Locus 3521

Sequence ID	3R_DroMel_CAF1
Location	9,512,425 – 9,512,623
Length	198
Max. P	0.999933

overview

Window 9

Location	9,512,425 – 9,512,545
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-43.46
Consensus MFE	-39.70
Energy contribution	-39.78
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-1.70
Structure conservation index	0.91
SVM decision value	1.89
SVM RNA-class probability	0.981686
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9512425 120 + 27905053
GUUUUGAGUCACCCGCUCUCUGGCCCUCGCCGCUGUUUGUUUUCUUCGCGCGCGUGUUUGCUCUCGCCGUGGGGCGAAAGCGCAGCGAUAAUAGUGGCUCAGAUAUAGUGUAUACUAUAU
..((((((((((.........(((....)))(((((..((((((.((.((((.(((........))))))).)).))))))))))).......))))))))))((((((....)))))). ( -44.00)
>DroSec_CAF1 142085 120 + 1
GUCUUGAGUCACCCGCUCUCUGGCCCUCGCCGCUGUUUGUUUUCUUCGCGCGCGUGUUUGCUUUCGCUGUGGGGCGAAAGCGCAGCGAUAAUAGUGGCUCAGAUGUAGUGUAUACUAUAU
...(((((((((.........(((....)))(((((..........(((....)))...(((((((((....)))))))))))))).......)))))))))(((((((....))))))) ( -42.00)
>DroSim_CAF1 132258 120 + 1
GUCUUGAGUCACCCGCUCUCUGGCCCUCGCCGCUGUUUGUUUUCUUCGCGCGCGUGUUUGCUCUCGCUGUGGGGCGAAAGCGCAGCGAUAAUAGUGGCUCAGAUAUAGUGUAUACUAUAU
(((..((((.....))))...)))....(((((((((........((((((((...((((((((......)))))))).)))).)))).)))))))))....(((((((....))))))) ( -43.20)
>DroEre_CAF1 149998 120 + 1
GUUUUGAGACACCCGCUCUCGCGCCCUCGCCGCUGUUUGUUUUCUUCGCGCGCGUGUUUGCUCUCGCCGUGGGGCGAAAGCGCAGCGAUAAUAGUGGCUCAGAUAUGGUGUAUACUACAC
((......((((((((....))).....(((((((((........((((((((...((((((((......)))))))).)))).)))).)))))))))........))))).....)).. ( -43.70)
>DroYak_CAF1 143778 120 + 1
GUUUUGAGUCACCCGCUCUCGCGCCCUCGCCGCUGUUUGUUUUCUUCGCGCGCGUGUUUGCUCUCGCCGUGGGGCGAAAGCGCAGCGAUAAUAGUGGCUCAGAUAUAGUGUAUACUAUAU
..((((((((((.((((...((((..(((((((.....)).....(((((.(((.(......).)))))))))))))..))))))))......))))))))))((((((....)))))). ( -44.40)
>consensus
GUUUUGAGUCACCCGCUCUCUGGCCCUCGCCGCUGUUUGUUUUCUUCGCGCGCGUGUUUGCUCUCGCCGUGGGGCGAAAGCGCAGCGAUAAUAGUGGCUCAGAUAUAGUGUAUACUAUAU
...(((((((((..((......))......((((((..((((((.((.((((.(((........))))))).)).))))))))))))......)))))))))(((((((....))))))) (-39.70 = -39.78 +   0.08)

alignment

secondary structure

dotplot

Window 0

Location	9,512,425 – 9,512,545
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-44.24
Consensus MFE	-40.64
Energy contribution	-40.60
Covariance contribution	-0.04
Combinations/Pair	1.09
Mean z-score	-3.27
Structure conservation index	0.92
SVM decision value	4.65
SVM RNA-class probability	0.999933
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9512425 120 - 27905053
AUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAAACAAACAGCGGCGAGGGCCAGAGAGCGGGUGACUCAAAAC
..........((((...((((.(((.......((((((((((((((((....))))))))).....((....)).............))))))).))))))).....))))......... ( -43.90)
>DroSec_CAF1 142085 120 - 1
AUAUAGUAUACACUACAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACAGCGAAAGCAAACACGCGCGCGAAGAAAACAAACAGCGGCGAGGGCCAGAGAGCGGGUGACUCAAGAC
..........((((...((((.(((.......(((((((((((((((......)))))))).....((....)).............))))))).))))))).....))))......... ( -40.80)
>DroSim_CAF1 132258 120 - 1
AUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACAGCGAGAGCAAACACGCGCGCGAAGAAAACAAACAGCGGCGAGGGCCAGAGAGCGGGUGACUCAAGAC
..........((((...((((.(((.......(((((((((((((((......)))))))).....((....)).............))))))).))))))).....))))......... ( -40.90)
>DroEre_CAF1 149998 120 - 1
GUGUAGUAUACACCAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAAACAAACAGCGGCGAGGGCGCGAGAGCGGGUGUCUCAAAAC
(((((...)))))......((((.((((....((((((((((((((((....))))))))).....((....)).............)))))))...(((....))))))).)))).... ( -47.30)
>DroYak_CAF1 143778 120 - 1
AUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAAACAAACAGCGGCGAGGGCGCGAGAGCGGGUGACUCAAAAC
(((((((....))))))).((((.((((....((((((((((((((((....))))))))).....((....)).............)))))))...(((....))))))).)))).... ( -48.30)
>consensus
AUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAAACAAACAGCGGCGAGGGCCAGAGAGCGGGUGACUCAAAAC
(((((((....))))))).((((.((((....(((((((((((((((......)))))))).....((....)).............)))))))..((......)).)))).)))).... (-40.64 = -40.60 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	9,512,465 – 9,512,585
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.65
Mean single sequence MFE	-40.02
Consensus MFE	-28.24
Energy contribution	-27.84
Covariance contribution	-0.40
Combinations/Pair	1.18
Mean z-score	-2.75
Structure conservation index	0.71
SVM decision value	1.63
SVM RNA-class probability	0.968559
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9512465 120 - 27905053
CUGUGCGAUGGGGUUUUCGGUAUGAGUAGGUUUACUAUACAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAA
.(((((((((((((((..(((((.(((..((.((((((....)))))).)))))))))).))))).)))))...((((.(((((((((....)))))))))...)).)))))))...... ( -41.90)
>DroSec_CAF1 142125 103 - 1
CUGUGCG-----------------AGUGGGUCUACUAUGCAUAUAGUAUACACUACAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACAGCGAAAGCAAACACGCGCGCGAAGAAA
..(((((-----------------(((((.((((((((....))))))............)).)))))...........((((((((......)))))))).....)))))......... ( -32.20)
>DroSim_CAF1 132298 103 - 1
CUGUGCG-----------------AGUGGGUAUACUAUGCAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACAGCGAGAGCAAACACGCGCGCGAAGAAA
..(((((-----------------((((((((((((((....))))))))).(.......)..)))))...........((((((((......)))))))).....)))))......... ( -35.40)
>DroEre_CAF1 150038 116 - 1
----GCGAUGGGGUUUUCGGUAUGAGUGGGGCUACUAUACGUGUAGUAUACACCAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAA
----..((((((((((..((((((.(((..(((((.......)))))...))))))))).))))).))))).((((((((((((((((....)))))))))......))).))))..... ( -47.00)
>DroYak_CAF1 143818 116 - 1
----GCGCUGGGGUUUUCGGUAUGAGUGGGGCUACUAUGAAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAA
----((((.(.(((((.((((...(((((((((.....((.((((((....))))))))..)))).)))))...)))).(((((((((....))))))))))))).).)))))....... ( -43.60)
>consensus
CUGUGCG_UGGGGUUUUCGGUAUGAGUGGGUCUACUAUGCAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCGCUUUCGCCCCACGGCGAGAGCAAACACGCGCGCGAAGAAA
....(((..................((((((.((((((....)))))).)).)))).................(((((.((((((((......))))))))...)).))))))....... (-28.24 = -27.84 +  -0.40)

alignment

secondary structure

dotplot

Window 2

Location	9,512,505 – 9,512,623
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.86
Mean single sequence MFE	-36.88
Consensus MFE	-23.36
Energy contribution	-23.06
Covariance contribution	-0.30
Combinations/Pair	1.18
Mean z-score	-2.38
Structure conservation index	0.63
SVM decision value	1.35
SVM RNA-class probability	0.945389
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9512505 118 - 27905053
UCCGCAGUGCGCGCGUGUAUCU--GUAAAUGUAUCCGUAUCUGUGCGAUGGGGUUUUCGGUAUGAGUAGGUUUACUAUACAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCG
..(((((((.(((((.((((..--(((....)))..)))).)))))((((((((((..(((((.(((..((.((((((....)))))).)))))))))).))))).)))))..))))))) ( -36.20)
>DroSec_CAF1 142165 101 - 1
UCCGCAGUGCGCGCGUGUAUCU--GUAAAUGUAUCCGUAUCUGUGCG-----------------AGUGGGUCUACUAUGCAUAUAGUAUACACUACAUCUGAGCCACUAUUAUCGCUGCG
..(((((((((((((.((((..--(((....)))..)))).))))))-----------------(((((.((((((((....))))))............)).))))).....))))))) ( -30.50)
>DroSim_CAF1 132338 103 - 1
UCCGCAGUGCGCGCGUGUAUCUGUGUAAAUGUAUCCGUAUCUGUGCG-----------------AGUGGGUAUACUAUGCAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCG
..(((((((((((((.((((..(((......)))..)))).))))))-----------------((((((((((((((....))))))))).(.......)..))))).....))))))) ( -33.60)
>DroEre_CAF1 150078 112 - 1
UUCGCAGUGUGCGCGUGUAUCU--GUAUCUGUAUCCGU------GCGAUGGGGUUUUCGGUAUGAGUGGGGCUACUAUACGUGUAGUAUACACCAUAUCUGAGCCACUAUUAUCGCUGCG
..(((((((.(((((..(((..--......)))..)))------))((((((((((..((((((.(((..(((((.......)))))...))))))))).))))).)))))..))))))) ( -44.40)
>DroYak_CAF1 143858 112 - 1
UUCGCAGUGUGCGCGUGUAUCU--GUAUCUGUGUCCGC------GCGCUGGGGUUUUCGGUAUGAGUGGGGCUACUAUGAAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCG
..(((((((((((((..(((..--......)))..)))------))))((((((((..(((((.((((....((((((....))))))..))))))))).))))).))).....)))))) ( -39.70)
>consensus
UCCGCAGUGCGCGCGUGUAUCU__GUAAAUGUAUCCGUAUCUGUGCG_UGGGGUUUUCGGUAUGAGUGGGUCUACUAUGCAUAUAGUAUACACUAUAUCUGAGCCACUAUUAUCGCUGCG
..(((((((.....(((..((..............((((....))))..................((((((.((((((....)))))).)).))))....))..)))......))))))) (-23.36 = -23.06 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:17 2006