Locus 2083

Sequence ID	X_DroMel_CAF1
Location	5,677,315 – 5,677,474
Length	159
Max. P	0.992286

overview

Window 6

Location	5,677,315 – 5,677,434
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	85.75
Mean single sequence MFE	-39.20
Consensus MFE	-30.91
Energy contribution	-30.03
Covariance contribution	-0.88
Combinations/Pair	1.19
Mean z-score	-2.06
Structure conservation index	0.79
SVM decision value	0.41
SVM RNA-class probability	0.726663
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5677315 119 - 22224390
CAGCGCAUACAGUUAGUAUGCGAACUUCCAAU-CGGGAGGUAGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAUCAAAAGUAGCAAUGGAAAAUAUAUGAUGAUGGUGCACUUCC
...(((((((.....))))))).((((((...-..))))))(((((.(((...(((((.......)))))....(((((((...(((...........))).)))))))))))))))... ( -38.20)
>DroSec_CAF1 16218 118 - 1
CAGCGCAUACAGCUAGUAUGCGAACUCCCGAU-UCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAUAAAAGUAGCAACGGAAAAUGU-UACUAAUGUUAAACUUUA
...(((((((.....))))))).(((...(((-(((..(.(((.(((...)))))).)..))))))..)))((((((((((..(((((((........)))-))))..)))).)))))). ( -38.00)
>DroSim_CAF1 17224 118 - 1
CAGCGCAUACAGCUAGUAUGCGAACUCCCGAUCUCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAUAAAAGUAGCAACGGAAAUUGU-UACAAACGUUA-ACUUUA
...(((((((.....))))))).((.((((....)))).))((.....))...(((((.......)))))((((((((((....(((((((......))))-)))....))))-)))))) ( -41.40)
>consensus
CAGCGCAUACAGCUAGUAUGCGAACUCCCGAU_UCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAUAAAAGUAGCAACGGAAAAUGU_UACUAAUGUUA_ACUUUA
..((((((((.....))))))..((.((((....)))).))......))....(((((.......))))).((((((((((..((((...(((.....))).))))..))))).))))). (-30.91 = -30.03 +  -0.88)

alignment

secondary structure

dotplot

Window 7

Location	5,677,355 – 5,677,474
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.42
Mean single sequence MFE	-54.77
Consensus MFE	-51.48
Energy contribution	-51.93
Covariance contribution	0.45
Combinations/Pair	1.09
Mean z-score	-3.48
Structure conservation index	0.94
SVM decision value	2.32
SVM RNA-class probability	0.992286
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5677355 119 + 22224390
GAUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACUACCUCCCG-AUUGGAAGUUCGCAUACUAACUGUAUGCGCUGCCGCCGGCGGCGAGGGGUCAGCUCCCAGGGGAUAAACUAG
(((..((((.(((((.......))))).(((((((((((.((.....-...)).))).(((((((.....)))))))..))))))))....)))).)))...(((....)))........ ( -49.50)
>DroSec_CAF1 16257 119 + 1
AUUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACCACACCCGA-AUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCGAGGGGACUCGCUCCAAAGGAUAAACUAG
..........(((((.......))))).(((((((((..((.((((.-..)))).)).(((((((.....))))))).)))))))((.((((((....))))))))...))......... ( -56.30)
>DroSim_CAF1 17262 120 + 1
AUUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACCACACCCGAGAUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCGAGGGGACUCGCUCCAAAGGAUAAACUAG
..........(((((.......))))).(((((((((..((.((((....)))).)).(((((((.....))))))).)))))))((.((((((....))))))))...))......... ( -58.50)
>consensus
AUUAACUUCACCGGGAUUCGAACCCGGACCGGCGGCACCACACCCGA_AUCGGGAGUUCGCAUACUAGCUGUAUGCGCUGCCGCCGGCGGCGAGGGGACUCGCUCCAAAGGAUAAACUAG
..........(((((.......))))).(((((((((..((.((((....)))).)).(((((((.....))))))).)))))))((.((((((....))))))))...))......... (-51.48 = -51.93 +   0.45)

alignment

secondary structure

dotplot

Window 8

Location	5,677,355 – 5,677,474
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.42
Mean single sequence MFE	-55.63
Consensus MFE	-50.60
Energy contribution	-50.27
Covariance contribution	-0.33
Combinations/Pair	1.06
Mean z-score	-3.03
Structure conservation index	0.91
SVM decision value	1.90
SVM RNA-class probability	0.982044
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5677355 119 - 22224390
CUAGUUUAUCCCCUGGGAGCUGACCCCUCGCCGCCGGCGGCAGCGCAUACAGUUAGUAUGCGAACUUCCAAU-CGGGAGGUAGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAUC
...(((..(((....)))...)))...(((((((((((((((.(((((((.....))))))).((((((...-..))))))..))))))))))..(((.......))))))))....... ( -55.70)
>DroSec_CAF1 16257 119 - 1
CUAGUUUAUCCUUUGGAGCGAGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAU-UCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAU
..........((((.(.(((((....))))))((((((((((.(((((((.....))))))..((.((((..-.)))).))).))))))))))(((((.......))))).))))..... ( -54.50)
>DroSim_CAF1 17262 120 - 1
CUAGUUUAUCCUUUGGAGCGAGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAUCUCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAU
..........((((.(.(((((....))))))((((((((((.(((((((.....))))))..((.((((....)))).))).))))))))))(((((.......))))).))))..... ( -56.70)
>consensus
CUAGUUUAUCCUUUGGAGCGAGUCCCCUCGCCGCCGGCGGCAGCGCAUACAGCUAGUAUGCGAACUCCCGAU_UCGGGUGUGGUGCCGCCGGUCCGGGUUCGAAUCCCGGUGAAGUUAAU
((((........))))...........(((((((((((((((.(((((((.....))))))).((.((((....)))).))..))))))))))..(((.......))))))))....... (-50.60 = -50.27 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:50 2006