Locus 303

Sequence ID 3L_DroMel_CAF1
Location 868,950 – 869,098
Length 148
Max. P 0.814109
window453 window454 window455

overview

Window 3

Location 868,950 – 869,066
Length 116
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 82.83
Mean single sequence MFE -26.27
Consensus MFE -15.82
Energy contribution -17.30
Covariance contribution 1.48
Combinations/Pair 1.09
Mean z-score -2.29
Structure conservation index 0.60
SVM decision value 0.66
SVM RNA-class probability 0.814109
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 868950 116 + 23771897
AUUCAUUCGGUGAAUGUAUAAAACCAUGUAUAUC-AAGAAGUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU-UAUUGCUAUCUAUAUGUGUCAUAAUAGCAUAUACUGCAG
.....(((..(((.((((((......))))))))-).))).(((((..(.(((...(((...((((((((.(((((..-..))))).)))...)))))...))).))).)..))))). ( -25.20)
>DroSec_CAF1 11873 114 + 1
AU--AUGUGGUGAAUGUAUAAAUCCAUGUAUAUC-GAGAAGUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU-UCUUGCUAUCUAUAUGUGCCAUACUUGCAUAUACUGCUG
((--(((..((((((((((((((...(((((...-.....)))))..)))))))).))))).((((((((.(((((..-..))))).)))...))))).....)..)))))....... ( -27.50)
>DroSim_CAF1 6894 114 + 1
AU--AUGUGGUGAAUGUAUAAAUCCAUGUAUAUC-GAGAAGUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU-UCUUGCUAUCUAUAUGUGCCAUAAUUGCAUAUACUGCUG
((--(((..((...(((((((((...(((((...-.....)))))..)))))))))......((((((((.(((((..-..))))).)))...)))))....))..)))))....... ( -28.80)
>DroEre_CAF1 11902 107 + 1
AU--AUUGUGUGGAUGUAUAAAACCUUGAAUACC-AAGAAGUGCAACGUUUGUAUAAUUCAAGCACAAGAAAGAAACUUU--------CUAUAUGUGCCAUAAUUGCAUAUACUGCAG
..--((((((..(((((.......((((.....)-))).......)))))..))))))....(((((((((((...))))--------))...)))))......((((.....)))). ( -23.54)
>DroYak_CAF1 11941 110 + 1
UU--AUUGC------AUAUAAAUGCAUGAAUAUUGAAAAAACGCAGCGUUUGUAUAAUUCAAGCACAAGAAAGAAACUUUCUUGCUAUCUAUAUGUGCCAUAAUUGCAUACACUGCAG
((--((.((------(((((..(((.(((((..((...(((((...))))).))..))))).)))((((((((...)))))))).......))))))).)))).((((.....)))). ( -26.30)
>consensus
AU__AUUGGGUGAAUGUAUAAAUCCAUGUAUAUC_AAGAAGUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU_UCUUGCUAUCUAUAUGUGCCAUAAUUGCAUAUACUGCAG
..........................................((((.((.((((........((((((((.(((((.....))))).)))...)))))......)))).)).)))).. (-15.82 = -17.30 +   1.48)

alignment

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secondary structure

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Window 4

Location 868,950 – 869,066
Length 116
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 82.83
Mean single sequence MFE -23.49
Consensus MFE -14.11
Energy contribution -15.55
Covariance contribution 1.44
Combinations/Pair 1.05
Mean z-score -2.03
Structure conservation index 0.60
SVM decision value 0.26
SVM RNA-class probability 0.658883
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 868950 116 - 23771897
CUGCAGUAUAUGCUAUUAUGACACAUAUAGAUAGCAAUA-AAUUGCUUUCUUGUGCUUAAAUUAUACAAACGCUGCACUUCUU-GAUAUACAUGGUUUUAUACAUUCACCGAAUGAAU
.(((((..(.((.(((..(((((((...(((.(((((..-..))))).))))))).)))....))))).)..)))))......-..................(((((...)))))... ( -20.10)
>DroSec_CAF1 11873 114 - 1
CAGCAGUAUAUGCAAGUAUGGCACAUAUAGAUAGCAAGA-AAUUGCUUUCUUGUGCUUAAAUUAUACAAACGCUGCACUUCUC-GAUAUACAUGGAUUUAUACAUUCACCACAU--AU
..((((..(.((..(((..((((((...(((.(((((..-..))))).)))))))))...)))...)).)..)))).......-........(((((......)))))......--.. ( -24.90)
>DroSim_CAF1 6894 114 - 1
CAGCAGUAUAUGCAAUUAUGGCACAUAUAGAUAGCAAGA-AAUUGCUUUCUUGUGCUUAAAUUAUACAAACGCUGCACUUCUC-GAUAUACAUGGAUUUAUACAUUCACCACAU--AU
..((((..(.((.((((..((((((...(((.(((((..-..))))).)))))))))..))))...)).)..)))).......-........(((((......)))))......--.. ( -25.50)
>DroEre_CAF1 11902 107 - 1
CUGCAGUAUAUGCAAUUAUGGCACAUAUAG--------AAAGUUUCUUUCUUGUGCUUGAAUUAUACAAACGUUGCACUUCUU-GGUAUUCAAGGUUUUAUACAUCCACACAAU--AU
.....(((((((((((...((((((...((--------((((...))))))))))))..............))))))..((((-(.....)))))...)))))...........--.. ( -19.83)
>DroYak_CAF1 11941 110 - 1
CUGCAGUGUAUGCAAUUAUGGCACAUAUAGAUAGCAAGAAAGUUUCUUUCUUGUGCUUGAAUUAUACAAACGCUGCGUUUUUUCAAUAUUCAUGCAUUUAUAU------GCAAU--AA
..(((((((.((.((((..((((((...(((.(((......))))))....))))))..))))...)).)))))))................(((((....))------)))..--.. ( -27.10)
>consensus
CUGCAGUAUAUGCAAUUAUGGCACAUAUAGAUAGCAAGA_AAUUGCUUUCUUGUGCUUAAAUUAUACAAACGCUGCACUUCUU_GAUAUACAUGGAUUUAUACAUUCACCAAAU__AU
..((((..(.((.......((((((...(((.(((((.....))))).))))))))).........)).)..)))).......................................... (-14.11 = -15.55 +   1.44)

alignment

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secondary structure

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Window 5

Location 868,989 – 869,098
Length 109
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 90.52
Mean single sequence MFE -23.63
Consensus MFE -16.94
Energy contribution -18.42
Covariance contribution 1.48
Combinations/Pair 1.07
Mean z-score -2.20
Structure conservation index 0.72
SVM decision value 0.40
SVM RNA-class probability 0.721362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 868989 109 + 23771897
GUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU-UAUUGCUAUCUAUAUGUGUCAUAAUAGCAUAUACUGCAGUAUUCUUUAUACUGGAUUCUUUGUUCUCCAAA
.(((((..(.(((...(((...((((((((.(((((..-..))))).)))...)))))...))).))).)..)))))((((.....))))((((..........)))).. ( -22.90)
>DroSec_CAF1 11910 109 + 1
GUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU-UCUUGCUAUCUAUAUGUGCCAUACUUGCAUAUACUGCUGUAUUCUUUAUACUGGAUUCUUUGUUCUCCAAA
((((((((((((.......))))).(((((((....))-))))).......(((((((.......)))))))..))))))).........((((..........)))).. ( -25.70)
>DroSim_CAF1 6931 109 + 1
GUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU-UCUUGCUAUCUAUAUGUGCCAUAAUUGCAUAUACUGCUGUAUUCUUUAUACUGGAUUCUUUGUUCUCCAAA
(((((((((.(((.(((((...((((((((.(((((..-..))))).)))...)))))...))))).))).)).))))))).........((((..........)))).. ( -27.60)
>DroEre_CAF1 11939 102 + 1
GUGCAACGUUUGUAUAAUUCAAGCACAAGAAAGAAACUUU--------CUAUAUGUGCCAUAAUUGCAUAUACUGCAGUAUUCUUUAUACUGGCUUCUUUGUUCUCAAAA
.......((..((((((.....(((((((((((...))))--------))...)))))....((((((.....)))))).....))))))..))...((((....)))). ( -20.60)
>DroYak_CAF1 11973 110 + 1
ACGCAGCGUUUGUAUAAUUCAAGCACAAGAAAGAAACUUUCUUGCUAUCUAUAUGUGCCAUAAUUGCAUACACUGCAGUAUUCUUUAUACUGGUUUCUUUGUUCUCCAAA
..((((.((.((((........(((((((((((...))))))...........)))))......)))).)).))))(((((.....)))))................... ( -21.34)
>consensus
GUGCAGCGUUUGUAUAAUUUAAGCACAAGAAAGCAAUU_UCUUGCUAUCUAUAUGUGCCAUAAUUGCAUAUACUGCAGUAUUCUUUAUACUGGAUUCUUUGUUCUCCAAA
..((((.((.((((........((((((((.(((((.....))))).)))...)))))......)))).)).)))).((((.....)))).................... (-16.94 = -18.42 +   1.48)

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 09:38:46 2006