Locus 7493

Sequence ID	X_DroMel_CAF1
Location	18,680,076 – 18,680,275
Length	199
Max. P	0.718829

overview

Window 2

Location	18,680,076 – 18,680,196
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.89
Mean single sequence MFE	-53.17
Consensus MFE	-40.78
Energy contribution	-41.57
Covariance contribution	0.78
Combinations/Pair	1.08
Mean z-score	-2.11
Structure conservation index	0.77
SVM decision value	0.09
SVM RNA-class probability	0.579454
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18680076 120 - 22224390
GCUAUGCCUGGUGGAUGCGGCCGCCACUGCCGCUGCCUUGAUCUUGGCCAAGGGCAGAUCCGAUUCGGCAUCUUUGUUCAUUGCCGUGGUCGCAAUGGUUGCUGAGCCACCCGAAGUGGC
(((((..(.(((((...((((.(((((((((.(((((........)))..)))))))...((((((((((...........))))).)))))...)))).))))..))))).)..))))) ( -51.60)
>DroSim_CAF1 5615 118 - 1
GCUAUGCCUGGUGGAAGCGGCCGCCACAGCCGCUGCCUUGAUCU-GGCCAAG-GCAGAUCCGAUUCGGCAUCUUUGUUUAUUGCCGUGGUCGCAAUGGCUGCUGAGCCACCAGCAGUGGC
(((((..(((((((...((((.((((..((..((((((((....-...))))-))))....(((((((((...........))))).))))))..)))).))))..)))))))..))))) ( -57.10)
>DroYak_CAF1 5458 120 - 1
GCUGUGCCUGGUGGAAGCGGCCGCCACAGCCGCUGCCUUGAUCUUGGCCAGCGGCAGAUCCGAUUCGGCAUCCUUGUUCAUUCCCGUGGUCGCAAUAGCAGCAGAGCCUCCUGUUGCGGC
.....(((........((((((((....(((((((((........)).))))))).((((((...))).))).............))))))))....(((((((......)))))))))) ( -50.80)
>consensus
GCUAUGCCUGGUGGAAGCGGCCGCCACAGCCGCUGCCUUGAUCUUGGCCAAGGGCAGAUCCGAUUCGGCAUCUUUGUUCAUUGCCGUGGUCGCAAUGGCUGCUGAGCCACCAGAAGUGGC
(((((..(.(((((...((((.((((..((..((((((((........))).)))))....(((((((((...........))))).))))))..)))).))))..))))).)..))))) (-40.78 = -41.57 +   0.78)

alignment

secondary structure

dotplot

Window 3

Location	18,680,116 – 18,680,236
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	75.28
Mean single sequence MFE	-37.83
Consensus MFE	-28.00
Energy contribution	-29.33
Covariance contribution	1.33
Combinations/Pair	1.00
Mean z-score	-1.29
Structure conservation index	0.74
SVM decision value	0.39
SVM RNA-class probability	0.718829
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18680116 120 + 22224390
UGAACAAAGAUGCCGAAUCGGAUCUGCCCUUGGCCAAGAUCAAGGCAGCGGCAGUGGCGGCCGCAUCCACCAGGCAUAGCAUGGAAAAGGAGACCAACAUCAGUUCGGGCAGUAGUGCCU
.((((....(((((.....((((.((((.((((......))))))))(((((.......)))))))))....))))).(.(((.....(....)...)))).))))(((((....))))) ( -38.50)
>DroSim_CAF1 5655 118 + 1
UAAACAAAGAUGCCGAAUCGGAUCUGC-CUUGGCC-AGAUCAAGGCAGCGGCUGUGGCGGCCGCUUCCACCAGGCAUAGCAUGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
....((...(((((......(((((((-....).)-)))))..((.((((((((...)))))))).))....)))))....))..................................... ( -33.30)
>DroYak_CAF1 5498 120 + 1
UGAACAAGGAUGCCGAAUCGGAUCUGCCGCUGGCCAAGAUCAAGGCAGCGGCUGUGGCGGCCGCUUCCACCAGGCACAGCAUGGAAAAGGAGACCAACAUCAGUUCGGGCAGUAGCGCCU
.((((...(((((((....((.....))(((((((........((.((((((((...)))))))).))....))).)))).)))....(....)...)))).))))((((......)))) ( -41.70)
>consensus
UGAACAAAGAUGCCGAAUCGGAUCUGCCCUUGGCCAAGAUCAAGGCAGCGGCUGUGGCGGCCGCUUCCACCAGGCAUAGCAUGGAAAAGGAGACCAACAUCAGUUCGGGCAGUAG_GCCU
....((...(((((......(((((((.....))..)))))..((.((((((((...)))))))).))....)))))....)).......................((((......)))) (-28.00 = -29.33 +   1.33)

alignment

secondary structure

dotplot

Window 4

Location	18,680,156 – 18,680,275
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	55.99
Mean single sequence MFE	-34.77
Consensus MFE	-21.90
Energy contribution	-23.38
Covariance contribution	1.47
Combinations/Pair	1.04
Mean z-score	-0.75
Structure conservation index	0.63
SVM decision value	0.36
SVM RNA-class probability	0.703140
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18680156 119 + 22224390
CAAGGCAGCGGCAGUGGCGGCCGCAUCCACCAGGCAUAGCAUGGAAAAGGAGACCAACAUCAGUUCGGGCAGUAGUGCCUCCGCUUCCAGCAAGGCCAAUUCCGCGGAGAUGCAGCGCA-
....((.(((((.......)))(((((.....(((...((.(((((..((((.(((((....))).))(((....)))))))..)))))))...)))...((....))))))).)))).- ( -41.30)
>DroSim_CAF1 5693 120 + 1
CAAGGCAGCGGCUGUGGCGGCCGCUUCCACCAGGCAUAGCAUGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
...((.((((((((...)))))))).)).(((.((...)).)))............................................................................ ( -20.10)
>DroYak_CAF1 5538 119 + 1
CAAGGCAGCGGCUGUGGCGGCCGCUUCCACCAGGCACAGCAUGGAAAAGGAGACCAACAUCAGUUCGGGCAGUAGCGCCUCCGCCUCCAGCAAGGCCAAUUCCGCGGAGAUGCAGCGCA-
...((.((((((((...)))))))).))....(((...((.((((...((((.(((((....))).))((....))..))))...))))))...)))......(((.........))).- ( -42.90)
>consensus
CAAGGCAGCGGCUGUGGCGGCCGCUUCCACCAGGCAUAGCAUGGAAAAGGAGACCAACAUCAGUUCGGGCAGUAG_GCCUCCGC_UCCAGCAAGGCCAAUUCCGCGGAGAUGCAGCGCA_
...((.((((((((...)))))))).)).(((.((...)).)))...........................((.(((.((((((...................)))))).))).)).... (-21.90 = -23.38 +   1.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:40:20 2006