Locus 3836

Sequence ID 2R_DroMel_CAF1
Location 12,658,400 – 12,658,622
Length 222
Max. P 0.868494
window6191 window6192 window6193

overview

Window 1

Location 12,658,400 – 12,658,507
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.24
Mean single sequence MFE -44.10
Consensus MFE -30.37
Energy contribution -28.68
Covariance contribution -1.69
Combinations/Pair 1.53
Mean z-score -1.58
Structure conservation index 0.69
SVM decision value 0.63
SVM RNA-class probability 0.805078
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12658400 107 - 20766785
GUUGAAUCGUUCUAUUCGGCAGCGUGAGGAUUUGCCCAGUGUUCUUUGUGGUG-----CCU--------CGCAUCGUUCGGGACGCAGGGCUUCGAUGAUCGCUCGGUAGAAACGGAUAG
......(((((((((..(((..(....)((((.((((.(((((((..((((((-----(..--------.)))))))..))))))).))))......)))))))..)))).))))).... ( -37.30)
>DroPse_CAF1 19448 118 - 1
GUUAAAUCGUCCUAUUCGGCAGCGUGAGGUUUUGCCCAGCGCCCUUUCUGGUGCGGCACUUC-GGUGUCCGUGUCGUUCGGGGCGCAGAGCUUCGAUGAUCGCUCGGUA-AAACGGAUAG
...........((((((.....(....)((((((((..(((((((...(((..((((((...-.))).)))..)))...))))))).((((..........))))))))-)))))))))) ( -52.30)
>DroGri_CAF1 19778 114 - 1
GGUGAAUCGUUUUAUUCGGCAGCGUGAGGUUUUGCGUGAUGCCCUUUGCGGUAUGA--CUUCGGUUAUCCGUGUUG---UGGGCGUGGCGCUUCGAUGAUCGCUCGGUA-ACACGAAUAG
......((((.((((..(((..(....).....((((.((((((..(((((.((((--(....))))))))))...---.)))))).))))..........)))..)))-).)))).... ( -44.20)
>DroYak_CAF1 18328 107 - 1
GUUGAAUCGUUCUAUUCGGCAGCGUGAGGAUUUGUCCAGUGUCCUUUGUGGUG-----CUU--------CGCACUGUUCGGAACGCAGGGCUUCGAUGAUCGCUCGGUAACCACGGAUAG
...........(((((((...((.((((((((.((((.((((((...(..(((-----(..--------.))))..)..)).)))).))))......)))).)))))).....))))))) ( -30.90)
>DroAna_CAF1 15447 118 - 1
GGUGAAUCGUUCUAUUCGGCAGCGUGAGGAUUUGUCCAGCGGCCUUUGUGGUGUGGCGCUUC-GGUGUCCGCAUCCUCCGGGUCGUCGGGCUUCGAUGAUCGCUCGGUA-ACACGAAUAG
...........(((((((...((.((((((((.((((.(((((((..(.((((((((((...-.))).))))))))...))))))).))))......)))).)))))).-...))))))) ( -47.60)
>DroPer_CAF1 19376 118 - 1
GUUAAAUCGUCCUAUUCGGCAGCGUGAGGUUUUGCCCAGCGCCCUUUCUGGUGCGGCACUUC-GGUGUCCGUGUCGUUCGGGGCGCAGAGCUUCGAUGAUCGCUCGGUA-AAACGGAUAG
...........((((((.....(....)((((((((..(((((((...(((..((((((...-.))).)))..)))...))))))).((((..........))))))))-)))))))))) ( -52.30)
>consensus
GUUGAAUCGUUCUAUUCGGCAGCGUGAGGAUUUGCCCAGCGCCCUUUGUGGUG_GG__CUUC_GGUGUCCGCAUCGUUCGGGGCGCAGGGCUUCGAUGAUCGCUCGGUA_AAACGGAUAG
...........(((((((...((.((((.....((((.(((((((...((((((((............))))))))...))))))).))))..((.....)))))))).....))))))) (-30.37 = -28.68 +  -1.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,658,507 – 12,658,622
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.14
Mean single sequence MFE -32.60
Consensus MFE -24.35
Energy contribution -24.72
Covariance contribution 0.36
Combinations/Pair 1.07
Mean z-score -2.04
Structure conservation index 0.75
SVM decision value 0.86
SVM RNA-class probability 0.868494
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12658507 115 + 20766785
UCAUCAACGCGGGUGCACUUGGCUUUCAGCUAGUGUGAAAGUAUGUGAAGACUGACUACAGAAAUGAUCCUGUGAAGUAUAGUCUUAAGUU-----UUUGCUGCCCAACCUGUGGAUCUU
.......((((((((((((.(((.....))))))))....(((.(..(((((((((((((....))...((....))..)))))...))))-----))..))))...)))))))...... ( -32.50)
>DroVir_CAF1 28349 115 + 1
UCAUCAACGCGGGUGUGACUUGCUUUCAGAAAGUGUGAAAGUAAGUGAAGACUGACUACAGAAAUGAUCCUGUGAAGUAUAGUCUUAACUU-----UUCAAUGCCCACCAAAAUGCUCUA
..........((((((.(((((((((((.......))))))))))).((((((((((((((........))))..))).))))))).....-----....)))))).............. ( -31.70)
>DroGri_CAF1 19892 115 + 1
UCAUCAACGCGGGUGUGAAGUGCUUUCAGAUAGUGUGAAAGUAAGUGAAGACUGACUACAGAAAUGAUCCUGUGAAGUAUAGUCUUAAUUU-----UACAACGCCCAUCAAUGGGCUCUA
...(((.(((..((.(((((...))))).)).))))))..(((((..((((((((((((((........))))..))).)))))))...))-----)))...(((((....))))).... ( -32.10)
>DroWil_CAF1 18151 115 + 1
UCAUCAACGCGGGUGUAUGUGGCUUUCUUUCAAUGUGAAAGUAAGUGAAGACUGACUACAGAAAUGAUCCUGUGAAGUAUAGUCUUAAAUU-----UUCAACGCCCGUCAAUGGCCCCUU
((((....((((((((.....((((.(((((.....))))).)))).((((((((((((((........))))..))).))))))).....-----....))))))))..))))...... ( -32.90)
>DroMoj_CAF1 55233 115 + 1
UCAUCAGCGUGGGUAUGGUGUGCUUUCAUUUUGUGUGAAAGUAAGUGAAGACUGACUACAGAAAUGAUCCUGUGAAGUAUAGUCUUAAAUU-----UUCAACGCUCACCGAAGCGCUCUA
.....(((((.(((..(((((((((((((.....)))))))).....((((((((((((((........))))..))).))))))).....-----....))))).)))...)))))... ( -33.40)
>DroAna_CAF1 15565 115 + 1
UCAUCAACGCGGGUGUGCUUAGCUUUCAUCUAAUGUGAAAGUAUGUGAAGACUGACUACAGAAAUGAUCCUGUGAAGUAUAGUCUUAAAGAUACAAUCCAUCGCCCGA-----CGAUGUU
.((((....((((((((....((((((((.....)))))))).((((((((((((((((((........))))..))).))))))).....))))...)).)))))).-----.)))).. ( -33.00)
>consensus
UCAUCAACGCGGGUGUGAUUUGCUUUCAGAUAGUGUGAAAGUAAGUGAAGACUGACUACAGAAAUGAUCCUGUGAAGUAUAGUCUUAAAUU_____UUCAACGCCCAACAAAGGGCUCUA
..........((((((.....(((((((.......))))))).....((((((((((((((........))))..))).)))))))..............)))))).............. (-24.35 = -24.72 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,658,507 – 12,658,622
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.14
Mean single sequence MFE -27.30
Consensus MFE -18.24
Energy contribution -18.22
Covariance contribution -0.03
Combinations/Pair 1.08
Mean z-score -1.46
Structure conservation index 0.67
SVM decision value 0.09
SVM RNA-class probability 0.580850
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12658507 115 - 20766785
AAGAUCCACAGGUUGGGCAGCAAA-----AACUUAAGACUAUACUUCACAGGAUCAUUUCUGUAGUCAGUCUUCACAUACUUUCACACUAGCUGAAAGCCAAGUGCACCCGCGUUGAUGA
...(((.((.((.((.((......-----.....((((((..(((..((((((....))))))))).))))))......((((((.......))))))....)).)).))..)).))).. ( -24.30)
>DroVir_CAF1 28349 115 - 1
UAGAGCAUUUUGGUGGGCAUUGAA-----AAGUUAAGACUAUACUUCACAGGAUCAUUUCUGUAGUCAGUCUUCACUUACUUUCACACUUUCUGAAAGCAAGUCACACCCGCGUUGAUGA
.....((((...(((((...(((.-----((((.((((((..(((..((((((....))))))))).)))))).)))).((((((.......))))))....)))..)))))...)))). ( -30.50)
>DroGri_CAF1 19892 115 - 1
UAGAGCCCAUUGAUGGGCGUUGUA-----AAAUUAAGACUAUACUUCACAGGAUCAUUUCUGUAGUCAGUCUUCACUUACUUUCACACUAUCUGAAAGCACUUCACACCCGCGUUGAUGA
.......(((..(((((.((.((.-----.....((((((..(((..((((((....))))))))).))))))......((((((.......))))))......)))))).)))..))). ( -25.80)
>DroWil_CAF1 18151 115 - 1
AAGGGGCCAUUGACGGGCGUUGAA-----AAUUUAAGACUAUACUUCACAGGAUCAUUUCUGUAGUCAGUCUUCACUUACUUUCACAUUGAAAGAAAGCCACAUACACCCGCGUUGAUGA
.......(((..(((((.((((..-----.....((((((..(((..((((((....))))))))).))))))..(((.(((((.....))))).)))...)).)).)))..))..))). ( -28.60)
>DroMoj_CAF1 55233 115 - 1
UAGAGCGCUUCGGUGAGCGUUGAA-----AAUUUAAGACUAUACUUCACAGGAUCAUUUCUGUAGUCAGUCUUCACUUACUUUCACACAAAAUGAAAGCACACCAUACCCACGCUGAUGA
.....(((....)))(((((.(..-----.....((((((..(((..((((((....))))))))).))))))......((((((.......))))))..........).)))))..... ( -25.30)
>DroAna_CAF1 15565 115 - 1
AACAUCG-----UCGGGCGAUGGAUUGUAUCUUUAAGACUAUACUUCACAGGAUCAUUUCUGUAGUCAGUCUUCACAUACUUUCACAUUAGAUGAAAGCUAAGCACACCCGCGUUGAUGA
..(((((-----.((((.((((((..((((....((((((..(((..((((((....))))))))).))))))...))))..)).))))........((...))...))))...))))). ( -29.30)
>consensus
AAGAGCCCAUUGAUGGGCGUUGAA_____AAUUUAAGACUAUACUUCACAGGAUCAUUUCUGUAGUCAGUCUUCACUUACUUUCACACUAAAUGAAAGCAAAGCACACCCGCGUUGAUGA
.............((((.................((((((..(((..((((((....))))))))).))))))......((((((.......)))))).........))))......... (-18.24 = -18.22 +  -0.03)

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 11:05:09 2006