Locus 8709

Sequence ID 3R_DroMel_CAF1
Location 23,285,133 – 23,285,368
Length 235
Max. P 0.977681
window13982 window13983 window13984 window13985

overview

Window 2

Location 23,285,133 – 23,285,227
Length 94
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 79.24
Mean single sequence MFE -19.70
Consensus MFE -13.97
Energy contribution -15.63
Covariance contribution 1.67
Combinations/Pair 1.00
Mean z-score -3.18
Structure conservation index 0.71
SVM decision value 1.80
SVM RNA-class probability 0.977681
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23285133 94 + 27905053
CCGGGUUGGCUUUU-GCAAAAGUGCAGUGAACAUUUUCAUUGCAAUUAAAUUUAGCACUAAAAGUUGGCAACAAAAAA-AAAAA--AAAAAAAGAAGG-
....((..((((((-((.(((.(((((((((....)))))))))......))).)))...)))))..)).........-.....--............- ( -21.20)
>DroGri_CAF1 96514 83 + 1
ACAAG-UUGCCACU-G--CAAGUGGA-UGAAAAUUUUCAUUGCAAUUAAAUUUAGCACAAAAAGUUUCCAAAAAAAAAGGGAAAUAA-----------A
...((-(((((((.-.--...)))((-((((....))))))))))))................((((((..........))))))..-----------. ( -14.50)
>DroSec_CAF1 82794 96 + 1
CCGGGUUGGCUUUU-GCAAAAGUGCAGUGAACAUUUUCAUUGCAAUUAAAUUUAGCACAAAAAGUUGGCAACAAAAAA-AAAAAUAAAAAAAGGAAGG-
....((..((((((-((.(((.(((((((((....)))))))))......))).)))...)))))..)).........-...................- ( -21.20)
>DroSim_CAF1 85934 96 + 1
CCGGGUUGGCUUUU-GCAAAAGUGCAGUGAACAUUUUCAUUGCAAUUAAAUUUAGCACAAAAAGUUGGCAACAAAAAA-AAAAAUAAAAAAAGGAAGG-
....((..((((((-((.(((.(((((((((....)))))))))......))).)))...)))))..)).........-...................- ( -21.20)
>DroEre_CAF1 88340 74 + 1
------UGGCUUUU-GCGAAAGUGCAGUGAACAUUUUCAUUGCAAUUAAAUUUAGCACAAAAAGUUGGCAACAA-------------AAA----AAGG-
------(((((...-((....))((((((((....))))))))..........))).)).....(((....)))-------------...----....- ( -17.10)
>DroYak_CAF1 85399 93 + 1
CCGGGUUGGCUUUUGGCGAAAGUGCAGUGAACAUUUUCAUUGCAAUUAAAUUUAGCACAAAAAGUUGGCAACAGAGAA-AAAAAAAGAAA----AAGG-
....((..((((((.((.(((.(((((((((....)))))))))......))).))...))))))..)).........-...........----....- ( -23.00)
>consensus
CCGGGUUGGCUUUU_GCAAAAGUGCAGUGAACAUUUUCAUUGCAAUUAAAUUUAGCACAAAAAGUUGGCAACAAAAAA_AAAAAUAAAAA____AAGG_
....((..((((((.((.(((.(((((((((....)))))))))......))).))...))))))..)).............................. (-13.97 = -15.63 +   1.67)

alignment

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secondary structure

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Window 3

Location 23,285,199 – 23,285,303
Length 104
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 74.85
Mean single sequence MFE -19.59
Consensus MFE -14.90
Energy contribution -15.73
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.05
Structure conservation index 0.76
SVM decision value 0.76
SVM RNA-class probability 0.842509
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23285199 104 - 27905053
UAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGCCACUGACAGUAACAUGACAUCUUUCUC--CCUUCU---UUUUUU--UU--UUU-U--UUUUUGUUGC
..((((((((.((.((((....))))...))(((...--....))).))))))))....((((((.............--......---......--..--...-.--....)))))) ( -21.85)
>DroGri_CAF1 96576 98 - 1
UAAGUGGCAAUGCAAACGGCAACAUUUUGGCGAGCAC--UUUUCUCUGUGCCACUGACAGUUACACGACAUUCGUUUUUU--------------UUAUU--UCCCU--UUUUUUUUGG
...(((((..(((.....))).....(..(.(.((((--........))))).)..)..)))))(((.....))).....--------------.....--.....--.......... ( -16.00)
>DroEre_CAF1 88400 90 - 1
UAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGCCACUGACAGUAACAUGACAUCUUUCUC--CCUU-------UUU-----------------UUGUUGC
..((((((((.((.((((....))))...))(((...--....))).))))))))....((((((.............--....-------...-----------------.)))))) ( -22.40)
>DroWil_CAF1 90815 102 - 1
UAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCACACUUCACUCUUUGCCAGUGACAGUUACAUGACAUUUUUUUU-------------UUCUUGUU--UUU-UCGCUUUUUUGGC
.(((((((..(((.((((....))))...))).)).)))))........(((((.((.(((.....((((........-------------....))))--...-..))))).))))) ( -20.20)
>DroMoj_CAF1 98240 113 - 1
UAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGCCACUGACAGCUACACGACAUUUCUUUUUUUCUGUGUGAUUUU-UUUUUUCCCCCU--UUUUUUUUGC
..((((((((.((.((((....))))...))(((...--....))).))))))))......((((((...............)))))).....-............--.......... ( -22.56)
>DroAna_CAF1 78572 87 - 1
UAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGGCAGUGACAGUAACAUGACAUCUC-------CUU-------U---UAUU------------UUUUGGC
...(((((..(((.((((....))))...))).))((--(((((((....).))))).)))..)))........-------...-------.---....------------....... ( -14.50)
>consensus
UAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC__UUCACUCUUUGCCACUGACAGUAACAUGACAUCUUUUUU___CUU_______UU_UU_UU__U___U__UUUUUUUUGC
..((((((((.((.((((....))))...))(((.........))).))))))))............................................................... (-14.90 = -15.73 +   0.83)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,285,227 – 23,285,341
Length 114
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 80.98
Mean single sequence MFE -25.85
Consensus MFE -20.32
Energy contribution -21.32
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.08
Structure conservation index 0.79
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23285227 114 - 27905053
AACACACCCAUGCUCUUGCGA-CCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGCCACUGACAGUAACAUGACAUCUUUCUC-
..........(((....))).-......((((((.((((..((((((((.((.((((....))))...))(((...--....))).))))))))))))...))))))..........- ( -27.70)
>DroVir_CAF1 94162 101 - 1
----CGCCCA----UCUGACG-CUGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUCUGCCACUGACAGUUACACGACAUUU------
----......----.......-.........((((((....(((((((..((.((((....))))...))(((...--....)))..)))))))......))))))......------ ( -24.80)
>DroWil_CAF1 90839 101 - 1
-------CCA--------CGC-UUGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCACACUUCACUCUUUGCCAGUGACAGUUACAUGACAUUUUUUUU-
-------...--------.((-(((((...((((.((((.....)))).(((.....)))))))...)))))))..((((((((.......))))).))).................- ( -23.90)
>DroYak_CAF1 85492 114 - 1
CACACACCCAUGCGCCUGCGA-CCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGCCACUGACAGUAACAUGACAUCUUUCUU-
((((((.....(((.......-.))).....))))))....((((((((.((.((((....))))...))(((...--....))).)))))))).......................- ( -28.70)
>DroMoj_CAF1 98276 107 - 1
----CGCCCA----UCUGUCG-CUGGCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGCCACUGACAGCUACACGACAUUUCUUUUU
----.(((..----.......-..)))....((((((((..((((((((.((.((((....))))...))(((...--....))).))))))))...))).)))))............ ( -28.90)
>DroAna_CAF1 78587 94 - 1
-----------------ACGAGUCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC--UUCACUCUUUGGCAGUGACAGUAACAUGACAUCUC-----
-----------------..((((((((...((((.((((.....)))).(((.....)))))))...)))))..((--(((((((....).))))).)))..........)))----- ( -21.10)
>consensus
____C_CCCA_____CUGCGA_CCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCAC__UUCACUCUUUGCCACUGACAGUAACAUGACAUCUUU_UU_
............................((((((.((((..((((((((.((.((((....))))...))(((.........))).))))))))))))...))))))........... (-20.32 = -21.32 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 23,285,265 – 23,285,368
Length 103
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 87.84
Mean single sequence MFE -27.40
Consensus MFE -23.05
Energy contribution -23.68
Covariance contribution 0.63
Combinations/Pair 1.04
Mean z-score -1.66
Structure conservation index 0.84
SVM decision value 0.52
SVM RNA-class probability 0.765926
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23285265 103 - 27905053
CCCAGCU-------------ACCACCACCUUUGCCGCACCAACACACCCAUGCUCUUGCGACCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCACU
....(((-------------.(((......(((((((...(((((((....((....))(.....).....)))))))...)))))))...(((((....))))))))..)))... ( -28.20)
>DroSec_CAF1 82928 108 - 1
CCCAGCUACU-------CCCACCACCACC-UUGCUGCACCAACACACCCAUGCUCCUGCGACCGCCCUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCACU
........((-------((((........-((((..(...(((((((....((....))(......)....)))))))...)..))))...(((((....)))))))).))).... ( -25.40)
>DroSim_CAF1 86068 115 - 1
CCCAGCUACUACCUCCACCCACCCCCACC-UUGCCGCACCAACACACCCAUGCUCCUGCGACCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCACU
....(((......................-(((((((...(((((((....((....))(.....).....)))))))...)))))))(((.((((....))))...))))))... ( -27.80)
>DroEre_CAF1 88452 101 - 1
CCCAACU-------------GCCC-CAAC-UUGCGGCAGCCACACACCCAUGCUCCUGCGACCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCACU
......(-------------((((-(((.-.((((...(((((((((.((((.....((....))...)))).))))....)))))..))))((((....)))))))).).))).. ( -28.20)
>consensus
CCCAGCU_____________ACCACCACC_UUGCCGCACCAACACACCCAUGCUCCUGCGACCGCCUUUAUGUGUGUUUAAGUGGCAAUGCAAAUGGCAACAUUUUGGCGAGCACU
....(((.......................(((((((...(((((((....((....))(.....).....)))))))...)))))))(((.((((....))))...))))))... (-23.05 = -23.68 +   0.63)

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 13:17:46 2006