Locus 7175

Sequence ID	X_DroMel_CAF1
Location	17,983,530 – 17,983,662
Length	132
Max. P	0.829883

overview

Window 1

Location	17,983,530 – 17,983,629
Length	99
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.09
Mean single sequence MFE	-38.90
Consensus MFE	-30.21
Energy contribution	-31.27
Covariance contribution	1.06
Combinations/Pair	1.23
Mean z-score	-1.81
Structure conservation index	0.78
SVM decision value	0.71
SVM RNA-class probability	0.829883
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17983530 99 - 22224390
-------GCUGGAGGCAACCUGGUCGGGAGCAGAUUCCGCCCAAACACCUCCGUGGAUCCCCCGGUUGCUCAAUAUCUCU-------------CUAGCUUCGGUU-UUUCUCCCAUUUUC
-------((((((((((((((((.(((((.....))))).)))..(((....)))........)))))).........))-------------)))))...((..-......))...... ( -29.80)
>DroSim_CAF1 14177 118 - 1
CUCCCCAGCUGGAGGCAACCUGGUCGGGAGCGAAUUCCGGCCAGACACCUCCGUGGAUCCCCCGGUUGCUCAAGCUCUCAGUUUCGCUGCG-AGUAGCUUCGGUU-UUUUUCCCAUUUCC
..........(((((....((((((((((.....))))))))))...)))))(.(((....((((..(((...((((.(((.....))).)-)))))).))))..-....))))...... ( -43.60)
>DroEre_CAF1 15224 118 - 1
UUCCCCAGCUGGAGGCAACCUGGUCGGGAGCGGAUUCCGACCAGACACCUCCGUGGAUCCCCCGGUUGCUCCAUCUCCCGGUUUCUCUGGA-CGUAGCUCCGGCU-UUUCUCCCAUUUCC
......(((((((((((((((((((((((.....)))))))))).......((.((....)))))))))........((((.....)))).-.....))))))))-.............. ( -43.90)
>DroYak_CAF1 13534 120 - 1
CUGCCCAGCUGGAGGCAACCUGGUCGGGAGCAGAUUCCGCCCGGACACCUUCGUGGAUCCCCCGGCUGUUCAAUCUCUCAGUUUCUCUGGGUAGUAGCUUCGGUUUUUUCUCCCAUUUUC
.((..(((((((.((....((((.(((((.....))))).)))).(((....)))....)))))))))..))...............((((.((.(((....)))....))))))..... ( -38.30)
>consensus
CUCCCCAGCUGGAGGCAACCUGGUCGGGAGCAGAUUCCGCCCAGACACCUCCGUGGAUCCCCCGGUUGCUCAAUCUCUCAGUUUCUCUGGG_AGUAGCUUCGGUU_UUUCUCCCAUUUCC
......(((((((((((((((((((((((.....)))))))))..(((....)))........))))))........((((.....)))).......))))))))............... (-30.21 = -31.27 +   1.06)

alignment

secondary structure

dotplot

Window 2

Location	17,983,556 – 17,983,662
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.28
Mean single sequence MFE	-40.35
Consensus MFE	-32.39
Energy contribution	-32.95
Covariance contribution	0.56
Combinations/Pair	1.19
Mean z-score	-1.51
Structure conservation index	0.80
SVM decision value	0.15
SVM RNA-class probability	0.606140
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17983556 106 - 22224390
CCAGCUCCCAGUUUCUUGGC-UCCGCCAUUUUUU-------------GCUGGAGGCAACCUGGUCGGGAGCAGAUUCCGCCCAAACACCUCCGUGGAUCCCCCGGUUGCUCAAUAUCUCU
....((((.(((....((((-...))))......-------------)))))))(((((((((.(((((.....))))).)))..(((....)))........))))))........... ( -32.60)
>DroSim_CAF1 14215 120 - 1
CCAGCCCGCAGUUCCUUGGGUUCCGCACUUUUUUUGGUGUCUCCCCAGCUGGAGGCAACCUGGUCGGGAGCGAAUUCCGGCCAGACACCUCCGUGGAUCCCCCGGUUGCUCAAGCUCUCA
..(((..((((..((..(((.(((((.......((((.......))))..(((((....((((((((((.....))))))))))...)))))))))).)))..))))))....))).... ( -46.60)
>DroEre_CAF1 15262 117 - 1
CCAGCCCGCAGUUAUUUGGU-UCCGCACUU-UU-UAGUGUUUCCCCAGCUGGAGGCAACCUGGUCGGGAGCGGAUUCCGACCAGACACCUCCGUGGAUCCCCCGGUUGCUCCAUCUCCCG
.....((((......((((.-...(((((.-..-.)))))....))))..(((((....((((((((((.....))))))))))...))))))))).......((.....))........ ( -40.70)
>DroYak_CAF1 13574 118 - 1
CCAGCCGGCAGUCCUUUGAU-UCCGCACUUUUU-UAGUGUCUGCCCAGCUGGAGGCAACCUGGUCGGGAGCAGAUUCCGCCCGGACACCUUCGUGGAUCCCCCGGCUGUUCAAUCUCUCA
.(((((((..((((..(((.-((((((((....-.))))(((((((.((..(.(....))..))..)).))))).......)))).....))).))))...)))))))............ ( -41.50)
>consensus
CCAGCCCGCAGUUCCUUGGU_UCCGCACUUUUU_UAGUGUCUCCCCAGCUGGAGGCAACCUGGUCGGGAGCAGAUUCCGCCCAGACACCUCCGUGGAUCCCCCGGUUGCUCAAUCUCUCA
.(((((..(((....)))...((((((((......)))............(((((....((((((((((.....))))))))))...))))))))))......)))))............ (-32.39 = -32.95 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:01 2006