Locus 1099

Sequence ID 3L_DroMel_CAF1
Location 3,212,141 – 3,212,287
Length 146
Max. P 0.968804
window1699 window1700 window1701 window1702

overview

Window 9

Location 3,212,141 – 3,212,247
Length 106
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 72.60
Mean single sequence MFE -38.02
Consensus MFE -11.72
Energy contribution -13.11
Covariance contribution 1.39
Combinations/Pair 1.35
Mean z-score -2.06
Structure conservation index 0.31
SVM decision value -0.00
SVM RNA-class probability 0.533011
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3212141 106 + 23771897
GUUUGUUUACAGCCGAUUCCGCAGAAUCAAUUCUACCCUGGAUUGGUGGCUGGUCCCUGGCCGCCUGGCACUGUAG---CAGCUACUACCGCCCAUGGGCAAAACUUCU
....((((...((((((((....)))))(((((......)))))((((((..(...)..)))))).)))...((((---......)))).(((....))).)))).... ( -33.80)
>DroGri_CAF1 10346 105 + 1
UU----CUGCAGCCCAUUCAGCAGCAGCCGUUCUACGCCGGCCUGAUGGCUGCCCCUUGGCAGACGACUGCUGCUGUGGCAGCCACAGCGGCGCAUGGCCAAAACUUCU
..----..((((((...((((.....((((........)))))))).))))))...(((((.......(((((((((((...)))))))))))....)))))....... ( -43.70)
>DroEre_CAF1 7631 106 + 1
GUUUGCUUACAGCCGAUUCCGCAGAAUCAAUUUUACCCCGGCUUGGUGGCUGGACCCUGGCCGCCUGGCACUGUAG---CAGCCACUGCCGCCCAUGGGCAAAAUUUCU
(.(((((.((((..(((((....)))))............(((.((((((..(...)..)))))).))).))))))---))).)......(((....)))......... ( -37.70)
>DroYak_CAF1 7483 106 + 1
GUUUGUUUACAGCCGAUUCCGCAGAAUCAAUUUUACCCCGGCUUGGUGGCUGGACCCUGGCCGCCUGGCACUGUAG---CAGCCACUGCCGCCCAUGGGCAAAACUUUU
((((...(((((..(((((....)))))............(((.((((((..(...)..)))))).))).)))))(---(((...)))).(((....))).)))).... ( -36.80)
>DroMoj_CAF1 7786 109 + 1
AUCUCUUCGCAGCCCUUUCAGCAGCAACAAUUCUAUACAGGGCUGAUGGCUGCUCCGUGGCAACCGACCACCGUAGCAGCAGCCACAGCGGCGCAGGGCCAAAAUUUUU
...........(((((....((.((......(((....)))((((.(((((((((.(((((....).)))).)....)))))))))))).))))))))).......... ( -35.10)
>DroAna_CAF1 7543 99 + 1
-------CUUAGCCGAUUCAGCAAAAUCAGUUCUAUCCCAGCAUUGUGGCUGGGCCAUGGCCACCGGGAACAGUGG---CAACCACUGCCCCGCAUGGCCAGAACUUCU
-------.......((((......))))((((((..((((((......))))))....(((((.((((..((((((---...)))))).))))..)))))))))))... ( -41.00)
>consensus
GUUUGUUUACAGCCGAUUCAGCAGAAUCAAUUCUACCCCGGCUUGGUGGCUGGACCCUGGCCGCCGGGCACUGUAG___CAGCCACUGCCGCCCAUGGCCAAAACUUCU
...........((((.....((((........((((....((..(((((((((...)))))))))..))...)))).........))))......))).)......... (-11.72 = -13.11 +   1.39) 

alignment

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secondary structure

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dotplot

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Window 0

Location 3,212,141 – 3,212,247
Length 106
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 72.60
Mean single sequence MFE -43.17
Consensus MFE -17.91
Energy contribution -17.27
Covariance contribution -0.63
Combinations/Pair 1.48
Mean z-score -2.37
Structure conservation index 0.41
SVM decision value 1.63
SVM RNA-class probability 0.968804
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3212141 106 - 23771897
AGAAGUUUUGCCCAUGGGCGGUAGUAGCUG---CUACAGUGCCAGGCGGCCAGGGACCAGCCACCAAUCCAGGGUAGAAUUGAUUCUGCGGAAUCGGCUGUAAACAAAC
...((((((((((.(((((.(((((....)---))))...))).((.(((..(....).))).))....))))))))))))(((((....))))).............. ( -34.80)
>DroGri_CAF1 10346 105 - 1
AGAAGUUUUGGCCAUGCGCCGCUGUGGCUGCCACAGCAGCAGUCGUCUGCCAAGGGGCAGCCAUCAGGCCGGCGUAGAACGGCUGCUGCUGAAUGGGCUGCAG----AA
.........(((.....))).(((..((..(((((((((((((((((((((....))).(((........)))..)).)))))))))))))..)))))..)))----.. ( -49.50)
>DroEre_CAF1 7631 106 - 1
AGAAAUUUUGCCCAUGGGCGGCAGUGGCUG---CUACAGUGCCAGGCGGCCAGGGUCCAGCCACCAAGCCGGGGUAAAAUUGAUUCUGCGGAAUCGGCUGUAAGCAAAC
...((((((((((...(((((((.((....---...)).)))).((.(((..(....).))).))..))).))))))))))(((((....))))).((.....)).... ( -40.90)
>DroYak_CAF1 7483 106 - 1
AAAAGUUUUGCCCAUGGGCGGCAGUGGCUG---CUACAGUGCCAGGCGGCCAGGGUCCAGCCACCAAGCCGGGGUAAAAUUGAUUCUGCGGAAUCGGCUGUAAACAAAC
...((((((((((...(((((((.((....---...)).)))).((.(((..(....).))).))..))).))))))))))(((((....))))).............. ( -39.70)
>DroMoj_CAF1 7786 109 - 1
AAAAAUUUUGGCCCUGCGCCGCUGUGGCUGCUGCUACGGUGGUCGGUUGCCACGGAGCAGCCAUCAGCCCUGUAUAGAAUUGUUGCUGCUGAAAGGGCUGCGAAGAGAU
........((((.(((.(((((((((((....))))))))))))))..))))....((((((.(((((...(((.........))).)))))...))))))........ ( -46.40)
>DroAna_CAF1 7543 99 - 1
AGAAGUUCUGGCCAUGCGGGGCAGUGGUUG---CCACUGUUCCCGGUGGCCAUGGCCCAGCCACAAUGCUGGGAUAGAACUGAUUUUGCUGAAUCGGCUAAG-------
...((((((((((((.(((((((((((...---)))))).)))))))))))....((((((......))))))..))))))(((((....))))).......------- ( -47.70)
>consensus
AGAAGUUUUGCCCAUGCGCGGCAGUGGCUG___CUACAGUGCCAGGCGGCCAGGGACCAGCCACCAAGCCGGGGUAGAAUUGAUUCUGCGGAAUCGGCUGUAAACAAAC
...........((.((.((.((....((((......)))).....)).)))).))..(((((.......((((((.......)))))).......)))))......... (-17.91 = -17.27 +  -0.63) 

alignment

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secondary structure

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dotplot

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Window 1

Location 3,212,170 – 3,212,287
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.52
Mean single sequence MFE -44.72
Consensus MFE -11.92
Energy contribution -13.90
Covariance contribution 1.97
Combinations/Pair 1.26
Mean z-score -2.61
Structure conservation index 0.27
SVM decision value 0.63
SVM RNA-class probability 0.805079
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3212170 117 + 23771897
AUUCUACCCUGGAUUGGUGGCUGGUCCCUGGCCGCCUGGCACUGUAG---CAGCUACUACCGCCCAUGGGCAAAACUUCUACGAGCUCGGAGGAAACAUAUUUACCACCAAUCCUUUACC
..........((((((((((..(((.....))).((.(((...((((---......)))).(((....))).............))).)).(....).......))))))))))...... ( -37.50)
>DroPse_CAF1 27234 114 + 1
AUUCUAUCCCGGCUUGAUGGCUGGUCCAUGGCCACCCGGCACUGUGA------CCGCUGCCGGCCACGGCCAGAACUUCUAUGAGAUUGGUGGCAACAUCUAUGCCACCAAUCCGUUGGC
........((((((....)))))).((((((((..((((((.((...------.)).))))))....)))))........(((.(((((((((((.......))))))))))))))))). ( -48.70)
>DroGri_CAF1 10371 120 + 1
GUUCUACGCCGGCCUGAUGGCUGCCCCUUGGCAGACGACUGCUGCUGUGGCAGCCACAGCGGCGCAUGGCCAAAACUUCUAUGAGAUUGGUGGCAAUAUAUUUGCAACCAAUGGGCUAGC
.......((((..(((.(((((((((..((((((....))))))..).)))))))))))))))((.(((((....(((....)))((((((.((((.....)))).)))))).))))))) ( -52.50)
>DroEre_CAF1 7660 117 + 1
AUUUUACCCCGGCUUGGUGGCUGGACCCUGGCCGCCUGGCACUGUAG---CAGCCACUGCCGCCCAUGGGCAAAAUUUCUACGACCUGGGAGGAAACAUCUUUACCACCAAUCCUUUAGC
..........((.(((((((..((((((.((.((...((((.((...---....)).))))(((....)))..........)).)).))).(....).)))...))))))).))...... ( -38.60)
>DroYak_CAF1 7512 117 + 1
AUUUUACCCCGGCUUGGUGGCUGGACCCUGGCCGCCUGGCACUGUAG---CAGCCACUGCCGCCCAUGGGCAAAACUUUUACGAGCUCGGAGGAAACAUCUUUACCACCAAUCCUUUGGC
......(((((((((((((((((.((....(((....)))...))..---)))))))....(((....)))..........))))).))).))..............((((....)))). ( -41.30)
>DroMoj_CAF1 7815 120 + 1
AUUCUAUACAGGGCUGAUGGCUGCUCCGUGGCAACCGACCACCGUAGCAGCAGCCACAGCGGCGCAGGGCCAAAAUUUUUAUGAAUUUGGUGGCAAUAUAUUUGCUGCCAAUGGCCUGGC
............((((.(((((((((.(((((....).)))).)....))))))))))))...((.((((((((((((....))))))((..((((.....))))..))..)))))).)) ( -49.70)
>consensus
AUUCUACCCCGGCUUGAUGGCUGGUCCCUGGCCGCCUGGCACUGUAG___CAGCCACUGCCGCCCAUGGCCAAAACUUCUACGAGCUUGGAGGAAACAUAUUUACCACCAAUCCUUUAGC
..........(((....((((((.......(((....)))..........))))))..)))(((....))).................((.((...........)).))........... (-11.92 = -13.90 +   1.97) 

alignment

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secondary structure

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dotplot

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Window 2

Location 3,212,170 – 3,212,287
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.52
Mean single sequence MFE -46.62
Consensus MFE -18.11
Energy contribution -19.78
Covariance contribution 1.67
Combinations/Pair 1.38
Mean z-score -2.32
Structure conservation index 0.39
SVM decision value 0.94
SVM RNA-class probability 0.886868
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3212170 117 - 23771897
GGUAAAGGAUUGGUGGUAAAUAUGUUUCCUCCGAGCUCGUAGAAGUUUUGCCCAUGGGCGGUAGUAGCUG---CUACAGUGCCAGGCGGCCAGGGACCAGCCACCAAUCCAGGGUAGAAU
......(((((((((((.....((.((((((((.((.(((((.(((((((((....)))))....)))).---)))).).))....)))..))))).))))))))))))).......... ( -42.80)
>DroPse_CAF1 27234 114 - 1
GCCAACGGAUUGGUGGCAUAGAUGUUGCCACCAAUCUCAUAGAAGUUCUGGCCGUGGCCGGCAGCGG------UCACAGUGCCGGGUGGCCAUGGACCAGCCAUCAAGCCGGGAUAGAAU
......((((((((((((.......)))))))))))).......((((((((.(((((((....)))------))))......((.((((....).))).)).....))))))))..... ( -51.80)
>DroGri_CAF1 10371 120 - 1
GCUAGCCCAUUGGUUGCAAAUAUAUUGCCACCAAUCUCAUAGAAGUUUUGGCCAUGCGCCGCUGUGGCUGCCACAGCAGCAGUCGUCUGCCAAGGGGCAGCCAUCAGGCCGGCGUAGAAC
(((((..(.(((((.((((.....)))).)))))((.....)).)..)))))..((((((((((((((((((.(....((((....))))....))))))))).)))..))))))).... ( -49.50)
>DroEre_CAF1 7660 117 - 1
GCUAAAGGAUUGGUGGUAAAGAUGUUUCCUCCCAGGUCGUAGAAAUUUUGCCCAUGGGCGGCAGUGGCUG---CUACAGUGCCAGGCGGCCAGGGUCCAGCCACCAAGCCGGGGUAAAAU
(((...((.((((((((...((....))..(((.((((((.........(((....)))((((.((....---...)).))))..)))))).)))....)))))))).))..)))..... ( -47.30)
>DroYak_CAF1 7512 117 - 1
GCCAAAGGAUUGGUGGUAAAGAUGUUUCCUCCGAGCUCGUAAAAGUUUUGCCCAUGGGCGGCAGUGGCUG---CUACAGUGCCAGGCGGCCAGGGUCCAGCCACCAAGCCGGGGUAAAAU
(((...((.((((((((.....((..((((..(.((.(((.........(((....)))((((.((....---...)).))))..))))))))))..)))))))))).))..)))..... ( -44.20)
>DroMoj_CAF1 7815 120 - 1
GCCAGGCCAUUGGCAGCAAAUAUAUUGCCACCAAAUUCAUAAAAAUUUUGGCCCUGCGCCGCUGUGGCUGCUGCUACGGUGGUCGGUUGCCACGGAGCAGCCAUCAGCCCUGUAUAGAAU
((..(((((.((((((........))))))..(((((......))))))))))..))(((((((((((....))))))))))).((((((......)))))).................. ( -44.10)
>consensus
GCCAAAGGAUUGGUGGCAAAGAUGUUGCCACCAAGCUCAUAGAAGUUUUGCCCAUGGGCGGCAGUGGCUG___CUACAGUGCCAGGCGGCCAGGGACCAGCCACCAAGCCGGGGUAGAAU
......((.((((((((.............(.(((((......))))).).((.(((.((.(.(..((((......))))..).).)).))).))....)))))))).)).......... (-18.11 = -19.78 +   1.67) 

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 09:59:01 2006