Locus 6684

Sequence ID	2L_DroMel_CAF1
Location	18,720,899 – 18,721,021
Length	122
Max. P	0.992418

overview

Window 4

Location	18,720,899 – 18,720,990
Length	91
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	65.23
Mean single sequence MFE	-20.78
Consensus MFE	-12.88
Energy contribution	-13.12
Covariance contribution	0.24
Combinations/Pair	1.11
Mean z-score	-1.98
Structure conservation index	0.62
SVM decision value	1.91
SVM RNA-class probability	0.982246
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18720899 91 + 22407834
UAGAAUAUUU-------CGGUA-------AUAAACUAGAUUUU---------------UCCGCCAGAAGCAAGGUCACACUAGGCUUAAGUGUGGCCAGCCUUUAAUUUAUUUCACAACU
..(((.(((.-------.(((.-------..............---------------...((.....))..(((((((((.......))))))))).)))...)))....)))...... ( -18.60)
>DroSec_CAF1 13608 90 + 1
UAGAAUAUCCCUAAAUACGGUA-------AUAAACAUGAUUUG-----------------------ACACAUGAUGACACUAGACUUAAGUGUGACCAGCCUUUAAUAUAAUUCAAACAC
..((((.....((((..((((.-------.....((((.....-----------------------...))))...(((((.......))))).))).)..)))).....))))...... ( -10.20)
>DroSim_CAF1 12047 109 + 1
UAGAAUAUUUCUAAAUCCGGUA-------AUAAACAGGAUUUAAUGGGGAUC----CCCCCGCCAGAAGCAAGGUCACACUAGACUUAAGUGUGACCAGCCAUUAAUAUAAUACACAACU
.......(((((((((((.((.-------....)).)))))))..((((...----.))))....))))...(((((((((.......)))))))))....................... ( -30.60)
>DroEre_CAF1 13764 107 + 1
UAGAAUAUCCCCAAAUCAUGUUAUAAACAUUAAACA---UCUAAA----------CAUUCCGCCAGAAACAAGGUCACACUGGACCUAAGUGUGACCAGCCUUUAAUGUAAUUCAAAUUG
..........................((((((((..---......----------..(((.....)))....(((((((((.......)))))))))....))))))))........... ( -20.70)
>DroYak_CAF1 13809 120 + 1
UAGAAUAUAUAGAUAUAGAAUAUUAAAUAAUAAACAGGAUUUAAUGAGGAUGAGCUAUUGCACCAGAAGAAAGGUCACACUAGACUCAAGUGUGACCAGCGUUUAAUGUAAUUCAAAGUG
..((((((((..........((((((((..(....)..)))))))).(((((.((....))...........(((((((((.......)))))))))..))))).)))).))))...... ( -23.80)
>consensus
UAGAAUAUCUCUAAAUACGGUA_______AUAAACAGGAUUUAA______________UCCGCCAGAAGCAAGGUCACACUAGACUUAAGUGUGACCAGCCUUUAAUAUAAUUCAAAACG
........................................................................(((((((((.......)))))))))....................... (-12.88 = -13.12 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	18,720,925 – 18,721,021
Length	96
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	68.83
Mean single sequence MFE	-23.83
Consensus MFE	-15.99
Energy contribution	-15.17
Covariance contribution	-0.81
Combinations/Pair	1.26
Mean z-score	-1.85
Structure conservation index	0.67
SVM decision value	2.33
SVM RNA-class probability	0.992418
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18720925 96 + 22407834
UUU---------------UCCGCCAGAAGCAAGGUCACACUAGGCUUAAGUGUGGCCAGCCUUUAAUUUAUUUCACAACUUUAAAAUUUGACGACUUAA--------U-UUUUUGUGUAU
...---------------.......((((...(((((((((.......)))))))))...)))).........(((((....((((((.........))--------)-))))))))... ( -17.90)
>DroSim_CAF1 12080 106 + 1
UUAAUGGGGAUC----CCCCCGCCAGAAGCAAGGUCACACUAGACUUAAGUGUGACCAGCCAUUAAUAUAAUACACAACUUUUAUAUUUGACAACUUAC--------A--UUUUGCGUAU
.....((((...----.)))).......(((((((((((((.......))))))))).......(((((((..........)))))))...........--------.--..)))).... ( -27.80)
>DroEre_CAF1 13801 101 + 1
CUAAA----------CAUUCCGCCAGAAACAAGGUCACACUGGACCUAAGUGUGACCAGCCUUUAAUGUAAUUCAAAUUGUUUAAGUCUUACG-CUUAC--------UUUUUUAGUGAUU
.....----------.....(((.(((((...(((((((((.......))))))))).........................(((((.....)-)))).--------.))))).)))... ( -21.00)
>DroYak_CAF1 13849 118 + 1
UUAAUGAGGAUGAGCUAUUGCACCAGAAGAAAGGUCACACUAGACUCAAGUGUGACCAGCGUUUAAUGUAAUUCAAAGUGUUGAAAUCUUACG-CUUACCUUUUACCUUUUUUAGUG-UU
((((.((((....((....))...(((((...(((((((((.......)))))))))(((((.....(...(((((....)))))..)..)))-))...))))).))))..))))..-.. ( -28.60)
>consensus
UUAAU___________AUUCCGCCAGAAGCAAGGUCACACUAGACUUAAGUGUGACCAGCCUUUAAUGUAAUUCAAAACGUUUAAAUCUGACG_CUUAC________U_UUUUAGUGUAU
....................(((.((((....(((((((((.......)))))))))..................(((.........)))...................)))).)))... (-15.99 = -15.17 +  -0.81)

alignment

secondary structure

dotplot

Window 6

Location	18,720,925 – 18,721,021
Length	96
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	68.83
Mean single sequence MFE	-25.05
Consensus MFE	-13.72
Energy contribution	-14.91
Covariance contribution	1.19
Combinations/Pair	1.16
Mean z-score	-1.85
Structure conservation index	0.55
SVM decision value	1.29
SVM RNA-class probability	0.940458
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18720925 96 - 22407834
AUACACAAAAA-A--------UUAAGUCGUCAAAUUUUAAAGUUGUGAAAUAAAUUAAAGGCUGGCCACACUUAAGCCUAGUGUGACCUUGCUUCUGGCGGA---------------AAA
...........-.--------.....((((((.((((((......)))))).......((((.((.((((((.......)))))).))..)))).)))))).---------------... ( -20.20)
>DroSim_CAF1 12080 106 - 1
AUACGCAAAA--U--------GUAAGUUGUCAAAUAUAAAAGUUGUGUAUUAUAUUAAUGGCUGGUCACACUUAAGUCUAGUGUGACCUUGCUUCUGGCGGGGG----GAUCCCCAUUAA
((((((((..--.--------.((.(((....))).))....))))))))....(((..(((.(((((((((.......)))))))))..)))..))).((((.----...))))..... ( -32.60)
>DroEre_CAF1 13801 101 - 1
AAUCACUAAAAAA--------GUAAG-CGUAAGACUUAAACAAUUUGAAUUACAUUAAAGGCUGGUCACACUUAGGUCCAGUGUGACCUUGUUUCUGGCGGAAUG----------UUUAG
.............--------.((((-(((..(.((.(((((((((((......)))))....(((((((((.......)))))))))))))))..)))...)))----------)))). ( -21.80)
>DroYak_CAF1 13849 118 - 1
AA-CACUAAAAAAGGUAAAAGGUAAG-CGUAAGAUUUCAACACUUUGAAUUACAUUAAACGCUGGUCACACUUGAGUCUAGUGUGACCUUUCUUCUGGUGCAAUAGCUCAUCCUCAUUAA
..-(((((...((((.........((-(((..((((((((....)))))....)))..)))))(((((((((.......)))))))))..)))).))))).................... ( -25.60)
>consensus
AAACACAAAAA_A________GUAAG_CGUAAAAUUUAAAAAUUGUGAAUUACAUUAAAGGCUGGUCACACUUAAGUCUAGUGUGACCUUGCUUCUGGCGGAAU___________AUUAA
...........................(((((((.........................(((.(((((((((.......)))))))))..)))))))))).................... (-13.72 = -14.91 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:21 2006