Locus 5249

Sequence ID 2R_DroMel_CAF1
Location 17,084,355 – 17,084,462
Length 107
Max. P 0.946024
window8384 window8385 window8386

overview

Window 4

Location 17,084,355 – 17,084,449
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 87.36
Mean single sequence MFE -25.50
Consensus MFE -19.44
Energy contribution -19.22
Covariance contribution -0.22
Combinations/Pair 1.10
Mean z-score -2.32
Structure conservation index 0.76
SVM decision value -0.05
SVM RNA-class probability 0.509088
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17084355 94 - 20766785
GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGCAGGCCAAUCCGCUUUGCCCGCCGGCACCAAAUUGCACAGCAACAGCAGCA
((..........(((((((......))))))).((.((((((((.(((.((......))))).).))))......((((...))))))))))). ( -26.00)
>DroVir_CAF1 31682 88 - 1
GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUAUCGCCUGCGGCCAAUCCGUUUUGCCCCCUGGCCACAAAUUGCACAGCGGC------A
............(((((((......))))))).......(((((.(((((....(.....)....))))).))....((...)))))------. ( -20.90)
>DroGri_CAF1 28154 88 - 1
CCACAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUAUGGCCGGCGGCCAAUCCGUUUUGCCCCUUGGCCACAAAUUGCACAGCGGC------A
............(((((((......))))))).....(((((...)))))..(((((.(((...(((....)))...))).))))).------. ( -24.50)
>DroSec_CAF1 21722 94 - 1
GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGCAGGCCAAUCCGCUUUGCCCGCCGGCACCAAAUUGCACAGCAACAGCAGCA
((..........(((((((......))))))).((.((((((((.(((.((......))))).).))))......((((...))))))))))). ( -26.00)
>DroSim_CAF1 21893 94 - 1
GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGCGGGCCAAUCCGCUUUGCCCGCCGGCACCAAAUUGCACAGCAACAGCAGCA
((..........(((((((......))))))).((.((((((((((((.((......))))))).))))......((((...))))))))))). ( -32.10)
>DroYak_CAF1 23713 85 - 1
GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGCAGGCCAAUCCGCUUUGCCCGCCGGCAACAAAUUGCACAGCA---------
(((.........(((((((......))))))).((.(((((.((((((......)).))))..)))))))......)))......--------- ( -23.50)
>consensus
GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGCAGGCCAAUCCGCUUUGCCCGCCGGCAACAAAUUGCACAGCAAC______A
(((.........(((((((......))))))).......(((((.(((.((......))))).).)))).......)))............... (-19.44 = -19.22 +  -0.22)

alignment

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secondary structure

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Window 5

Location 17,084,371 – 17,084,462
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.29
Mean single sequence MFE -27.50
Consensus MFE -15.40
Energy contribution -15.68
Covariance contribution 0.28
Combinations/Pair 1.16
Mean z-score -2.07
Structure conservation index 0.56
SVM decision value 1.36
SVM RNA-class probability 0.946024
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17084371 91 + 20766785
CAAUUUGGUGCCGGCGGGCAAAGCGGAUUGGCCUGCGGCCAGACAUGUGAAUAAAAUUACAUUCACUAUUUUAUAUGC----CACAUGGCU-----------UGUU--------------
(((((((.((((....))))...)))))))(((((.(((.......((((((........))))))..........))----).)).))).-----------....-------------- ( -26.03)
>DroVir_CAF1 31692 96 + 1
CAAUUUGUGGCCAGGGGGCAAAACGGAUUGGCCGCAGGCGAUACAUGUGAAUAAAAUUACAUUCACUAUUUUAUAUGC----CACACAGAU----------ACAUAUAUA----------
.....(((((((((..(......)...)))))))))(((((((...((((((........)))))).....))).)))----)........----------.........---------- ( -24.30)
>DroWil_CAF1 63947 94 + 1
CAAUUUGUGGCCUGCGGGUCCAGCGGAUUGGCCUGGAGCCAUACAUGUGAAUAAAAUUACAUUCACUAUUUUAUAUAGACGAUAUAUG--------------UAUA------------CA
.....((((((.(.((((.((((....)))))))).)))))))...((((((........)))))).....((((((.....))))))--------------....------------.. ( -23.80)
>DroMoj_CAF1 27499 107 + 1
CAAUUUGUGGCCGCGGGGCAAAACGGAUUGGCCGCCGGCCAUACAUGUGAAUAAAAUUACAUUCACUAUUUUAUAUGC----CACAUAGGUAUCCAAACGUACAUAUAUA--------C-
.....((((((((.(.(((...........))).)))))))))...((((((........))))))........((((----(.....))))).................--------.- ( -28.00)
>DroAna_CAF1 24002 93 + 1
CAAUUUGCUGCCGGCGGGGCAAGCGGAUUGGCCUCCGGCCAGACAUGUGAAUAAAAUUACAUUCACUAUUUUAUAUGC----CACAUGGUG-----------UAUAUA------------
.....(((((((((.(((.(((.....))).))))))).))).)).((((((........)))))).....(((((((----(....))))-----------))))..------------ ( -30.20)
>DroPer_CAF1 56005 102 + 1
CAAUUUGUGGGCCGGGGGCAAAGCGGAUUGGCCUGCGGCCAGACAUGUGAAUAAAAUUACAUUCACUAUUUUAUAUGC----CAUAUG--------------UAUAUAGGAGUGUAUUCG
((...(((.(((((.((((.((.....)).)))).)))))..)))..))........(((((((.((((..((((((.----..))))--------------)).))))))))))).... ( -32.70)
>consensus
CAAUUUGUGGCCGGCGGGCAAAGCGGAUUGGCCUCCGGCCAGACAUGUGAAUAAAAUUACAUUCACUAUUUUAUAUGC____CACAUGG_U___________UAUAUA____________
.(((((((.(((....)))...)))))))(((.....)))......((((((........))))))...................................................... (-15.40 = -15.68 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,084,371 – 17,084,462
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.29
Mean single sequence MFE -24.97
Consensus MFE -14.22
Energy contribution -14.17
Covariance contribution -0.05
Combinations/Pair 1.22
Mean z-score -1.87
Structure conservation index 0.57
SVM decision value 0.99
SVM RNA-class probability 0.895765
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17084371 91 - 20766785
--------------AACA-----------AGCCAUGUG----GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGCAGGCCAAUCCGCUUUGCCCGCCGGCACCAAAUUG
--------------....-----------.(((.((((----((.......((.(((((((......))))))))).....))))))((((((......)))...))))))......... ( -26.00)
>DroVir_CAF1 31692 96 - 1
----------UAUAUAUGU----------AUCUGUGUG----GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUAUCGCCUGCGGCCAAUCCGUUUUGCCCCCUGGCCACAAAUUG
----------.........----------.....((((----((..........(((((((......))))))).......((..((((.....))))...))......))))))..... ( -23.30)
>DroWil_CAF1 63947 94 - 1
UG------------UAUA--------------CAUAUAUCGUCUAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUAUGGCUCCAGGCCAAUCCGCUGGACCCGCAGGCCACAAAUUG
((------------((((--------------(((((((.....))))).....(((((((......))))))).)))))((((.(.(((((......))).)).)..)))))))..... ( -21.00)
>DroMoj_CAF1 27499 107 - 1
-G--------UAUAUAUGUACGUUUGGAUACCUAUGUG----GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUAUGGCCGGCGGCCAAUCCGUUUUGCCCCGCGGCCACAAAUUG
-.--------..(((((((((((..((...)).)))).----))))))).....(((((((......))))))).....((((((.(((.(((......)))..)))))))))....... ( -31.40)
>DroAna_CAF1 24002 93 - 1
------------UAUAUA-----------CACCAUGUG----GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGGAGGCCAAUCCGCUUGCCCCGCCGGCAGCAAAUUG
------------......-----------(((...)))----((..........(((((((......))))))).((.(((((.((.(((..........))))))))))))))...... ( -25.00)
>DroPer_CAF1 56005 102 - 1
CGAAUACACUCCUAUAUA--------------CAUAUG----GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUCUGGCCGCAGGCCAAUCCGCUUUGCCCCCGGCCCACAAAUUG
...........(((((..--------------..))))----)...........(((((((......))))))).(((..(((((..(((.((......)))))..))))).)))..... ( -23.10)
>consensus
____________UAUAUA___________A_CCAUGUG____GCAUAUAAAAUAGUGAAUGUAAUUUUAUUCACAUGUAUGGCCGCAGGCCAAUCCGCUUUGCCCCCCGGCCACAAAUUG
.................................(((((.....)))))......(((((((......))))))).(((.(((((...))))).........(((....))).)))..... (-14.22 = -14.17 +  -0.05)

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 11:40:10 2006