Locus 227

Sequence ID	2L_DroMel_CAF1
Location	635,905 – 635,995
Length	90
Max. P	0.999941

overview

Window 1

Location	635,905 – 635,995
Length	90
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	91.85
Mean single sequence MFE	-19.12
Consensus MFE	-17.52
Energy contribution	-17.92
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.89
Structure conservation index	0.92
SVM decision value	4.71
SVM RNA-class probability	0.999941
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 635905 90 + 22407834
UCCGCUGGCGAGCGAAAUGCGAUAAAAUGCAAAUCUCUCUUGAAGCUAAAAGGACACCAGCCAGCAAUUGAAAUCUAAAACAAAAAAAA-A
...(((((((((.((..((((......))))..)).)))............((...)).))))))........................-. ( -20.00)
>DroSec_CAF1 24669 83 + 1
UCCGCUGGCGAGCGAAAUGCGAUAAAAUGCAAAUCUCUCUUGAAGCUAAAAGUACACCAGCCAGCAAUUGAAAUCUAAAAAC--------A
...(((((((((.((..((((......))))..)).))).....((.....))......)))))).................--------. ( -19.60)
>DroSim_CAF1 24568 83 + 1
UCCGCUGGCGAGCGAAAUGCGAUAAAAUGCAAAUCUCUCUUGAAGCUAAAAGGACACCAGCCAGCAAUUGAAAUCUAAAAAC--------A
...(((((((((.((..((((......))))..)).)))............((...)).)))))).................--------. ( -20.00)
>DroEre_CAF1 29077 91 + 1
UCCGCUGGCGAGCAAAAUGCGAUAAAAUGCAAAUCUCUCUUGAAGCUAAAAGGACACCAGCCAGCAAUUGAAAUCUAAAAAAAAAAAAACA
...((((((.(((....((((......))))..((......)).)))....((...)).)))))).......................... ( -18.00)
>DroYak_CAF1 28244 89 + 1
UCCGCUGGCGAGCAAAAUGCGAUAAAAUGCAAAUCUCUCUUGAAGCUAAAAGGACACCAGCCAGCAAUUGAAAUCUAAAAAAC--GAAAUA
...((((((.(((....((((......))))..((......)).)))....((...)).))))))..................--...... ( -18.00)
>consensus
UCCGCUGGCGAGCGAAAUGCGAUAAAAUGCAAAUCUCUCUUGAAGCUAAAAGGACACCAGCCAGCAAUUGAAAUCUAAAAAA____AAA_A
...(((((((((.((..((((......))))..)).)))............(.....).)))))).......................... (-17.52 = -17.92 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	635,905 – 635,995
Length	90
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	91.85
Mean single sequence MFE	-22.28
Consensus MFE	-22.48
Energy contribution	-22.24
Covariance contribution	-0.24
Combinations/Pair	1.05
Mean z-score	-2.24
Structure conservation index	1.01
SVM decision value	4.53
SVM RNA-class probability	0.999915
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 635905 90 - 22407834
U-UUUUUUUUGUUUUAGAUUUCAAUUGCUGGCUGGUGUCCUUUUAGCUUCAAGAGAGAUUUGCAUUUUAUCGCAUUUCGCUCGCCAGCGGA
.-......................(((((((((((.((.......)).))).(((.((..(((........)))..)).))))))))))). ( -23.10)
>DroSec_CAF1 24669 83 - 1
U--------GUUUUUAGAUUUCAAUUGCUGGCUGGUGUACUUUUAGCUUCAAGAGAGAUUUGCAUUUUAUCGCAUUUCGCUCGCCAGCGGA
.--------...............(((((((((((.((.......)).))).(((.((..(((........)))..)).))))))))))). ( -23.40)
>DroSim_CAF1 24568 83 - 1
U--------GUUUUUAGAUUUCAAUUGCUGGCUGGUGUCCUUUUAGCUUCAAGAGAGAUUUGCAUUUUAUCGCAUUUCGCUCGCCAGCGGA
.--------...............(((((((((((.((.......)).))).(((.((..(((........)))..)).))))))))))). ( -23.10)
>DroEre_CAF1 29077 91 - 1
UGUUUUUUUUUUUUUAGAUUUCAAUUGCUGGCUGGUGUCCUUUUAGCUUCAAGAGAGAUUUGCAUUUUAUCGCAUUUUGCUCGCCAGCGGA
........................(((((((((((.((.......)).))).(((..(..(((........)))..)..))))))))))). ( -20.90)
>DroYak_CAF1 28244 89 - 1
UAUUUC--GUUUUUUAGAUUUCAAUUGCUGGCUGGUGUCCUUUUAGCUUCAAGAGAGAUUUGCAUUUUAUCGCAUUUUGCUCGCCAGCGGA
......--................(((((((((((.((.......)).))).(((..(..(((........)))..)..))))))))))). ( -20.90)
>consensus
U_UUU____UUUUUUAGAUUUCAAUUGCUGGCUGGUGUCCUUUUAGCUUCAAGAGAGAUUUGCAUUUUAUCGCAUUUCGCUCGCCAGCGGA
........................(((((((((((.((.......)).))).(((.((..(((........)))..)).))))))))))). (-22.48 = -22.24 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:33 2006