Locus 3740

Sequence ID	3R_DroMel_CAF1
Location	10,151,126 – 10,151,275
Length	149
Max. P	0.825472

overview

Window 5

Location	10,151,126 – 10,151,235
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	85.78
Mean single sequence MFE	-31.50
Consensus MFE	-18.98
Energy contribution	-21.06
Covariance contribution	2.08
Combinations/Pair	1.19
Mean z-score	-2.93
Structure conservation index	0.60
SVM decision value	0.70
SVM RNA-class probability	0.825472
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10151126 109 - 27905053
CCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCUAUGGAAAAUCAAAGCCGUGGCUUAUCAAAUCCUCCAAAUCAGGAGGAAUCCCCUCACCAAUGGGGUGAACCAGCA
...((.(((................((.(((((.((((..........))))))))).))...((((((......)))))).)))))(((((.....)))))....... ( -33.80)
>DroSec_CAF1 9734 109 - 1
CCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCAUUGGAAAAUCAAAGCCAUGGCUUAUCAAGUCCUCCAAACCAGGAGGAAUGCCCUCACGAAUGGGGUGAACCAGCA
(((.((((.............(((.((.(((((((.((..........))))))))).)))))((((((......))))))....)))).....)))((....)).... ( -33.90)
>DroSim_CAF1 8820 109 - 1
CCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCUUUGGAAAAUCAAAUCCAUGGCUUAUCAAGUCCUCCAAAUCUGGAGGAAUCCCCUCACGAAUGGGGUGAACCAGCA
(((.((((.............(((.((.(((((..((((........)))).))))).)))))(((((((....)))))))....)))).....)))((....)).... ( -35.70)
>DroEre_CAF1 9911 109 - 1
CCAGGAGGAAAGUUCAAGUAACUUAGAAAAGCCUGUGAAAUAUCAAAGCCAAGGCUUAUCAAAUUCCCAAAGUCAGGAGGAAUCCCCUAGCGAAUGGGGUCUGACAGCA
...((.((((((((.....))))).((.((((((.(((....)))......)))))).))...)))))...((((((......((((........)))))))))).... ( -27.80)
>DroYak_CAF1 8940 109 - 1
CAGUGCGGAAAGUUCAAGUAACUUAGAAAAGCCUUUGAAUAAUCAAAGCUCAGGCUUAUCCACUACCCAAAAUCCGGAGGAAUCCCCUUACGAAUGGGGUGAACCAGCA
...(((((((((((.....)))))....((((((((((....)))).....)))))).)))..(((((...((.((((((.....)))).)).)).))))).....))) ( -26.30)
>consensus
CCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCUUUGGAAAAUCAAAGCCAUGGCUUAUCAAAUCCUCCAAAUCAGGAGGAAUCCCCUCACGAAUGGGGUGAACCAGCA
...........(((((.........((.((((((.(((..........))))))))).))...((((((......))))))..((((........)))))))))..... (-18.98 = -21.06 +   2.08)

alignment

secondary structure

dotplot

Window 6

Location	10,151,155 – 10,151,275
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.17
Mean single sequence MFE	-34.52
Consensus MFE	-22.42
Energy contribution	-23.54
Covariance contribution	1.12
Combinations/Pair	1.17
Mean z-score	-2.32
Structure conservation index	0.65
SVM decision value	0.22
SVM RNA-class probability	0.637994
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10151155 120 + 27905053
CCUCCUGAUUUGGAGGAUUUGAUAAGCCACGGCUUUGAUUUUCCAUAGGCUUUUCUAAGGUAUUUGAACUUUCCUCCUGGGCUUCCAAACUUCUAAAGCUUUCUUCUGGCUGGGAGGUAU
((((((...(((((((.((((..(((((..(((((((......)).))))).....(((((......))))).......))))).)))))))))))((((.......))))))))))... ( -32.40)
>DroSec_CAF1 9763 120 + 1
CCUCCUGGUUUGGAGGACUUGAUAAGCCAUGGCUUUGAUUUUCCAAUGGCUUUUCUAAGGUAUUUGAACUUUCCUCCUGGGCUUCAAGACUUCUAAAGCUUUCUUCUGGCUGGGAGGUAU
(((((..(((.(((((((((((.(((((((((..........)).))))))).)).)))((......))..)))))).((((((..((....)).))))))......)))..)))))... ( -39.20)
>DroSim_CAF1 8849 120 + 1
CCUCCAGAUUUGGAGGACUUGAUAAGCCAUGGAUUUGAUUUUCCAAAGGCUUUUCUAAGGUAUUUGAACUUUCCUCCUGGGCUUCAAGACUUCUAAAGCUUUCUUCUGGCUGGGAGGUAU
(((((......))))).(((((.(((((.((((........))))..))))).)).))).............(((((..(.((..((((............))))..)))..)))))... ( -37.10)
>DroEre_CAF1 9940 120 + 1
CCUCCUGACUUUGGGAAUUUGAUAAGCCUUGGCUUUGAUAUUUCACAGGCUUUUCUAAGUUACUUGAACUUUCCUCCUGGACUUCCAAACUUCUAAAGCUUUCUUCUUGUUGGGGGGUAU
(((((..((....(((((.....((((....))))....)))))..(((((((...(((((....(((...(((....))).)))..)))))..))))))).......))..)))))... ( -31.00)
>DroYak_CAF1 8969 120 + 1
CCUCCGGAUUUUGGGUAGUGGAUAAGCCUGAGCUUUGAUUAUUCAAAGGCUUUUCUAAGUUACUUGAACUUUCCGCACUGGCUUCCAAACUUCUAAAGCUUUCUUCUUGUUGGGGGGUAU
((((((((.((..((((.((((.((((((.....((((....)))))))))).))))...))))..))...))).....(((((...........)))))...........))))).... ( -32.90)
>consensus
CCUCCUGAUUUGGAGGACUUGAUAAGCCAUGGCUUUGAUUUUCCAAAGGCUUUUCUAAGGUAUUUGAACUUUCCUCCUGGGCUUCCAAACUUCUAAAGCUUUCUUCUGGCUGGGAGGUAU
((((((((((.((((((......((((....))))............((((((...(((......(((...(((....))).)))....)))..)))))))))))).))))))))))... (-22.42 = -23.54 +   1.12)

alignment

secondary structure

dotplot

Window 7

Location	10,151,155 – 10,151,275
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.17
Mean single sequence MFE	-29.92
Consensus MFE	-19.94
Energy contribution	-21.18
Covariance contribution	1.24
Combinations/Pair	1.20
Mean z-score	-2.18
Structure conservation index	0.67
SVM decision value	0.25
SVM RNA-class probability	0.652826
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10151155 120 - 27905053
AUACCUCCCAGCCAGAAGAAAGCUUUAGAAGUUUGGAAGCCCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCUAUGGAAAAUCAAAGCCGUGGCUUAUCAAAUCCUCCAAAUCAGGAGG
...(((((.............(((((.........)))))...((((((..((......))....((.(((((.((((..........))))))))).))...))))))......))))) ( -32.40)
>DroSec_CAF1 9763 120 - 1
AUACCUCCCAGCCAGAAGAAAGCUUUAGAAGUCUUGAAGCCCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCAUUGGAAAAUCAAAGCCAUGGCUUAUCAAGUCCUCCAAACCAGGAGG
...(((((.............(((((((.....)))))))...((((((..((......))(((.((.(((((((.((..........))))))))).)))))))))))......))))) ( -35.30)
>DroSim_CAF1 8849 120 - 1
AUACCUCCCAGCCAGAAGAAAGCUUUAGAAGUCUUGAAGCCCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCUUUGGAAAAUCAAAUCCAUGGCUUAUCAAGUCCUCCAAAUCUGGAGG
...(((((.((..........(((((((.....)))))))...((((((..((......))(((.((.(((((..((((........)))).))))).)))))))))))....))))))) ( -36.10)
>DroEre_CAF1 9940 120 - 1
AUACCCCCCAACAAGAAGAAAGCUUUAGAAGUUUGGAAGUCCAGGAGGAAAGUUCAAGUAACUUAGAAAAGCCUGUGAAAUAUCAAAGCCAAGGCUUAUCAAAUUCCCAAAGUCAGGAGG
....((.((.....((((....)))).((..((.((((.(((....)))(((((.....))))).((.((((((.(((....)))......)))))).))...)))).))..)).)).)) ( -23.20)
>DroYak_CAF1 8969 120 - 1
AUACCCCCCAACAAGAAGAAAGCUUUAGAAGUUUGGAAGCCAGUGCGGAAAGUUCAAGUAACUUAGAAAAGCCUUUGAAUAAUCAAAGCUCAGGCUUAUCCACUACCCAAAAUCCGGAGG
....((.((.....((((....))))....((.((((((((.(.((.((..(((((((...(((....)))..)))))))..))...)).).))))..))))..)).........)).)) ( -22.60)
>consensus
AUACCUCCCAGCCAGAAGAAAGCUUUAGAAGUUUGGAAGCCCAGGAGGAAAGUUCAAAUACCUUAGAAAAGCCUUUGGAAAAUCAAAGCCAUGGCUUAUCAAAUCCUCCAAAUCAGGAGG
...(((((.............(((((.........)))))...(((((((((.........))).((.((((((.(((..........))))))))).))...))))))......))))) (-19.94 = -21.18 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:56 2006