Locus 3768

Sequence ID 2L_DroMel_CAF1
Location 10,981,496 – 10,981,696
Length 200
Max. P 0.923925
window5936 window5937 window5938 window5939 window5940

overview

Window 6

Location 10,981,496 – 10,981,616
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.89
Mean single sequence MFE -37.82
Consensus MFE -24.95
Energy contribution -24.07
Covariance contribution -0.88
Combinations/Pair 1.35
Mean z-score -1.92
Structure conservation index 0.66
SVM decision value 0.34
SVM RNA-class probability 0.694179
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10981496 120 + 22407834
ACGUAAAGUUGAAAAGUCAGAGCAAAAGGAAAUUGAACGAAACGCGGCGCCAUUGGAUGUGGCUUCAAUCUUGGCCAGACGUGUGGCUAUCGAAUUAUCCGAGUCCGAGGAUUCGGAUAG
.((...(((((....(((.(.((...((((..(((((((.....))..(((((.....)))))))))))))).))).)))...)))))..))...((((((((((....)))))))))). ( -35.50)
>DroVir_CAF1 7354 120 + 1
ACGCAAGGUAGAAAAGUCCGAGCUGAAGGAAAUUGAACGCAAUACGGCAAUGCUGGAUGUAGCCUCGAUUUUGGCCAGGCGAGUGGCCAUUGAGCUAUCGGAGUCAGAAGAUUCGGAUAG
.(....)........((((.((((.((.((((((((..((.(((((((...))))..))).)).))))))))(((((......))))).)).))))....(((((....))))))))).. ( -34.40)
>DroGri_CAF1 8415 120 + 1
GCGAAAGGUGGAAAAGUCGGAGCUAAAGGAAAUUGAACGUAAUACGGCAAUGCUGGAUGUGGCCUCAAUAUUGGCCAGGCGAGUGGCCAUCGAGCUGUCGGAGUCGGAGGACUCCGAUAG
((....(((((...(.(((.................((((....((((...)))).))))((((........))))...))).)..)))))..))((((((((((....)))))))))). ( -42.40)
>DroWil_CAF1 9327 120 + 1
GCGAAAGGUGGAGAAAUCCGAGCAAAAGGAAAUUGAACGUAAUACGGCACUUUUGGAUGUGGCAUCUAUAUUGGCAAGACGGGUGGCAAUUGAGUUAUCCGAAUCAGAGGAUUCGGAUAG
((......((((....)))).)).......(((((..(((......((.....((((((...)))))).....))...))).....)))))....((((((((((....)))))))))). ( -31.30)
>DroMoj_CAF1 7648 120 + 1
GCGGAAGGUAGAAAAGUCGGAGUUGAAGGAAAUUGAACGCAAUACGGCAAUGUUGGAUGUGGCAUCGAUUUUGGCCAGGCGAGUGGCCAUUGAGCUGUCGGAGUCGGAAGAUUCCGACAG
((....(((...((((((((.(((.((.....)).)))((.((.((((...)))).))...)).)))))))).))).(((.....))).....))((((((((((....)))))))))). ( -42.30)
>DroAna_CAF1 9325 120 + 1
GCGAAAGGUGGAAAAGUCUGAGCAGAAGGAAUUUGAACGUAAUACGGCACCUUUGGACGUCGCCUCCAUCUUGGCCAGACGCGUGGCAAUUGAACUGUCCGAGUCGGAGGACUCGGACAG
((.(((((((......(((....)))...........((.....)).))))))).(.(((((((........)))..)))))...)).......(((((((((((....))))))))))) ( -41.00)
>consensus
GCGAAAGGUGGAAAAGUCCGAGCAAAAGGAAAUUGAACGUAAUACGGCAAUGUUGGAUGUGGCCUCAAUAUUGGCCAGACGAGUGGCCAUUGAGCUAUCCGAGUCGGAGGAUUCGGAUAG
...................((((..............((.....))(((........))).)).)).....((((((......)))))).....(((((((((((....))))))))))) (-24.95 = -24.07 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,981,536 – 10,981,656
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.39
Mean single sequence MFE -43.30
Consensus MFE -29.80
Energy contribution -28.80
Covariance contribution -1.00
Combinations/Pair 1.50
Mean z-score -2.36
Structure conservation index 0.69
SVM decision value 0.62
SVM RNA-class probability 0.800889
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10981536 120 + 22407834
AACGCGGCGCCAUUGGAUGUGGCUUCAAUCUUGGCCAGACGUGUGGCUAUCGAAUUAUCCGAGUCCGAGGAUUCGGAUAGCGAAGACGACAGCGAGGGCUGGAUGGAACCGAACGAAACA
....(((.(((((.....)))))(((.((((.((((...(((((.(((.(((...((((((((((....)))))))))).))))).).))).))..)))))))).))))))......... ( -43.60)
>DroVir_CAF1 7394 120 + 1
AAUACGGCAAUGCUGGAUGUAGCCUCGAUUUUGGCCAGGCGAGUGGCCAUUGAGCUAUCGGAGUCAGAAGAUUCGGAUAGCGAGGAUGACAGCGAGGGAUGGAUGGAACCCAAUGAGACC
.....(((..(((((....((.((((.....((((((......))))))....((((((.(((((....))))).)))))))))).)).))))).(((..........))).....).)) ( -42.10)
>DroGri_CAF1 8455 120 + 1
AAUACGGCAAUGCUGGAUGUGGCCUCAAUAUUGGCCAGGCGAGUGGCCAUCGAGCUGUCGGAGUCGGAGGACUCCGAUAGUGAAGAUGACAGCGAGGGUUGGAUGGAACCGAACGAAACC
....(((....(((.(.(.(((((........))))).)).)))..(((((..((((((((((((....))))))))))))........((((....)))))))))..)))......... ( -48.20)
>DroWil_CAF1 9367 120 + 1
AAUACGGCACUUUUGGAUGUGGCAUCUAUAUUGGCAAGACGGGUGGCAAUUGAGUUAUCCGAAUCAGAGGAUUCGGAUAGUGAAGAUGAUAGCGAGGGUUGGAUGGAACCCAAUGAAACC
......((.....((((((...)))))).....))......(((..((......(((((((((((....)))))))))))...............(((((......)))))..))..))) ( -31.50)
>DroMoj_CAF1 7688 120 + 1
AAUACGGCAAUGUUGGAUGUGGCAUCGAUUUUGGCCAGGCGAGUGGCCAUUGAGCUGUCGGAGUCGGAAGAUUCCGACAGUGAAGAUGACAGCGAGGGUUGGAUGGAAACCAAUGAAACC
.....((...((((((......((((.....((((((......))))))....((((((((((((....))))))))))))...)))).((((....))))........))))))...)) ( -45.70)
>DroAna_CAF1 9365 120 + 1
AAUACGGCACCUUUGGACGUCGCCUCCAUCUUGGCCAGACGCGUGGCAAUUGAACUGUCCGAGUCGGAGGACUCGGACAGCGAUGACGACAGCGAGGGGUGGAUGGAGCCAAACGAGACA
.....(((......((......))(((((((..(((...(((((.(..((((..(((((((((((....)))))))))))))))..).)).)))...))))))))))))).......... ( -48.70)
>consensus
AAUACGGCAAUGUUGGAUGUGGCCUCAAUAUUGGCCAGACGAGUGGCCAUUGAGCUAUCCGAGUCGGAGGAUUCGGAUAGCGAAGAUGACAGCGAGGGUUGGAUGGAACCCAACGAAACC
..((((.((....))..)))).((((.....((((((......))))))((..((((((((((((....))))))))))))...)).......))))....................... (-29.80 = -28.80 +  -1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,981,536 – 10,981,656
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.39
Mean single sequence MFE -36.14
Consensus MFE -20.75
Energy contribution -20.92
Covariance contribution 0.17
Combinations/Pair 1.30
Mean z-score -2.61
Structure conservation index 0.57
SVM decision value 0.35
SVM RNA-class probability 0.698121
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10981536 120 - 22407834
UGUUUCGUUCGGUUCCAUCCAGCCCUCGCUGUCGUCUUCGCUAUCCGAAUCCUCGGACUCGGAUAAUUCGAUAGCCACACGUCUGGCCAAGAUUGAAGCCACAUCCAAUGGCGCCGCGUU
.........((((((.(((..(((..((.(((.((..(((.(((((((.((....)).)))))))...)))..)).)))))...)))...))).)).((((.......)))))))).... ( -34.60)
>DroVir_CAF1 7394 120 - 1
GGUCUCAUUGGGUUCCAUCCAUCCCUCGCUGUCAUCCUCGCUAUCCGAAUCUUCUGACUCCGAUAGCUCAAUGGCCACUCGCCUGGCCAAAAUCGAGGCUACAUCCAGCAUUGCCGUAUU
(((......(((..........)))..((((....((((((((((.((.((....)).)).))))))....((((((......)))))).....)))).......))))...)))..... ( -36.70)
>DroGri_CAF1 8455 120 - 1
GGUUUCGUUCGGUUCCAUCCAACCCUCGCUGUCAUCUUCACUAUCGGAGUCCUCCGACUCCGACAGCUCGAUGGCCACUCGCCUGGCCAAUAUUGAGGCCACAUCCAGCAUUGCCGUAUU
(((.......((((......))))...((((.........((.((((((((....)))))))).))(((((((((((......))))))...)))))........))))...)))..... ( -38.10)
>DroWil_CAF1 9367 120 - 1
GGUUUCAUUGGGUUCCAUCCAACCCUCGCUAUCAUCUUCACUAUCCGAAUCCUCUGAUUCGGAUAACUCAAUUGCCACCCGUCUUGCCAAUAUAGAUGCCACAUCCAAAAGUGCCGUAUU
(((..(...(((((......)))))..((.(((........((((((((((....)))))))))).....((((.((.......)).))))...)))))...........).)))..... ( -25.50)
>DroMoj_CAF1 7688 120 - 1
GGUUUCAUUGGUUUCCAUCCAACCCUCGCUGUCAUCUUCACUGUCGGAAUCUUCCGACUCCGACAGCUCAAUGGCCACUCGCCUGGCCAAAAUCGAUGCCACAUCCAACAUUGCCGUAUU
(((....((((....((((........((((((.........((((((....))))))...))))))....((((((......)))))).....))))......))))....)))..... ( -35.80)
>DroAna_CAF1 9365 120 - 1
UGUCUCGUUUGGCUCCAUCCACCCCUCGCUGUCGUCAUCGCUGUCCGAGUCCUCCGACUCGGACAGUUCAAUUGCCACGCGUCUGGCCAAGAUGGAGGCGACGUCCAAAGGUGCCGUAUU
..........(((.((.........(((((..((((...((((((((((((....))))))))))))......((((......))))...))))..)))))........)).)))..... ( -46.13)
>consensus
GGUUUCAUUGGGUUCCAUCCAACCCUCGCUGUCAUCUUCACUAUCCGAAUCCUCCGACUCCGACAGCUCAAUGGCCACUCGCCUGGCCAAAAUCGAGGCCACAUCCAACAGUGCCGUAUU
((((((..................................((((((((.((....)).)))))))).......((((......)))).......)))))).................... (-20.75 = -20.92 +   0.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,981,576 – 10,981,696
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.33
Mean single sequence MFE -46.25
Consensus MFE -29.40
Energy contribution -28.90
Covariance contribution -0.50
Combinations/Pair 1.38
Mean z-score -3.50
Structure conservation index 0.64
SVM decision value 1.16
SVM RNA-class probability 0.923925
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10981576 120 + 22407834
GUGUGGCUAUCGAAUUAUCCGAGUCCGAGGAUUCGGAUAGCGAAGACGACAGCGAGGGCUGGAUGGAACCGAACGAAACAUCGGCUUGAUCCCUGAUUAACUCGUUAAAGCCUGACAUAA
((((((((.(((...((((((((((....)))))))))).))).......((((((..(.((((.((.((((........)))).)).))))..).....))))))..))))..)))).. ( -42.90)
>DroVir_CAF1 7434 120 + 1
GAGUGGCCAUUGAGCUAUCGGAGUCAGAAGAUUCGGAUAGCGAGGAUGACAGCGAGGGAUGGAUGGAACCCAAUGAGACCUCUGCUUGAUCCCUGAUGGCUUCGGUUAAACCGGAUAAAA
.....((((((..((((((.(((((....))))).))))))..((((.(.(((((((..(.(.(((...))).).)..)))).)))).))))..))))))(((((.....)))))..... ( -46.20)
>DroGri_CAF1 8495 120 + 1
GAGUGGCCAUCGAGCUGUCGGAGUCGGAGGACUCCGAUAGUGAAGAUGACAGCGAGGGUUGGAUGGAACCGAACGAAACCUCCGCUUGAUCUCUGAUGGCUUCGGUUAAGCUGGAUAAAA
.....(((((((.((((((((((((....))))))))))))..((((.(.((((..(((((..((....))..)..))))..))))).)))).)))))))(((((.....)))))..... ( -48.70)
>DroWil_CAF1 9407 120 + 1
GGGUGGCAAUUGAGUUAUCCGAAUCAGAGGAUUCGGAUAGUGAAGAUGAUAGCGAGGGUUGGAUGGAACCCAAUGAAACCUCUGCUUGAUCGCUGAUGGCUUCAUUAAAGCCAGAUAAAA
...((((..........((((((((....))))))))((((((((....(((((((((((......))))).........((.....))))))))....))))))))..))))....... ( -40.40)
>DroMoj_CAF1 7728 120 + 1
GAGUGGCCAUUGAGCUGUCGGAGUCGGAAGAUUCCGACAGUGAAGAUGACAGCGAGGGUUGGAUGGAAACCAAUGAAACCUCUGCUUGAUCCCUGAUGGCUUCGGUUAAGCCGGAUAAAA
.....((((((..((((((((((((....))))))))))))...(((.(.((((((((((((.(....))))))....)))).)))).)))...))))))(((((.....)))))..... ( -50.60)
>DroAna_CAF1 9405 120 + 1
GCGUGGCAAUUGAACUGUCCGAGUCGGAGGACUCGGACAGCGAUGACGACAGCGAGGGGUGGAUGGAGCCAAACGAGACAUCGGCUUGAUCCCUGAUGAACUCGCUCAAGCCGGACCUAA
...((((.((((..(((((((((((....)))))))))))))))......((((((.((.((((.(((((............))))).))))))......))))))...))))....... ( -48.70)
>consensus
GAGUGGCCAUUGAGCUAUCCGAGUCGGAGGAUUCGGAUAGCGAAGAUGACAGCGAGGGUUGGAUGGAACCCAACGAAACCUCUGCUUGAUCCCUGAUGGCUUCGGUUAAGCCGGAUAAAA
....(((((((..((((((((((((....))))))))))))...))))..(((((((..((...(....)...))...)))).))).......................)))........ (-29.40 = -28.90 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,981,576 – 10,981,696
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.33
Mean single sequence MFE -39.22
Consensus MFE -21.42
Energy contribution -21.73
Covariance contribution 0.31
Combinations/Pair 1.23
Mean z-score -3.51
Structure conservation index 0.55
SVM decision value 0.98
SVM RNA-class probability 0.894469
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10981576 120 - 22407834
UUAUGUCAGGCUUUAACGAGUUAAUCAGGGAUCAAGCCGAUGUUUCGUUCGGUUCCAUCCAGCCCUCGCUGUCGUCUUCGCUAUCCGAAUCCUCGGACUCGGAUAAUUCGAUAGCCACAC
........((((.....((.....))..((((..((((((........))))))..))))))))...(((((((.......(((((((.((....)).)))))))...)))))))..... ( -38.10)
>DroVir_CAF1 7434 120 - 1
UUUUAUCCGGUUUAACCGAAGCCAUCAGGGAUCAAGCAGAGGUCUCAUUGGGUUCCAUCCAUCCCUCGCUGUCAUCCUCGCUAUCCGAAUCUUCUGACUCCGAUAGCUCAAUGGCCACUC
.......(((.....)))..(((((..(((((..(((.((((......(((((...)))))..)))))))...))))).((((((.((.((....)).)).))))))...)))))..... ( -36.40)
>DroGri_CAF1 8495 120 - 1
UUUUAUCCAGCUUAACCGAAGCCAUCAGAGAUCAAGCGGAGGUUUCGUUCGGUUCCAUCCAACCCUCGCUGUCAUCUUCACUAUCGGAGUCCUCCGACUCCGACAGCUCGAUGGCCACUC
....................((((((.(((((..((((..((((......((......))))))..))))...)))))..((.((((((((....)))))))).))...))))))..... ( -39.00)
>DroWil_CAF1 9407 120 - 1
UUUUAUCUGGCUUUAAUGAAGCCAUCAGCGAUCAAGCAGAGGUUUCAUUGGGUUCCAUCCAACCCUCGCUAUCAUCUUCACUAUCCGAAUCCUCUGAUUCGGAUAACUCAAUUGCCACCC
.......((((...(((((((((.((.((......)).)))))))))))(((((......)))))................((((((((((....))))))))))........))))... ( -37.60)
>DroMoj_CAF1 7728 120 - 1
UUUUAUCCGGCUUAACCGAAGCCAUCAGGGAUCAAGCAGAGGUUUCAUUGGUUUCCAUCCAACCCUCGCUGUCAUCUUCACUGUCGGAAUCUUCCGACUCCGACAGCUCAAUGGCCACUC
.......(((.....)))..(((((..(((((..(((.((((.....((((.......)))).)))))))...)))....((((((((.((....)).))))))))))..)))))..... ( -36.10)
>DroAna_CAF1 9405 120 - 1
UUAGGUCCGGCUUGAGCGAGUUCAUCAGGGAUCAAGCCGAUGUCUCGUUUGGCUCCAUCCACCCCUCGCUGUCGUCAUCGCUGUCCGAGUCCUCCGACUCGGACAGUUCAAUUGCCACGC
...(((.((((...((((((........((((..((((((........))))))..))))....)))))))))).....((((((((((((....))))))))))))......))).... ( -48.10)
>consensus
UUUUAUCCGGCUUAACCGAAGCCAUCAGGGAUCAAGCAGAGGUUUCAUUGGGUUCCAUCCAACCCUCGCUGUCAUCUUCACUAUCCGAAUCCUCCGACUCCGACAGCUCAAUGGCCACUC
........(((................(((((..(((.((((........(....).......)))))))...)))))..((((((((.((....)).)))))))).......))).... (-21.42 = -21.73 +   0.31)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:42 2006