Locus 2483

Sequence ID	2L_DroMel_CAF1
Location	6,827,675 – 6,827,835
Length	160
Max. P	0.999852

overview

Window 4

Location	6,827,675 – 6,827,765
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	76.95
Mean single sequence MFE	-12.22
Consensus MFE	-1.88
Energy contribution	-1.32
Covariance contribution	-0.56
Combinations/Pair	1.43
Mean z-score	-1.57
Structure conservation index	0.15
SVM decision value	0.10
SVM RNA-class probability	0.585155
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6827675 90 + 22407834
GGGCGAUCCAAAUCCAAAUCGGAAACCCAAUCGGAAUCCAAAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAA
(((((((.....(((.....))).........(((.(((.................))).)))..))))...(((....)))..)))... ( -14.63)
>DroPse_CAF1 40880 75 + 1
GGGGAAUGUGAAUGGAAAUGG--------AUUGAAAU-------UAAAUCCAAAUCGAAAUCCCAACUGAAAUCCAAAUCGAAAUUGAAA
.((((...(((((....))((--------(((.....-------..)))))...)))...)))).......................... ( -12.00)
>DroSec_CAF1 31826 90 + 1
GCGCAAUCCAAAUCCAAAUCGGAAACCCAAUCGGAAUCCCAAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAA
......((((..(((.....))).........(((.(((.................))).)))...............))))........ ( -11.23)
>DroSim_CAF1 23684 90 + 1
GCGCAAUCCAAAUCCAAAUCGGAAACCCAAUCGGAAUCCCAAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAA
......((((..(((.....))).........(((.(((.................))).)))...............))))........ ( -11.23)
>DroPer_CAF1 32734 75 + 1
GGGGAAUGUGAAUGGAAAUGG--------AUUGAAAU-------UAAAUCCAAAUCGAAAUCCCAACUGAAAUCCAAAUCGAAAUUGAAA
.((((...(((((....))((--------(((.....-------..)))))...)))...)))).......................... ( -12.00)
>consensus
GGGCAAUCCAAAUCCAAAUCGGAAACCCAAUCGGAAUCC_AAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAA
......................................................((((........))))........(((....))).. ( -1.88 =  -1.32 +  -0.56)

alignment

secondary structure

dotplot

Window 5

Location	6,827,675 – 6,827,765
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	76.95
Mean single sequence MFE	-26.19
Consensus MFE	-16.54
Energy contribution	-20.70
Covariance contribution	4.16
Combinations/Pair	1.19
Mean z-score	-4.20
Structure conservation index	0.63
SVM decision value	4.26
SVM RNA-class probability	0.999852
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6827675 90 - 22407834
UUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUUUGGAUUCCGAUUGGGUUUCCGAUUUGGAUUUGGAUCGCCC
...(((.(((((.(((((.(((.....))).))))).))))).)))((((..(((((.((((((....)))))).)))))..)))).... ( -34.10)
>DroPse_CAF1 40880 75 - 1
UUUCAAUUUCGAUUUGGAUUUCAGUUGGGAUUUCGAUUUGGAUUUA-------AUUUCAAU--------CCAUUUCCAUUCACAUUCCCC
.(((((.......)))))........((((....((..((((((..-------.....)))--------)))..)).........)))). ( -11.62)
>DroSec_CAF1 31826 90 - 1
UUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUUGGGAUUCCGAUUGGGUUUCCGAUUUGGAUUUGGAUUGCGC
((..((..((((.(((((.(((((((((((((((((((((....)))))))))))))))))))))..)))))..))))))..))...... ( -36.80)
>DroSim_CAF1 23684 90 - 1
UUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUUGGGAUUCCGAUUGGGUUUCCGAUUUGGAUUUGGAUUGCGC
((..((..((((.(((((.(((((((((((((((((((((....)))))))))))))))))))))..)))))..))))))..))...... ( -36.80)
>DroPer_CAF1 32734 75 - 1
UUUCAAUUUCGAUUUGGAUUUCAGUUGGGAUUUCGAUUUGGAUUUA-------AUUUCAAU--------CCAUUUCCAUUCACAUUCCCC
.(((((.......)))))........((((....((..((((((..-------.....)))--------)))..)).........)))). ( -11.62)
>consensus
UUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUU_GGAUUCCGAUUGGGUUUCCGAUUUGGAUUUGGAUUGCCC
...........((((((((((.((((((((.((((((((((((((......)))))))))))))).)))))))).))))))))))..... (-16.54 = -20.70 +   4.16)

alignment

secondary structure

dotplot

Window 6

Location	6,827,692 – 6,827,805
Length	113
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	98.82
Mean single sequence MFE	-17.90
Consensus MFE	-17.50
Energy contribution	-17.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.14
Structure conservation index	0.98
SVM decision value	1.11
SVM RNA-class probability	0.916633
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6827692 113 + 22407834
AUCGGAAACCCAAUCGGAAUCCAAAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAAUCGAAAUCCGAACAACCCAAGUCGAAAUCGAAAUCUCAAC
.(((((...((....))........((((..(((.....))).........((..(((....)))..))....))))..)))))..........(((....)))......... ( -17.50)
>DroSec_CAF1 31843 113 + 1
AUCGGAAACCCAAUCGGAAUCCCAAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAAUCGAAAUCCGAACAAGCCAAGUCGAAAUCGAAAUCUCAAC
.(((((.........((....))..((((..(((.....))).........((..(((....)))..))....))))..)))))..........(((....)))......... ( -18.10)
>DroSim_CAF1 23701 113 + 1
AUCGGAAACCCAAUCGGAAUCCCAAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAAUCGAAAUCCGAACAAGCCAAGUCGAAAUCGAAAUCUCAAC
.(((((.........((....))..((((..(((.....))).........((..(((....)))..))....))))..)))))..........(((....)))......... ( -18.10)
>consensus
AUCGGAAACCCAAUCGGAAUCCCAAUCGAAAUCCCAAUCGGAAUCCCAAUCGAAAUCCAAAUGGAAAUCCAAAUCGAAAUCCGAACAAGCCAAGUCGAAAUCGAAAUCUCAAC
.(((((...((....))........((((..(((.....))).........((..(((....)))..))....))))..)))))..........(((....)))......... (-17.50 = -17.50 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	6,827,692 – 6,827,805
Length	113
Sequences	3
Columns	113
Reading direction	reverse
Mean pairwise identity	98.82
Mean single sequence MFE	-44.30
Consensus MFE	-43.03
Energy contribution	-43.37
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-6.11
Structure conservation index	0.97
SVM decision value	0.86
SVM RNA-class probability	0.867607
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6827692 113 - 22407834
GUUGAGAUUUCGAUUUCGACUUGGGUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUUUGGAUUCCGAUUGGGUUUCCGAU
(((((((((.(((...((((....)))).))))))))))))(((((..((((.(((((.((((((((..(((((....)))))..))).))))).))))).))))..))))). ( -44.70)
>DroSec_CAF1 31843 113 - 1
GUUGAGAUUUCGAUUUCGACUUGGCUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUUGGGAUUCCGAUUGGGUUUCCGAU
(((((((((.(((...(((......))).))))))))))))(((((..((((.((((((..((((((..(((((....)))))..))))))..).))))).))))..))))). ( -44.10)
>DroSim_CAF1 23701 113 - 1
GUUGAGAUUUCGAUUUCGACUUGGCUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUUGGGAUUCCGAUUGGGUUUCCGAU
(((((((((.(((...(((......))).))))))))))))(((((..((((.((((((..((((((..(((((....)))))..))))))..).))))).))))..))))). ( -44.10)
>consensus
GUUGAGAUUUCGAUUUCGACUUGGCUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUCCGAUUGGGAUUUCGAUUGGGAUUCCGAUUGGGUUUCCGAU
(((((((((.(((...(((......))).))))))))))))(((((..((((.((((((((((((((..(((((....)))))..))))))))).))))).))))..))))). (-43.03 = -43.37 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	6,827,732 – 6,827,835
Length	103
Sequences	3
Columns	103
Reading direction	reverse
Mean pairwise identity	98.71
Mean single sequence MFE	-27.47
Consensus MFE	-27.40
Energy contribution	-27.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	1.00
SVM decision value	0.95
SVM RNA-class probability	0.888181
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6827732 103 - 22407834
GCGAAUGUGUGUGCAUGAUUUACGGAUUGAGUUGAGAUUUCGAUUUCGACUUGGGUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUC
.(((((((....)))).....((((.(..(((((((((....)))))))))..).)))))))(((..(((((..((..(((....)))..)))))))..))). ( -27.30)
>DroSec_CAF1 31883 103 - 1
ACGAAUGUGUGUGCAUGAUUUACGGAUUGAGUUGAGAUUUCGAUUUCGACUUGGCUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUC
.(((((((....)))).....(((..(..(((((((((....)))))))))..)..))))))(((..(((((..((..(((....)))..)))))))..))). ( -27.70)
>DroSim_CAF1 23741 103 - 1
GCGAAUGUGUGUGCAUGAUUUACGGAUUGAGUUGAGAUUUCGAUUUCGACUUGGCUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUC
.(((((((....)))).....(((..(..(((((((((....)))))))))..)..))))))(((..(((((..((..(((....)))..)))))))..))). ( -27.40)
>consensus
GCGAAUGUGUGUGCAUGAUUUACGGAUUGAGUUGAGAUUUCGAUUUCGACUUGGCUUGUUCGGAUUUCGAUUUGGAUUUCCAUUUGGAUUUCGAUUGGGAUUC
.(((((((....)))).....((((.(..(((((((((....)))))))))..).)))))))(((..(((((..((..(((....)))..)))))))..))). (-27.40 = -27.40 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:58 2006