(((......)))......(((((((((.......))))))))).-------- ( -24.80)
>DroAna_CAF1 127310 98 + 1
--------------UACCUGCCCCUU--UUCUGUCCCCUCU-----UGGGUAAUUGGGUCACUUGUAUGCGAAAAAGCAGCGAACUGUUGCAUGCGAAGUACAUGCAACAUCAAGGAUA
--------------..(((((((..(--(.....(((....-----.))).))..))))...((((.(((......)))))))..(((((((((.......)))))))))...)))... ( -25.90)
>DroPer_CAF1 133145 115 + 1
CCGCCCUGCGACUGCCCCUGCCCCU---UCC-CCUGCCCCUACCCCUCUGUAAUUGGGUCACUUCUAUGCGAAAAAGCAGCGAACUGUUGCAUGCAAAGUACAUGCGACAUCCAGGAGA
....((((((.((((...(((....---...-...((((.(((......)))...)))).........))).....))))))...(((((((((.......)))))))))..))))... ( -28.01)
>consensus
C_A__C__CGCCCACAUCUGCCCAUU__CCC_ACUGCCUUU_____CCCGUAAUUGGGUCACUUGUAUGCGAAAAAGCAGCGAACUGUUGCAUGCAAAGUACAUGCAACAU________
...................(((((..............................)))))...((((.(((......)))))))..(((((((((.......)))))))))......... (-16.28 = -16.98 +   0.70)

alignment

secondary structure

dotplot

Window 7

Location	9,362,822 – 9,362,925
Length	103
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	76.19
Mean single sequence MFE	-36.41
Consensus MFE	-21.38
Energy contribution	-22.10
Covariance contribution	0.73
Combinations/Pair	1.15
Mean z-score	-2.27
Structure conservation index	0.59
SVM decision value	1.70
SVM RNA-class probability	0.972620
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9362822 103 - 27905053
--------AUGUUGCAUUUACUUUGCAUGCAACAGUUCGCUGCUUUUUCGCAUACAAGUGACCCAAUUACGGG-----AAAGGCAGU-GGGUUGAUGGCCUGAUGUGGGCG--GGCUGG
--------.(((((((.......)))).))).(((..((((((((((((((......))))(((......)))-----)))))))))-)..)))..((((((.......))--)))).. ( -38.60)
>DroSim_CAF1 141264 103 - 1
--------AUGUUGCAUGUACUUUGCAUGCAACAGUUCGCUGCUUUUUCGCAUACAAGUGACCCAAUUACGGG-----AAAGGCAGU-GGGUUGAUGGGCUGAUGUGGACG--AGGUGG
--------.((((((((((.....))))))))))..(((((((((((((((......))))(((......)))-----)))))))))-))(((.(((......))).))).--...... ( -36.50)
>DroEre_CAF1 132961 96 - 1
--------AUGUUGCAUGUACUUUGCAUGCAACAGUUCGCUGCUUUUUCGCAUACAAGUGACCCAAUUACGGG-----AAAGGCAGU-GGA--AGUGGGCAGAUGUGGGCG--G-----
--------.((((((((((.....)))))))))).((((((((((((((((......))))(((......)))-----)))))))))-)))--.((..((....))..)).--.----- ( -37.20)
>DroYak_CAF1 133259 98 - 1
--------AUGUUGCAUGUACUUUGCAUGCAACAGUUCGCUGCUUUUUCGCAUACAAGUGACCCAAUUACGGC-----AAAGGCAGU-GGG--AGUGGGCAAAUGUAGGGG--G--U-G
--------.((((((((((.....))))))))))(..(.((((....((((......))))((((.((((.((-----....)).))-)).--..)))).....)))).).--.--)-. ( -34.30)
>DroAna_CAF1 127310 98 - 1
UAUCCUUGAUGUUGCAUGUACUUCGCAUGCAACAGUUCGCUGCUUUUUCGCAUACAAGUGACCCAAUUACCCA-----AGAGGGGACAGAA--AAGGGGCAGGUA--------------
...(((...((((((((((.....))))))))))....(((.(((((((((......))))........(((.-----...))).....))--))).))))))..-------------- ( -30.80)
>DroPer_CAF1 133145 115 - 1
UCUCCUGGAUGUCGCAUGUACUUUGCAUGCAACAGUUCGCUGCUUUUUCGCAUAGAAGUGACCCAAUUACAGAGGGGUAGGGGCAGG-GGA---AGGGGCAGGGGCAGUCGCAGGGCGG
..((((((((((.((((((.....)))))).)).((((.((((((((((.(.........((((..........))))........)-.))---)))))))))))).))).)))))... ( -41.03)
>consensus
________AUGUUGCAUGUACUUUGCAUGCAACAGUUCGCUGCUUUUUCGCAUACAAGUGACCCAAUUACGGG_____AAAGGCAGU_GGA__AAUGGGCAGAUGUGGGCG__G__U_G
.........((((((((((.....))))))))))(..((((((((((((((......)))).((......))......))))))))).........)..)................... (-21.38 = -22.10 +   0.73)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:37 2006