Locus 4289

Sequence ID	2R_DroMel_CAF1
Location	14,100,143 – 14,100,274
Length	131
Max. P	0.963639

overview

Window 3

Location	14,100,143 – 14,100,238
Length	95
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.59
Mean single sequence MFE	-30.32
Consensus MFE	-16.93
Energy contribution	-17.69
Covariance contribution	0.75
Combinations/Pair	1.36
Mean z-score	-2.12
Structure conservation index	0.56
SVM decision value	1.56
SVM RNA-class probability	0.963639
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14100143 95 + 20766785
--UCGU----------------------GUGGGCUCGCAAAGUAAUGCGACAGGCGUUAAAUGCGCCGGCAAUCGAUUUGAUUUGCAGUCG-CGAUGCGAAUUUAAUUGAAAUGAAAAAU
--((((----------------------((.(((..(((...((((((.....))))))..)))))).))..((((((.((((((((....-...)))))))).)))))).))))..... ( -30.50)
>DroVir_CAF1 14147 105 + 1
CACUGCUUGCGU------------AACAGUAUGUACCGAAAGUAAUGUGACAGGCGUUAAAUGCGCU-GCAAUCGAUUUGAUUUGCAAUCUAUGAU--GGCUUUAAUUGAAAAAAACCAA
...(((..((((------------(...........(....)((((((.....))))))..))))).-))).((((((......((.(((...)))--.))...)))))).......... ( -17.80)
>DroPse_CAF1 10170 117 + 1
--ACUCUUAUGCAAGAGCCAGCACAACAGUGGGCUCGCAAAGUAAUGUGACAGGCGCUAAAUGUGCUGGCAAUCGAUUUGAUUUGCAAGCU-CGAUGCGAAUUUAAUUGAAAUGAAAAAU
--..((((....))))(((((((((..((((.(.(((((......))))))...))))...)))))))))..((((((.((((((((....-...)))))))).)))))).......... ( -37.40)
>DroGri_CAF1 14403 97 + 1
--CUGCUUGCGU------------AACAGUCGGUACCGAAAGUAAUGUGACAGGCGUUAAAUGCGAU-GCAAUCGAUUUGAUUUGCAAUCUGUGAU--GACUUUAAUUGAAAAA------
--(((.(..(((------------.((..(((....)))..)).)))..))))(((((......)))-))..((((((....(..(.....)..).--......))))))....------ ( -20.20)
>DroEre_CAF1 4415 112 + 1
--UCGCUUGCGUAAGAGCA-----AACAGUGGGCUCGAAAAGUAAUGCGACAGGCGUUAAAUGCGCCGGCAAUCGAUUUGAUUUGCCGUCG-CGAUGCGAAUUUAAUUGAAAUGAAAAAU
--((((((((....((((.-----........)))).....))))((((((.(((((.....)))))(((((((.....)).)))))))))-))..)))).................... ( -37.30)
>DroPer_CAF1 10117 117 + 1
--ACGCUUAUGCAAGAGCCAGCACAACAGUGGGCUCGCAAAGUAAUGUGACAGGCGCUAAAUGUGCUGGCAAUCGAUUUGAUUUGCAAUCU-CGAUGCGAAUUUAAUUGAAAUGAAAAAU
--..((....))....(((((((((..((((.(.(((((......))))))...))))...)))))))))..((((((.((((((((....-...)))))))).)))))).......... ( -38.70)
>consensus
__ACGCUUGCGU____________AACAGUGGGCUCGCAAAGUAAUGUGACAGGCGUUAAAUGCGCUGGCAAUCGAUUUGAUUUGCAAUCU_CGAUGCGAAUUUAAUUGAAAUGAAAAAU
....((((((..................))))))...........(((....(((((.....))))).))).((((((.((((((((........)))))))).)))))).......... (-16.93 = -17.69 +   0.75)

alignment

secondary structure

dotplot

Window 4

Location	14,100,159 – 14,100,274
Length	115
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	84.93
Mean single sequence MFE	-37.44
Consensus MFE	-26.89
Energy contribution	-27.08
Covariance contribution	0.20
Combinations/Pair	1.13
Mean z-score	-2.28
Structure conservation index	0.72
SVM decision value	0.05
SVM RNA-class probability	0.558771
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14100159 115 + 20766785
AGUAAUGCGACAGGCGUUAAAUGCGCCGGCAAUCGAUUUGAUUUGCAGUCGCGAUGCGAAUUUAAUUGAAAUGAAAAAUAGCC----GCCCAUAGCCGCACGGUGGGCAGUUGUGCGCC
......(((((((((((.....)))))(((..((((((.((((((((.......)))))))).))))))..(....)...)))----((((...(((....)))))))...))).))). ( -40.80)
>DroPse_CAF1 10208 106 + 1
AGUAAUGUGACAGGCGCUAAAUGUGCUGGCAAUCGAUUUGAUUUGCAAGCUCGAUGCGAAUUUAAUUGAAAUGAAAAAUAGCCAGCCCCCCUU--UCAGGCAGUGGGC-----------
............(((((.....)))))(((..((((((.((((((((.......)))))))).))))))..(....)...))).(((((((..--...))..).))))----------- ( -28.10)
>DroSim_CAF1 22437 113 + 1
AGUAAUGCGACAGGCGUUAAAUGCGCCGGCAAUCGAUUUGAUUUGCAGUCGCGAUGCGAAUUUAAUUGAAAUGAAAAAUAGCC----GCCCAU--UCGCACGGUGGGCAGUUGUGCGGC
.((..((((((.(((((.....)))))(((..((((((.((((((((.......)))))))).))))))..(....)...)))----((((((--(.....))))))).))))))..)) ( -41.00)
>DroEre_CAF1 4448 112 + 1
AGUAAUGCGACAGGCGUUAAAUGCGCCGGCAAUCGAUUUGAUUUGCCGUCGCGAUGCGAAUUUAAUUGAAAUGAAAAAUAGCC----GCGCAU--UCGCGCGGUGGGCAGUUG-GCGGU
.(((.((((((.(((((.....)))))(((((((.....)).))))))))))).)))....(((((((............(((----((((..--..)))))))...))))))-).... ( -44.06)
>DroYak_CAF1 19811 112 + 1
AGUAAUGCGACAGGCGUUAAAUGCGCCGGCAAUCGAUUUGAUUCGCAGUCGCGAUGCGAAUUUAAUUGAAAUGAAAAAUAGCC----GCCCAU--UCGCACAGUGGGCAGUUG-GCGGU
..((((((.....))))))....(((((((..((((((.((((((((.......)))))))).))))))..............----((((((--(.....))))))).))))-))).. ( -42.60)
>DroPer_CAF1 10155 106 + 1
AGUAAUGUGACAGGCGCUAAAUGUGCUGGCAAUCGAUUUGAUUUGCAAUCUCGAUGCGAAUUUAAUUGAAAUGAAAAAUAGCCAGCCCCCCUU--UCAGGCAGUGGGC-----------
............(((((.....)))))(((..((((((.((((((((.......)))))))).))))))..(....)...))).(((((((..--...))..).))))----------- ( -28.10)
>consensus
AGUAAUGCGACAGGCGUUAAAUGCGCCGGCAAUCGAUUUGAUUUGCAGUCGCGAUGCGAAUUUAAUUGAAAUGAAAAAUAGCC____GCCCAU__UCGCACAGUGGGCAGUUG_GCGG_
............(((((.....)))))(((..((((((.((((((((.......)))))))).)))))).((.....)).)))....((((((.........))))))........... (-26.89 = -27.08 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:16 2006