Locus 2031

Sequence ID	X_DroMel_CAF1
Location	5,586,962 – 5,587,060
Length	98
Max. P	0.965750

overview

Window 6

Location	5,586,962 – 5,587,060
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	81.28
Mean single sequence MFE	-47.36
Consensus MFE	-35.76
Energy contribution	-35.78
Covariance contribution	0.02
Combinations/Pair	1.04
Mean z-score	-1.68
Structure conservation index	0.76
SVM decision value	0.42
SVM RNA-class probability	0.729101
Prediction	RNA
WARNING	Sequence 3: Base composition out of range.

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5586962 98 + 22224390
CCGGCAUUCCGGGCAUCCCGGGACCCGAACCACCGCCGGGCGAAGAGCCCGGGGAUGAGGGACCCGGUCCAGUGGGCGAGCCCGAUCCGGAAGGUGAG
.((.(.((((((((...(((((.(((....((((.((((((.....)))))))).)).))).)))))......(((....)))).)))))))).)).. ( -49.50)
>DroSec_CAF1 15108 98 + 1
CGGCCAUUCCGGGCAUCCCGGGACCCGAAACACCGCCGGGCGAAGAGCCCGGGGAUGAGGGGCCCGGUCCAGUGGGCGGGCCCGAUCCGGAAGGUGAG
..(((.(((((((((((((((...........)))((((((.....)))))))))))..(((((((.(((...))))))))))..))))))))))... ( -55.10)
>DroSim_CAF1 15081 98 + 1
CGGCCAUUCCGGGCAUCCCGGGACCCGAAACACCGCCGGGCGAAGAGCCCGGGGAUGAGGGGCCCGGUCCAGUGGGCGGGCCNNNNNNNNNNNNNNNN
.((((.(((((((...)))))))(((....((((.((((((.....)))))))).)).)))(((((......))))).))))................ ( -46.50)
>DroEre_CAF1 15577 90 + 1
--------CCAGGCAUCCCGGGACCCGAGCCACCGCCUGGCGACGAGCCAGGGGAUGAGGGCCCCGGUCCAGUGGGCGAACCCGAUCCGGAUGGUGAG
--------.....(((((((((.(((....((((.((((((.....)))))))).)).))).)))))(((..((((....))))....))).)))).. ( -40.70)
>DroYak_CAF1 15638 90 + 1
--------CCAGGCAUCCCGGGACCGGAGCCACCGCCUGGCGACGAGCCAGGGGACGAGGGGCCCGGUCCAGUGGGCGAACCCGAUCCGGAAGGUGAG
--------.....((((((((((((((.(((.((.((((((.....))))))......))))))))))))..((((....))))...)))..)))).. ( -45.00)
>consensus
C_G_CAUUCCGGGCAUCCCGGGACCCGAACCACCGCCGGGCGAAGAGCCCGGGGAUGAGGGGCCCGGUCCAGUGGGCGAGCCCGAUCCGGAAGGUGAG
...........((....(((((.(((......((.((((((.....))))))))....))).))))).))...(((....)))...((....)).... (-35.76 = -35.78 +   0.02)

alignment

secondary structure

dotplot

Window 7

Location	5,586,962 – 5,587,060
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	81.28
Mean single sequence MFE	-48.76
Consensus MFE	-39.04
Energy contribution	-38.60
Covariance contribution	-0.44
Combinations/Pair	1.15
Mean z-score	-2.23
Structure conservation index	0.80
SVM decision value	1.59
SVM RNA-class probability	0.965750
Prediction	RNA
WARNING	Sequence 3: Base composition out of range.

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5586962 98 - 22224390
CUCACCUUCCGGAUCGGGCUCGCCCACUGGACCGGGUCCCUCAUCCCCGGGCUCUUCGCCCGGCGGUGGUUCGGGUCCCGGGAUGCCCGGAAUGCCGG
........((((.((((((((.((....)).(((((.((((((((.((((((.....)))))).)))))...))).))))))).))))))....)))) ( -52.90)
>DroSec_CAF1 15108 98 - 1
CUCACCUUCCGGAUCGGGCCCGCCCACUGGACCGGGCCCCUCAUCCCCGGGCUCUUCGCCCGGCGGUGUUUCGGGUCCCGGGAUGCCCGGAAUGGCCG
....((((((((((((((....)))......((((((((..((((.((((((.....)))))).))))....))).))))))))..)))))).))... ( -51.50)
>DroSim_CAF1 15081 98 - 1
NNNNNNNNNNNNNNNNGGCCCGCCCACUGGACCGGGCCCCUCAUCCCCGGGCUCUUCGCCCGGCGGUGUUUCGGGUCCCGGGAUGCCCGGAAUGGCCG
................((((..((....((.((((((((..((((.((((((.....)))))).))))....))).)))))....)).))...)))). ( -44.90)
>DroEre_CAF1 15577 90 - 1
CUCACCAUCCGGAUCGGGUUCGCCCACUGGACCGGGGCCCUCAUCCCCUGGCUCGUCGCCAGGCGGUGGCUCGGGUCCCGGGAUGCCUGG--------
....((((((((...(((....))).)))))((((((((((((((.((((((.....)))))).)))))...)))))))))......)))-------- ( -48.50)
>DroYak_CAF1 15638 90 - 1
CUCACCUUCCGGAUCGGGUUCGCCCACUGGACCGGGCCCCUCGUCCCCUGGCUCGUCGCCAGGCGGUGGCUCCGGUCCCGGGAUGCCUGG--------
....((....))..(((((...(((...((((((((((......((((((((.....)))))).)).))).))))))).)))..))))).-------- ( -46.00)
>consensus
CUCACCUUCCGGAUCGGGCUCGCCCACUGGACCGGGCCCCUCAUCCCCGGGCUCUUCGCCCGGCGGUGGUUCGGGUCCCGGGAUGCCCGGAAUG_C_G
.............((((((...(((...(((((.((.....((((.((((((.....)))))).))))..)).))))).)))..))))))........ (-39.04 = -38.60 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:37 2006