Locus 1735

Sequence ID	2L_DroMel_CAF1
Location	4,758,562 – 4,758,711
Length	149
Max. P	0.999944

overview

Window 7

Location	4,758,562 – 4,758,672
Length	110
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-26.29
Consensus MFE	-22.36
Energy contribution	-22.00
Covariance contribution	-0.36
Combinations/Pair	1.10
Mean z-score	-1.70
Structure conservation index	0.85
SVM decision value	1.20
SVM RNA-class probability	0.930121
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4758562 110 - 22407834
CCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU--AUUUUAUUUAUGCCUCAUGUGCGCUUAGUUAUUCUGGGUUUUUGUGGUAAU
.((((..((((.(((((.....((..((((((((((....))))))))))..))(((((--((..............))))).))...)))))...))))....)))).... ( -26.44)
>DroSec_CAF1 206871 110 - 1
CCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU--AUUUUAUUUAUGCCUCAUGUGCGCUUAGUUAUUCUGGGUUUUUGUGGUAAU
.((((..((((.(((((.....((..((((((((((....))))))))))..))(((((--((..............))))).))...)))))...))))....)))).... ( -26.44)
>DroSim_CAF1 183793 110 - 1
CCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU--AUUUUAUUUAUGCCUCAUGUGCGCUUAGUUAUUCUGGGUUUUUGUGGUAAU
.((((..((((.(((((.....((..((((((((((....))))))))))..))(((((--((..............))))).))...)))))...))))....)))).... ( -26.44)
>DroEre_CAF1 195556 112 - 1
CCUAUUUGCUUUGUAACACUUACACUCGAAUGGCUUACGUAAGCCAUUUGCUUGGCCAUAUAUUUUAUUUAUGCCUCAUGGGCGCUUAGCUAUUCUGGGUUUUCGUGGUAAU
......................((..((((((((((....))))))))))..))(((((.............(((.....)))((((((.....))))))....)))))... ( -27.10)
>DroYak_CAF1 193557 110 - 1
CCUCUUUGCUUUGUAACACUUACACUCGAAUGGCUUACGUAAGCCAUUUGCUUAGCCAU--AUUUUAUUUAUGCCUCAUGUGCGUUUAGCUACGCUGGGUUUUUGUGGUAAU
...........((((.....))))..((((((((((....))))))))))....(((((--(..........((((..(((((.....)).)))..))))...))))))... ( -25.02)
>consensus
CCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU__AUUUUAUUUAUGCCUCAUGUGCGCUUAGUUAUUCUGGGUUUUUGUGGUAAU
.......(((.((((.....))))..((((((((((....))))))))))...)))...............((((.((.....((((((.....))))))...)).)))).. (-22.36 = -22.00 +  -0.36)

alignment

secondary structure

dotplot

Window 8

Location	4,758,595 – 4,758,711
Length	116
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	91.23
Mean single sequence MFE	-26.22
Consensus MFE	-23.80
Energy contribution	-23.56
Covariance contribution	-0.24
Combinations/Pair	1.13
Mean z-score	-1.74
Structure conservation index	0.91
SVM decision value	1.94
SVM RNA-class probability	0.983232
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4758595 116 + 22407834
AUGAGGCAUAAAUAAAAU--AUGGCCAGGCAAAUGGCUUACGUAAGCCAUCCGAGUGUAAGUGUUACAAAGCAAAUGGGAUAAUGGACU-GACUGCCUGGCAGAGAUAAAAGUAAUCUA
......((((.......)--)))((((((((..((((((....))))))((((..(.((..((((....))))..)).)....))))..-...))))))))..((((.......)))). ( -29.60)
>DroSec_CAF1 206904 116 + 1
AUGAGGCAUAAAUAAAAU--AUGGCCAGGCAAAUGGCUUACGUAAGCCAUCCGAGUGUAAGUGUUACAAAGCAAAUGGGAUAAUGGACU-GACUGCCUGGCAGAGAUAAAAGUAAUCUA
......((((.......)--)))((((((((..((((((....))))))((((..(.((..((((....))))..)).)....))))..-...))))))))..((((.......)))). ( -29.60)
>DroSim_CAF1 183826 116 + 1
AUGAGGCAUAAAUAAAAU--AUGGCCAGGCAAAUGGCUUACGUAAGCCAUCCGAGUGUAAGUGUUACAAAGCAAAUGGGAUAAUGGACU-GACUGCCUGGCAGAGAUAAAAGUAAUCUA
......((((.......)--)))((((((((..((((((....))))))((((..(.((..((((....))))..)).)....))))..-...))))))))..((((.......)))). ( -29.60)
>DroEre_CAF1 195589 114 + 1
AUGAGGCAUAAAUAAAAUAUAUGGCCAAGCAAAUGGCUUACGUAAGCCAUUCGAGUGUAAGUGUUACAAAGCAAAUAGGAUAUA-----GGAUGGCCUGGCAGGGAUAAAAGUAAUCUA
.....((..........(((..(((((......)))))...))).(((((((..((((...((((....))))......)))).-----)))))))...))..((((.......)))). ( -21.80)
>DroYak_CAF1 193590 117 + 1
AUGAGGCAUAAAUAAAAU--AUGGCUAAGCAAAUGGCUUACGUAAGCCAUUCGAGUGUAAGUGUUACAAAGCAAAGAGGAUAUAGGUUAGGAUGGCAUGGCAGGGAUAAAAGUAAUCUA
....(.(((.........--...(((((((.....))))).))..((((((((..((((.....))))...)......(((....))).)))))))))).)..((((.......)))). ( -20.50)
>consensus
AUGAGGCAUAAAUAAAAU__AUGGCCAGGCAAAUGGCUUACGUAAGCCAUCCGAGUGUAAGUGUUACAAAGCAAAUGGGAUAAUGGACU_GACUGCCUGGCAGAGAUAAAAGUAAUCUA
.......................(((((((....(((((....)))))((((...(((............)))....)))).............)))))))..((((.......)))). (-23.80 = -23.56 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	4,758,595 – 4,758,711
Length	116
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	91.23
Mean single sequence MFE	-23.52
Consensus MFE	-23.16
Energy contribution	-23.20
Covariance contribution	0.04
Combinations/Pair	1.10
Mean z-score	-2.45
Structure conservation index	0.98
SVM decision value	4.73
SVM RNA-class probability	0.999944
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4758595 116 - 22407834
UAGAUUACUUUUAUCUCUGCCAGGCAGUC-AGUCCAUUAUCCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU--AUUUUAUUUAUGCCUCAU
.((((.......))))..(((((((....-.....................((((.....))))...(((((((((....))))))))))))))))(((--(.......))))...... ( -26.80)
>DroSec_CAF1 206904 116 - 1
UAGAUUACUUUUAUCUCUGCCAGGCAGUC-AGUCCAUUAUCCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU--AUUUUAUUUAUGCCUCAU
.((((.......))))..(((((((....-.....................((((.....))))...(((((((((....))))))))))))))))(((--(.......))))...... ( -26.80)
>DroSim_CAF1 183826 116 - 1
UAGAUUACUUUUAUCUCUGCCAGGCAGUC-AGUCCAUUAUCCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU--AUUUUAUUUAUGCCUCAU
.((((.......))))..(((((((....-.....................((((.....))))...(((((((((....))))))))))))))))(((--(.......))))...... ( -26.80)
>DroEre_CAF1 195589 114 - 1
UAGAUUACUUUUAUCCCUGCCAGGCCAUCC-----UAUAUCCUAUUUGCUUUGUAACACUUACACUCGAAUGGCUUACGUAAGCCAUUUGCUUGGCCAUAUAUUUUAUUUAUGCCUCAU
..................(((((((.....-----................((((.....))))...(((((((((....))))))))))))))))....................... ( -22.90)
>DroYak_CAF1 193590 117 - 1
UAGAUUACUUUUAUCCCUGCCAUGCCAUCCUAACCUAUAUCCUCUUUGCUUUGUAACACUUACACUCGAAUGGCUUACGUAAGCCAUUUGCUUAGCCAU--AUUUUAUUUAUGCCUCAU
...............................................(((.((((.....))))..((((((((((....))))))))))...)))(((--(.......))))...... ( -14.30)
>consensus
UAGAUUACUUUUAUCUCUGCCAGGCAGUC_AGUCCAUUAUCCCAUUUGCUUUGUAACACUUACACUCGGAUGGCUUACGUAAGCCAUUUGCCUGGCCAU__AUUUUAUUUAUGCCUCAU
..................(((((((..........................((((.....))))...(((((((((....))))))))))))))))....................... (-23.16 = -23.20 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:51 2006