Locus 4525

Sequence ID	3R_DroMel_CAF1
Location	12,016,154 – 12,016,252
Length	98
Max. P	0.991868

overview

Window 5

Location	12,016,154 – 12,016,252
Length	98
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	93.96
Mean single sequence MFE	-29.54
Consensus MFE	-21.94
Energy contribution	-21.98
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-2.22
Structure conservation index	0.74
SVM decision value	0.32
SVM RNA-class probability	0.689376
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12016154 98 + 27905053
UCGAUGGGAGAAAGAUAUGGGAGUGCG--UAUAUGUGGCCAGAAAAUUAUGUAUACGCAGCGUUUCCUCAUUGAGAGGCGCUGCUGACGCAAAAUAAAUG
.......................((((--(((((((((........))))))))))(((((((((((.....).))))))))))....)))......... ( -26.60)
>DroSec_CAF1 121011 100 + 1
UCGAUGGGAGAAAGAUAUGGGAGUGCGUGUAUAUGUGGCCAGAAAAUUGUGUAUACGCAGCGUUUCCUCAUUGAGAGGCGCUGCUGACGCAAAAUAAAUG
.......................((((((((((((..(........)..)))))))(((((((((((.....).))))))))))..)))))......... ( -29.10)
>DroSim_CAF1 121293 100 + 1
UCGAUGGGAGAAAGAUAUGGGAGUGCGUGUAUAUGUGGCCAGAAAAUUAUGUAUACGCAGCGUUUCCUCAUUGAGAGGCGCUGCUGACGCAAAAUAAAUG
.......................(((((((((((((((........))))))))))(((((((((((.....).))))))))))..)))))......... ( -29.50)
>DroEre_CAF1 120720 98 + 1
UCCACGUCCGAAAGAUAUGAGAGUGCG--UAUAUGUGGCCAGAAAAUUAUGUAUACGCAGCGUUUCCUCAUUGUGAGGAGCUGCUGACGCAAAAUAAAUG
....(((((....)..........(((--(((((((((........))))))))))))((((.((((((.....)))))).))))))))........... ( -29.30)
>DroYak_CAF1 123834 98 + 1
UCGACGUUCGAAAGAUAUGCGAGUGCG--UAUAUGUGGCCAGAAAAUUAUGUAUACGCAGCGUUUCCUCAUUGAGAGGCGCUGCUGACGCAAAAUAAAUG
(((.(((((....)).)))))).((((--(((((((((........))))))))))(((((((((((.....).))))))))))....)))......... ( -33.20)
>consensus
UCGAUGGGAGAAAGAUAUGGGAGUGCG__UAUAUGUGGCCAGAAAAUUAUGUAUACGCAGCGUUUCCUCAUUGAGAGGCGCUGCUGACGCAAAAUAAAUG
.......................((((..((((..(((........)))..)))).(((((((((((.....).))))))))))...))))......... (-21.94 = -21.98 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	12,016,154 – 12,016,252
Length	98
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	93.96
Mean single sequence MFE	-23.02
Consensus MFE	-19.16
Energy contribution	-19.36
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.34
Structure conservation index	0.83
SVM decision value	2.29
SVM RNA-class probability	0.991868
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12016154 98 - 27905053
CAUUUAUUUUGCGUCAGCAGCGCCUCUCAAUGAGGAAACGCUGCGUAUACAUAAUUUUCUGGCCACAUAUA--CGCACUCCCAUAUCUUUCUCCCAUCGA
.........(((((..((((((((((.....))))...))))))((...((........))...))....)--))))....................... ( -21.20)
>DroSec_CAF1 121011 100 - 1
CAUUUAUUUUGCGUCAGCAGCGCCUCUCAAUGAGGAAACGCUGCGUAUACACAAUUUUCUGGCCACAUAUACACGCACUCCCAUAUCUUUCUCCCAUCGA
.........(((((..((((((((((.....))))...))))))(((((..((......))......))))))))))....................... ( -23.10)
>DroSim_CAF1 121293 100 - 1
CAUUUAUUUUGCGUCAGCAGCGCCUCUCAAUGAGGAAACGCUGCGUAUACAUAAUUUUCUGGCCACAUAUACACGCACUCCCAUAUCUUUCUCCCAUCGA
.........(((((..((((((((((.....))))...))))))(((((..........((....))))))))))))....................... ( -22.80)
>DroEre_CAF1 120720 98 - 1
CAUUUAUUUUGCGUCAGCAGCUCCUCACAAUGAGGAAACGCUGCGUAUACAUAAUUUUCUGGCCACAUAUA--CGCACUCUCAUAUCUUUCGGACGUGGA
.......((..((((.((((((((((.....)))))...)))))(((((..........((....))))))--)..................))))..)) ( -25.50)
>DroYak_CAF1 123834 98 - 1
CAUUUAUUUUGCGUCAGCAGCGCCUCUCAAUGAGGAAACGCUGCGUAUACAUAAUUUUCUGGCCACAUAUA--CGCACUCGCAUAUCUUUCGAACGUCGA
.........((((...((((((((((.....))))...))))))(((((..........((....))))))--).....))))......(((.....))) ( -22.50)
>consensus
CAUUUAUUUUGCGUCAGCAGCGCCUCUCAAUGAGGAAACGCUGCGUAUACAUAAUUUUCUGGCCACAUAUA__CGCACUCCCAUAUCUUUCUCCCAUCGA
.........((((...((((((((((.....))))...))))))((...((........))...)).......))))....................... (-19.16 = -19.36 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:23 2006