Locus 7306

Sequence ID	3L_DroMel_CAF1
Location	19,560,811 – 19,560,950
Length	139
Max. P	0.811171

overview

Window 2

Location	19,560,811 – 19,560,910
Length	99
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	73.56
Mean single sequence MFE	-41.20
Consensus MFE	-12.84
Energy contribution	-12.20
Covariance contribution	-0.64
Combinations/Pair	1.50
Mean z-score	-2.35
Structure conservation index	0.31
SVM decision value	0.65
SVM RNA-class probability	0.811171
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19560811 99 - 23771897
AUAAGUGGUGGAAAGUUGCUGGAUAUAAGUCCUAGUUCCUUGUGUUCCCUCAAACAGCAGAGGAGAGGAGGAGCAGCUAAAC---AGAAGGUGUCG---GCAGCG--
..............(((((((.((((...((.(((((.(((.(.(((((((........)))).))).).))).)))))...---.))..))))))---))))).-- ( -29.10)
>DroVir_CAF1 4374 101 - 1
AUAAGCGGUGGCAAGCUGCUGGACAUAAGCCCCAGUUCGCUGUGUUCCCUGAAACAGCAGCGGCGUCAGGGC---GCCAAAGCAAAGAACUUGCUU---GUGGCCAG
...((((((.....))))))((.(((((((...(((((((((((((......)))).))))(((((....))---)))........))))).))))---))).)).. ( -41.90)
>DroPse_CAF1 4322 105 - 1
AUCAGUGGCGGCAAGCUGCUGGACAUCAGUCCCAGUUCGCUGGGCUCCCUCAAGCAGCAGCGGCGCGGAGGGGUAGCCAAGCAGCAGAAGGUGCCCCACUCCGCG--
...(((((.((((..(((((((((....))))......(((.(((((((((..((.((....)))).)))))..)))).))))))))....))))))))).....-- ( -49.10)
>DroYak_CAF1 4549 99 - 1
AUAAGCGGUGGAAAGUUACUGGAUAUAAGUCCAAGUUCCUUGUGCUCCCUUAAACAGCAGAGGAGAGGAGGAGGAGCUAAAC---AGAAGGUGUCG---GCAGCG--
....((.((.((.......(((((....)))))((((((((.(.(((((((........)))).))).).))))))))....---........)).---)).)).-- ( -33.00)
>DroAna_CAF1 5102 99 - 1
AUCAGCGGCGGCAAGCUGCUGGACAUCAGUCCGAGCUCGCUGUGCUCCCUGAAGCAGCAAAGGAGAGUAGGCGGCGGCAAGC---AGAAGGCCAUC---GCCACC--
....(((..(((...(((((((((....))))..((.(((((((((((((..........))).))))..)))))))).)))---))...)))..)---))....-- ( -45.00)
>DroPer_CAF1 4340 105 - 1
AUCAGUGGCGGCAAGCUGCUGGACAUCAGUCCCAGUUCGCUGGGCUCCCUCAAGCAGCAGCGGCGCGGAGGGGUAGCCAAGCAGCAGAAGGUGCCCCACUCCGCG--
...(((((.((((..(((((((((....))))......(((.(((((((((..((.((....)))).)))))..)))).))))))))....))))))))).....-- ( -49.10)
>consensus
AUAAGCGGCGGCAAGCUGCUGGACAUAAGUCCCAGUUCGCUGUGCUCCCUCAAACAGCAGAGGAGAGGAGGAGGAGCCAAAC___AGAAGGUGCCC___GCCGCG__
......((((((.(((((..((((....))))))))).)))......((((...(......).....))))....)))............................. (-12.84 = -12.20 +  -0.64)

alignment

secondary structure

dotplot

Window 3

Location	19,560,833 – 19,560,950
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.17
Mean single sequence MFE	-45.59
Consensus MFE	-24.62
Energy contribution	-26.02
Covariance contribution	1.40
Combinations/Pair	1.34
Mean z-score	-1.91
Structure conservation index	0.54
SVM decision value	0.20
SVM RNA-class probability	0.630328
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19560833 117 - 23771897
CAGUAAUUCUCCCCUGAGAAUUGUUGUCGAUAAUAAUUCCAUAAGUGGUGGAAAGUUGCUGGAUAUAAGUCCUAGUUCCUUGUGUUCCCUCAAACAGCAGAGGAGAGGAGGAGCAGC
.(((((((.(((((((.(((((((((....))))))))))).....)).))).)))))))((((....))))..(((((((...(((((((........)))).))))))))))... ( -36.50)
>DroVir_CAF1 4401 114 - 1
CAGCGCUUCGCCGUUGCGCAUUGUCGUUGACAAUAAUUCCAUAAGCGGUGGCAAGCUGCUGGACAUAAGCCCCAGUUCGCUGUGUUCCCUGAAACAGCAGCGGCGUCAGGGC---GC
..(((((((((((((((..((((((...))))))............((..((((((.(((((.........)))))..))).)))..)).......)))))))))...))))---)) ( -44.70)
>DroPse_CAF1 4350 117 - 1
CAGCAACUCUCCGCUGCGGAUUGUGGUGGACAACAAUUCCAUCAGUGGCGGCAAGCUGCUGGACAUCAGUCCCAGUUCGCUGGGCUCCCUCAAGCAGCAGCGGCGCGGAGGGGUAGC
..((..((((((((.(((((((((((((((.......)))))(((..((.....))..)))..)).)))))).....(((((.(((......)))..)))))))))))))))...)) ( -51.70)
>DroGri_CAF1 5487 114 - 1
CAAUGACUCACCACUGCGCAUUGUUGUGGACAACAAUUCGAUAAGUGGUGGCAAGCUGCUGGACAUAAGUCCAAGCUCGCUGUGCUCCCUCAAGCAACAGCGGCGUCAGGGC---GG
...((((.(((((((.((.(((((((....))))))).))...)))))))((.((((..(((((....)))))))))(((((((((......))).))))))))))))....---.. ( -49.30)
>DroAna_CAF1 5124 117 - 1
CAGCAACUCCCCCCUCAGGAUCGUCGUCGACAACAAUUCCAUCAGCGGCGGCAAGCUGCUGGACAUCAGUCCGAGCUCGCUGUGCUCCCUGAAGCAGCAAAGGAGAGUAGGCGGCGG
..((.((((.((..........(((((((.(.............))))))))..((((((((((....))))((((.......)))).....))))))...)).))))..))..... ( -39.62)
>DroPer_CAF1 4368 117 - 1
CAGCAACUCUCCGCUGCGGAUUGUGGUGGACAACAAUUCCAUCAGUGGCGGCAAGCUGCUGGACAUCAGUCCCAGUUCGCUGGGCUCCCUCAAGCAGCAGCGGCGCGGAGGGGUAGC
..((..((((((((.(((((((((((((((.......)))))(((..((.....))..)))..)).)))))).....(((((.(((......)))..)))))))))))))))...)) ( -51.70)
>consensus
CAGCAACUCUCCGCUGCGGAUUGUCGUGGACAACAAUUCCAUAAGUGGCGGCAAGCUGCUGGACAUAAGUCCCAGUUCGCUGUGCUCCCUCAAGCAGCAGCGGCGAGGAGGCG_AGC
........((((.(((((((((((........)))))))....((((((.....))))))((((....))))....((((((((((......)))).)))))).)))).)))).... (-24.62 = -26.02 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:37 2006