Locus 1926

Sequence ID	X_DroMel_CAF1
Location	5,301,494 – 5,301,669
Length	175
Max. P	0.572819

overview

Window 9

Location	5,301,494 – 5,301,592
Length	98
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	85.13
Mean single sequence MFE	-27.35
Consensus MFE	-19.33
Energy contribution	-19.32
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.71
SVM decision value	0.08
SVM RNA-class probability	0.572819
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5301494 98 + 22224390
ACAUCGCACAGCCAAGUGGAAGUGCGC-UGUUAAAUGAGCGUGUUGCCCGCGGAAAGUCCAACAGCAAAACUAGCAACUUGCAACUUGCAACAUGCCAA
(((.(((((..((....))..))))).-)))....((.(((((((((....((.....))....((((..........)))).....))))))))))). ( -31.40)
>DroSec_CAF1 38309 87 + 1
ACAUCGCACAGCCAAGUGCAAG--CGC-UGUUAAAUGAGCGUGUUGCCCGCGGAAGGUCCA---------CUUGCAACUUGCUACUUGCAACAUGCCAC
.....(((....((((((((((--(((-(........)))))(((((..(.((.....)).---------)..))))))))).))))).....)))... ( -25.40)
>DroSim_CAF1 29145 87 + 1
ACAUCGCACAGCCAAGUGGAAG--CGC-UGUUAAAUGAGCGUGUUGCCCGCGGAAGGUCCA---------CUUGCAACUUGCUACUUGCAACAUGCCAC
.....(((..((.(((((((.(--(((-(........)))))........(....).))))---------)))))...((((.....))))..)))... ( -24.80)
>DroYak_CAF1 40128 82 + 1
----CGCACAUCCAAGUGGAUG--CGUUUGUUAAAUGAGCGUGUUGC-CGCGGAAGGUCCA---------CUGGCAACUUGCAGCUUGCAACAUGCCA-
----.((.(((((....)))))--.))........((.(((((((((-.((((.....)).---------...((.....)).))..)))))))))))- ( -27.80)
>consensus
ACAUCGCACAGCCAAGUGGAAG__CGC_UGUUAAAUGAGCGUGUUGCCCGCGGAAGGUCCA_________CUUGCAACUUGCAACUUGCAACAUGCCAC
......(((......))).................((.(((((((((....((.....)).............((.....)).....))))))))))). (-19.33 = -19.32 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	5,301,572 – 5,301,669
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.58
Mean single sequence MFE	-34.16
Consensus MFE	-23.72
Energy contribution	-23.16
Covariance contribution	-0.56
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.69
SVM decision value	-0.02
SVM RNA-class probability	0.521335
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5301572 97 + 22224390
-------------UGCAACUUGCAACAUGCCAA--------CGCCGUGUGGCACUUUGUUGGGCAAAAGGACCUGAUUGCCAGCAAGGAUAC--CAACGAUGCUGCUUGUAAAAGCCGAA
-------------(((((...(((.(.(((((.--------.......)))))(((((((((.(((.((...))..))))))))))))....--....).)))...)))))......... ( -24.80)
>DroSec_CAF1 38376 96 + 1
-------------UGCUACUUGCAACAUGCCAC--------CGCCGUGUGGCACUUUGUUG-GCGAAAGGAGCUGAUUGCCAGCAAGGAUAC--CAGCCAUGCUGCUUGUAAAAGCCGAA
-------------.(((..((((((..((((((--------......))))))((((((((-((((.((...))..))))))))))))....--((((...)))).)))))).))).... ( -32.30)
>DroSim_CAF1 29212 96 + 1
-------------UGCUACUUGCAACAUGCCAC--------CGCCGUGUGGCACUUUGUUG-GCGAAAGGAGCUGAUUGCCAGCAAGGAUAC--CAGCCAUGCUGCUUGUAAAAGCCGAA
-------------.(((..((((((..((((((--------......))))))((((((((-((((.((...))..))))))))))))....--((((...)))).)))))).))).... ( -32.30)
>DroEre_CAF1 39762 113 + 1
GCCGCCUGCAGCUUGCAGCUUGCAACAUGCCACCGCUACCCCGCCGUGUGGCACUUUGUUG-GCAAGAGGACCUGAUUGCCAGCAAGGAUGCCG------UGCUGCUUGUAAAAGCCGAA
..((.((...((..(((((..(((...(((((((((......).)).))))))((((((((-((((..(....)..)))))))))))).)))..------.)))))..))...)).)).. ( -45.10)
>DroYak_CAF1 40191 97 + 1
-------------UGCAGCUUGCAACAUGCCA---------CGCGGUGUUGCACUUUGUUG-GCAAGAGGAGCUGAUUGCCAGCAAGGAUACUGCAAGGAUGCUGCUUGUAAAAGCCGAA
-------------(((((..((((((((((..---------.)).))))))))((((((((-((((..(....)..))))))))))))...)))))......(.((((....)))).).. ( -36.30)
>consensus
_____________UGCAACUUGCAACAUGCCAC________CGCCGUGUGGCACUUUGUUG_GCAAAAGGAGCUGAUUGCCAGCAAGGAUAC__CAACCAUGCUGCUUGUAAAAGCCGAA
..............((...((((((((.((............(((....))).((((((((.((((..(....)..)))))))))))).............)))).))))))..)).... (-23.72 = -23.16 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:00 2006