Locus 3666

Sequence ID	3L_DroMel_CAF1
Location	10,725,435 – 10,725,575
Length	140
Max. P	0.992746

overview

Window 6

Location	10,725,435 – 10,725,551
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.02
Mean single sequence MFE	-32.55
Consensus MFE	-31.68
Energy contribution	-31.85
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.45
Structure conservation index	0.97
SVM decision value	2.35
SVM RNA-class probability	0.992746
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725435 116 + 23771897
GGGGGAAGAU----AGACAGAUAAACAAAGUUGCAGUUGUGUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUA
..........----...............(((((.((.(((((((((..((.......))..))))))))).))......((((((.(......)..)))))).......)))))..... ( -32.70)
>DroSec_CAF1 59288 116 + 1
GGGGGAAGAU----AGACAGAUAAACAAAGUUGCAGUUGUGUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUA
..........----...............(((((.((.(((((((((..((.......))..))))))))).))......((((((.(......)..)))))).......)))))..... ( -32.70)
>DroSim_CAF1 61460 116 + 1
GGGGGAAGAU----AGACAGAUAAACAAAGUUGCAGUUGUGUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUA
..........----...............(((((.((.(((((((((..((.......))..))))))))).))......((((((.(......)..)))))).......)))))..... ( -32.70)
>DroEre_CAF1 64094 116 + 1
GGGGGAAGAU----AGACAGAUAAACAAAGUUGCAGUUGAGUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUA
..........----...............(((((.((...(((((((..((.......))..)))))))...))......((((((.(......)..)))))).......)))))..... ( -28.90)
>DroYak_CAF1 73858 116 + 1
GGGGGAAGAU----AGACAGAUAAACAAAGUUGCAGUUGUGUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUA
..........----...............(((((.((.(((((((((..((.......))..))))))))).))......((((((.(......)..)))))).......)))))..... ( -32.70)
>DroAna_CAF1 61411 118 + 1
-GCAGAAGAUACUCAGAUAGAUAGACAAAGUUGCAGU-GUGUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACACUGCGGCACAUAGAGCGACAGAUA
-............................(((((.((-(((((((((..((.......))..)))))))).)))......(((((((.........))))))).......)))))..... ( -35.60)
>consensus
GGGGGAAGAU____AGACAGAUAAACAAAGUUGCAGUUGUGUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUA
.............................(((((.((.(((((((((..((.......))..))))))))).))......((((((...........)))))).......)))))..... (-31.68 = -31.85 +   0.17)

alignment

secondary structure

dotplot

Window 7

Location	10,725,471 – 10,725,575
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.30
Mean single sequence MFE	-32.27
Consensus MFE	-29.16
Energy contribution	-29.68
Covariance contribution	0.53
Combinations/Pair	1.04
Mean z-score	-1.58
Structure conservation index	0.90
SVM decision value	0.90
SVM RNA-class probability	0.878335
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10725471 104 + 23771897
GUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUACAUCUGCACACGCAGAUACA---GAUA-------------
(((((((..((.......))..))))))).....((((..((((((.(......)..)))))).(((...)))....))))((((((....))))))...---....------------- ( -32.80)
>DroSec_CAF1 59324 98 + 1
GUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUACAUCUGCACACGCAGAUA----------------------
(((((((..((.......))..))))))).....((((..((((((.(......)..)))))).(((...)))....))))((((((....)))))).---------------------- ( -32.80)
>DroSim_CAF1 61496 104 + 1
GUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUACAUCUGCACACGCAGAUACA---GAUA-------------
(((((((..((.......))..))))))).....((((..((((((.(......)..)))))).(((...)))....))))((((((....))))))...---....------------- ( -32.80)
>DroEre_CAF1 64130 104 + 1
GUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUACAUCUGCACACGCAGAUACA---GAUA-------------
(((((((..((.......))..))))))).....((((..((((((.(......)..)))))).(((...)))....))))((((((....))))))...---....------------- ( -32.80)
>DroYak_CAF1 73894 120 + 1
GUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUACAUCUGCACACGCAGAUACAGCAGAUACGGCAGAGACAGA
(((((((..((.......))..)))))))....(((((..((((((.(......)..)))))).(((...)))........((((((....)))))).......)))))........... ( -34.60)
>DroAna_CAF1 61449 104 + 1
GUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACACUGCGGCACAUAGAGCGACAGAUACAGAUGCAGAUGGAGAUGAA---GAUA-------------
(((((((..((.......))..)))))))....(((....(((((((.........))))))).(((...(((.(.......).)))..)))...)))..---....------------- ( -27.80)
>consensus
GUGACAGAAGCGAAGCGAGCAAUUGUCACAUUACGUAUACGCCGCGGGAGCAGACAGUGCGGCACGCAGAGCGACAGAUACAUCUGCACACGCAGAUACA___GAUA_____________
(((((((..((.......))..))))))).....((((..((((((...........)))))).(((...)))....))))((((((....))))))....................... (-29.16 = -29.68 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:03:46 2006