Locus 4302

Sequence ID	3R_DroMel_CAF1
Location	11,422,171 – 11,422,286
Length	115
Max. P	0.823452

overview

Window 9

Location	11,422,171 – 11,422,286
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.95
Mean single sequence MFE	-28.02
Consensus MFE	-22.36
Energy contribution	-22.92
Covariance contribution	0.56
Combinations/Pair	1.14
Mean z-score	-1.43
Structure conservation index	0.80
SVM decision value	0.10
SVM RNA-class probability	0.581854
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11422171 115 + 27905053
UAUGAAUGAAUAUUCGAGCAUUCGCA----UCCAUUCUUCUUUUUUCUCCGCAAAGCGUUUUUUCUGUUGCUUCCCACAUAAAAGUUCAUCAGCGAGAAUAUUGGCGGGAAGAAAAAA-G
...(((((.((...((......)).)----).)))))..(((((((((((((.((..((((((.(((..((((.........))))....))).)))))).)).))))..))))))))-) ( -23.70)
>DroSec_CAF1 169646 116 + 1
UAUGAAUGAAUAUUCGAGCAUUCGUA----UCCAUUCUUCUUUUUUCUCCGCAAAGCGUUUUUUCUGAUGCUUCCCACAUAAAAGUUCAUCAGCGAGAAUAUUGGCGGGAAGAAAGAAGA
((((((((..........))))))))----.....((((((((((((.((((.((..((((((.(((((((((.........)))..)))))).)))))).)).)))))))))))))))) ( -36.60)
>DroSim_CAF1 162472 115 + 1
UAUGAAUGAAUAUUCGAGCAUUCGCA----UCCAUUCUUCUUUUUUCUCCGCAAAGCGUUUUUUCUGUUGCUUCCCACAUAAAAGUUCAUCAGCGAGAAUAUUGGCGGGAAGAAAGAA-A
...(((((.((...((......)).)----).)))))((((((((((.((((.((..((((((.(((..((((.........))))....))).)))))).)).))))))))))))))-. ( -28.10)
>DroEre_CAF1 157711 112 + 1
UAUGAAUGAAUAUUCGAGCAUUCGCA----UGCAUUCUUCU-CUUUCUCUGCAAAGCGUUU-UUCUGUUGCUUCCCGCAUAAAAGUUCAUCAGCGAGAAUAUUGGCGGGAAGAAAGGA--
...(((((..(((.((......)).)----)))))))...(-(((((...(((..(((...-...))))))(((((((...((.((((........)))).)).))))))))))))).-- ( -25.90)
>DroYak_CAF1 161903 116 + 1
UAUGAAUGAAUAUUCGAGCAUUCGCAUUCAUGCAUUCUUUU-UUCUCUCUGCAAAGCGUUU-UUCUGUUGCUUCCCGCAUAAAAGUUCAUCAGCGAGAAUAUUGGCGGGAAGAAGGAG--
((((((((...((......))...)))))))).........-....((((....((((...-...)))).((((((((...((.((((........)))).)).))))))))..))))-- ( -25.80)
>consensus
UAUGAAUGAAUAUUCGAGCAUUCGCA____UCCAUUCUUCUUUUUUCUCCGCAAAGCGUUUUUUCUGUUGCUUCCCACAUAAAAGUUCAUCAGCGAGAAUAUUGGCGGGAAGAAAGAA__
...(((((......((......))........)))))((((((((((.((((.((..((((((.(((..((((.........))))....))).)))))).)).)))))))))))))).. (-22.36 = -22.92 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	11,422,171 – 11,422,286
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.95
Mean single sequence MFE	-28.96
Consensus MFE	-21.98
Energy contribution	-22.02
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-2.05
Structure conservation index	0.76
SVM decision value	0.69
SVM RNA-class probability	0.823452
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11422171 115 - 27905053
C-UUUUUUCUUCCCGCCAAUAUUCUCGCUGAUGAACUUUUAUGUGGGAAGCAACAGAAAAAACGCUUUGCGGAGAAAAAAGAAGAAUGGA----UGCGAAUGCUCGAAUAUUCAUUCAUA
(-((((((((((.........((((((((((.......))).)))))))((((.((........)))))))))))))))))..(((((((----(((((....)))..)))))))))... ( -31.60)
>DroSec_CAF1 169646 116 - 1
UCUUCUUUCUUCCCGCCAAUAUUCUCGCUGAUGAACUUUUAUGUGGGAAGCAUCAGAAAAAACGCUUUGCGGAGAAAAAAGAAGAAUGGA----UACGAAUGCUCGAAUAUUCAUUCAUA
..((((((.(((((((...........((((((..(((((.....)))))))))))............)))).))).))))))(((((((----(((((....)))..)))))))))... ( -31.80)
>DroSim_CAF1 162472 115 - 1
U-UUCUUUCUUCCCGCCAAUAUUCUCGCUGAUGAACUUUUAUGUGGGAAGCAACAGAAAAAACGCUUUGCGGAGAAAAAAGAAGAAUGGA----UGCGAAUGCUCGAAUAUUCAUUCAUA
.-((((((.(((((((.....((((((((((.......))).)))))))((............))...)))).))).))))))(((((((----(((((....)))..)))))))))... ( -30.60)
>DroEre_CAF1 157711 112 - 1
--UCCUUUCUUCCCGCCAAUAUUCUCGCUGAUGAACUUUUAUGCGGGAAGCAACAGAA-AAACGCUUUGCAGAGAAAG-AGAAGAAUGCA----UGCGAAUGCUCGAAUAUUCAUUCAUA
--((((((((((((((.((..(((........)))..))...)))))))((((.((..-.....))))))...)))))-.)).(((((.(----(((((....)))..))).)))))... ( -25.90)
>DroYak_CAF1 161903 116 - 1
--CUCCUUCUUCCCGCCAAUAUUCUCGCUGAUGAACUUUUAUGCGGGAAGCAACAGAA-AAACGCUUUGCAGAGAGAA-AAAAGAAUGCAUGAAUGCGAAUGCUCGAAUAUUCAUUCAUA
--(((((..(((((((.((..(((........)))..))...)))))))((((.((..-.....)))))))).)))..-......(((.((((((((((....)))..))))))).))). ( -24.90)
>consensus
__UUCUUUCUUCCCGCCAAUAUUCUCGCUGAUGAACUUUUAUGUGGGAAGCAACAGAAAAAACGCUUUGCGGAGAAAAAAGAAGAAUGGA____UGCGAAUGCUCGAAUAUUCAUUCAUA
..((((((.(((((((.((..(((........)))..))...)))))))((((.((........)))))))))))).......(((((((......(((....)))....)))))))... (-21.98 = -22.02 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:20 2006