Locus 1039

Sequence ID	X_DroMel_CAF1
Location	3,023,825 – 3,023,985
Length	160
Max. P	0.593636

overview

Window 5

Location	3,023,825 – 3,023,945
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.25
Mean single sequence MFE	-39.72
Consensus MFE	-35.85
Energy contribution	-35.85
Covariance contribution	0.00
Combinations/Pair	1.10
Mean z-score	-1.37
Structure conservation index	0.90
SVM decision value	0.12
SVM RNA-class probability	0.593636
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3023825 120 + 22224390
GCAUUCAAAUCUAUUUGGAGAUUGACAAUCGCAAAUGCACCGAAUGCUUUACGCACGCCGUUGAGGCAGCCGAAUUUCUGGCUGCCACGGCGGCCAAACAUCAGCUGCGGAACGAUUUUC
................((((((((......((....)).(((...(((........(((((((.((((((((......)))))))).)))))))........)))..)))..)))))))) ( -42.89)
>DroSec_CAF1 4244 120 + 1
GCAUUCAAAUCUAUUUGGAGAUUGACAAUCGCAAGUGCACCGAGUGCUUCACCCACGCCGUGGAGGCGGCCGAGUUCCUGGCUGCCACGGCGGCCAAACAUCAGCUGAGGAACGACUUCC
((((((.(((((......))))).......((....))...)))))).........(((((.(.((((((((......)))))))).).)))))............((((.....)))). ( -40.40)
>DroEre_CAF1 4262 120 + 1
GCAUACAAAUCUAUCUGGAGAUUGAUAACCGCAAGUGCACCGAGUGCUUCACACACGCCGUGGAGGCAGCCGAAUUUCUGGCUGCCACGGCGGCCAAACAUCAGCUGAGGAACGACUUUC
.............(((..((.(((((....(.(((..(.....)..))))......(((((.(.((((((((......)))))))).).))))).....)))))))..)))......... ( -38.70)
>DroYak_CAF1 4190 120 + 1
GCAUACAAAUCUAUCUGGAGAUUGACAAUCGCAAGUGCACCGAAUGCUUCACCCACGCAGUGGAGGCGGCCGAAUUCCUGGCUGCCACGGCAGCCAAACAUCAGCUGCGGAAUGACUUCC
(((....(((((......)))))......(....)))).((.....((((((.......))))))(((((.((.....(((((((....)))))))....)).))))))).......... ( -36.90)
>consensus
GCAUACAAAUCUAUCUGGAGAUUGACAAUCGCAAGUGCACCGAAUGCUUCACCCACGCCGUGGAGGCAGCCGAAUUCCUGGCUGCCACGGCGGCCAAACAUCAGCUGAGGAACGACUUCC
((((((.(((((......))))).......((....))...)))))).........(((((.(.((((((((......)))))))).).)))))..............((((....)))) (-35.85 = -35.85 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	3,023,825 – 3,023,945
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.25
Mean single sequence MFE	-43.77
Consensus MFE	-38.21
Energy contribution	-38.40
Covariance contribution	0.19
Combinations/Pair	1.11
Mean z-score	-1.40
Structure conservation index	0.87
SVM decision value	0.09
SVM RNA-class probability	0.576794
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3023825 120 - 22224390
GAAAAUCGUUCCGCAGCUGAUGUUUGGCCGCCGUGGCAGCCAGAAAUUCGGCUGCCUCAACGGCGUGCGUAAAGCAUUCGGUGCAUUUGCGAUUGUCAAUCUCCAAAUAGAUUUGAAUGC
((.((((((...(((.(.(((((((.(((((((((((((((........)))))))...)))))).))...))))))).).)))....)))))).))(((((......)))))....... ( -48.00)
>DroSec_CAF1 4244 120 - 1
GGAAGUCGUUCCUCAGCUGAUGUUUGGCCGCCGUGGCAGCCAGGAACUCGGCCGCCUCCACGGCGUGGGUGAAGCACUCGGUGCACUUGCGAUUGUCAAUCUCCAAAUAGAUUUGAAUGC
...((((((......((((((((((.(((((((((((.(((........))).)))...)))))...))).))))).)))))......)))))).(((((((......))).)))).... ( -41.10)
>DroEre_CAF1 4262 120 - 1
GAAAGUCGUUCCUCAGCUGAUGUUUGGCCGCCGUGGCAGCCAGAAAUUCGGCUGCCUCCACGGCGUGUGUGAAGCACUCGGUGCACUUGCGGUUAUCAAUCUCCAGAUAGAUUUGUAUGC
((.(..(((......((((((((((.(((((((((((((((........)))))))...))))))...)).))))).)))))......)))..).))(((((......)))))....... ( -43.10)
>DroYak_CAF1 4190 120 - 1
GGAAGUCAUUCCGCAGCUGAUGUUUGGCUGCCGUGGCAGCCAGGAAUUCGGCCGCCUCCACUGCGUGGGUGAAGCAUUCGGUGCACUUGCGAUUGUCAAUCUCCAGAUAGAUUUGUAUGC
((((....))))(((.(.(((((((((((((....))))))))...((((.(((((......).)))).))))))))).).)))...(((((..(((.(((....))).))))))))... ( -42.90)
>consensus
GAAAGUCGUUCCGCAGCUGAUGUUUGGCCGCCGUGGCAGCCAGAAAUUCGGCCGCCUCCACGGCGUGGGUGAAGCACUCGGUGCACUUGCGAUUGUCAAUCUCCAAAUAGAUUUGAAUGC
((.((((((......((((((((((.(((((((((((((((........)))))))...))))))...)).))))).)))))......)))))).))(((((......)))))....... (-38.21 = -38.40 +   0.19)

alignment

secondary structure

dotplot

Window 7

Location	3,023,865 – 3,023,985
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.42
Mean single sequence MFE	-44.85
Consensus MFE	-36.59
Energy contribution	-36.52
Covariance contribution	-0.06
Combinations/Pair	1.21
Mean z-score	-1.39
Structure conservation index	0.82
SVM decision value	-0.04
SVM RNA-class probability	0.511945
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3023865 120 + 22224390
CGAAUGCUUUACGCACGCCGUUGAGGCAGCCGAAUUUCUGGCUGCCACGGCGGCCAAACAUCAGCUGCGGAACGAUUUUCAGAUACACAGUGUUAGGGGCAUCAAGAAUCCCGGCGAUGA
....(((.....))).(((((((.((((((((......)))))))).)))))))....((((.((((.(((..((((..(.(((((...))))).)..).))).....))))))))))). ( -47.00)
>DroSec_CAF1 4284 120 + 1
CGAGUGCUUCACCCACGCCGUGGAGGCGGCCGAGUUCCUGGCUGCCACGGCGGCCAAACAUCAGCUGAGGAACGACUUCCAGAUACACAGUGUGCGGGGCAUCAAGAAUCCCGGCGAUGA
...(((.......)))(((((.(.((((((((......)))))))).).)))))....((((.((((.(((..((..(((.(.(((.....)))).)))..)).....))))))))))). ( -43.90)
>DroEre_CAF1 4302 120 + 1
CGAGUGCUUCACACACGCCGUGGAGGCAGCCGAAUUUCUGGCUGCCACGGCGGCCAAACAUCAGCUGAGGAACGACUUUCAGAUACACAGCGUGCGGGGCAUCAAGAAUCCCGGCGAUGA
...(((.....)))..(((((.(.((((((((......)))))))).).)))))....((((.((((.(...(........)...).))))..((.(((.((.....))))).)))))). ( -45.90)
>DroYak_CAF1 4230 120 + 1
CGAAUGCUUCACCCACGCAGUGGAGGCGGCCGAAUUCCUGGCUGCCACGGCAGCCAAACAUCAGCUGCGGAAUGACUUCCAGAUACACAGCGUUCGUGGUAUUAAGAAUCCCGGCGACGA
..(((((..(((..((((.(((...(((((.((.....(((((((....)))))))....)).)))))((((....)))).....))).))))..))))))))........((....)). ( -42.60)
>consensus
CGAAUGCUUCACCCACGCCGUGGAGGCAGCCGAAUUCCUGGCUGCCACGGCGGCCAAACAUCAGCUGAGGAACGACUUCCAGAUACACAGCGUGCGGGGCAUCAAGAAUCCCGGCGAUGA
...(((((((...(((((.(((...(((((.((.....(((((((....)))))))....)).)))))((((....)))).....))).))))).))))))).................. (-36.59 = -36.52 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:05 2006