Locus 3845

Sequence ID 2R_DroMel_CAF1
Location 12,706,889 – 12,706,983
Length 94
Max. P 0.655977
window6212 window6213

overview

Window 2

Location 12,706,889 – 12,706,983
Length 94
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 70.04
Mean single sequence MFE -30.68
Consensus MFE -13.25
Energy contribution -14.75
Covariance contribution 1.50
Combinations/Pair 1.19
Mean z-score -1.72
Structure conservation index 0.43
SVM decision value 0.26
SVM RNA-class probability 0.655977
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12706889 94 + 20766785
UCGAGCAGCCAGCAGCUGUUGGUGGCUAAAAC-GGGGAAA---CCGGGCUUCCGGAAAGUUGACGGAAGGGGAAAAAGCCGUC--GCUACCGGCGAGUGU
...(((.((((((....)))))).)))....(-.((....---)).)((((((((..(((.(((((............)))))--))).)))).)))).. ( -35.60)
>DroSec_CAF1 53186 84 + 1
UCGAGCAGCCAGCAGCUGUUGGUGGCUAAAAC-GGGGAAA---CCGGGCAUCCGGCACGUUGGUGGAGGGG-GAAAAGC-----------CGGCGAGUGU
....((.((((((....))))))((((....(-.((....---)).)...(((..(((....)))..))).-....)))-----------).))...... ( -28.50)
>DroSim_CAF1 59164 94 + 1
UCGAGCAGCCACCAGCUGUUGGUGGCUAAAAC-GGGGAAA---CCGGGCAUCCGGCACGUUGGUGGAGGGGGGAAAAGCCGUC--GCUACCGGCGAGUGU
....(((((((((((...)))))))))....(-.((....---)).))).....((.(((((((((.((.((......)).))--.))))))))).)).. ( -42.10)
>DroEre_CAF1 53881 82 + 1
UCGAGCAGCCAGCAGCUGCUGGUGGCUAAAACCGGGGAAA---CCGGGUAGCCGGAAAAU-------AGGUGGAGGGGAGGGG--------GGUGAGUGU
((.(.(.((((((....))))))(((((...((((.....---)))).))))).......-------.).).)).........--------......... ( -28.50)
>DroYak_CAF1 56273 95 + 1
UCGAGCAGCCAGCAGCUGUUGGUGGCUAAAACGGGGGAAA---UCGGGUAACCGGAAAACCCGGAAAAGGGGGAAAAGGGGGA--GCUACCGGCGAGUGU
(((((((((.....))))))(((((((....(........---((((....))))....(((......)))......)....)--))))))..))).... ( -30.60)
>DroAna_CAF1 52032 81 + 1
UCGAGC-------AGCUGUUUGUGGCUAAAAC-CACAAAAAAAAAGGCCAG--GGCGAGU---------GAGGAAGAGAGGGCAGGAGUCCGGCGAGUGU
(((.((-------.(((.(((((((......)-))))))......)))...--.))....---------..........((((....))))..))).... ( -18.80)
>consensus
UCGAGCAGCCAGCAGCUGUUGGUGGCUAAAAC_GGGGAAA___CCGGGCAUCCGGAAAGUUGG_GGAAGGGGGAAAAGCGGGC__GCUACCGGCGAGUGU
((((((.((((((....)))))).)))................((((....))))......................................))).... (-13.25 = -14.75 +   1.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,706,889 – 12,706,983
Length 94
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 70.04
Mean single sequence MFE -24.80
Consensus MFE -6.17
Energy contribution -8.00
Covariance contribution 1.83
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.25
SVM decision value 0.01
SVM RNA-class probability 0.540873
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12706889 94 - 20766785
ACACUCGCCGGUAGC--GACGGCUUUUUCCCCUUCCGUCAACUUUCCGGAAGCCCGG---UUUCCCC-GUUUUAGCCACCAACAGCUGCUGGCUGCUCGA
......(((((((((--...((((.......((((((.........))))))..(((---.....))-)....)))).......)))))))))....... ( -29.70)
>DroSec_CAF1 53186 84 - 1
ACACUCGCCG-----------GCUUUUC-CCCCUCCACCAACGUGCCGGAUGCCCGG---UUUCCCC-GUUUUAGCCACCAACAGCUGCUGGCUGCUCGA
......((((-----------((.....-..........((((.(((((....))))---).....)-)))..(((........)))))))))....... ( -21.80)
>DroSim_CAF1 59164 94 - 1
ACACUCGCCGGUAGC--GACGGCUUUUCCCCCCUCCACCAACGUGCCGGAUGCCCGG---UUUCCCC-GUUUUAGCCACCAACAGCUGGUGGCUGCUCGA
......(((((..((--(.((((.....................))))..)))))))---).....(-(...(((((((((.....)))))))))..)). ( -31.30)
>DroEre_CAF1 53881 82 - 1
ACACUCACC--------CCCCUCCCCUCCACCU-------AUUUUCCGGCUACCCGG---UUUCCCCGGUUUUAGCCACCAGCAGCUGCUGGCUGCUCGA
.........--------................-------.......(((((.((((---.....))))...))))).(.((((((.....)))))).). ( -22.90)
>DroYak_CAF1 56273 95 - 1
ACACUCGCCGGUAGC--UCCCCCUUUUCCCCCUUUUCCGGGUUUUCCGGUUACCCGA---UUUCCCCCGUUUUAGCCACCAACAGCUGCUGGCUGCUCGA
......(((((((((--(...........(((......)))......(((((..((.---.......))...)))))......))))))))))....... ( -26.60)
>DroAna_CAF1 52032 81 - 1
ACACUCGCCGGACUCCUGCCCUCUCUUCCUC---------ACUCGCC--CUGGCCUUUUUUUUUGUG-GUUUUAGCCACAAACAGCU-------GCUCGA
........((..(..(((.............---------....((.--...)).......((((((-((....)))))))))))..-------)..)). ( -16.50)
>consensus
ACACUCGCCGGUAGC__GCCCGCUUUUCCCCCUUCC_CCAACUUGCCGGAUGCCCGG___UUUCCCC_GUUUUAGCCACCAACAGCUGCUGGCUGCUCGA
.............................................((((....))))...............((((((.((.....)).))))))..... ( -6.17 =  -8.00 +   1.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:27 2006