Locus 638

Sequence ID	2R_DroMel_CAF1
Location	3,199,877 – 3,199,968
Length	91
Max. P	0.997922

overview

Window 5

Location	3,199,877 – 3,199,968
Length	91
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	78.68
Mean single sequence MFE	-37.68
Consensus MFE	-29.80
Energy contribution	-31.10
Covariance contribution	1.30
Combinations/Pair	1.00
Mean z-score	-2.90
Structure conservation index	0.79
SVM decision value	2.96
SVM RNA-class probability	0.997922
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3199877 91 + 20766785
CAGACGGCGUCUGCUGGCCGUCAUCGGAUCUGGAGGC--------CAGACCAAGAGAUCUGAAGUAGCUGGCCUGGCAGCAGGCCGAAAGCCAGGCCAA
..((((((........)))))).((((((((...((.--------....))...))))))))......(((((((((............))))))))). ( -40.40)
>DroSec_CAF1 6990 99 + 1
CAGACGGCGUCUGCUGGCCGUCAUCGGAUCUGGAGGCCUGGAGGCCAGACCAAGAGAUCUGAAGUAGCUGGCCUGGCAGCAGGCCGAAAGCCAGGCCAA
..((((((........)))))).((((((((((.((((....))))...))...))))))))......(((((((((............))))))))). ( -47.30)
>DroSim_CAF1 10757 96 + 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNAUCUGGAGGCC---AGACCAGACCAAGAGAUCUGAAGUAGCUGGCCUGGCAGCAGGCCGAAAGCCAGGCCAA
............................(((((...))---))).((((.(....).)))).......(((((((((............))))))))). ( -25.50)
>DroEre_CAF1 7108 86 + 1
CAGACGGCGUCUGCUGGCCGUCAUCGGAUCUGGAGGC-------------CAAAAGAUCUGAAGUAGCUGGCCUGGCAGCAGGCCGAUAGCCAGGCCAA
..((((((........)))))).((((((((......-------------....))))))))......(((((((((............))))))))). ( -39.20)
>DroYak_CAF1 7260 86 + 1
CAGACGUCGUCUGCUGGCCGUCGUCGGAUCUGGAGGC-------------CAAAAGAUCUGAAGUAGCUGGCCUGGCAGAAGGCCGAUAGCCAGGCCAA
.........(((((((((((.(.((((((((......-------------....))))))))....).))))).)))))).((((........)))).. ( -36.00)
>consensus
CAGACGGCGUCUGCUGGCCGUCAUCGGAUCUGGAGGC________CAGACCAAGAGAUCUGAAGUAGCUGGCCUGGCAGCAGGCCGAAAGCCAGGCCAA
..((((((........)))))).((((((((.......................))))))))......(((((((((............))))))))). (-29.80 = -31.10 +   1.30)

alignment

secondary structure

dotplot

Window 6

Location	3,199,877 – 3,199,968
Length	91
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	78.68
Mean single sequence MFE	-36.24
Consensus MFE	-27.46
Energy contribution	-29.66
Covariance contribution	2.20
Combinations/Pair	1.00
Mean z-score	-2.83
Structure conservation index	0.76
SVM decision value	2.86
SVM RNA-class probability	0.997457
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3199877 91 - 20766785
UUGGCCUGGCUUUCGGCCUGCUGCCAGGCCAGCUACUUCAGAUCUCUUGGUCUG--------GCCUCCAGAUCCGAUGACGGCCAGCAGACGCCGUCUG
((((((((((............))))))))))..............((((((((--------(...))))).)))).((((((........)))))).. ( -37.90)
>DroSec_CAF1 6990 99 - 1
UUGGCCUGGCUUUCGGCCUGCUGCCAGGCCAGCUACUUCAGAUCUCUUGGUCUGGCCUCCAGGCCUCCAGAUCCGAUGACGGCCAGCAGACGCCGUCUG
((((((((((............)))))))))).....((.(((((...(((((((...)))))))...))))).)).((((((........)))))).. ( -46.50)
>DroSim_CAF1 10757 96 - 1
UUGGCCUGGCUUUCGGCCUGCUGCCAGGCCAGCUACUUCAGAUCUCUUGGUCUGGUCU---GGCCUCCAGAUNNNNNNNNNNNNNNNNNNNNNNNNNNN
.(((((((((............)))))))))((((..(((((((....)))))))..)---)))................................... ( -32.30)
>DroEre_CAF1 7108 86 - 1
UUGGCCUGGCUAUCGGCCUGCUGCCAGGCCAGCUACUUCAGAUCUUUUG-------------GCCUCCAGAUCCGAUGACGGCCAGCAGACGCCGUCUG
((((((((((............)))))))))).....((.(((((...(-------------(...))))))).)).((((((........)))))).. ( -33.30)
>DroYak_CAF1 7260 86 - 1
UUGGCCUGGCUAUCGGCCUUCUGCCAGGCCAGCUACUUCAGAUCUUUUG-------------GCCUCCAGAUCCGACGACGGCCAGCAGACGACGUCUG
((((((((((............))))))))))......(((((((.(((-------------(((((..........)).)))))).))).....)))) ( -31.20)
>consensus
UUGGCCUGGCUUUCGGCCUGCUGCCAGGCCAGCUACUUCAGAUCUCUUGGUCUG________GCCUCCAGAUCCGAUGACGGCCAGCAGACGCCGUCUG
((((((((((............)))))))))).....((.(((((...((((.........))))...))))).)).((((((........)))))).. (-27.46 = -29.66 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:23 2006