Locus 5087

Sequence ID	2L_DroMel_CAF1
Location	14,517,406 – 14,517,562
Length	156
Max. P	0.969157

overview

Window 6

Location	14,517,406 – 14,517,502
Length	96
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	92.74
Mean single sequence MFE	-35.32
Consensus MFE	-28.00
Energy contribution	-28.24
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.35
Structure conservation index	0.79
SVM decision value	1.64
SVM RNA-class probability	0.969157
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14517406 96 - 22407834
AUGUCAUGCGACGCUGGAAAAGAUGACACCACUCUGCGGGAAACGGCCAGAG--------GAGCAGAGGGAUGAGCGUGAAAUACGAGUCCUUCGGCAUGUAGC
....(((((...(((((...........)).((((((.(....).).)))))--------.))).(((((((...((((...)))).))))))).))))).... ( -33.10)
>DroSec_CAF1 48998 96 - 1
AUGUCAUGCGACGCUGGAAAAGAUGACACCACUCUGCGGGAAACGGCCAGAG--------GAGCCGAGGGAUGAGCGUGAAAUACGAGUCCUUCGGCAUGUAGC
..(((....)))((((.(.............((((((.(....).).)))))--------..((((((((((...((((...)))).)))))))))).).)))) ( -38.10)
>DroSim_CAF1 34131 96 - 1
AUGUCAUGCGACGCUGGAAAAGAUGACACCACUCUGCGGGAAACGGCCAGAG--------GAGCCGAGGGAUGAGCGUGAAAUACGAGUCCUUCGGCAUGUAGC
..(((....)))((((.(.............((((((.(....).).)))))--------..((((((((((...((((...)))).)))))))))).).)))) ( -38.10)
>DroEre_CAF1 42410 104 - 1
AUGUCAUCCGACGGUGGAAAAGAUGACACCACUCUGCGGGAAACAACCAGAGGAGCACAGGAGCAGAGGGAUGAGCGUGAAAUACGAGUCCUUCGGCAUGUAGC
(((((.(((...((((..........)))).(((((..(....)...))))).......)))...(((((((...((((...)))).))))))))))))..... ( -35.30)
>DroYak_CAF1 38965 96 - 1
AUGUCACCCGACGCUGGAAAAGAUGACACCACUCUGCGGGGAACGGCAGGAG--------GAGCAGAGGGAUGAGCGUGAAAUACGAGUCCUUCGGCAUGUAGC
..(((....)))((((.(..........((.(.((((.(....).))))).)--------).((.(((((((...((((...)))).))))))).)).).)))) ( -32.00)
>consensus
AUGUCAUGCGACGCUGGAAAAGAUGACACCACUCUGCGGGAAACGGCCAGAG________GAGCAGAGGGAUGAGCGUGAAAUACGAGUCCUUCGGCAUGUAGC
..(((....)))((((.(.............((((((.(....).)).))))..........((.(((((((...((((...)))).))))))).)).).)))) (-28.00 = -28.24 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	14,517,462 – 14,517,562
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.84
Mean single sequence MFE	-33.23
Consensus MFE	-22.25
Energy contribution	-21.97
Covariance contribution	-0.28
Combinations/Pair	1.04
Mean z-score	-2.53
Structure conservation index	0.67
SVM decision value	0.23
SVM RNA-class probability	0.646210
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14517462 100 - 22407834
GGAGGUG-UCACAG--------CAAAACAGCUAC-----------CAGCGACAAUGACAACGGUUCCACAUUGUUGUCACAUGUCAUGCGACGCUGGAAAAGAUGACACCACUCUGCGGG
...((((-((((((--------(......))).(-----------((((.....((((((((((.....))))))))))...(((....))))))))....).))))))).......... ( -36.10)
>DroPse_CAF1 52004 107 - 1
AAAUGUG-UCACAG--------CAAAACAGCUACCAAGCGACAGCCAGCGACAAUGACAACGGUUCCACAUUGUUGUCACAUGUCAUCCGACGCAGAAAAAGAUGACACGGCCAUG----
...((((-((((((--------(......))).....(((...(....)((((.((((((((((.....))))))))))..))))......))).......).)))))))......---- ( -29.00)
>DroSim_CAF1 34187 100 - 1
GGAGGUG-UCACAG--------CAAAACAGCUAC-----------CAGCGACAAUGACAACGGUUCCACAUUGUUGUCACAUGUCAUGCGACGCUGGAAAAGAUGACACCACUCUGCGGG
...((((-((((((--------(......))).(-----------((((.....((((((((((.....))))))))))...(((....))))))))....).))))))).......... ( -36.10)
>DroEre_CAF1 42474 109 - 1
GGCGGGGAUCACAGCAAAGCAGCAAAACAGCUAC-----------CAGCGACAAUGACAACGGUUCCACAUUGUUGUCACAUGUCAUCCGACGGUGGAAAAGAUGACACCACUCUGCGGG
.((((((.((...((...(.(((......))).)-----------..))((((.((((((((((.....))))))))))..))))....)).((((..........)))).))))))... ( -33.10)
>DroYak_CAF1 39021 100 - 1
GGAGGUG-UCACAG--------CAAAACAGCUAC-----------CAGCGACAAUGACAACGGUUCCACAUUGUUGUCACAUGUCACCCGACGCUGGAAAAGAUGACACCACUCUGCGGG
...((((-((((((--------(......))).(-----------((((.....((((((((((.....))))))))))...(((....))))))))....).))))))).......... ( -36.10)
>DroPer_CAF1 56987 107 - 1
AAAUGUG-UCACAG--------CAAAACAGCUACCAAGCGACAGCCAGCGACAAUGACAACGGUUCCACAUUGUUGUCACAUGUCAUCCGACGCAGAAAAAGAUGACACGGCCAUG----
...((((-((((((--------(......))).....(((...(....)((((.((((((((((.....))))))))))..))))......))).......).)))))))......---- ( -29.00)
>consensus
GGAGGUG_UCACAG________CAAAACAGCUAC___________CAGCGACAAUGACAACGGUUCCACAUUGUUGUCACAUGUCAUCCGACGCUGGAAAAGAUGACACCACUCUGCGGG
...((((.((((.................(((..............)))((((.((((((((((.....))))))))))..))))................).))))))).......... (-22.25 = -21.97 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:38 2006