Locus 1130

Sequence ID	3L_DroMel_CAF1
Location	3,299,147 – 3,299,306
Length	159
Max. P	0.869098

overview

Window 9

Location	3,299,147 – 3,299,266
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.22
Mean single sequence MFE	-41.52
Consensus MFE	-27.81
Energy contribution	-28.00
Covariance contribution	0.19
Combinations/Pair	1.15
Mean z-score	-2.30
Structure conservation index	0.67
SVM decision value	0.86
SVM RNA-class probability	0.869098
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3299147 119 + 23771897
AACCAGAAGAACAUUCUAAUA-AUGGCUCAAAUUAAAGGAUUGUUUGCUCUCCUCGCUGUGGUGACCAUUGUCCUAAUGGUGGCCAACUCGGCUUCGGCCGUGGAUUGCCCAUCUGGAAG
..(((((.(((((.(((..((-((.......))))..))).)))))((..(((.(....((((.(((((((...))))))).))))....(((....)))).)))..))...)))))... ( -41.60)
>DroSim_CAF1 5093 119 + 1
AACCAGAAGAAUAUUCUAAAA-AUGGCUCAAAUUAAAGGAUUGUUUGCUCUCCUCGCUGUGGUGACCAUUGUCCUAAUGGUGGCCAACUCGGCUUCGGCCGUGGAUUGCCCAUCUGGAAG
..((((((((....)))....-..(((.........((((..(....)..))))(((..((((.(((((((...))))))).))))....(((....))))))....)))..)))))... ( -38.00)
>DroEre_CAF1 5001 119 + 1
AACCAGAAGCUCAUUACAAAA-AUGGCUCAGAUUAAAGGCUUGUUCGCUGUGCUCGCUGUGGUGGCCAUUGUCCUAAUGGCCGCCAACUCGUCUUCGGCUGUGGAUUGCCAGUCUGGAAC
..((((((((.((((.....)-)))))).........(((..((((((...(((((...((((((((((((...))))))))))))...)).....))).)))))).)))..)))))... ( -44.70)
>DroYak_CAF1 4305 120 + 1
UACCAAGACUUAAUAGUAAAACAUGGCUCAGAUGAAAGGCUUGUUCGCUGUGCUCGCUGUGGUGGCCAUUGUCCUUUUGGCCGCCGACUCGUCUUCGGCCGUGGAUUGCCUAUCUGGAAC
........((..(((((((..(((((((.((((((..(((..((.......))..))).(((((((((.........)))))))))..))))))..)))))))..))).))))..))... ( -41.80)
>consensus
AACCAGAAGAACAUUCUAAAA_AUGGCUCAAAUUAAAGGAUUGUUCGCUCUCCUCGCUGUGGUGACCAUUGUCCUAAUGGCCGCCAACUCGGCUUCGGCCGUGGAUUGCCCAUCUGGAAC
..(((((...............((((((..................((.......))..(((((((((((.....)))))))))))..........))))))((....))..)))))... (-27.81 = -28.00 +   0.19)

alignment

secondary structure

dotplot

Window 0

Location	3,299,186 – 3,299,306
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-53.37
Consensus MFE	-42.90
Energy contribution	-43.90
Covariance contribution	1.00
Combinations/Pair	1.05
Mean z-score	-2.90
Structure conservation index	0.80
SVM decision value	0.68
SVM RNA-class probability	0.820364
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3299186 120 + 23771897
UUGUUUGCUCUCCUCGCUGUGGUGACCAUUGUCCUAAUGGUGGCCAACUCGGCUUCGGCCGUGGAUUGCCCAUCUGGAAGAUUCAGUGGUCCUUGCUGGGCCUGGGAUGGAGAGCAGUGC
....(((((((((((((..((((.(((((((...))))))).))))....(((....)))))))....((((.(((((...))))).(((((.....)))))))))..)))))))))... ( -54.40)
>DroSim_CAF1 5132 120 + 1
UUGUUUGCUCUCCUCGCUGUGGUGACCAUUGUCCUAAUGGUGGCCAACUCGGCUUCGGCCGUGGAUUGCCCAUCUGGAAGAUUCAGUGGUCCUUGCUGGGCCUGGGAUGGAGAGCAGUGC
....(((((((((((((..((((.(((((((...))))))).))))....(((....)))))))....((((.(((((...))))).(((((.....)))))))))..)))))))))... ( -54.40)
>DroEre_CAF1 5040 120 + 1
UUGUUCGCUGUGCUCGCUGUGGUGGCCAUUGUCCUAAUGGCCGCCAACUCGUCUUCGGCUGUGGAUUGCCAGUCUGGAACUUUCAGUGGUCCUUGCUGGGCCUGGGAUGGAGAGCAGUGC
.....((((((.(((....((((((((((((...))))))))))))...(((((..(((.........(((((..(((.((......)))))..))))))))..)))))))).)))))). ( -51.30)
>consensus
UUGUUUGCUCUCCUCGCUGUGGUGACCAUUGUCCUAAUGGUGGCCAACUCGGCUUCGGCCGUGGAUUGCCCAUCUGGAAGAUUCAGUGGUCCUUGCUGGGCCUGGGAUGGAGAGCAGUGC
......(((((((......((((.(((((((...))))))).)))).(((((.((((((...((((..(..(((.....)))...)..))))..)))))).)))))..)))))))..... (-42.90 = -43.90 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	3,299,186 – 3,299,306
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-40.80
Consensus MFE	-32.76
Energy contribution	-33.77
Covariance contribution	1.00
Combinations/Pair	1.06
Mean z-score	-2.30
Structure conservation index	0.80
SVM decision value	0.15
SVM RNA-class probability	0.608748
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3299186 120 - 23771897
GCACUGCUCUCCAUCCCAGGCCCAGCAAGGACCACUGAAUCUUCCAGAUGGGCAAUCCACGGCCGAAGCCGAGUUGGCCACCAUUAGGACAAUGGUCACCACAGCGAGGAGAGCAAACAA
....((((((((.((.(.((((.(((..(((((((((.......))).)))....))).((((....)))).)))))))((((((.....)))))).......).))))))))))..... ( -43.70)
>DroSim_CAF1 5132 120 - 1
GCACUGCUCUCCAUCCCAGGCCCAGCAAGGACCACUGAAUCUUCCAGAUGGGCAAUCCACGGCCGAAGCCGAGUUGGCCACCAUUAGGACAAUGGUCACCACAGCGAGGAGAGCAAACAA
....((((((((.((.(.((((.(((..(((((((((.......))).)))....))).((((....)))).)))))))((((((.....)))))).......).))))))))))..... ( -43.70)
>DroEre_CAF1 5040 120 - 1
GCACUGCUCUCCAUCCCAGGCCCAGCAAGGACCACUGAAAGUUCCAGACUGGCAAUCCACAGCCGAAGACGAGUUGGCGGCCAUUAGGACAAUGGCCACCACAGCGAGCACAGCGAACAA
((..(((((.........((.((.....)).)).(((............((((........)))).........(((.(((((((.....))))))).)))))).)))))..))...... ( -35.00)
>consensus
GCACUGCUCUCCAUCCCAGGCCCAGCAAGGACCACUGAAUCUUCCAGAUGGGCAAUCCACGGCCGAAGCCGAGUUGGCCACCAUUAGGACAAUGGUCACCACAGCGAGGAGAGCAAACAA
....((((((((.((.(.((((.(((..(((((.(((.......)))...))...))).((((....)))).)))))))((((((.....)))))).......).))))))))))..... (-32.76 = -33.77 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:56 2006