Locus 8247

Sequence ID 3L_DroMel_CAF1
Location 21,660,454 – 21,660,605
Length 151
Max. P 0.964731
window13487 window13488 window13489

overview

Window 7

Location 21,660,454 – 21,660,568
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.45
Mean single sequence MFE -48.95
Consensus MFE -26.34
Energy contribution -26.98
Covariance contribution 0.64
Combinations/Pair 1.33
Mean z-score -1.80
Structure conservation index 0.54
SVM decision value 0.43
SVM RNA-class probability 0.732195
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21660454 114 + 23771897
UUGAUCGCAAGCG-U-----AGGGCCUGGUGAGGAUUCCCUCGCCGCCGGCGGCGAAGACAGCGAUAUGCCGCUGUCUGUGAGCAGAGAGACGGCAUCCUCCUUGGACACACUACGACGG
.....((....((-(-----((.(((.((.((((((.((.((((((....))))))((((((((......))))))))..............)).)))))))).)).)...))))).)). ( -46.90)
>DroVir_CAF1 22823 111 + 1
UUAAUUGCCGUGG---------CAGCCGGCGAAAAAUCGCGAGCCGCUGGCGGCGAGGACAGCGAUAUACCGCUGUCCGUAAGCACAGAGACAGCAUCCUCCUUGGAUAGGCUGCGACGA
........(((.(---------(((((.((((....)))).....((((.(.((..((((((((......))))))))....))...)...))))((((.....)))).)))))).))). ( -51.70)
>DroEre_CAF1 36725 114 + 1
UUGAUCGAAAGUG-U-----GUGGCCUGGUGAGGAUUCCCUCGCCGCCGGCGGCGAGGACAAUGAUAUGCCGCUGUCCGUGAGCAGAGAUACGGCAUCCUCUUUGGACACGCUGCGGCGG
.....((...(((-(-----(((..(..(.(((((...((((((((....)))))))).........(((((.(((((....)....)))))))))))))).)..).))))).))..)). ( -48.10)
>DroYak_CAF1 45744 114 + 1
UUGAUCGAAAGUG-U-----GUGGCCUGGUGAGGAUUCCCUCGCCGCCGGCGGCGAGGACAACGAUAUGCCGCUGUCUGUGAGCAGAGAGACGGCAUCCUCCUUGGACACACUACGACGG
....(((..((((-(-----((..((.((.(((((...((((((((....)))))))).........(((((((.((((....)))).)).)))))))))))).))))))))).)))... ( -55.70)
>DroMoj_CAF1 25475 111 + 1
UUAAUGGCCGUCG---------CAGCGGGCGAGGAUUCACGCGCCGCCGGCGGCGAUGACAGCGAAAUACCGCUAUCCGUGAGCAGAGAGACGGCAUCCUCUUUCGAGAGGCUGCGACGG
.......((((((---------((((....((((((((((((((((....)))))..((.((((......)))).)))))))((.(.....).))))))))...(....))))))))))) ( -50.30)
>DroAna_CAF1 36287 120 + 1
UUGAUGGCCGUUGCUGCGACAAGAACCGGGGAAGAGCAUCGAUCCGUCGGCGGCGAGGAGAGCGAGAUCCCGCUGUCUGUGUGCAGGGAGACGGCAUCCUCUUUGGACAAACUGCGACGA
((((((..(....((.((........)).))..)..))))))..(((((((((((.(((........))))))))))..(((.(((((((........))))))).)))......)))). ( -41.00)
>consensus
UUGAUCGCAAGUG_U_______GACCUGGUGAGGAUUCCCGCGCCGCCGGCGGCGAGGACAGCGAUAUGCCGCUGUCCGUGAGCAGAGAGACGGCAUCCUCCUUGGACACACUGCGACGG
...........................((((.((....)).))))((((.(.((..((((((((......))))))))....))...)...)))).(((.....)))............. (-26.34 = -26.98 +   0.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,660,454 – 21,660,568
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.45
Mean single sequence MFE -47.12
Consensus MFE -24.33
Energy contribution -24.72
Covariance contribution 0.39
Combinations/Pair 1.32
Mean z-score -2.42
Structure conservation index 0.52
SVM decision value 1.57
SVM RNA-class probability 0.964731
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21660454 114 - 23771897
CCGUCGUAGUGUGUCCAAGGAGGAUGCCGUCUCUCUGCUCACAGACAGCGGCAUAUCGCUGUCUUCGCCGCCGGCGGCGAGGGAAUCCUCACCAGGCCCU-----A-CGCUUGCGAUCAA
..(((((((((((.((...((((((((((.((.((((....)))).)))))).........(((((((((....))))))))).))))))....))...)-----)-))).))))))... ( -48.80)
>DroVir_CAF1 22823 111 - 1
UCGUCGCAGCCUAUCCAAGGAGGAUGCUGUCUCUGUGCUUACGGACAGCGGUAUAUCGCUGUCCUCGCCGCCAGCGGCUCGCGAUUUUUCGCCGGCUG---------CCACGGCAAUUAA
..(..(((((..((((.....)))))))))..).........(((((((((....)))))))))..((((...((((((.((((....)))).)))))---------)..))))...... ( -49.30)
>DroEre_CAF1 36725 114 - 1
CCGCCGCAGCGUGUCCAAAGAGGAUGCCGUAUCUCUGCUCACGGACAGCGGCAUAUCAUUGUCCUCGCCGCCGGCGGCGAGGGAAUCCUCACCAGGCCAC-----A-CACUUUCGAUCAA
..((....))(((.((...(((((((((((...((((....))))..))))).........(((((((((....))))))))).))))))....)).)))-----.-............. ( -43.60)
>DroYak_CAF1 45744 114 - 1
CCGUCGUAGUGUGUCCAAGGAGGAUGCCGUCUCUCUGCUCACAGACAGCGGCAUAUCGUUGUCCUCGCCGCCGGCGGCGAGGGAAUCCUCACCAGGCCAC-----A-CACUUUCGAUCAA
..((((.(((((((((...((((((((((.((.((((....)))).)))))).........(((((((((....))))))))).))))))....))..))-----)-))))..))))... ( -53.60)
>DroMoj_CAF1 25475 111 - 1
CCGUCGCAGCCUCUCGAAAGAGGAUGCCGUCUCUCUGCUCACGGAUAGCGGUAUUUCGCUGUCAUCGCCGCCGGCGGCGCGUGAAUCCUCGCCCGCUG---------CGACGGCCAUUAA
((((((((((.........((((((((.(.....).))(((((((((((((....))))))))..(((((....))))))))))))))))....))))---------))))))....... ( -53.82)
>DroAna_CAF1 36287 120 - 1
UCGUCGCAGUUUGUCCAAAGAGGAUGCCGUCUCCCUGCACACAGACAGCGGGAUCUCGCUCUCCUCGCCGCCGACGGAUCGAUGCUCUUCCCCGGUUCUUGUCGCAGCAACGGCCAUCAA
............((((.....))))(((((....(((((((..(((.(.((((....((((((((((....))).)))..)).))...))))).)))..))).))))..)))))...... ( -33.60)
>consensus
CCGUCGCAGCGUGUCCAAAGAGGAUGCCGUCUCUCUGCUCACAGACAGCGGCAUAUCGCUGUCCUCGCCGCCGGCGGCGAGGGAAUCCUCACCAGGCC_______A_CAACGGCGAUCAA
...................((((((((((.((.((((....)))).)))))))........(((((((((....))))).)))).))))).............................. (-24.33 = -24.72 +   0.39)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,660,488 – 21,660,605
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.71
Mean single sequence MFE -39.62
Consensus MFE -25.91
Energy contribution -25.55
Covariance contribution -0.36
Combinations/Pair 1.33
Mean z-score -1.83
Structure conservation index 0.65
SVM decision value 0.69
SVM RNA-class probability 0.824022
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21660488 117 - 23771897
GAAUCCAAAUAA---UAAAAACCAAACAAAUGGUACGCAGCCGUCGUAGUGUGUCCAAGGAGGAUGCCGUCUCUCUGCUCACAGACAGCGGCAUAUCGCUGUCUUCGCCGCCGGCGGCGA
............---.....((((......)))).(((.((((.((...((((..((..((((......))))..))..))))((((((((....)))))))).....)).)))).))). ( -39.90)
>DroVir_CAF1 22854 115 - 1
UAAUAGACAUAA---AACUAACACA--GCAUGGUACGCAGUCGUCGCAGCCUAUCCAAGGAGGAUGCUGUCUCUGUGCUUACGGACAGCGGUAUAUCGCUGUCCUCGCCGCCAGCGGCUC
............---.........(--((((((...((((.((((....(((.....)))..))))))))..)))))))...(((((((((....)))))))))..((((....)))).. ( -41.30)
>DroEre_CAF1 36759 117 - 1
GAAUCGAAAUAA---UAAAAACCAAACAAAUGGUACGCAGCCGCCGCAGCGUGUCCAAAGAGGAUGCCGUAUCUCUGCUCACGGACAGCGGCAUAUCAUUGUCCUCGCCGCCGGCGGCGA
............---.....((((......)))).....((((((((.(((.(..(((.((..(((((((...((((....))))..))))))).)).)))..).))).).))))))).. ( -44.30)
>DroYak_CAF1 45778 116 - 1
GAAUUGAAAUAA---UAAAA-GCAAACAAAUGGUACGCAGCCGUCGUAGUGUGUCCAAGGAGGAUGCCGUCUCUCUGCUCACAGACAGCGGCAUAUCGUUGUCCUCGCCGCCGGCGGCGA
............---.....-((..((.....))..)).(((((((..(((.(..(((.((..((((((.((.((((....)))).)))))))).)).)))..).)))..).)))))).. ( -40.50)
>DroMoj_CAF1 25506 115 - 1
UAAUAGACAUAA---AACUAACUCA--GCAUGGUACGCAGCCGUCGCAGCCUCUCGAAAGAGGAUGCCGUCUCUCUGCUCACGGAUAGCGGUAUUUCGCUGUCAUCGCCGCCGGCGGCGC
.....(((....---..........--(((((((.....))))).))(((..(((....)))(((((((.((.((((....)))).)))))))))..))))))..(((((....))))). ( -40.50)
>DroAna_CAF1 36327 115 - 1
--AGCUAAAUAACCAUUAAACCCG---AAAUGGUACGUAGUCGUCGCAGUUUGUCCAAAGAGGAUGCCGUCUCCCUGCACACAGACAGCGGGAUCUCGCUCUCCUCGCCGCCGACGGAUC
--.((((....((((((.......---.))))))...))))((((((.((((((....((.(((.......)))))....)))))).((((((........))).))).).))))).... ( -31.20)
>consensus
GAAUCGAAAUAA___UAAAAACCAA__AAAUGGUACGCAGCCGUCGCAGCGUGUCCAAAGAGGAUGCCGUCUCUCUGCUCACAGACAGCGGCAUAUCGCUGUCCUCGCCGCCGGCGGCGA
.......................................((((((((.((.((..((.(((((......))))).))..))..((((((((....))))))))...)).).))))))).. (-25.91 = -25.55 +  -0.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:27 2006