Locus 6530

Sequence ID 3R_DroMel_CAF1
Location 17,234,201 – 17,234,379
Length 178
Max. P 0.999440
window10623 window10624 window10625 window10626 window10627 window10628

overview

Window 3

Location 17,234,201 – 17,234,299
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.35
Mean single sequence MFE -32.48
Consensus MFE -24.14
Energy contribution -25.14
Covariance contribution 1.00
Combinations/Pair 1.09
Mean z-score -2.03
Structure conservation index 0.74
SVM decision value 1.88
SVM RNA-class probability 0.981156
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17234201 98 + 27905053
----------------------AUUGAAAUUAAAAGAAAUCGGUAAAUAAUAGCCUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUAAAGCAGUUCUCUUGCUGCUUGCCGAAGCAGUU
----------------------.................(((((.......(((..((((....))))..))).(((......)))..(((((((......))))))))))))....... ( -28.00)
>DroSec_CAF1 29852 111 + 1
GUUGAGUGCCGUU---------AUUCAAAUUAAAAGAAAUCGGUAAAUAAUAGCUUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUGAAGCAGUUCUGUGGCUGCUUGCCGAAGCAGUU
.(((((((....)---------))))))...........(((((.......(((((((((....))))))))).(((......)))..(((((((......))))))))))))....... ( -34.80)
>DroSim_CAF1 31024 111 + 1
GUUGCGUGCCGCU---------AUUCAAAUUAAAAGAAAUCGGUAAACAAUUGCUUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUGAAGCAGUUCUCUGGCUGCUUGCCGAAGCAGUU
((((..(((((..---------.(((.........)))..)))))..)))).((((((((....))))))))..((.((((...((.((((((((......))))))).).)))))).)) ( -34.80)
>DroEre_CAF1 31662 118 + 1
ACUUAUUGU--UAAUUUAAAACUUUCAGAUUAAAAGUAAUCAGUUAGUAAUGGCAUAACCGCUAGGUGGAGCACGAGUGCGAUCUGUAAAGCAGUUCACUCGCUGCUAGCCGAAGCAGUC
....(((((--(........(((..(.(((((....))))).)..)))..((((....((((...))))((((((((((....(((.....)))..)))))).)))).)))).)))))). ( -32.10)
>DroYak_CAF1 50025 118 + 1
GUUCAUUGU--UCAUUUAAAACUUGUAUAUAAAAAGAAAUCUGUAAGUAAUGGCAUCACCGCUAGGUGGUGCUCGAGUGCGAUCUCUAAAGCAGUUUUCUUGCUGCUCGCCGAAGCAGUC
.........--......................((((((.((((.......(((((((((....))))))))).(((......)))....)))).))))))((((((......)))))). ( -32.70)
>consensus
GUUGAGUGC__UU_________AUUCAAAUUAAAAGAAAUCGGUAAAUAAUAGCAUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUAAAGCAGUUCUCUGGCUGCUUGCCGAAGCAGUU
.......................................(((((((......((((((((....))))))))..(((......)))....(((((......))))))))))))....... (-24.14 = -25.14 +   1.00)

alignment

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secondary structure

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Window 4

Location 17,234,201 – 17,234,299
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.35
Mean single sequence MFE -27.40
Consensus MFE -19.30
Energy contribution -19.66
Covariance contribution 0.36
Combinations/Pair 1.17
Mean z-score -1.28
Structure conservation index 0.70
SVM decision value 0.02
SVM RNA-class probability 0.545259
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17234201 98 - 27905053
AACUGCUUCGGCAAGCAGCAAGAGAACUGCUUUAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAGGCUAUUAUUUACCGAUUUCUUUUAAUUUCAAU----------------------
..((((((....)))))).(((((((.((((........))))....(((..((((....))))..))).............))))))).........---------------------- ( -24.90)
>DroSec_CAF1 29852 111 - 1
AACUGCUUCGGCAAGCAGCCACAGAACUGCUUCAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAAGCUAUUAUUUACCGAUUUCUUUUAAUUUGAAU---------AACGGCACUCAAC
....((....))((((((........))))))..(((......)))(((...((((....))))..((..(((((((..((((......)))))))))---------))..)).)))... ( -28.20)
>DroSim_CAF1 31024 111 - 1
AACUGCUUCGGCAAGCAGCCAGAGAACUGCUUCAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAAGCAAUUGUUUACCGAUUUCUUUUAAUUUGAAU---------AGCGGCACGCAAC
..(((((((((.((((((...(((...((((........)))))))..(((.((((....)))).)))..)))))).)))).(((.........))).---------)))))........ ( -29.80)
>DroEre_CAF1 31662 118 - 1
GACUGCUUCGGCUAGCAGCGAGUGAACUGCUUUACAGAUCGCACUCGUGCUCCACCUAGCGGUUAUGCCAUUACUAACUGAUUACUUUUAAUCUGAAAGUUUUAAAUUA--ACAAUAAGU
(((((((..((..((((.((((((..(((.....)))....))))))))))...)).)))))))..............(((((((((((.....))))))....)))))--......... ( -27.90)
>DroYak_CAF1 50025 118 - 1
GACUGCUUCGGCGAGCAGCAAGAAAACUGCUUUAGAGAUCGCACUCGAGCACCACCUAGCGGUGAUGCCAUUACUUACAGAUUUCUUUUUAUAUACAAGUUUUAAAUGA--ACAAUGAAC
(.((((((....)))))))((((((.(((.....(((......)))(.(((.((((....)))).))))........))).))))))...........((((.....))--))....... ( -26.20)
>consensus
AACUGCUUCGGCAAGCAGCAAGAGAACUGCUUUAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAAGCCAUUAUUUACCGAUUUCUUUUAAUUUGAAU_________AA__ACAAUCAAC
....((....))((((((........))))))..(((......)))..(((.((((....)))).))).................................................... (-19.30 = -19.66 +   0.36)

alignment

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secondary structure

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Window 5

Location 17,234,219 – 17,234,339
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.36
Mean single sequence MFE -39.94
Consensus MFE -28.48
Energy contribution -29.88
Covariance contribution 1.40
Combinations/Pair 1.07
Mean z-score -3.64
Structure conservation index 0.71
SVM decision value 3.60
SVM RNA-class probability 0.999440
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17234219 120 + 27905053
CGGUAAAUAAUAGCCUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUAAAGCAGUUCUCUUGCUGCUUGCCGAAGCAGUUGAUGCGCUGCUUGUCGAAGCAGUUGAUGCACUGCUUGCAC
((((.......(((..((((....))))..))).(((......)))..(((((((......)))))))))))(((((((.(...((((((((....)))))).))...)))))))).... ( -43.80)
>DroSec_CAF1 29883 96 + 1
CGGUAAAUAAUAGCUUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUGAAGCAGUUCUGUGGCUGCUUGCCGAAGCAGUUGAU------------------------GAACUGCUUGCAU
.((((......(((((((((....)))))))))....)))).....(((((((((((...((((((((....))))))))...------------------------))))))))).)). ( -39.90)
>DroSim_CAF1 31055 96 + 1
CGGUAAACAAUUGCUUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUGAAGCAGUUCUCUGGCUGCUUGCCGAAGCAGUUGAU------------------------GAACUGCUUGCAU
.((((.((....((((((((....))))))))....))..))))..(((((((((((..(((((((((....)))))))))..------------------------))))))))).)). ( -40.40)
>DroEre_CAF1 31700 96 + 1
CAGUUAGUAAUGGCAUAACCGCUAGGUGGAGCACGAGUGCGAUCUGUAAAGCAGUUCACUCGCUGCUAGCCGAAGCAGUCGAU------------------------UUACUGCUUGCAU
..((((....))))......((..(((..((((((((((....(((.....)))..)))))).)))).))).(((((((....------------------------..))))))))).. ( -34.40)
>DroYak_CAF1 50063 96 + 1
CUGUAAGUAAUGGCAUCACCGCUAGGUGGUGCUCGAGUGCGAUCUCUAAAGCAGUUUUCUUGCUGCUCGCCGAAGCAGUCGAU------------------------UCACUGCUUGCAU
.((((((((.((((((((((....))))))))((((.(((..((.....((((((......))))))....)).))).)))).------------------------.)).)))))))). ( -41.20)
>consensus
CGGUAAAUAAUAGCAUCACCACUAGGUGGAGCUCGAGUGCUAUCUCUAAAGCAGUUCUCUGGCUGCUUGCCGAAGCAGUUGAU________________________GAACUGCUUGCAU
..((((......((((((((....))))))))((((.((((.((....(((((((......)))))))...)))))).))))................................)))).. (-28.48 = -29.88 +   1.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,234,219 – 17,234,339
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.36
Mean single sequence MFE -33.38
Consensus MFE -22.95
Energy contribution -23.11
Covariance contribution 0.16
Combinations/Pair 1.13
Mean z-score -2.47
Structure conservation index 0.69
SVM decision value 2.02
SVM RNA-class probability 0.985852
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17234219 120 - 27905053
GUGCAAGCAGUGCAUCAACUGCUUCGACAAGCAGCGCAUCAACUGCUUCGGCAAGCAGCAAGAGAACUGCUUUAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAGGCUAUUAUUUACCG
((((.((((((......))))))((...((((((..(.((..((((((....))))))...)))..))))))..))....))))...(((..((((....))))..)))........... ( -40.90)
>DroSec_CAF1 29883 96 - 1
AUGCAAGCAGUUC------------------------AUCAACUGCUUCGGCAAGCAGCCACAGAACUGCUUCAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAAGCUAUUAUUUACCG
.((.(((((((((------------------------.....((((((....)))))).....)))))))))))(((......))).((((.((((....)))).))))........... ( -33.20)
>DroSim_CAF1 31055 96 - 1
AUGCAAGCAGUUC------------------------AUCAACUGCUUCGGCAAGCAGCCAGAGAACUGCUUCAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAAGCAAUUGUUUACCG
.((.(((((((((------------------------.((..((((((....))))))...)))))))))))))(((......)))..(((.((((....)))).)))............ ( -33.30)
>DroEre_CAF1 31700 96 - 1
AUGCAAGCAGUAA------------------------AUCGACUGCUUCGGCUAGCAGCGAGUGAACUGCUUUACAGAUCGCACUCGUGCUCCACCUAGCGGUUAUGCCAUUACUAACUG
..(.(((((((..------------------------....))))))))(((((((.(((((((..(((.....)))....)))))))(((......))).)))).)))........... ( -30.60)
>DroYak_CAF1 50063 96 - 1
AUGCAAGCAGUGA------------------------AUCGACUGCUUCGGCGAGCAGCAAGAAAACUGCUUUAGAGAUCGCACUCGAGCACCACCUAGCGGUGAUGCCAUUACUUACAG
.((.(((.((((.------------------------.((((.(((.((...((((((........))))))....))..))).))))(((.((((....)))).))))))).))).)). ( -28.90)
>consensus
AUGCAAGCAGUGC________________________AUCAACUGCUUCGGCAAGCAGCAAGAGAACUGCUUUAGAGAUAGCACUCGAGCUCCACCUAGUGGUGAAGCCAUUAUUUACCG
.((((((((((..............................)))))))....((((((........))))))........))).....(((.((((....)))).)))............ (-22.95 = -23.11 +   0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,234,259 – 17,234,379
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.27
Mean single sequence MFE -33.37
Consensus MFE -21.26
Energy contribution -21.27
Covariance contribution 0.00
Combinations/Pair 1.08
Mean z-score -2.33
Structure conservation index 0.64
SVM decision value 1.65
SVM RNA-class probability 0.969696
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17234259 120 + 27905053
UAUCUCUAAAGCAGUUCUCUUGCUGCUUGCCGAAGCAGUUGAUGCGCUGCUUGUCGAAGCAGUUGAUGCACUGCUUGCACAUUGCGCUCGCACAGUCAUCAACUGACUACCGGGUAUAUC
........(((((((......))))))).(((.(((((((((((.((((..((.(((.(((((.(.((((.....))))))))))..)))))))))))))))))).))..)))....... ( -42.50)
>DroSec_CAF1 29923 96 + 1
UAUCUCUGAAGCAGUUCUGUGGCUGCUUGCCGAAGCAGUUGAU------------------------GAACUGCUUGCAUAUUGACCUCCUACAGACAUCAACUGACUACCGGGUAUAUC
(((..((((((((((((...((((((((....))))))))...------------------------))))))))).....((((..((.....))..))))........)))..))).. ( -27.40)
>DroSim_CAF1 31095 96 + 1
UAUCUCUGAAGCAGUUCUCUGGCUGCUUGCCGAAGCAGUUGAU------------------------GAACUGCUUGCAUAGUGUCCUCGCAUAGACAUCAACUGACUACCGGGUAUAUC
(((..((((((((((((..(((((((((....)))))))))..------------------------))))))))).....(((((........)))))...........)))..))).. ( -30.20)
>consensus
UAUCUCUGAAGCAGUUCUCUGGCUGCUUGCCGAAGCAGUUGAU________________________GAACUGCUUGCAUAUUGACCUCGCACAGACAUCAACUGACUACCGGGUAUAUC
........(((((((......))))))).(((.((((((((((............................((....))...(((....))).....)))))))).))..)))....... (-21.26 = -21.27 +   0.00)

alignment

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secondary structure

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Window 8

Location 17,234,259 – 17,234,379
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.27
Mean single sequence MFE -34.20
Consensus MFE -19.57
Energy contribution -19.57
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.57
SVM decision value 0.83
SVM RNA-class probability 0.860319
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17234259 120 - 27905053
GAUAUACCCGGUAGUCAGUUGAUGACUGUGCGAGCGCAAUGUGCAAGCAGUGCAUCAACUGCUUCGACAAGCAGCGCAUCAACUGCUUCGGCAAGCAGCAAGAGAACUGCUUUAGAGAUA
.......((((.((.(((((((((.((((.(((((((...)))).((((((......)))))))))....))))..))))))))))))))).((((((........))))))........ ( -43.40)
>DroSec_CAF1 29923 96 - 1
GAUAUACCCGGUAGUCAGUUGAUGUCUGUAGGAGGUCAAUAUGCAAGCAGUUC------------------------AUCAACUGCUUCGGCAAGCAGCCACAGAACUGCUUCAGAGAUA
.............(((.((((((.((.....)).)))))).((.(((((((((------------------------.....((((((....)))))).....)))))))))))..))). ( -29.30)
>DroSim_CAF1 31095 96 - 1
GAUAUACCCGGUAGUCAGUUGAUGUCUAUGCGAGGACACUAUGCAAGCAGUUC------------------------AUCAACUGCUUCGGCAAGCAGCCAGAGAACUGCUUCAGAGAUA
......((((((((.((.....)).)))).)).))...((.((.(((((((((------------------------.((..((((((....))))))...))))))))))))).))... ( -29.90)
>consensus
GAUAUACCCGGUAGUCAGUUGAUGUCUGUGCGAGGACAAUAUGCAAGCAGUUC________________________AUCAACUGCUUCGGCAAGCAGCCAGAGAACUGCUUCAGAGAUA
.......((((.((.((((((((..((.....)).......((....))............................)))))))))))))).((((((........))))))........ (-19.57 = -19.57 +  -0.00)

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 12:23:41 2006