Locus 7577

Sequence ID 3L_DroMel_CAF1
Location 20,367,571 – 20,367,731
Length 160
Max. P 0.994995
window12309 window12310 window12311 window12312

overview

Window 9

Location 20,367,571 – 20,367,691
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.33
Mean single sequence MFE -42.91
Consensus MFE -36.98
Energy contribution -37.77
Covariance contribution 0.78
Combinations/Pair 1.08
Mean z-score -1.96
Structure conservation index 0.86
SVM decision value 0.46
SVM RNA-class probability 0.745575
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20367571 120 + 23771897
CCAUUGGCAGGGACCUCUGCGGUUGCAGCAAGGAUAUCUCAUUUUCGUGGCAGCCUUGAUGGCCUUGGUGUUCAUUAAAUACCUGCCUGAAUGGACUGCCUGGGCUGUAUUGGCUGCCAU
.........(((((((((((....))))..)))...))))......(((((((((...(((((((.((((((((((.............))))))).))).)))))))...))))))))) ( -46.62)
>DroYak_CAF1 21330 120 + 1
CCAUUGGCAGGGCCCUCUGCGGUUGCAGCAAGGAUAUCUUAUUUUUGUGGCAGCCCUAAUGGCUUUGGUGUUCAUAAAAUACCUGCCUGAAUGGACUGCCUGGGCUGUAUUGGCUGCCAU
....(((((((((((...((((((((.(((((((((...))))))))).))))))(((..(((...((((((.....)))))).)))....)))...))..))))).......)))))). ( -45.51)
>DroAna_CAF1 8841 120 + 1
ACAUUGGCAGGGUCCCCUGAGGUUACAGCAGGGAUAUCUCAUAUUUGUGGCUGCCCUAAUGGCUUUGGUAUUUAUCAAAUACCUACCGGAAUGGACGGCCUGGGCUGUAUUGGCUGCAAU
..((((.((((....)))).(((((((((.(((....)))........(((((.((...(((....((((((.....))))))..)))....)).)))))...))))))...))).)))) ( -36.60)
>consensus
CCAUUGGCAGGGACCUCUGCGGUUGCAGCAAGGAUAUCUCAUUUUUGUGGCAGCCCUAAUGGCUUUGGUGUUCAUAAAAUACCUGCCUGAAUGGACUGCCUGGGCUGUAUUGGCUGCCAU
....((((((...((..(((((((...((((((((.....))))))))(((((((.....(((...((((((.....)))))).))).....)).)))))..)))))))..)))))))). (-36.98 = -37.77 +   0.78)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,367,571 – 20,367,691
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.33
Mean single sequence MFE -35.70
Consensus MFE -30.99
Energy contribution -31.67
Covariance contribution 0.67
Combinations/Pair 1.13
Mean z-score -1.70
Structure conservation index 0.87
SVM decision value 0.16
SVM RNA-class probability 0.611875
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20367571 120 - 23771897
AUGGCAGCCAAUACAGCCCAGGCAGUCCAUUCAGGCAGGUAUUUAAUGAACACCAAGGCCAUCAAGGCUGCCACGAAAAUGAGAUAUCCUUGCUGCAACCGCAGAGGUCCCUGCCAAUGG
.((((((......((((...(((((((......(((.(((.(((...))).)))...))).....)))))))........(((.....)))))))..(((.....)))..)))))).... ( -34.70)
>DroYak_CAF1 21330 120 - 1
AUGGCAGCCAAUACAGCCCAGGCAGUCCAUUCAGGCAGGUAUUUUAUGAACACCAAAGCCAUUAGGGCUGCCACAAAAAUAAGAUAUCCUUGCUGCAACCGCAGAGGGCCCUGCCAAUGG
.((((((........((((.((((((((.....(((.(((.(((...))).)))...)))....))))))))....................((((....)))).)))).)))))).... ( -41.30)
>DroAna_CAF1 8841 120 - 1
AUUGCAGCCAAUACAGCCCAGGCCGUCCAUUCCGGUAGGUAUUUGAUAAAUACCAAAGCCAUUAGGGCAGCCACAAAUAUGAGAUAUCCCUGCUGUAACCUCAGGGGACCCUGCCAAUGU
.(((((((.......((((..((((.......)))).((((((.....))))))..........)))).............((......)))))))))...((((....))))....... ( -31.10)
>consensus
AUGGCAGCCAAUACAGCCCAGGCAGUCCAUUCAGGCAGGUAUUUAAUGAACACCAAAGCCAUUAGGGCUGCCACAAAAAUGAGAUAUCCUUGCUGCAACCGCAGAGGACCCUGCCAAUGG
.((((((.............((((((((.....(((.(((.(((...))).)))...)))....))))))))..............((((..((((....))))))))..)))))).... (-30.99 = -31.67 +   0.67)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,367,611 – 20,367,731
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 77.65
Mean single sequence MFE -39.94
Consensus MFE -27.65
Energy contribution -27.99
Covariance contribution 0.34
Combinations/Pair 1.11
Mean z-score -2.46
Structure conservation index 0.69
SVM decision value 2.53
SVM RNA-class probability 0.994995
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20367611 120 + 23771897
AUUUUCGUGGCAGCCUUGAUGGCCUUGGUGUUCAUUAAAUACCUGCCUGAAUGGACUGCCUGGGCUGUAUUGGCUGCCAUUUCUAUUUGGGGUAAGUUUGACACAGCUUGAAGGCCAAGA
......(((((((((...(((((((.((((((((((.............))))))).))).)))))))...))))))))).....(((((..((((((......))))))....))))). ( -44.02)
>DroYak_CAF1 21370 118 + 1
AUUUUUGUGGCAGCCCUAAUGGCUUUGGUGUUCAUAAAAUACCUGCCUGAAUGGACUGCCUGGGCUGUAUUGGCUGCCAUUUCUAUUUGGGGUGAGCUGGAUGCAGCUUUAAGGGU--GG
(((((((.(((((.((....(((...((((((.....)))))).))).....)).))))).(((((((((..(((..(((..(.....)..))))))..).)))))))))))))))--.. ( -43.30)
>DroAna_CAF1 8881 108 + 1
AUAUUUGUGGCUGCCCUAAUGGCUUUGGUAUUUAUCAAAUACCUACCGGAAUGGACGGCCUGGGCUGUAUUGGCUGCAAUUUCCAUUUGGGGUAAGCUUU----------UCUCGU--AG
.(((..(.(((((((((((.((....((((((.....))))))..))((((..(.(((((...........))))))...))))..))))))).))))..----------.)..))--). ( -32.50)
>consensus
AUUUUUGUGGCAGCCCUAAUGGCUUUGGUGUUCAUAAAAUACCUGCCUGAAUGGACUGCCUGGGCUGUAUUGGCUGCCAUUUCUAUUUGGGGUAAGCUUGA__CAGCUU_AAGGGU__GG
......(((((((((...((((((..(((((((((...............)))))).)))..))))))...)))))))))((((....))))............................ (-27.65 = -27.99 +   0.34)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,367,611 – 20,367,731
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 77.65
Mean single sequence MFE -27.87
Consensus MFE -21.47
Energy contribution -21.70
Covariance contribution 0.23
Combinations/Pair 1.11
Mean z-score -1.81
Structure conservation index 0.77
SVM decision value 1.42
SVM RNA-class probability 0.951939
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20367611 120 - 23771897
UCUUGGCCUUCAAGCUGUGUCAAACUUACCCCAAAUAGAAAUGGCAGCCAAUACAGCCCAGGCAGUCCAUUCAGGCAGGUAUUUAAUGAACACCAAGGCCAUCAAGGCUGCCACGAAAAU
..((((((........).)))))..................((((((((......((....))..........(((.(((.(((...))).)))...))).....))))))))....... ( -30.00)
>DroYak_CAF1 21370 118 - 1
CC--ACCCUUAAAGCUGCAUCCAGCUCACCCCAAAUAGAAAUGGCAGCCAAUACAGCCCAGGCAGUCCAUUCAGGCAGGUAUUUUAUGAACACCAAAGCCAUUAGGGCUGCCACAAAAAU
..--........(((((....)))))...............((((((((......((....))..........(((.(((.(((...))).)))...))).....))))))))....... ( -30.10)
>DroAna_CAF1 8881 108 - 1
CU--ACGAGA----------AAAGCUUACCCCAAAUGGAAAUUGCAGCCAAUACAGCCCAGGCCGUCCAUUCCGGUAGGUAUUUGAUAAAUACCAAAGCCAUUAGGGCAGCCACAAAUAU
..--......----------...(((...(((....((((...((.(((...........))).))...))))(((.((((((.....))))))...)))....))).)))......... ( -23.50)
>consensus
CC__ACCCUU_AAGCUG__UCAAGCUUACCCCAAAUAGAAAUGGCAGCCAAUACAGCCCAGGCAGUCCAUUCAGGCAGGUAUUUAAUGAACACCAAAGCCAUUAGGGCUGCCACAAAAAU
.........................................((((((((......((....))..........(((.(((.(((...))).)))...))).....))))))))....... (-21.47 = -21.70 +   0.23)

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 12:50:41 2006