Locus 6480

Sequence ID	X_DroMel_CAF1
Location	16,258,627 – 16,258,787
Length	160
Max. P	0.982500

overview

Window 2

Location	16,258,627 – 16,258,747
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.66
Mean single sequence MFE	-40.36
Consensus MFE	-38.42
Energy contribution	-38.46
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.80
Structure conservation index	0.95
SVM decision value	1.92
SVM RNA-class probability	0.982500
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16258627 120 - 22224390
AUGCGCGCGCGCAAAGAGAGAGCGCCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUACGCAGCAGGCAGCUACAGCGCAAAAUUAUAUGUAAUUGGCC
.(((((..((((.........))(((((.((.((((((.....)).)))))).))..(((.....((((....))))..)))....))).))....)))))................... ( -37.40)
>DroSec_CAF1 6941 119 - 1
AUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUACGCAGCAGGCAGC-ACAGCGCAAAAUUAUAUGUAAUUGGCC
.((((((.((((.....(.(((.((((((((.((.....))..))))))))))))..(((.....((((....))))..))).....)).))-.).)))))................... ( -41.00)
>DroSim_CAF1 7082 119 - 1
AUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUACGCAGCAGGCAGC-ACAGCGCAAAAUUAUAUGUAAUUGGCC
.((((((.((((.....(.(((.((((((((.((.....))..))))))))))))..(((.....((((....))))..))).....)).))-.).)))))................... ( -41.00)
>DroEre_CAF1 7067 119 - 1
AUGCGCGCGCGCAAAGAGAGAGCGGCGGUGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGGAAUUCCUUGAAAAAGGUACGCAGCAGGCAGC-ACAGCGCAAAAUUAUAUGUAAUUGGCC
.((((((.((((...(.(((.((((((((...((.....)).)))))))).))))..(((.....((((....))))..))).....)).))-.).)))))................... ( -41.40)
>DroYak_CAF1 6918 119 - 1
AUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUACGCAGCAGGCAGC-ACAGCGCAAAAUUAUAUGUAAUUGGCC
.((((((.((((.....(.(((.((((((((.((.....))..))))))))))))..(((.....((((....))))..))).....)).))-.).)))))................... ( -41.00)
>consensus
AUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUACGCAGCAGGCAGC_ACAGCGCAAAAUUAUAUGUAAUUGGCC
.(((((..((((.....(.(((.((((((((.((.....))..))))))))))))..(((.....((((....))))..))).....)).))....)))))................... (-38.42 = -38.46 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	16,258,667 – 16,258,787
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-47.08
Consensus MFE	-44.86
Energy contribution	-45.50
Covariance contribution	0.64
Combinations/Pair	1.02
Mean z-score	-1.16
Structure conservation index	0.95
SVM decision value	0.18
SVM RNA-class probability	0.621629
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16258667 120 + 22224390
GUACCUUUUUCAAGGAAUUUCGCUUGGAGGGCAGCAGUUGCUCUCUGCUCCGCCGGCGCUCUCUCUUUGCGCGCGCGCAUCCUUGCAAGGAAAUUGAAGUGACGGAGACGGAACAGGCGG
...((((....)))).....((((((..((((((...))))))((((((((((((((((.........)))).)).)).((((....))))............)))).)))).)))))). ( -42.30)
>DroSec_CAF1 6980 120 + 1
GUACCUUUUUCAAGGAAUUUCGCUUGGAGGGCAGCAGUUGCUCUCUGCUCCGCCGCCGCUCUCUCUUUGCGCGCGCGCAUCCUUGCAAGGAAAUUGAAGUGGCGGAGACGGAACAGGCUG
...((((....))))......(((((((((((((...))))))))...((((((((((((.((....((((....))))((((....))))....))))))))))...)))).))))).. ( -46.40)
>DroSim_CAF1 7121 120 + 1
GUACCUUUUUCAAGGAAUUUCGCUUGGAGGGCAGCAGUUGCUCUCUGCUCCGCCGCCGCUCUCUCUUUGCGCGCGCGCAUCCUUGCAAGGAAAUUGAAGUGGCGGAGACGGAACAGGCUG
...((((....))))......(((((((((((((...))))))))...((((((((((((.((....((((....))))((((....))))....))))))))))...)))).))))).. ( -46.40)
>DroEre_CAF1 7106 120 + 1
GUACCUUUUUCAAGGAAUUCCGCUUGGAGGGCAGCAGUUGCUCUCUGCUCCACCGCCGCUCUCUCUUUGCGCGCGCGCAUCCUUGCAAGGAAAUGGAAGUGGCGGAGACGGAACAGGCGG
...((((....))))....(((((((((((((((...))))))))...(((.((((((((..(....((((....))))((((....))))...)..))))))))....))).))))))) ( -49.80)
>DroYak_CAF1 6957 120 + 1
GUACCUUUUUCAAGGAAUUUCGCUUGGAGGGCAGCAGUUGCUCUCUGCUCCGCCGCCGCUCUCUCUUUGCGCGCGCGCAUCCUUGCGAGGAAAUGGAAGUGGCGGAGACGGAACAGGCGG
...((((....)))).....((((((((((((((...))))))))...((((((((((((..(....((((....))))((((....))))...)..))))))))...)))).)))))). ( -50.50)
>consensus
GUACCUUUUUCAAGGAAUUUCGCUUGGAGGGCAGCAGUUGCUCUCUGCUCCGCCGCCGCUCUCUCUUUGCGCGCGCGCAUCCUUGCAAGGAAAUUGAAGUGGCGGAGACGGAACAGGCGG
...((((....))))....(((((((((((((((...))))))))...((((((((((((.((....((((....))))((((....))))....))))))))))...)))).))))))) (-44.86 = -45.50 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	16,258,667 – 16,258,787
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-44.38
Consensus MFE	-42.08
Energy contribution	-41.96
Covariance contribution	-0.12
Combinations/Pair	1.05
Mean z-score	-1.63
Structure conservation index	0.95
SVM decision value	1.79
SVM RNA-class probability	0.977346
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16258667 120 - 22224390
CCGCCUGUUCCGUCUCCGUCACUUCAAUUUCCUUGCAAGGAUGCGCGCGCGCAAAGAGAGAGCGCCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUAC
.(((.(((((((((..(((...(((....((((....))))((((....))))..)))...)))..)))))))))(((.(((.....))).)))...))).....((((....))))... ( -39.90)
>DroSec_CAF1 6980 120 - 1
CAGCCUGUUCCGUCUCCGCCACUUCAAUUUCCUUGCAAGGAUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUAC
..((.(((((((((.(((((.(((.....((((....))))((((....))))..))).).)))).)))))))))(((.(((.....))).)))...))......((((....))))... ( -44.30)
>DroSim_CAF1 7121 120 - 1
CAGCCUGUUCCGUCUCCGCCACUUCAAUUUCCUUGCAAGGAUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUAC
..((.(((((((((.(((((.(((.....((((....))))((((....))))..))).).)))).)))))))))(((.(((.....))).)))...))......((((....))))... ( -44.30)
>DroEre_CAF1 7106 120 - 1
CCGCCUGUUCCGUCUCCGCCACUUCCAUUUCCUUGCAAGGAUGCGCGCGCGCAAAGAGAGAGCGGCGGUGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGGAAUUCCUUGAAAAAGGUAC
((((.(((((((...(((((.((..(...((((....))))((((....))))....)..)).))))))))))))(((.(((.....))).)))...))))....((((....))))... ( -46.80)
>DroYak_CAF1 6957 120 - 1
CCGCCUGUUCCGUCUCCGCCACUUCCAUUUCCUCGCAAGGAUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUAC
.(((.(((((((((.((((..((..(...((((....))))((((....))))..)..)).)))).)))))))))(((.(((.....))).)))...))).....((((....))))... ( -46.60)
>consensus
CCGCCUGUUCCGUCUCCGCCACUUCAAUUUCCUUGCAAGGAUGCGCGCGCGCAAAGAGAGAGCGGCGGCGGAGCAGAGAGCAACUGCUGCCCUCCAAGCGAAAUUCCUUGAAAAAGGUAC
..((.(((((((((.(((((.(((.....((((....))))((((....))))..))).).)))).)))))))))(((.(((.....))).)))...))......((((....))))... (-42.08 = -41.96 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:53 2006