Locus 533

Sequence ID	2R_DroMel_CAF1
Location	2,825,740 – 2,825,869
Length	129
Max. P	0.988782

overview

Window 8

Location	2,825,740 – 2,825,854
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	84.12
Mean single sequence MFE	-39.86
Consensus MFE	-28.84
Energy contribution	-29.16
Covariance contribution	0.32
Combinations/Pair	1.10
Mean z-score	-2.98
Structure conservation index	0.72
SVM decision value	2.13
SVM RNA-class probability	0.988782
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2825740 114 - 20766785
AAACUGAAACUGCAUCUGAAUUCGAAUCCGAGUCCGAAGCCCGGGCAGCUGCAUUCAGCUACAGCAUUCAACUUGGCAACAGGAAGUGGCAGCGGUAUUGUUGCCGCUUAUCUG
...(((((..((((.((....(((....)))(((((.....))))))).)))))))))...(((.......((((....))))(((((((((((....)))))))))))..))) ( -39.30)
>DroSec_CAF1 14767 114 - 1
AAACUGAAACUGCAUCUGAAUCCGAAUCCGAGUCCGAAGCCCGGGCAGCUGCAUACAGCUUCAGCAUUCAACUUGGCAACAGGAAGUGGCAGCGGUAUUGUUGCCACUUAUCUG
....((((..(((..................(((((.....)))))(((((....)))))...))))))).((((....))))(((((((((((....)))))))))))..... ( -38.70)
>DroSim_CAF1 27962 114 - 1
AAACUGAAACUGCAUCUGAAUUCGAAUCCGAGUCCGAAGCCCGGGCAGCUGCAUACAGCUUCAGCAUUCAACUUGGCAACAGGAAGUGGCAGCGGUAUUGUUGCCGCUUAUCUG
....((((..(((........(((....)))(((((.....)))))(((((....)))))...))))))).((((....))))(((((((((((....)))))))))))..... ( -39.10)
>DroEre_CAF1 14603 89 - 1
AAAAC------------GAAACUGCAGCCGAAUCUUAAGCCCGGGCAGCUGCAUUCAGC-------------UUGGCAACAGGAAGUGGCAGCGUUAUUGUUGCCGCUUAUCUG
.....------------.........(((((.......((....)).((((....))))-------------)))))..(((((((((((((((....))))))))))).)))) ( -33.00)
>DroYak_CAF1 15087 114 - 1
AAACUAAAACUGAAGCUGAAACUGCAUCUGAUUCCGAAGCCCGGGCAGCUGCAUUCAGCUUCAGCAUUCAACUUGGCAACAGGAAGUGGCAGCGGUAUUGUUGCCGCUUAUCUG
.........(((((((((((..((((.(((...(((.....))).))).))))))))))))))).......((((....))))(((((((((((....)))))))))))..... ( -49.20)
>consensus
AAACUGAAACUGCAUCUGAAUCCGAAUCCGAGUCCGAAGCCCGGGCAGCUGCAUUCAGCUUCAGCAUUCAACUUGGCAACAGGAAGUGGCAGCGGUAUUGUUGCCGCUUAUCUG
...........................(((((((((.....)))))(((((....)))))............))))...(((((((((((((((....))))))))))).)))) (-28.84 = -29.16 +   0.32)

alignment

secondary structure

dotplot

Window 9

Location	2,825,777 – 2,825,869
Length	92
Sequences	4
Columns	92
Reading direction	forward
Mean pairwise identity	92.57
Mean single sequence MFE	-33.73
Consensus MFE	-26.00
Energy contribution	-26.87
Covariance contribution	0.87
Combinations/Pair	1.09
Mean z-score	-3.23
Structure conservation index	0.77
SVM decision value	0.92
SVM RNA-class probability	0.882450
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2825777 92 + 20766785
GCCAAGUUGAAUGCUGUAGCUGAAUGCAGCUGCCCGGGCUUCGGACUCGGAUUCGAAUUCAGAUGCAGUUUCAGUUUCAGUUUCAAUUUUAG
...((((((((.((((.(((((((....(((((((((((....).)))))..((.......)).)))))))))))).))))))))))))... ( -32.30)
>DroSec_CAF1 14804 92 + 1
GCCAAGUUGAAUGCUGAAGCUGUAUGCAGCUGCCCGGGCUUCGGACUCGGAUUCGGAUUCAGAUGCAGUUUCAGUUUCAGUUUCAAUUUUAG
...((((((((.((((((((((..((((.(((.(((((.((((....)))))))))...))).))))....))))))))))))))))))... ( -35.40)
>DroSim_CAF1 27999 92 + 1
GCCAAGUUGAAUGCUGAAGCUGUAUGCAGCUGCCCGGGCUUCGGACUCGGAUUCGAAUUCAGAUGCAGUUUCAGUUUCAGUUUCAAUUUUAG
...((((((((.((((((((((..((((.(((.((((((....).))))).........))).))))....))))))))))))))))))... ( -34.60)
>DroYak_CAF1 15124 92 + 1
GCCAAGUUGAAUGCUGAAGCUGAAUGCAGCUGCCCGGGCUUCGGAAUCAGAUGCAGUUUCAGCUUCAGUUUUAGUUUCAGUUUCAGUUUGAG
..(((..((((.((((((((((((((((.(((.(((.....)))...))).))))..))))))))))))............))))..))).. ( -32.62)
>consensus
GCCAAGUUGAAUGCUGAAGCUGAAUGCAGCUGCCCGGGCUUCGGACUCGGAUUCGAAUUCAGAUGCAGUUUCAGUUUCAGUUUCAAUUUUAG
...((((((((.(((((((((((.((((.(((.(((.....)))..(((....)))...))).))))...)))))))))))))))))))... (-26.00 = -26.87 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:05 2006