Locus 4283

Sequence ID	3R_DroMel_CAF1
Location	11,407,295 – 11,407,452
Length	157
Max. P	0.988147

overview

Window 3

Location	11,407,295 – 11,407,412
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.90
Mean single sequence MFE	-36.85
Consensus MFE	-26.00
Energy contribution	-26.72
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-1.79
Structure conservation index	0.71
SVM decision value	0.02
SVM RNA-class probability	0.541159
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11407295 117 + 27905053
CGACGGUCCUGGCCACGCCCACUGCCAAAC-CAC--ACAUCAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUG
....(((....))).(((((....(((...-...--............))).)))))..((((((((((.........((..(((((((((.....))).))))))..)))))))))))) ( -35.87)
>DroSec_CAF1 154959 118 + 1
CGACGGGCCGCGCCACGCCCACUGCCACACCCCC--ACAUCAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUG
....((((........)))).(((((.(.((...--.............)).)))))).((((((((((.........((..(((((((((.....))).))))))..)))))))))))) ( -36.69)
>DroSim_CAF1 146414 118 + 1
CGGCGGGCCGGGCCACACCCACUGCCACACCCGC--ACAUCAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUG
.(((((...(((.....))).)))))....((((--.(..(((....)))..).)))).((((((((((.........((..(((((((((.....))).))))))..)))))))))))) ( -42.50)
>DroEre_CAF1 142692 111 + 1
CGCC------GGCCACGCCCACCGCCACCC-CAC--ACAUCCUCAUAAUGGAGGCCGGACAAUUAUGCGGCAAUUAAAAGAGCUCGGACGUGCAACACGAGUUGAGUCCUCGCGUAAUAG
.(((------((((..((.....)).....-...--...(((.......))))))))).).((((((((((..........))..((((...((((....)))).)))).)))))))).. ( -35.60)
>DroYak_CAF1 146406 114 + 1
CGACG-----GGCCACGCCCACUGCCACCC-CACACACAUCAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCGCGCAUAAUGG
....(-----(((...)))).(((((..((-..................))..)))))...((((((((..........(..(((((((((.....))).))))))..).)))))))).. ( -33.57)
>consensus
CGACGG_CC_GGCCACGCCCACUGCCACAC_CAC__ACAUCAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUG
...............(((((....(((.....................))).)))))..((((((((((.........((..(((((((((.....))).))))))..)))))))))))) (-26.00 = -26.72 +   0.72)

alignment

secondary structure

dotplot

Window 4

Location	11,407,332 – 11,407,452
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.08
Mean single sequence MFE	-32.02
Consensus MFE	-26.34
Energy contribution	-26.46
Covariance contribution	0.12
Combinations/Pair	1.17
Mean z-score	-2.30
Structure conservation index	0.82
SVM decision value	2.11
SVM RNA-class probability	0.988147
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11407332 120 + 27905053
CAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUGUAGAAAAAUUUCACAAAUAUCCAGAAAGUAAUGGCUGCAA
..............(((((((((((((((.........((..(((((((((.....))).))))))..)))))))))))))...................(((........))))))).. ( -30.40)
>DroSec_CAF1 154997 120 + 1
CAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUGUAGAAAAAUGUCGCAAAUAUCCAGCAAGUAAUGGCUGCAA
........((((..(((((((((((((((.........((..(((((((((.....))).))))))..))))))))))))).........)))).....))))(((.((....))))).. ( -34.00)
>DroSim_CAF1 146452 120 + 1
CAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUGUAGAAAAAUGUCGCAAAUAUCCAGCAAGUAAUGGCUGCAA
........((((..(((((((((((((((.........((..(((((((((.....))).))))))..))))))))))))).........)))).....))))(((.((....))))).. ( -34.00)
>DroEre_CAF1 142723 120 + 1
CCUCAUAAUGGAGGCCGGACAAUUAUGCGGCAAUUAAAAGAGCUCGGACGUGCAACACGAGUUGAGUCCUCGCGUAAUAGUGCAAAAAUAUCGCAAACAUUCAGCAAGUAAUGGCUGCAA
((((......))))..(.((.((((((((((..........))..((((...((((....)))).)))).)))))))).)).).........(((..(((((.....).))))..))).. ( -32.70)
>DroYak_CAF1 146440 120 + 1
CAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCGCGCAUAAUGGUAGAAAAAUAUCGCAAACAUUCAGCAAGUAAUGGCCGCAA
..............((((...(((((((((...........((((((((((.....))).)))))))))))((..((((...((......)).....))))..))..)))))..)))).. ( -29.00)
>consensus
CAUCAUAAUGGAGGGCGGACAAUUAUGCGGCAAUUAAAAGAGCUCAAACGUGGAAAACGAUUUGAGUCCUCGCGUAAUUGUAGAAAAAUAUCGCAAAUAUCCAGCAAGUAAUGGCUGCAA
..............(((((((((((((((.........((..(((((((((.....))).))))))..)))))))))))))...................(((........))))))).. (-26.34 = -26.46 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:35 2006