Locus 7653

Sequence ID 3L_DroMel_CAF1
Location 20,568,076 – 20,568,302
Length 226
Max. P 0.987783
window12434 window12435 window12436 window12437 window12438 window12439

overview

Window 4

Location 20,568,076 – 20,568,182
Length 106
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 91.19
Mean single sequence MFE -23.85
Consensus MFE -18.94
Energy contribution -19.50
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.08
Structure conservation index 0.79
SVM decision value 0.77
SVM RNA-class probability 0.844955
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20568076 106 + 23771897
CCCCGUCUCACAAAUUAGCUCCAUUACAACGCUGGAACGAUUGAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAAAAACGCAAAAUACAAA
.................((((((.........))))..((((....))))..((((((..(((((((.....)))))))..)))))).......)).......... ( -24.50)
>DroSec_CAF1 12856 106 + 1
CCCCGUCUCACAAAUUAGCUCCAUUACAUCGCACGAACGAUCCAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAGAAACGCAAAAUACAAA
..............................((.....(((....))).(((.((((((..(((((((.....)))))))..)))))).)))...)).......... ( -25.80)
>DroSim_CAF1 6512 106 + 1
CCCCGUCUCACAAAUUAGCUCCAUUACAUCGCUCGAACGAUCCAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAGAAACGAAAAAUACAAA
............................(((.((((........))))(((.((((((..(((((((.....)))))))..)))))).)))..))).......... ( -25.70)
>DroEre_CAF1 6420 106 + 1
CCCGGUCUCCCAAAUUAGCUCCAUUACAGAGUCCGUCCGAUCCAUCGAUCUUGCCUGUGAAAUCCAUUUCAAGUGGUUUCAGCAGCCCGAAAACGCAAAAUACAAG
..(((.(((...................))).)))...((((....))))((((((((((((.((((.....))))))))).))).........))))........ ( -19.41)
>consensus
CCCCGUCUCACAAAUUAGCUCCAUUACAUCGCUCGAACGAUCCAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAAAAACGCAAAAUACAAA
.................((...................((((....))))..((((((..(((((((.....)))))))..)))))).......)).......... (-18.94 = -19.50 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,568,116 – 20,568,222
Length 106
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 92.45
Mean single sequence MFE -29.05
Consensus MFE -25.14
Energy contribution -25.45
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -3.39
Structure conservation index 0.87
SVM decision value 2.09
SVM RNA-class probability 0.987783
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20568116 106 + 23771897
UUGAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAAAAACGCAAAAUACAAAAUACCCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACC
............((((((..(((((((.....)))))))..))))))......(((..(.(((((.......))))).)..)))....((((....))))...... ( -28.00)
>DroSec_CAF1 12896 106 + 1
UCCAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAGAAACGCAAAAUACAAACCCCUCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACC
........(((.((((((..(((((((.....)))))))..)))))).)))..(((..(.(((((.......))))).)..)))....((((....))))...... ( -31.20)
>DroSim_CAF1 6552 106 + 1
UCCAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAGAAACGAAAAAUACAAACCCCUCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACC
...((((.(((.((((((..(((((((.....)))))))..)))))).))).........(((((.......))))).....))))..((((....))))...... ( -29.90)
>DroEre_CAF1 6460 104 + 1
UCCAUCGAUCUUGCCUGUGAAAUCCAUUUCAAGUGGUUUCAGCAGCCCGAAAACGCAAAAUACAAGCCC--CUUGUAUUGGGCGAUACUCUCACUUGAGAAUAACC
....(((...((((...(((((.((((.....)))))))))))))..)))...(((..((((((((...--))))))))..)))....((((....))))...... ( -27.10)
>consensus
UCCAUCGAUCUUGGCUGUGAAAACCAUUUCAAGUGGUUUCAGCAGCCCAAAAACGCAAAAUACAAACCCCUCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACC
...((((.((..((((((..(((((((.....)))))))..)))))).............(((((.......)))))..)).))))..((((....))))...... (-25.14 = -25.45 +   0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,568,116 – 20,568,222
Length 106
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 92.45
Mean single sequence MFE -31.45
Consensus MFE -28.45
Energy contribution -28.57
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.77
Structure conservation index 0.90
SVM decision value 0.91
SVM RNA-class probability 0.879267
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20568116 106 - 23771897
GGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGGGUAUUUUGUAUUUUGCGUUUUUGGGCUGCUGAAACCACUUGAAAUGGUUUUCACAGCCAAGAUCGAUCAA
((((((((((....))))))..(((..((((((((.....))))))))..)))......(((((..(((((((.......)))))))..)))))..))))...... ( -31.60)
>DroSec_CAF1 12896 106 - 1
GGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGGUUUGUAUUUUGCGUUUCUGGGCUGCUGAAACCACUUGAAAUGGUUUUCACAGCCAAGAUCGAUGGA
...(((((((....))))))).(((..((((((((.....))))))))..)))..(((.(((((..(((((((.......)))))))..))))).)))........ ( -33.70)
>DroSim_CAF1 6552 106 - 1
GGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGGUUUGUAUUUUUCGUUUCUGGGCUGCUGAAACCACUUGAAAUGGUUUUCACAGCCAAGAUCGAUGGA
(((.((((((....)))))))))....((((((((.....))))))))..(((..(((.(((((..(((((((.......)))))))..))))).))).))).... ( -31.60)
>DroEre_CAF1 6460 104 - 1
GGUUAUUCUCAAGUGAGAGUAUCGCCCAAUACAAG--GGGCUUGUAUUUUGCGUUUUCGGGCUGCUGAAACCACUUGAAAUGGAUUUCACAGGCAAGAUCGAUGGA
(((.((((((....)))))))))((((........--))))(((.((((((((.((((((....)))))).).(((((((....))))).)))))))))))).... ( -28.90)
>consensus
GGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGGUUUGUAUUUUGCGUUUCUGGGCUGCUGAAACCACUUGAAAUGGUUUUCACAGCCAAGAUCGAUGGA
...(((((((....))))))).(((..((((((((.....))))))))..)))..(((.(((((.((((((((.......))).)))))))))).)))........ (-28.45 = -28.57 +   0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,568,142 – 20,568,262
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -29.41
Consensus MFE -24.83
Energy contribution -25.20
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.99
Structure conservation index 0.84
SVM decision value 0.78
SVM RNA-class probability 0.850058
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20568142 120 + 23771897
UUUCAAGUGGUUUCAGCAGCCCAAAAACGCAAAAUACAAAAUACCCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACCCUAGAGUCGUCGUUUGCUACACGAGUUGCCCAAAUCACUU
....(((((((((..(((((.......(((..(.(((((.......))))).)..)))....((((....))))............((((.((.....)))))))))))..))))))))) ( -27.00)
>DroSec_CAF1 12922 120 + 1
UUUCAAGUGGUUUCAGCAGCCCAGAAACGCAAAAUACAAACCCCUCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACCCUAGAGUCGUCGUUUGCUACACGAGUUGCCCAAAUCACUU
....(((((((((..(((((........)).............(((.((((..((((((((((((.................))))).)))))))..)))).))).)))..))))))))) ( -29.43)
>DroSim_CAF1 6578 120 + 1
UUUCAAGUGGUUUCAGCAGCCCAGAAACGAAAAAUACAAACCCCUCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACCCUAGAGUCGUCGUUUGCUACACGAGUUGCCCGAAUCACUU
....(((((((((..(((((.(......)...............((.((((..((((((((((((.................))))).)))))))..)))).)))))))..))))))))) ( -27.73)
>DroEre_CAF1 6486 115 + 1
UUUCAAGUGGUUUCAGCAGCCCGAAAACGCAAAAUACAAGCCC--CUUGUAUUGGGCGAUACUCUCACUUGAGAAUAACCCUAGAGUC---GUUUGCUACACGAGUUGCCCAAAUCACUU
....(((((((((..(((((.((.....((((((((((((...--))))))))(((..((.(((......))).))..))).......---..))))....)).)))))..))))))))) ( -33.50)
>consensus
UUUCAAGUGGUUUCAGCAGCCCAAAAACGCAAAAUACAAACCCCUCUUGUACUGAGCGAUACUCUCACUUGAGAAUAACCCUAGAGUCGUCGUUUGCUACACGAGUUGCCCAAAUCACUU
....(((((((((..(((((.(............(((((.......)))))..((((((((((((.................))))).))))))).......).)))))..))))))))) (-24.83 = -25.20 +   0.38)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,568,142 – 20,568,262
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -35.97
Consensus MFE -34.08
Energy contribution -33.83
Covariance contribution -0.25
Combinations/Pair 1.10
Mean z-score -1.63
Structure conservation index 0.95
SVM decision value 0.79
SVM RNA-class probability 0.851118
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20568142 120 - 23771897
AAGUGAUUUGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGGGUAUUUUGUAUUUUGCGUUUUUGGGCUGCUGAAACCACUUGAAA
(((((.(((.((((.((((....(((((..((((.....(((((((((((....)))))))..))))(((((....)))))))))..))))).....)))).)))).))).))))).... ( -35.50)
>DroSec_CAF1 12922 120 - 1
AAGUGAUUUGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGGUUUGUAUUUUGCGUUUCUGGGCUGCUGAAACCACUUGAAA
(((((.(((.((((....((.(((.(((((.(((.....(((((((((((....)))))))..))))((((((((.....))))))))))))))))))).)))))).))).))))).... ( -35.30)
>DroSim_CAF1 6578 120 - 1
AAGUGAUUCGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGGUUUGUAUUUUUCGUUUCUGGGCUGCUGAAACCACUUGAAA
(((((.((..((((....((.(((.((((((........(((((((((((....)))))))..))))((((((((.....))))))))..))))))))).))))))..)).))))).... ( -32.40)
>DroEre_CAF1 6486 115 - 1
AAGUGAUUUGGGCAACUCGUGUAGCAAAC---GACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCCCAAUACAAG--GGGCUUGUAUUUUGCGUUUUCGGGCUGCUGAAACCACUUGAAA
(((((.(((.((((.((((....((((..---.......(((((((((((....)))))))..))))((((((((--...)))))))))))).....)))).)))).))).))))).... ( -40.70)
>consensus
AAGUGAUUUGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGGUUUGUAUUUUGCGUUUCUGGGCUGCUGAAACCACUUGAAA
(((((.(((.((((.((((....((((............(((((((((((....)))))))..))))((((((((.....)))))))))))).....)))).)))).))).))))).... (-34.08 = -33.83 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,568,182 – 20,568,302
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.54
Mean single sequence MFE -34.62
Consensus MFE -28.46
Energy contribution -30.18
Covariance contribution 1.72
Combinations/Pair 1.08
Mean z-score -1.40
Structure conservation index 0.82
SVM decision value 0.06
SVM RNA-class probability 0.562693
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20568182 120 - 23771897
AUCGUCGUCGGCUUUCAAGGGUUUCUCAAGCGAUUUUCAUAAGUGAUUUGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGGGUAU
.(((((((..(((..((.(((((.((((((..((((....))))..)))))).))))).)).)))..))))))).....(((((((((((....)))))))..)))).((((....)))) ( -38.30)
>DroSec_CAF1 12962 120 - 1
AUCGUCGUCGGUUUUUAAGGGUUUCUCAAGCGAUUUUCAUAAGUGAUUUGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGG
.(((((((..(((.....(((((.((((((..((((....))))..)))))).)))))....)))..)))))))((((((.(.(((((((....))))))).).)).......))))... ( -36.01)
>DroAna_CAF1 34083 107 - 1
AUCGUCGUCUGCUUACAAGGGUUUCUCAAGCGAUUUUCAUAAGUGAUUCGGGCAACUCGUGUAGCAAAC---GACUUAAGGUUUCAUCUCAAGUGAGAGUAUAGUUCAAU----------
...(((((.((((.(((.(((((.((....(((...(((....))).))))).))))).))))))).))---)))...........((((....))))............---------- ( -26.20)
>DroSim_CAF1 6618 120 - 1
AUCGUCGUCGGCUUUCAAGGGUUUCUCAAGCGAUUUUCAUAAGUGAUUCGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAGAGGGG
.(((((((..(((..((.(((((.((....(((...(((....))).))))).))))).)).)))..)))))))((((((.(.(((((((....))))))).).)).......))))... ( -35.41)
>DroEre_CAF1 6526 115 - 1
AUCGUCGUCGGCUUUCAAGGGUUUCUCAAGCGAUUUUUAUAAGUGAUUUGGGCAACUCGUGUAGCAAAC---GACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCCCAAUACAAG--GGG
...(((((..(((..((.(((((.((((((..((((....))))..)))))).))))).)).)))..))---)))....(((((((((((....)))))))..))))........--... ( -37.20)
>consensus
AUCGUCGUCGGCUUUCAAGGGUUUCUCAAGCGAUUUUCAUAAGUGAUUUGGGCAACUCGUGUAGCAAACGACGACUCUAGGGUUAUUCUCAAGUGAGAGUAUCGCUCAGUACAAG_GGGG
.(((((((..(((..((.(((((.((((((..((((....))))..)))))).))))).)).)))..))))))).....(((((((((((....)))))))..))))............. (-28.46 = -30.18 +   1.72)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:51 2006