Locus 2564

Sequence ID	3R_DroMel_CAF1
Location	6,939,722 – 6,939,960
Length	238
Max. P	0.981806

overview

Window 4

Location	6,939,722 – 6,939,830
Length	108
Sequences	3
Columns	108
Reading direction	forward
Mean pairwise identity	98.77
Mean single sequence MFE	-37.67
Consensus MFE	-37.67
Energy contribution	-37.67
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	1.00
SVM decision value	1.90
SVM RNA-class probability	0.981806
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6939722 108 + 27905053
CAUAAUUAAAGGGGAAAACCUCAAAAGAGCCUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCCCUGGCCGCACA
..........((((....)))).....(((((((((....)))))..))))((((((((...))(.(((..(((((((....)..))))))..))).).))))))... ( -37.20)
>DroSim_CAF1 89710 108 + 1
CAUAAUUAAAGGGGAAAACCUCAAAAAAGCCUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCUCUGGCCGCACA
..........((((....)))).....(((((((((....)))))..))))((((((((...))(.(((..(((((((....)..))))))..))).).))))))... ( -37.90)
>DroYak_CAF1 90346 108 + 1
CAUAAUUAAAGGGGAAAACCUCAAAAAAGCCUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCUCUGGCCGCACA
..........((((....)))).....(((((((((....)))))..))))((((((((...))(.(((..(((((((....)..))))))..))).).))))))... ( -37.90)
>consensus
CAUAAUUAAAGGGGAAAACCUCAAAAAAGCCUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCUCUGGCCGCACA
..........((((....)))).....(((((((((....)))))..))))((((((((...))(.(((..(((((((....)..))))))..))).).))))))... (-37.67 = -37.67 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	6,939,752 – 6,939,858
Length	106
Sequences	3
Columns	106
Reading direction	forward
Mean pairwise identity	94.65
Mean single sequence MFE	-40.77
Consensus MFE	-36.54
Energy contribution	-36.54
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-3.01
Structure conservation index	0.90
SVM decision value	1.50
SVM RNA-class probability	0.959406
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6939752 106 + 27905053
CUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCCCUGGCCGCACAAUUGUUGCACGCACACAGUCUACAGACC
.(((((....)))))..(((((((((((...(((((((((.(((((((....)..))))))((.((....)).)).......)))))))))..))).)))))).)) ( -42.40)
>DroSim_CAF1 89740 99 + 1
CUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCUCUGGCCGCACAAUUGUUGCACGCACACAGUC-------C
.(((((....)))))..(((((((.......(((((((((.(((((((....)..))))))((.((....)).)).......))))))))))))))))-------. ( -36.31)
>DroYak_CAF1 90376 106 + 1
CUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCUCUGGCCGCACAAUUGUUGCACGCACACAGUCCACAGACC
.(((((....)))))..(((((((((((...(((((((((.(((((((....)..))))))((.((....)).)).......)))))))))..))).)))))).)) ( -43.60)
>consensus
CUUGAACUCAUUCAACUGGCUGUGGCUGCAUUGCGUGCAGUUUGGCCCGAAAGUUGGCCAAGUUGCUCUGGCCGCACAAUUGUUGCACGCACACAGUC_ACAGACC
.(((((....)))))..(((((((.......(((((((((.(((((((....)..))))))((.((....)).)).......))))))))))))))))........ (-36.54 = -36.54 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	6,939,752 – 6,939,858
Length	106
Sequences	3
Columns	106
Reading direction	reverse
Mean pairwise identity	94.65
Mean single sequence MFE	-42.63
Consensus MFE	-34.07
Energy contribution	-35.73
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-3.21
Structure conservation index	0.80
SVM decision value	0.70
SVM RNA-class probability	0.826141
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6939752 106 - 27905053
GGUCUGUAGACUGUGUGCGUGCAACAAUUGUGCGGCCAGGGCAACUUGGCCAACUUUCGGGCCAAACUGCACGCAAUGCAGCCACAGCCAGUUGAAUGAGUUCAAG
((.((((.(.(((((((((((((....(((.(((((((((....)))))))..(.....))))))..))))))).))))))).))))))..(((((....))))). ( -45.70)
>DroSim_CAF1 89740 99 - 1
G-------GACUGUGUGCGUGCAACAAUUGUGCGGCCAGAGCAACUUGGCCAACUUUCGGGCCAAACUGCACGCAAUGCAGCCACAGCCAGUUGAAUGAGUUCAAG
(-------(.(((((((((((((.......(((.......)))..((((((........))))))..))))))).))))))))........(((((....))))). ( -35.40)
>DroYak_CAF1 90376 106 - 1
GGUCUGUGGACUGUGUGCGUGCAACAAUUGUGCGGCCAGAGCAACUUGGCCAACUUUCGGGCCAAACUGCACGCAAUGCAGCCACAGCCAGUUGAAUGAGUUCAAG
((.((((((.(((((((((((((.......(((.......)))..((((((........))))))..))))))).))))))))))))))..(((((....))))). ( -46.80)
>consensus
GGUCUGU_GACUGUGUGCGUGCAACAAUUGUGCGGCCAGAGCAACUUGGCCAACUUUCGGGCCAAACUGCACGCAAUGCAGCCACAGCCAGUUGAAUGAGUUCAAG
((.((((.(.(((((((((((((.......(((.......)))..((((((........))))))..))))))).))))))).))))))..(((((....))))). (-34.07 = -35.73 +   1.67)

alignment

secondary structure

dotplot

Window 7

Location	6,939,792 – 6,939,891
Length	99
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	72.91
Mean single sequence MFE	-35.57
Consensus MFE	-14.91
Energy contribution	-15.85
Covariance contribution	0.94
Combinations/Pair	1.11
Mean z-score	-2.24
Structure conservation index	0.42
SVM decision value	0.02
SVM RNA-class probability	0.542023
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6939792 99 - 27905053
-GCCCAUAGGCAU------UUUUCCACUCCACUUGACUGUGGUCUGUAGA------------CUGUGUGCGUGCAACAAUUGUGCGGCCAGGGCAACUU--GGCCAACUUUCGGGCCAAA
-((((....((((------...((.((.((((......))))...)).))------------....))))(..((.....))..)(((((((....)))--)))).......)))).... ( -39.20)
>DroSim_CAF1 89780 92 - 1
-GCCCAUAGGCAU------UUUUCCACUCCACUUGACUGUG-------GA------------CUGUGUGCGUGCAACAAUUGUGCGGCCAGAGCAACUU--GGCCAACUUUCGGGCCAAA
-((((....((((------.....((.(((((......)))-------))------------.)).))))(..((.....))..)((((((......))--)))).......)))).... ( -32.90)
>DroWil_CAF1 102976 115 - 1
UGCCACUUGCCACUUGCUACUUGCCACUCGAAAGCAAUUUGGUUAGCCGAUUUUGUGUGUUUGUGUAUGCGUGCAACAAAU--GCGGCU---GCAACUUGUGGCCAACUUUUUGCCCAAG
.(((((..((((.(((((..(((.....))).)))))..))))((((((..(((((.(((.(((....))).)))))))).--.)))))---)......)))))................ ( -30.80)
>DroYak_CAF1 90416 99 - 1
-GCCCAUCGGCAU------UUUUCCACUCCACUUGACUGUGGUCUGUGGA------------CUGUGUGCGUGCAACAAUUGUGCGGCCAGAGCAACUU--GGCCAACUUUCGGGCCAAA
-((((....((((------...(((((.((((......))))...)))))------------....))))(..((.....))..)((((((......))--)))).......)))).... ( -39.40)
>consensus
_GCCCAUAGGCAU______UUUUCCACUCCACUUGACUGUGGUCUGU_GA____________CUGUGUGCGUGCAACAAUUGUGCGGCCAGAGCAACUU__GGCCAACUUUCGGGCCAAA
.((.....(((.................((((......))))...........................((((((.....)))))))))...)).......((((........))))... (-14.91 = -15.85 +   0.94)

alignment

secondary structure

dotplot

Window 8

Location	6,939,858 – 6,939,960
Length	102
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	80.43
Mean single sequence MFE	-24.71
Consensus MFE	-16.54
Energy contribution	-16.43
Covariance contribution	-0.11
Combinations/Pair	1.10
Mean z-score	-1.87
Structure conservation index	0.67
SVM decision value	0.48
SVM RNA-class probability	0.754499
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6939858 102 + 27905053
ACAGUCAAGUGGAGUGGAAAAAUGCCUAUGGGCGUGUCC------CCACU--GGAAGGCCAAAUGCACUAGGAAAUUGUAUAGGAAAAAUCUUGGAAAAUUAUAGAACCA
.......(((((...(((...(((((....))))).)))------)))))--((...((.....)).(((...((((...(((((....)))))...)))).)))..)). ( -23.30)
>DroSim_CAF1 89839 91 + 1
ACAGUCAAGUGGAGUGGAAAAAUGCCUAUGGGCGUGUCC------CCACU--GGAAGGCCAA-----------AAAUAUAUAGGAAAAAUCUUGGAAAAUUAUAGAACAA
.(..((.(((((...(((...(((((....))))).)))------)))))--.))..)....-----------.......(((((....)))))................ ( -19.80)
>DroYak_CAF1 90482 110 + 1
ACAGUCAAGUGGAGUGGAAAAAUGCCGAUGGGCGUGUCCAUCCUUCCAGUGGGGAAGGCCAAAUGCACUAGGAAAAUUUGUAAGAAAUGUUUUGGAAACUUAUAAAACCA
..(((((..(((.(((((...(((((....))))).)))))((((((.....)))))))))..)).))).((....((((((((..............)))))))).)). ( -31.04)
>consensus
ACAGUCAAGUGGAGUGGAAAAAUGCCUAUGGGCGUGUCC______CCACU__GGAAGGCCAAAUGCACUAGGAAAAUAUAUAGGAAAAAUCUUGGAAAAUUAUAGAACCA
.(..((.(((((...(((...(((((....))))).)))......)))))...))..)......................(((((....)))))................ (-16.54 = -16.43 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:28 2006