Locus 5587

Sequence ID	2L_DroMel_CAF1
Location	15,855,573 – 15,855,782
Length	209
Max. P	0.904021

overview

Window 9

Location	15,855,573 – 15,855,667
Length	94
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.90
Mean single sequence MFE	-32.21
Consensus MFE	-23.11
Energy contribution	-23.44
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.72
SVM decision value	0.44
SVM RNA-class probability	0.737851
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15855573 94 - 22407834
---------CAUUCAACCCAUUUACAUGCAA----------------CGCAGGCAG-GGCGGAAACGGAAGUGCCGAGGCAGCUCUGAAAUAAUAUCAAAAAUGGCUGCCGGAGGCGGCA
---------..(((..(((.......(((..----------------.)))....)-))..)))((....))((((.(((((((.(((.......))).....))))))).....)))). ( -28.50)
>DroPse_CAF1 17649 105 - 1
---------------CUCCAUUUACAUGCAGUCCUGCAAGUCGACGGCGCAGGCCGAAGCGGAAACGGAAGUGCAGAGGCAGCUCAGAAAUAAUAUCAAAAAUGGCUGCCGGAGGCGGCA
---------------((((..............(((((..((..((((....))))...((....))))..))))).((((((.((................))))))))))))...... ( -39.09)
>DroSec_CAF1 27830 94 - 1
---------CAUUCAACCCAUUUACAUGCAA----------------CGCAGGCAG-GGCGGAAACGGAAGUGCCGAGGCAGCUCUGAAAUAAUAUCAAAAAUGGCUGCCGGAGGCGGCA
---------..(((..(((.......(((..----------------.)))....)-))..)))((....))((((.(((((((.(((.......))).....))))))).....)))). ( -28.50)
>DroSim_CAF1 28864 94 - 1
---------CAUUCAACCCAUUUACAUGCAA----------------CGCAGGCAG-GGCGGAAACGGAAGUGCCGAGGCAGCUCUGAAAUAAUAUCAAAAAUGGCUGCCGGAGGCGGCA
---------..(((..(((.......(((..----------------.)))....)-))..)))((....))((((.(((((((.(((.......))).....))))))).....)))). ( -28.50)
>DroEre_CAF1 15194 103 - 1
CAUGCAACCCAUUCAACCCAUUUACAUGCAA----------------CGCGGGCAG-GGCGGAAACGGAAGUGCCGAGGCAGCUCUGAAAUAAUAUCAAAAAUGGCUGCCGGAGGCGGCA
..(((......(((..(((.......(((..----------------.....))))-))..)))((....))(((..(((((((.(((.......))).....)))))))...))).))) ( -29.61)
>DroPer_CAF1 43410 105 - 1
---------------CUCCAUUUACAUGCAGUCCUGCAAGUCGACGGCGCAGGCCGAAGCGGAAACGGAAGUGCAGAGGCAGCUCAGAAAUAAUAUCAAAAAUGGCUGCCGGAGGCGGCA
---------------((((..............(((((..((..((((....))))...((....))))..))))).((((((.((................))))))))))))...... ( -39.09)
>consensus
_________CAUUCAACCCAUUUACAUGCAA________________CGCAGGCAG_GGCGGAAACGGAAGUGCCGAGGCAGCUCUGAAAUAAUAUCAAAAAUGGCUGCCGGAGGCGGCA
..........................(((..................(((........)))...((....))(((..(((((((...................)))))))...))).))) (-23.11 = -23.44 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	15,855,645 – 15,855,742
Length	97
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	89.90
Mean single sequence MFE	-20.76
Consensus MFE	-19.26
Energy contribution	-19.57
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.73
Structure conservation index	0.93
SVM decision value	1.03
SVM RNA-class probability	0.904021
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15855645 97 - 22407834
GCACCAUUGCAUUCUGAAGUUCUUGCACUCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAA-AAAGGGACUCC---------CAUUCAACCCAUUUACAUGCAA
......((((((..((((.....(((.....))).(((((((.....((((.....))))....-)))))))....---------...........)))).)))))) ( -17.40)
>DroSec_CAF1 27902 98 - 1
GCACCAUUGCAUUCUGAAGCUCUUGCACGCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAAAAAAGGGAGUCU---------CAUUCAACCCAUUUACAUGCAA
......((((((..((((((....)).......(((((((((.....((((.....)))).....)))))))))..---------...........)))).)))))) ( -21.70)
>DroSim_CAF1 28936 97 - 1
GCACCAUUGCAUUCUAAAGCUCUUGCACUCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAA-AAAGGGAGUCU---------CAUUCAACCCAUUUACAUGCAA
......((((((..((((((....)).......(((((((((.....((((.....))))....-)))))))))..---------...........)))).)))))) ( -21.20)
>DroEre_CAF1 15266 107 - 1
GCACCAUUGCAUUCUGAAGCUCCUGCACUCGGCACUCCCUUUGGCCCCGAUAAGCGAUCUCAAAAAAAGGGAGCCCCAUGCAACCCAUUCAACCCAUUUACAUGCAA
(((...........((((.....((((...((..((((((((......(((.....)))......))))))))..)).)))).....))))...........))).. ( -22.75)
>consensus
GCACCAUUGCAUUCUGAAGCUCUUGCACUCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAA_AAAGGGAGUCC_________CAUUCAACCCAUUUACAUGCAA
......((((((..((((.....(((.....)))((((((((.....((((.....)))).....)))))))).......................)))).)))))) (-19.26 = -19.57 +   0.31)

alignment

secondary structure

dotplot

Window 1

Location	15,855,667 – 15,855,782
Length	115
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	87.63
Mean single sequence MFE	-23.93
Consensus MFE	-21.46
Energy contribution	-21.40
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-1.67
Structure conservation index	0.90
SVM decision value	0.72
SVM RNA-class probability	0.833339
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15855667 115 - 22407834
UCAGUCGCCCACAUUAACUUCAAUUCGCUCCCUAGCACACGCACCAUUGCAUUCUGAAGUUCUUGCACUCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAA-AAAGGGACUCC
......((...((..(((((((....(((....)))....(((....)))....)))))))..))......))..(((((((.....((((.....))))....-))))))).... ( -22.90)
>DroSec_CAF1 27924 100 - 1
----------------ACUUCAAUUCGCUCCCUAGCACACGCACCAUUGCAUUCUGAAGCUCUUGCACGCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAAAAAAGGGAGUCU
----------------.(((((....(((....)))....(((....)))....))))).....((.....))(((((((((.....((((.....)))).....))))))))).. ( -24.30)
>DroSim_CAF1 28958 115 - 1
UCAGUCGCCCACAUUAACUUCAAUUCGCUCCCUAGCACACGCACCAUUGCAUUCUAAAGCUCUUGCACUCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAA-AAAGGGAGUCU
..........................(((((((.((....))....((((...((((((....(((.....)))....))))))....(((.....))))))).-..))))))).. ( -24.10)
>DroEre_CAF1 15297 116 - 1
UCAGUCGCCCACAUUAACUUCAAUUCGCUCCCUCGCACACGCACCAUUGCAUUCUGAAGCUCCUGCACUCGGCACUCCCUUUGGCCCCGAUAAGCGAUCUCAAAAAAAGGGAGCCC
..........................(((((((.((....))...(((((........((....))..((((..((......))..))))...))))).........))))))).. ( -24.40)
>consensus
UCAGUCGCCCACAUUAACUUCAAUUCGCUCCCUAGCACACGCACCAUUGCAUUCUGAAGCUCUUGCACUCUGCACUCCCUUUAGCCCCGAUAAGCGAUCGCAAA_AAAGGGAGUCC
..........................(((((((.((....))....((((...((((((....(((.....)))....))))))....(((.....)))))))....))))))).. (-21.46 = -21.40 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:57 2006