Locus 5404

Sequence ID 3R_DroMel_CAF1
Location 14,214,322 – 14,214,442
Length 120
Max. P 0.662313
window8798 window8799

overview

Window 8

Location 14,214,322 – 14,214,442
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -39.32
Consensus MFE -22.11
Energy contribution -24.83
Covariance contribution 2.72
Combinations/Pair 1.18
Mean z-score -1.94
Structure conservation index 0.56
SVM decision value -0.01
SVM RNA-class probability 0.530500
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14214322 120 + 27905053
ACCUUCGCCAAUCAGGCACUUGCUGCCCAGAUCCACGUUGAAAAGGUUCAGCGUGUGGUAGAUGCCCUUCAUUUUCUUGACCAUGGCGCUCCAGGUGGGCAGCUGUUUCAAGGCAGCCUG
............(((((....((((((((....(((((((((....)))))))))(((.((.((((..(((......)))....)))))))))..))))))))((((....))))))))) ( -46.30)
>DroVir_CAF1 93320 120 + 1
GCACUCGCCAAUCAAGCACUUGCUGCCCAGAUCCACAUUGAACAUGUUCAGCGUGUGAUAGAUGGCCUUCAUUUUCUUGACCAUGGCCGUCCAGUUGGGCAGCUGCUUCUUGAUUGCCUU
......(.((((((((.....(((((((((((((((.(((((....))))).))).))).(((((((.(((......)))....)))))))...))))))))).....)))))))).).. ( -48.90)
>DroGri_CAF1 78793 120 + 1
GCACUCGCCAAUCAAGCACUUGCUGCCCAGGUCCACAUUGAACAUGUUCAGGGUGAAGUAAAUGGCCUUCAUUUUCUUGAUCAUGGCCGACCAGGUGGGCAGCUGCUUCAGAAUCGCCUU
......((...(((((((...(((((((((((((((.(((((....))))).)))........((((.(((......)))....))))))))...)))))))))))))..))...))... ( -41.90)
>DroWil_CAF1 82022 120 + 1
AGCCUCGCCAAUUAGACAUUUGCUGCCCAGAUCCACAUUGAACAAGUUGAGGACAUGGUAAAUGGCCUUCAUUUUCUUCACCAUAGCCGACCAGGUGGGCAACUUUUUCAAAACCGCCUG
.((...((.(((.....))).))(((((..........((((.(((.(((((.(((.....)))..))))).))).)))).....(((.....))))))))..............))... ( -23.00)
>DroMoj_CAF1 98530 120 + 1
GCACUCGCCGAUCAUGCACUUGCUUCCCAGAUCCACAUUGAACAGGUUCAGCGUGUGGUAGAUGGCCUUCAUUUUCUUGACCAUGACCGUCCAGUUGGGCAGCUGCUUCUUGAUGGCCUU
......(((.((((.(((...(((.(((((..((((((((((....))))..))))))..(((((.(.(((......)))....).)))))...))))).))))))....)))))))... ( -35.80)
>DroAna_CAF1 78481 120 + 1
ACCCUCUCCAAUGAGGCACUUGCUGCCCAAGUCCACAUUGAAAAGGUUCAGGGUGUGAUAGAUGGCCUUCAUUUUCUUGAUCGAAGCAGUCCAGUUCGGCAAUUGCUUCAGGGCAGCUUU
..((((......)))).....(((((((................(((.(((((.((((.((.....))))))..))))))))((((((((((.....))..)))))))).)))))))... ( -40.00)
>consensus
ACACUCGCCAAUCAGGCACUUGCUGCCCAGAUCCACAUUGAACAGGUUCAGCGUGUGGUAGAUGGCCUUCAUUUUCUUGACCAUGGCCGUCCAGGUGGGCAGCUGCUUCAAGACAGCCUU
.............(((((...((((((((.((((((.(((((....))))).))).))).(((((((.(((......)))....)))))))....)))))))))))))............ (-22.11 = -24.83 +   2.72)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 14,214,322 – 14,214,442
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -40.15
Consensus MFE -25.48
Energy contribution -26.10
Covariance contribution 0.62
Combinations/Pair 1.31
Mean z-score -1.79
Structure conservation index 0.63
SVM decision value 0.27
SVM RNA-class probability 0.662313
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14214322 120 - 27905053
CAGGCUGCCUUGAAACAGCUGCCCACCUGGAGCGCCAUGGUCAAGAAAAUGAAGGGCAUCUACCACACGCUGAACCUUUUCAACGUGGAUCUGGGCAGCAAGUGCCUGAUUGGCGAAGGU
......(((((......((((((((..((((..(((....(((......)))..))).))))...((((.((((....)))).))))....))))))))...((((.....))))))))) ( -42.80)
>DroVir_CAF1 93320 120 - 1
AAGGCAAUCAAGAAGCAGCUGCCCAACUGGACGGCCAUGGUCAAGAAAAUGAAGGCCAUCUAUCACACGCUGAACAUGUUCAAUGUGGAUCUGGGCAGCAAGUGCUUGAUUGGCGAGUGC
..(.((((((((.....((((((((..((((.((((....(((......))).)))).))))((.((((.((((....)))).))))))..)))))))).....)))))))).)...... ( -48.40)
>DroGri_CAF1 78793 120 - 1
AAGGCGAUUCUGAAGCAGCUGCCCACCUGGUCGGCCAUGAUCAAGAAAAUGAAGGCCAUUUACUUCACCCUGAACAUGUUCAAUGUGGACCUGGGCAGCAAGUGCUUGAUUGGCGAGUGC
..(.(((((...(((((((((((((...((((((((....(((......))).))))........(((..((((....))))..)))))))))))))))...)))))))))).)...... ( -43.20)
>DroWil_CAF1 82022 120 - 1
CAGGCGGUUUUGAAAAAGUUGCCCACCUGGUCGGCUAUGGUGAAGAAAAUGAAGGCCAUUUACCAUGUCCUCAACUUGUUCAAUGUGGAUCUGGGCAGCAAAUGUCUAAUUGGCGAGGCU
.....((((((......((((((((...((((.((.....((((.((..(((.((.(((.....))).)))))..)).))))..)).))))))))))))....(((.....))))))))) ( -34.00)
>DroMoj_CAF1 98530 120 - 1
AAGGCCAUCAAGAAGCAGCUGCCCAACUGGACGGUCAUGGUCAAGAAAAUGAAGGCCAUCUACCACACGCUGAACCUGUUCAAUGUGGAUCUGGGAAGCAAGUGCAUGAUCGGCGAGUGC
...(((((((....((((((.((((..((((.((((....(((......))).)))).))))(((((...((((....)))).)))))...)))).)))...))).)))).)))...... ( -35.80)
>DroAna_CAF1 78481 120 - 1
AAAGCUGCCCUGAAGCAAUUGCCGAACUGGACUGCUUCGAUCAAGAAAAUGAAGGCCAUCUAUCACACCCUGAACCUUUUCAAUGUGGACUUGGGCAGCAAGUGCCUCAUUGGAGAGGGU
..((.((.(((((((((....((.....))..))))))..(((......)))))).)).)).............(((((((((((.(((((((.....))))).)).))))))))))).. ( -36.70)
>consensus
AAGGCGAUCAUGAAGCAGCUGCCCAACUGGACGGCCAUGGUCAAGAAAAUGAAGGCCAUCUACCACACCCUGAACCUGUUCAAUGUGGAUCUGGGCAGCAAGUGCCUGAUUGGCGAGGGC
.................((((((((..((((.((((....(((......))).)))).))))(((((...((((....)))).)))))...))))))))...((((.....))))..... (-25.48 = -26.10 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:53 2006