Locus 6571

Sequence ID 2R_DroMel_CAF1
Location 20,534,489 – 20,534,646
Length 157
Max. P 0.948970
window10458 window10459 window10460

overview

Window 8

Location 20,534,489 – 20,534,607
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.38
Mean single sequence MFE -29.02
Consensus MFE -18.88
Energy contribution -20.44
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -1.86
Structure conservation index 0.65
SVM decision value 0.34
SVM RNA-class probability 0.695363
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20534489 118 + 20766785
AAAGUUACUUGGCCCCGACGAGGGGAGUGUCAUCC-CUCGUCGAGUUUGUCUUCUGAAACA-UAUCACAAUAACACAUCAUUUGUCAAGGCAACAAAUGAUGUUGCAUGUAACCUUAUCA
...(((((...((..((((((((((.......)))-))))))).((((........)))).-............(((((((((((.......))))))))))).))..)))))....... ( -35.90)
>DroSim_CAF1 36374 118 + 1
ACAGUUACUUGGCCCCGGCGAGGGCAGUGUCAUCCCCUCGUCGAGUUUCGCUUC-AAAACA-UAUCACAAUAACACAUCAUUUGUCAAGGCAACAAAUGAUGUUGCAUGUAACCUUAUCA
...(((((...((..(((((((((.(......).)))))))))...........-......-............(((((((((((.......))))))))))).))..)))))....... ( -33.90)
>DroYak_CAF1 37843 119 + 1
AAAGUUACUUGGCCCCGGCGAGCGUAAUGUCAUCCCCUCGUUGAGUUUGGCUUCUGAAACA-UAUCACAAUAACACAUCAUUUGUCAAGGCAACAAAUGAUGUUGCAUGUAACCUUAUCA
...(((((.(((((((((((((.(..((...))..)))))))).)...)))..........-............(((((((((((.......)))))))))))..)).)))))....... ( -26.30)
>DroAna_CAF1 44351 100 + 1
AAAGUUGCUUG-CCCCGGCUGGG------UC-------------GUUCGGCUUUUGAAACACUAUCACAAUAACACAUCAUUUGUCAGGCAAACAAACGAUGUUGCAUGUAACCUUAUCA
...(((((.((-(...((((((.------..-------------..))))))......................(((((.(((((.......))))).))))).))).)))))....... ( -20.00)
>consensus
AAAGUUACUUGGCCCCGGCGAGGG_AGUGUCAUCC_CUCGUCGAGUUUGGCUUCUGAAACA_UAUCACAAUAACACAUCAUUUGUCAAGGCAACAAAUGAUGUUGCAUGUAACCUUAUCA
...(((((.((....(((((((..............)))))))...............................(((((((((((.......)))))))))))..)).)))))....... (-18.88 = -20.44 +   1.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,534,489 – 20,534,607
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.38
Mean single sequence MFE -36.27
Consensus MFE -23.25
Energy contribution -25.12
Covariance contribution 1.88
Combinations/Pair 1.03
Mean z-score -2.66
Structure conservation index 0.64
SVM decision value 1.39
SVM RNA-class probability 0.948970
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20534489 118 - 20766785
UGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA-UGUUUCAGAAGACAAACUCGACGAG-GGAUGACACUCCCCUCGUCGGGGCCAAGUAACUUU
....((((((((..((.((((((((((((.....))))))))))))(((.((.(((..-....))).)))))...(((((((((-((.........)))))))))))))...)))))))) ( -46.20)
>DroSim_CAF1 36374 118 - 1
UGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA-UGUUUU-GAAGCGAAACUCGACGAGGGGAUGACACUGCCCUCGCCGGGGCCAAGUAACUGU
......((((((..((.((((((((((((.....))))))))))))....((((..((-.....)-)..))))..((((.((((((.(......).)))))).))))))...)))))).. ( -38.40)
>DroYak_CAF1 37843 119 - 1
UGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA-UGUUUCAGAAGCCAAACUCAACGAGGGGAUGACAUUACGCUCGCCGGGGCCAAGUAACUUU
....((((((((..((.((((((((((((.....))))))))))))....((.(((..-....))).))))....(((..((((.(..........).))))..))).....)))))))) ( -33.20)
>DroAna_CAF1 44351 100 - 1
UGAUAAGGUUACAUGCAACAUCGUUUGUUUGCCUGACAAAUGAUGUGUUAUUGUGAUAGUGUUUCAAAAGCCGAAC-------------GA------CCCAGCCGGGG-CAAGCAACUUU
.((((..((((((.(((.(((((((((((.....))))))))))))))...))))))..))))......(((...(-------------(.------......)).))-).......... ( -27.30)
>consensus
UGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA_UGUUUCAGAAGCCAAACUCGACGAG_GGAUGACACU_CCCUCGCCGGGGCCAAGUAACUUU
.((((..((((((.(((.(((((((((((.....))))))))))))))...))))))..))))............((((.((((.(..........).)))).))))............. (-23.25 = -25.12 +   1.88)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,534,528 – 20,534,646
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.25
Mean single sequence MFE -31.85
Consensus MFE -25.58
Energy contribution -25.45
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -1.67
Structure conservation index 0.80
SVM decision value 0.43
SVM RNA-class probability 0.734897
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20534528 118 - 20766785
UGGCAA-ACCGUAACGUAACCGUCUGCAACGGAUAUGAGAUGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA-UGUUUCAGAAGACAAACUCGA
......-..(((..((((.((((.....)))).))))..))).....((((((.(((.(((((((((((.....))))))))))))))...)))))).-((((......))))....... ( -30.20)
>DroSim_CAF1 36414 117 - 1
UGCCAA-ACCGUAACGUAACCGUCUGCAGCGGAUAUGAGAUGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA-UGUUUU-GAAGCGAAACUCGA
.(((((-(.(((..((((.((((.....)))).))))..........((((((.(((.(((((((((((.....))))))))))))))...)))))))-)).)))-)..))......... ( -31.30)
>DroYak_CAF1 37883 118 - 1
UGCCAA-ACCGUAACGUAAGCGUCUGCAGCGGAUAUGAGAUGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA-UGUUUCAGAAGCCAAACUCAA
......-...((((((....))).)))...((...(((((((.....((((((.(((.(((((((((((.....))))))))))))))...)))))).-)))))))....))........ ( -30.70)
>DroAna_CAF1 44375 114 - 1
CGCCACCAACGGACUGU--GGGUCUGCAACGGAUGUGAGAUGAUAAGGUUACAUGCAACAUCGUUUGUUUGCCUGACAAAUGAUGUGUUAUUGUGAUAGUGUUUCAAAAGCCGAAC----
.........(((((...--..)))))...(((...(((((((.....((((((.(((.(((((((((((.....))))))))))))))...))))))..)))))))....)))...---- ( -35.20)
>consensus
UGCCAA_ACCGUAACGUAACCGUCUGCAACGGAUAUGAGAUGAUAAGGUUACAUGCAACAUCAUUUGUUGCCUUGACAAAUGAUGUGUUAUUGUGAUA_UGUUUCAGAAGCCAAACUCGA
.....................(((((...))))).(((((((.....((((((.(((.(((((((((((.....))))))))))))))...))))))..))))))).............. (-25.58 = -25.45 +  -0.13)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:05 2006