Locus 1573

Sequence ID	3R_DroMel_CAF1
Location	4,504,315 – 4,504,475
Length	160
Max. P	0.984435

overview

Window 8

Location	4,504,315 – 4,504,435
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.08
Mean single sequence MFE	-35.84
Consensus MFE	-28.26
Energy contribution	-28.22
Covariance contribution	-0.04
Combinations/Pair	1.15
Mean z-score	-1.43
Structure conservation index	0.79
SVM decision value	0.04
SVM RNA-class probability	0.552888
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4504315 120 - 27905053
UCUUAUUCGAGCUUGAGCCUCAGGUGGCCAGUUUUUUAAUUCUUCCUUGCCACAAGGCAAGCAAAAAGAGGCUGUAUAGUAGAAACUGCAGCCAGGAUCCUUGCACACCGUCUUGGAGCA
..........((((.((.....((((((.((..((((...((((.((((((....))))))....))))((((((..(((....)))))))))))))..)).)).))))...)).)))). ( -37.10)
>DroSec_CAF1 4295 120 - 1
UCUUAUUCGAGCUUGGGCCUCAGCUGGCCAAUUUUUUAGUUCUUCCUUGCCACAAGGCAAACAAAAAGAGGCUGUAUAGUAGAAACUGCAGCCAGGAUCCUUGCACACCGUCUUGGAGCA
........(((((..((((......))))........))))).....(((..((((((...........((((((..(((....))))))))).((...........))))))))..))) ( -34.10)
>DroSim_CAF1 4290 120 - 1
UCUUAUUCGAGCUUGGGCCUCAGCUGGCCAAUUUUUUAGUUCUUCCUUGCCACAAGGCAAGCAAAAAGAGGCUGUGUAGUAGAAACUGCAGCCAGGAUCCUUGCACACCGUCUUGGAGCA
...............((((......)))).........(((((..((((((....))))))......(((((.((((.((((...)))).((.((....)).)))))).)))))))))). ( -36.70)
>DroEre_CAF1 4298 120 - 1
UCGCAUUCGAGCUUGCGCCUCAACUGGCCAGUUCUUUAGUUCCACCUUGCCACAAGGCAAGCAAAAUGAGGAUGUAUAGUAAAAACUGCAGCCAGUAUCCUUGCAUACGGAUUUGGAGCA
........(((((.(.(((......)))))))))....(((((..((((((....))))))......(((..(((((.((((..((((....))))....)))))))))..)))))))). ( -34.20)
>DroYak_CAF1 4309 120 - 1
UCUUAUCCGAGCUUGCGCCUCAACUGGCCAGUUCUUUAGUUCUUCCUUGCCACAAGGCAAGCAAAAAGAGGCUGUGUAGUAAAAACUGCAGCCGGGAUCCUUGCACACUGACUUGGAGCA
.....(((((((.((((......((((((((((((((.....((.((((((....)))))).))))))).))))((((((....)))))))))))......))))....).))))))... ( -37.10)
>consensus
UCUUAUUCGAGCUUGCGCCUCAGCUGGCCAGUUUUUUAGUUCUUCCUUGCCACAAGGCAAGCAAAAAGAGGCUGUAUAGUAGAAACUGCAGCCAGGAUCCUUGCACACCGUCUUGGAGCA
.....((((((((((.(((......)))))).......(((((..((((((....))))))........((((((..(((....))))))))))))))...........).))))))... (-28.26 = -28.22 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	4,504,355 – 4,504,475
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.25
Mean single sequence MFE	-34.04
Consensus MFE	-27.36
Energy contribution	-27.28
Covariance contribution	-0.08
Combinations/Pair	1.19
Mean z-score	-2.44
Structure conservation index	0.80
SVM decision value	1.97
SVM RNA-class probability	0.984435
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4504355 120 + 27905053
ACUAUACAGCCUCUUUUUGCUUGCCUUGUGGCAAGGAAGAAUUAAAAAACUGGCCACCUGAGGCUCAAGCUCGAAUAAGAAAACAAAUGUCUGUCAGUCAAGGCAGGCAAACAUAAAUUA
.......(((((((((((.((((((....)))))).)))))..........((...)).))))))......................((((((((......))))))))........... ( -32.70)
>DroSec_CAF1 4335 120 + 1
ACUAUACAGCCUCUUUUUGUUUGCCUUGUGGCAAGGAAGAACUAAAAAAUUGGCCAGCUGAGGCCCAAGCUCGAAUAAGAAAGCAAAUGUCAGCCAGUCAGGGCAGGCAAACAUAAAUUA
...............(((((((((((((((((...................((((......))))...((((......))..))........))))..)))))))))))))......... ( -32.20)
>DroSim_CAF1 4330 120 + 1
ACUACACAGCCUCUUUUUGCUUGCCUUGUGGCAAGGAAGAACUAAAAAAUUGGCCAGCUGAGGCCCAAGCUCGAAUAAGAAAGCAAAUGUCAGUCAGUCAGGGCAGGCAAACAUGAAUUA
...........((..(((((((((((((((((...................((((......))))...((((......))..))........))))..)))))))))))))...)).... ( -32.30)
>DroEre_CAF1 4338 120 + 1
ACUAUACAUCCUCAUUUUGCUUGCCUUGUGGCAAGGUGGAACUAAAGAACUGGCCAGUUGAGGCGCAAGCUCGAAUGCGAAAGCAAUUGUCAGUCAGUCGAGGCAGCCAAACAUAAAUUA
.........((((.(((..((((((....))))).)..))).....((.(((((...(((((.(....)))))).(((....))).......)))))))))))................. ( -36.40)
>DroYak_CAF1 4349 120 + 1
ACUACACAGCCUCUUUUUGCUUGCCUUGUGGCAAGGAAGAACUAAAGAACUGGCCAGUUGAGGCGCAAGCUCGGAUAAGAAAGCAGUUGUCAGCCAGUCAAGGCAAAAAAAAUUAAAAAA
........((((.(((((.((((((....)))))).))))).....((.(((((....((((.(....)))))(((((........))))).))))))).))))................ ( -36.60)
>consensus
ACUAUACAGCCUCUUUUUGCUUGCCUUGUGGCAAGGAAGAACUAAAAAACUGGCCAGCUGAGGCCCAAGCUCGAAUAAGAAAGCAAAUGUCAGUCAGUCAAGGCAGGCAAACAUAAAUUA
...............(((((((((((((((((..................(((((......))).)).((((......))..))........))))..)))))))))))))......... (-27.36 = -27.28 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:54 2006