Locus 5984

Sequence ID	3L_DroMel_CAF1
Location	15,989,364 – 15,989,604
Length	240
Max. P	0.826892

overview

Window 8

Location	15,989,364 – 15,989,484
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-35.33
Consensus MFE	-33.78
Energy contribution	-33.27
Covariance contribution	-0.50
Combinations/Pair	1.12
Mean z-score	-1.72
Structure conservation index	0.96
SVM decision value	0.70
SVM RNA-class probability	0.826892
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15989364 120 - 23771897
UUCAAAUUGAUUUCGACCCGACUAUGCAAAUGUCGUAAAUAAAGCUGUAGAGGGUUUUCAGUUUUUGGUGUUUUCUCAACCGAGUUCUCACAACCUGGCCAGCGGCAUAAGUCGGAAGCU
.................((((((((((...(((.....)))..((((....(((((.(.((..((((((.........))))))..)).).)))))...)))).)))).))))))..... ( -30.80)
>DroSec_CAF1 18370 120 - 1
UUCAAAUUGAUUUCGACCCGACUAUGCAAAUGUCGUAAAUAAAGCCGUAGAGGGUUUUCAGUUUUCGGUGUUUUCGCAACCGAGUUCUCACAACCUGGCCAGCGGCUUAAGUCGGAAGCU
..........(((((((.((((.........))))......(((((((.(.(((((.(.((..((((((((....)).))))))..)).).)))))...).)))))))..)))))))... ( -36.30)
>DroSim_CAF1 19510 120 - 1
UUCAAAUUGAUUUCGACCCGACUAUGCAAAUGUCGUAAAUAAAGCUGUAGAGGGUUUUCAGUUUUCGGUGUUUUCUCCACCGAGUUCUCACAACCUGGCCAGCGGCUUAAGUCGGAAGCU
..........(((((((.((((.........))))......(((((((.(.(((((.(.((..(((((((.......)))))))..)).).)))))...).)))))))..)))))))... ( -36.00)
>DroEre_CAF1 19385 119 - 1
UUCAAAUUGAUUUCGACCCGACUAUGCUAAUGUCGUAAAUAAAGCUGUAGAGGGUU-UGGGUUUUCGGUGUUUUCUCAACCGAAUUCUCACAACCUGGCCAGCGGCUUAAGUCGGAAGCU
..........(((((((.((((.........))))......(((((((.(.(((((-((((..((((((.........))))))..)))).)))))...).)))))))..)))))))... ( -38.20)
>consensus
UUCAAAUUGAUUUCGACCCGACUAUGCAAAUGUCGUAAAUAAAGCUGUAGAGGGUUUUCAGUUUUCGGUGUUUUCUCAACCGAGUUCUCACAACCUGGCCAGCGGCUUAAGUCGGAAGCU
..........(((((((.((((.........))))......(((((((.(.(((((...((..((((((.........))))))..))...)))))...).)))))))..)))))))... (-33.78 = -33.27 +  -0.50)

alignment

secondary structure

dotplot

Window 9

Location	15,989,484 – 15,989,604
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-23.98
Consensus MFE	-21.12
Energy contribution	-21.06
Covariance contribution	-0.06
Combinations/Pair	1.10
Mean z-score	-1.57
Structure conservation index	0.88
SVM decision value	0.12
SVM RNA-class probability	0.593405
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15989484 120 + 23771897
AAUCCUUUGCAAGGGCAUAAAAAACGAGAUUAAAUUUGCCUGCGUGCGCAAAAAGCCACAGAAAAGGCGGAAAACAAAAACAGCAAAGAAAAAUAAGUUGCAGAUUGGUGAUGUGAAGGG
...((((..((..(.((.................(((((((.((((.((.....))))).)...)))))))...........((((...........))))....)).)..))..)))). ( -25.50)
>DroSec_CAF1 18490 120 + 1
AAUCCUUUGCAAGGGCAUAAAAAACGAGAUUAAAUUUGCCUGCGUGCGCAAAAAGCCACAGAAAAGGCGGAAAACAAAAACAGCAAAGAAAAAUAAGUUGCAGAUUGGCGAUGGGUUGGG
....((((((..(((((...................)))))((....)).....(((........)))..............))))))...(((..(((((......)))))..)))... ( -24.61)
>DroSim_CAF1 19630 120 + 1
AAUCCUUUGCAAGGGCAUAAAAAACGAGAUUAAAUUUGCCUGCGUGCGCAAAAAGCCACAGAAAAGGCGGAAAACAAAAACAGCAAAGAAAAAUAAGUUGCAGAUUGGCGAUGGGAUGGG
.(((((((((........................(((((((.((((.((.....))))).)...)))))))...........((((...........))))......)))).)))))... ( -24.50)
>DroEre_CAF1 19504 115 + 1
AAUCCUUUGCAAGGGCAUAAAAAACGAGAUUAAAUUUGCCUGCGUGCGCAAAAAGCCACAGAAAAGGCGGAAAACAGAAAGAGCAAAGAAAAAUAAGUUGCAGAUUGGGAAUGGG-----
..((((..(((.(((((...................)))))...)))((((...(((........)))(.....)......................)))).....)))).....----- ( -21.31)
>consensus
AAUCCUUUGCAAGGGCAUAAAAAACGAGAUUAAAUUUGCCUGCGUGCGCAAAAAGCCACAGAAAAGGCGGAAAACAAAAACAGCAAAGAAAAAUAAGUUGCAGAUUGGCGAUGGGAUGGG
....((((((..(((((...................)))))((....)).....(((........)))..............))))))........(((((......)))))........ (-21.12 = -21.06 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:00 2006