Locus 1905

Sequence ID X_DroMel_CAF1
Location 5,280,568 – 5,280,705
Length 137
Max. P 0.744832
window3102 window3103

overview

Window 2

Location 5,280,568 – 5,280,670
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.11
Mean single sequence MFE -31.58
Consensus MFE -18.58
Energy contribution -18.62
Covariance contribution 0.04
Combinations/Pair 1.16
Mean z-score -1.91
Structure conservation index 0.59
SVM decision value 0.46
SVM RNA-class probability 0.744832
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5280568 102 + 22224390
GCAAACAGUGGCGA---------AGAUGUUGUCUGGACAGCG-GCAGCUGGGAAUGGAU-------GGACAGAAAAGUGCAGCU-UGCAAGGUCAACAUGGCGUAUGCGCGAUGUUUGAG
.((((((.(.(((.---------..((((..(...(((....-(((((((.(..((...-------...))......).)))).-)))...)))...)..))))...))).))))))).. ( -31.40)
>DroSec_CAF1 17496 99 + 1
GCAAACAGGGGCGA---------AGAUGAUGUCUGGACAGCG-GGAGCGGG--UUGUGU-------GGACAGA-AAGUGCAGUU-UGCAAGGUCAACAUUGCGUAUGCGCGAUGUUUGAG
((((((....(((.---------......((((((.(((((.-.......)--)))).)-------)))))..-...))).)))-)))....(((((((((((....))))))).)))). ( -35.80)
>DroSim_CAF1 12251 99 + 1
GCAAACAGGGGCGA---------AGAUGAUGUCUGGACAGCG-GGAGCGGG--UUGUGU-------GGACAGA-AAGUGCAGUU-UGCAAGGUCAACAUUGCGUAUGCGCAAUGUUGGAG
((((((....(((.---------......((((((.(((((.-.......)--)))).)-------)))))..-...))).)))-)))....(((((((((((....))))))))))).. ( -39.00)
>DroEre_CAF1 17219 106 + 1
GCAAACAGCGGCGA---------AGAUGAAGACAGGGCAGCGGGCAGCGGGCGCAGGGUGGAA---UGACA-A-AAGUGCAGUUUUGCAAGGCCAACAUUGCGUAUGCGUGAUGUUUGGG
.((((((((.((..---------...((....)).....))..)).(((.((((((..(((..---((.((-(-((......)))))))...)))...)))))).)))....)))))).. ( -28.10)
>DroYak_CAF1 13614 117 + 1
GCAAACAGGGGCGAAGAAGGUGAAGAUGAAGACAGGACAGCG-GCAGCGGCAGCAUGAUGGAAGCAGGACAAA-AAGUGCAGUU-GGCAAGGUCAACACGGCGUAUGCGCGAUGUUGGAG
((........)).......................((((.((-((((((.(.((((..((.........))..-..)))).(((-(((...))))))..).))).))).)).)))).... ( -23.60)
>consensus
GCAAACAGGGGCGA_________AGAUGAUGUCUGGACAGCG_GCAGCGGG__CUGGGU_______GGACAGA_AAGUGCAGUU_UGCAAGGUCAACAUUGCGUAUGCGCGAUGUUUGAG
((........)).......................(((.((.....)).............................(((......)))..)))(((((((((....))))))))).... (-18.58 = -18.62 +   0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,280,599 – 5,280,705
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.71
Mean single sequence MFE -30.83
Consensus MFE -16.58
Energy contribution -17.14
Covariance contribution 0.56
Combinations/Pair 1.24
Mean z-score -1.87
Structure conservation index 0.54
SVM decision value 0.30
SVM RNA-class probability 0.677957
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5280599 106 - 22224390
UAAUUA-----CCAAGGUGUACAGCGGGUGUUUGAAAGUCCUCAAACAUCGCGCAUACGCCAUGUUGACCUUGCA-AGCUGCACUUUUCUGUCC-------AUCCAUUCCCAGCUGC-CG
...(((-----.((.((((((..((((((((((((......))))))))).))).)))))).)).)))....(((-.((((.............-------.........)))))))-.. ( -29.75)
>DroSec_CAF1 17527 106 - 1
UAAUUACAUCACCGAGGUGU--AGCGGGUGUAUUAAAGUCCUCAAACAUCGCGCAUACGCAAUGUUGACCUUGCA-AACUGCACUU-UCUGUCC-------ACACAA--CCCGCUCC-CG
....((((((.....)))))--)((((((((......(((....(((((.(((....))).))))))))..(((.-....)))...-.......-------..)).)--)))))...-.. ( -27.20)
>DroSim_CAF1 12282 106 - 1
UAAUUACAUCACCGAGGUGU--AGCGGGUGUAUUAAAGUCCUCCAACAUUGCGCAUACGCAAUGUUGACCUUGCA-AACUGCACUU-UCUGUCC-------ACACAA--CCCGCUCC-CG
....((((((.....)))))--)((((((((............((((((((((....))))))))))....(((.-....)))...-.......-------..)).)--)))))...-.. ( -33.30)
>DroEre_CAF1 17250 111 - 1
UAAUUACAGUGCCCAGCUA----GCGGGUGCAUUAAAGUUCCCAAACAUCACGCAUACGCAAUGUUGGCCUUGCAAAACUGCACUU-U-UGUCA---UUCCACCCUGCGCCCGCUGCCCG
...............((.(----(((((((((.........((((.(((..((....))..)))))))...((((....))))...-.-.....---........))))))))))))... ( -30.00)
>DroYak_CAF1 13654 117 - 1
UAAUGACAGUGCCCAGGUAGCGAGCGGGUGUAUUAAAGUCCUCCAACAUCGCGCAUACGCCGUGUUGACCUUGCC-AACUGCACUU-UUUGUCCUGCUUCCAUCAUGCUGCCGCUGC-CG
........(.((...(((((((((((((......(((((....((((((.(((....))).)))))).....((.-....))))))-)....))))))).......))))))...))-). ( -33.91)
>consensus
UAAUUACAGCACCCAGGUGU__AGCGGGUGUAUUAAAGUCCUCAAACAUCGCGCAUACGCAAUGUUGACCUUGCA_AACUGCACUU_UCUGUCC_______ACCCAA__CCCGCUGC_CG
......................((((((.((..........((.(((((.(((....))).)))))))...(((......))).......................)).))))))..... (-16.58 = -17.14 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:36 2006