Locus 506

Sequence ID 3L_DroMel_CAF1
Location 1,481,368 – 1,481,584
Length 216
Max. P 0.979834
window757 window758 window759 window760 window761

overview

Window 7

Location 1,481,368 – 1,481,485
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.81
Mean single sequence MFE -51.68
Consensus MFE -28.13
Energy contribution -27.80
Covariance contribution -0.33
Combinations/Pair 1.50
Mean z-score -1.65
Structure conservation index 0.54
SVM decision value 0.08
SVM RNA-class probability 0.573944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1481368 117 + 23771897
GGCCAGAAGGGCGGGCGGCGGAAGAGUGGGCACUACCGCCUGUAGAGGUUGCAGGCCAGCAGGAACCCCAAGCAAACUGGGAGCCACCGGAGUUGGUGCCUGGAAUAUUCCGGGCGG
.(((((..((((.((((((((...(((....))).)))))(((((...))))).))).)).((...((((.......))))..)).))....)))))(((((((....))))))).. ( -48.10)
>DroPse_CAF1 167605 117 + 1
GGCCAGCAGAGCAGGCGGCGGCAGUGACGGAACGACGGCCUGCAGAGGCUGGAGUCCCGCGGGCACGCCCAGGAGACUGGGCGUCACUGGGGUCGGAGCCUGGAAGAUUCCAGGAGG
..(((((...((((((.(((............)).).))))))....))))).(.(((.(((..((((((((....))))))))..)))))).)....((((((....))))))... ( -62.90)
>DroWil_CAF1 131039 117 + 1
GGCCAGCAGGGCAGGCGGCGGCAAUGUGGGAGCCACACUUUGCAGUGUGGGCAAACCUGUGGGAACGCCUAACAAACUGGGAGCCACUGCUGUUGGUGGCUGGAAAAUGCCAGGCGG
.(((((((..((((..(((.....(((((...)))))..((.((((.(((((...((....))...)))))....)))).))))).)))))))))))(.((((......)))).).. ( -46.90)
>DroYak_CAF1 133928 117 + 1
GGCCAGAAGAGCUGGCGGCGGAAGAGUAGGCACCACCGCCUGUAGAGGUUGCAGGCCAGCAGGAACUCCAAGCAGACUGGGAGCCACCGGAGUGGGUGCCUGGAAUAUUCCGGGCGG
.(((((.....)))))..(((((...((((((((.((((((((((...)))))))).....((..((((.((....)).))))...))))....)))))))).....)))))..... ( -48.20)
>DroAna_CAF1 135513 117 + 1
GGCCAGGAGGGCGGGCGGAGGCAGAGCCGGAGCGACAGGUUGAAGAGGUUGAAGUCCAGCUGGGACGCCCAACAGACUGGGUGCCACGGCGGAGGGUGCUUGGAAGAUUCCCGGAGG
..((.(((((((..((....))...))).(((((.(((.((....)).)))...(((.((((((.((((((......)))))))).)))))))...)))))......)))).))... ( -41.10)
>DroPer_CAF1 170235 117 + 1
GGCCAGCAGAGCAGGCGGCGGCAGUGACGGAACGACGGCCUGCAGAGGCUGGAGUCCCGCGGGCACGCCCAGGAGACUGGGCGUCACUGGGGUCGGAGCCUGGAAGAUUCCAGGAGG
..(((((...((((((.(((............)).).))))))....))))).(.(((.(((..((((((((....))))))))..)))))).)....((((((....))))))... ( -62.90)
>consensus
GGCCAGCAGAGCAGGCGGCGGCAGAGUCGGAACGACAGCCUGCAGAGGUUGCAGUCCAGCGGGAACGCCCAGCAGACUGGGAGCCACUGGGGUCGGUGCCUGGAAGAUUCCAGGAGG
.(((.(.....).)))(((......(..(((....(.((((....)))).)...)))..)......((((((....))))))))).((((((((...........)))))))).... (-28.13 = -27.80 +  -0.33) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,481,408 – 1,481,507
Length 99
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 79.04
Mean single sequence MFE -43.54
Consensus MFE -20.93
Energy contribution -20.93
Covariance contribution 0.00
Combinations/Pair 1.32
Mean z-score -2.06
Structure conservation index 0.48
SVM decision value -0.00
SVM RNA-class probability 0.533327
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1481408 99 + 23771897
UGUAGAGGUUGCAGGCCAGCAGGAACCCCAAGCAAACUGGGAGCCACCGGAGUUGGUGCCUGGAAUAUUCCGGGCGGCAGAAGAGC------GGGAGCGGCUUGA-
...........((((((.((.((...((((.......))))..)).(((...(((.((((((((....)))))))).))).....)------))..)))))))).- ( -39.70)
>DroPse_CAF1 167645 106 + 1
UGCAGAGGCUGGAGUCCCGCGGGCACGCCCAGGAGACUGGGCGUCACUGGGGUCGGAGCCUGGAAGAUUCCAGGAGGAAGCAGAGCCGCCACAGGAGCGGCUGGCA
.((....(((...(.(((.(((..((((((((....))))))))..)))))).)....((((((....))))))....)))..(((((((....).)))))).)). ( -54.70)
>DroSim_CAF1 125769 99 + 1
UGUAGAGGUUGCAGGCCAGCAGGAACUCCAAGCAAACUGGGAGCCACGGGAGUUGGUGCCUGGAAUAUUCCGGGCGGCAGAAGAGC------AGGAGCGGCUUGG-
...........((((((.((.....((((.((....)).))))((.......(((.((((((((....)))))))).)))......------.)).)))))))).- ( -35.34)
>DroYak_CAF1 133968 99 + 1
UGUAGAGGUUGCAGGCCAGCAGGAACUCCAAGCAGACUGGGAGCCACCGGAGUGGGUGCCUGGAAUAUUCCGGGCGGAAGAAGAGC------AGGAGCGGCUUGA-
...........((((((.((.((....))..((...((((......))))......((((((((....))))))))........))------....)))))))).- ( -34.30)
>DroAna_CAF1 135553 103 + 1
UGAAGAGGUUGAAGUCCAGCUGGGACGCCCAACAGACUGGGUGCCACGGCGGAGGGUGCUUGGAAGAUUCCCGGAGGAAGAAGAGCCGC---CGGAGCGGCCUGUA
...(.((((((...(((.((((((.((((((......)))))))).))))....(((((((......((((....))))...))).)))---)))).)))))).). ( -41.20)
>DroPer_CAF1 170275 106 + 1
UGCAGAGGCUGGAGUCCCGCGGGCACGCCCAGGAGACUGGGCGUCACUGGGGUCGGAGCCUGGAAGAUUCCAGGAGGAAGCAGAGCCGCCACGGGAGCGGCUGGCA
(((..(((((...(.(((.(((..((((((((....))))))))..)))))).)..)))))......((((....)))))))..((((((.(....).))).))). ( -56.00)
>consensus
UGUAGAGGUUGCAGGCCAGCAGGAACGCCAAGCAGACUGGGAGCCACCGGAGUCGGUGCCUGGAAGAUUCCGGGAGGAAGAAGAGC______AGGAGCGGCUUGA_
.....((((((...(((.((.((..((((.((....)).))))...))...)).))).((((((....)))))).......................))))))... (-20.93 = -20.93 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 9

Location 1,481,445 – 1,481,544
Length 99
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 70.92
Mean single sequence MFE -49.43
Consensus MFE -20.48
Energy contribution -22.15
Covariance contribution 1.67
Combinations/Pair 1.29
Mean z-score -1.97
Structure conservation index 0.41
SVM decision value 0.78
SVM RNA-class probability 0.847947
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1481445 99 + 23771897
UGGGAGCCACCGGAGUUGGUGCCUGGAAUAUUCCGGGCGGCAGAAGAGC------------GGGAGCGGCUUGA---GCCAAAGCAGGAUGCAGAGCAGCCGCGGAUGUGGCUG
....((((((.....(((.((((((((....)))))))).)))....((------------((..(((((....---)))...((.....))...))..))))....)))))). ( -43.10)
>DroVir_CAF1 137270 108 + 1
UGGGUCCGCCAAGACCGGGCGCCUGGUAUAUGCCAGGCGGCAGCAGUGC------AGCAGCGGGUGCUGUUGGCACCGCCAGAGCAGGAUGCAAGGCAGCCGCCGAGGUGGCCG
..((((......))))((.((((((((....))).((((((....((((------((((((....)))))).)))).(((...((.....))..))).)))))).))))).)). ( -54.50)
>DroPse_CAF1 167682 108 + 1
UGGGCGUCACUGGGGUCGGAGCCUGGAAGAUUCCAGGAGGAAGCAGAGC------CGCCACAGGAGCGGCUGGCAUGGCCAAGCCCGGAUUGAGGGCAGCCGCCGAUGUGGCAG
..(((....(((...((....((((((....)))))).))...))).))------)((((((...(((((((((...)))..((((.......))))))))))...)))))).. ( -52.00)
>DroWil_CAF1 131116 114 + 1
UGGGAGCCACUGCUGUUGGUGGCUGGAAAAUGCCAGGCGGGAGCAGUGCAGCAGCCGUUACCGGAGCUGUGGGCACGGCCAGAACCGGAUGAAGAGCAGCCGCUGAUGUGGCUG
....((((((....((..(((((((.....((((..((....))...(((((..(((....))).))))).))))(((......))).........)))))))..)))))))). ( -48.30)
>DroAna_CAF1 135590 105 + 1
UGGGUGCCACGGCGGAGGGUGCUUGGAAGAUUCCCGGAGGAAGAAGAGC------CGC---CGGAGCGGCCUGUACUGCGAGGGCGGGAUGCAAGGCAGCCGCUGUGGUUGCCG
..((((((((((((((((.((((((((....)))(((.((........)------).)---))))))).)))...((((....((.....))...))))))))))))).)))). ( -47.40)
>DroPer_CAF1 170312 108 + 1
UGGGCGUCACUGGGGUCGGAGCCUGGAAGAUUCCAGGAGGAAGCAGAGC------CGCCACGGGAGCGGCUGGCAUGGCCAAGCCCGGAUUGAGGGCAGCCGCCGAUGUGGCAG
..(((....(((...((....((((((....)))))).))...))).))------)((((((...(((((((((...)))..((((.......))))))))))...)))))).. ( -51.30)
>consensus
UGGGAGCCACUGGGGUCGGUGCCUGGAAGAUUCCAGGAGGAAGCAGAGC______CGC_ACGGGAGCGGCUGGCACGGCCAAAGCCGGAUGCAGGGCAGCCGCCGAUGUGGCAG
.....(((((...........((((((....))))))............................(((((((.(....((......))......).)))))))....))))).. (-20.48 = -22.15 +   1.67) 

alignment

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secondary structure

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dotplot

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Window 0

Location 1,481,445 – 1,481,544
Length 99
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 70.92
Mean single sequence MFE -42.93
Consensus MFE -14.64
Energy contribution -17.20
Covariance contribution 2.56
Combinations/Pair 1.14
Mean z-score -2.56
Structure conservation index 0.34
SVM decision value 1.85
SVM RNA-class probability 0.979834
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1481445 99 - 23771897
CAGCCACAUCCGCGGCUGCUCUGCAUCCUGCUUUGGC---UCAAGCCGCUCCC------------GCUCUUCUGCCGCCCGGAAUAUUCCAGGCACCAACUCCGGUGGCUCCCA
.((((((....(((((((((..((.....))...)))---...))))))....------------((......)).(((.(((....))).)))..........)))))).... ( -34.70)
>DroVir_CAF1 137270 108 - 1
CGGCCACCUCGGCGGCUGCCUUGCAUCCUGCUCUGGCGGUGCCAACAGCACCCGCUGCU------GCACUGCUGCCGCCUGGCAUAUACCAGGCGCCCGGUCUUGGCGGACCCA
.(((......((((((.(((..((.....))...)))(((((...((((....))))..------)))))))))))((((((......))))))))).(((((....))))).. ( -52.60)
>DroPse_CAF1 167682 108 - 1
CUGCCACAUCGGCGGCUGCCCUCAAUCCGGGCUUGGCCAUGCCAGCCGCUCCUGUGGCG------GCUCUGCUUCCUCCUGGAAUCUUCCAGGCUCCGACCCCAGUGACGCCCA
..((((((..(((((((((((.......))))..(((...))))))))))..))))))(------((.(((..((..((((((....))))))....))...)))....))).. ( -48.00)
>DroWil_CAF1 131116 114 - 1
CAGCCACAUCAGCGGCUGCUCUUCAUCCGGUUCUGGCCGUGCCCACAGCUCCGGUAACGGCUGCUGCACUGCUCCCGCCUGGCAUUUUCCAGCCACCAACAGCAGUGGCUCCCA
.((((((..(((((((((........((((..(((..........)))..))))...)))))))))...((((......((((........)))).....)))))))))).... ( -41.40)
>DroAna_CAF1 135590 105 - 1
CGGCAACCACAGCGGCUGCCUUGCAUCCCGCCCUCGCAGUACAGGCCGCUCCG---GCG------GCUCUUCUUCCUCCGGGAAUCUUCCAAGCACCCUCCGCCGUGGCACCCA
.((...((((.((((.(((.(((..((((((....))......((((((....---)))------)))...........))))......))))))....)))).))))...)). ( -35.20)
>DroPer_CAF1 170312 108 - 1
CUGCCACAUCGGCGGCUGCCCUCAAUCCGGGCUUGGCCAUGCCAGCCGCUCCCGUGGCG------GCUCUGCUUCCUCCUGGAAUCUUCCAGGCUCCGACCCCAGUGACGCCCA
..(((((...(((((((((((.......))))..(((...))))))))))...)))))(------((.(((..((..((((((....))))))....))...)))....))).. ( -45.70)
>consensus
CAGCCACAUCGGCGGCUGCCCUGCAUCCGGCCCUGGCCGUGCCAGCCGCUCCCGU_GCG______GCUCUGCUUCCGCCUGGAAUCUUCCAGGCACCAACCCCAGUGGCACCCA
..(((((....(((((((((..((.....))...)))......))))))............................(((((......)))))...........)))))..... (-14.64 = -17.20 +   2.56) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,481,485 – 1,481,584
Length 99
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 69.88
Mean single sequence MFE -48.55
Consensus MFE -16.51
Energy contribution -16.93
Covariance contribution 0.42
Combinations/Pair 1.32
Mean z-score -1.92
Structure conservation index 0.34
SVM decision value 0.23
SVM RNA-class probability 0.646333
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1481485 99 - 23771897
GCAGUGGUCACUAAGGUGGGUGCAAUGCCAGUGGUUUCGGCAGCCACAUCCGCGGCUGCUCUGCAUCCUGCUUUGGC---UCAAGCCGCUCCC------------GCUCUUCUG
((((((((..((((((((((((((..(((...)))...(((((((.(....).))))))).))))))).))))))).---....))))))...------------))....... ( -37.20)
>DroVir_CAF1 137310 104 - 1
----UUGCCGCCAAAGUGAACGCCAUGCCCGUGGUGAGUGCGGCCACCUCGGCGGCUGCCUUGCAUCCUGCUCUGGCGGUGCCAACAGCACCCGCUGCU------GCACUGCUG
----..(((((((.(((...((((((....))))))((.((((((.(....).))))))))........))).))))))).....(((((...((....------))..))))) ( -43.90)
>DroPse_CAF1 167722 108 - 1
GCAGUGGUCACGAAGGUGGGCAACAUGCCUUUGGUGAAUGCUGCCACAUCGGCGGCUGCCCUCAAUCCGGGCUUGGCCAUGCCAGCCGCUCCUGUGGCG------GCUCUGCUU
((((...((((((((((((....).))))))).))))..(((((((((..(((((((((((.......))))..(((...))))))))))..)))))))------)).)))).. ( -57.80)
>DroWil_CAF1 131156 114 - 1
GCCGUGGUGGCCAAAGUGGGUGCCAUGCCAGUGGUAAGUGCAGCCACAUCAGCGGCUGCUCUUCAUCCGGUUCUGGCCGUGCCCACAGCUCCGGUAACGGCUGCUGCACUGCUC
...(..(..(((...(((((..(...((((((((.(((.((((((.(....).)))))).)))...)))...))))).)..))))).((....))...)))..)..)....... ( -52.20)
>DroAna_CAF1 135630 105 - 1
GCUGUGGUGGCCAAGGUGGGUGCCAUGCCAGUAGUUUCGGCGGCAACCACAGCGGCUGCCUUGCAUCCCGCCCUCGCAGUACAGGCCGCUCCG---GCG------GCUCUUCUU
((((((((.(((..(((....)))..(((.........)))))).)))))))).(((((...((.....))....)))))...((((((....---)))------)))...... ( -46.40)
>DroPer_CAF1 170352 108 - 1
GCAGUGGUCACGAAGGUGGGCAACAUGCCUCUGGUGAAUGCUGCCACAUCGGCGGCUGCCCUCAAUCCGGGCUUGGCCAUGCCAGCCGCUCCCGUGGCG------GCUCUGCUU
((((...((((.(((((((....).))))).).))))..((((((((...(((((((((((.......))))..(((...))))))))))...))))))------)).)))).. ( -53.80)
>consensus
GCAGUGGUCACCAAGGUGGGCGCCAUGCCAGUGGUGAAUGCAGCCACAUCGGCGGCUGCCCUGCAUCCGGCCCUGGCCGUGCCAGCCGCUCCCGU_GCG______GCUCUGCUU
...((((((((....)))........(((.((((.....((((((.(....).)))))).......)).))...))).......)))))......................... (-16.51 = -16.93 +   0.42) 

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 09:43:48 2006