Locus 8478

Sequence ID 3R_DroMel_CAF1
Location 22,620,540 – 22,620,659
Length 119
Max. P 0.951403
window13637 window13638 window13639 window13640

overview

Window 7

Location 22,620,540 – 22,620,630
Length 90
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 81.47
Mean single sequence MFE -29.55
Consensus MFE -24.33
Energy contribution -24.17
Covariance contribution -0.17
Combinations/Pair 1.22
Mean z-score -1.64
Structure conservation index 0.82
SVM decision value 0.58
SVM RNA-class probability 0.787759
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22620540 90 + 27905053
CUGUUUU-----CCGCUGCGUGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUUAAAUCCGCUUCUGGAUAUACCCAGA
......(-----((((.(((((((((((.((....))))))))..)))))....)))))...(((((......))))).(((((......))))) ( -30.30)
>DroPse_CAF1 76191 95 + 1
CUGUUGCUGCUGCUGCUGCGUGUUGCUCACACAUGCGGCGCAAAUUAUGUCAACGUGGAUUUCUGAAGUCAACUCCGCACUCGGGGAUAUCCGUG
..(((((...(((.(((((((((.......))))))))))))......).))))(((((....((....))..))))).(.((((....)))).) ( -27.40)
>DroSec_CAF1 68801 90 + 1
CUGUUUU-----CCGCUGCGUGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUCUGGGUAUCCCCAGA
....(((-----.(((..(((((.......)))))..))).)))..........(((((((((......))))))))).((((((....)))))) ( -33.00)
>DroSim_CAF1 70592 90 + 1
CUGUUCU-----CCGCUGCGUGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUCUGGGUAUCUCCAGA
......(-----((((.(((((((((((.((....))))))))..)))))....)))))...(((((......))))).((((((....)))))) ( -30.30)
>DroYak_CAF1 71921 76 + 1
CUGCUUG-----CUGCUGCGUGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUC--------------
....(((-----(.((..(((((.......)))))..))))))...........(((((((((......)))))))))...-------------- ( -26.70)
>DroPer_CAF1 80367 92 + 1
CUGUUGCUGC---UGCUGCGUGUUGCUCACACAUGCGGCGCAAAUUAUGUCAACGUGGAUUUGUGAAGUCAACUCCGCACUCGGGGAUAUCCGUG
..((((((((---.(((((((((.......))))))))))))......).))))(((((.(((......))).))))).(.((((....)))).) ( -29.60)
>consensus
CUGUUUU_____CCGCUGCGUGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUCUGGGUAUAUCCAGA
.............((((((((((.......))))))))))..............(((((((((......)))))))))...((((....)))).. (-24.33 = -24.17 +  -0.17)

alignment

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secondary structure

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Window 8

Location 22,620,540 – 22,620,630
Length 90
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 81.47
Mean single sequence MFE -27.91
Consensus MFE -18.65
Energy contribution -19.22
Covariance contribution 0.57
Combinations/Pair 1.09
Mean z-score -2.11
Structure conservation index 0.67
SVM decision value 0.62
SVM RNA-class probability 0.802944
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22620540 90 - 27905053
UCUGGGUAUAUCCAGAAGCGGAUUUAACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACACGCAGCGG-----AAAACAG
((((((....))))))...((((((........)))))).(((((.......((((((((....)).))))))....))))).-----....... ( -27.10)
>DroPse_CAF1 76191 95 - 1
CACGGAUAUCCCCGAGUGCGGAGUUGACUUCAGAAAUCCACGUUGACAUAAUUUGCGCCGCAUGUGUGAGCAACACGCAGCAGCAGCAGCAACAG
..(((......)))..((((((.(((....)))...)))..............(((((.((.((((((.....)))))))).)).)))))).... ( -26.80)
>DroSec_CAF1 68801 90 - 1
UCUGGGGAUACCCAGAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACACGCAGCGG-----AAAACAG
((((((....))))))...(((((((......))))))).(((((.......((((((((....)).))))))....))))).-----....... ( -34.10)
>DroSim_CAF1 70592 90 - 1
UCUGGAGAUACCCAGAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACACGCAGCGG-----AGAACAG
(((((......)))))...(((((((......))))))).(((((.......((((((((....)).))))))....))))).-----....... ( -30.10)
>DroYak_CAF1 71921 76 - 1
--------------GAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACACGCAGCAG-----CAAGCAG
--------------...(((((((((......)))))))..((((.......((((((((....)).)))))).......)))-----)..)).. ( -25.44)
>DroPer_CAF1 80367 92 - 1
CACGGAUAUCCCCGAGUGCGGAGUUGACUUCACAAAUCCACGUUGACAUAAUUUGCGCCGCAUGUGUGAGCAACACGCAGCA---GCAGCAACAG
..(((......)))..((((((.(((......))).))).................((.((.((((((.....)))))))).---)).))).... ( -23.90)
>consensus
UCUGGAUAUACCCAGAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACACGCAGCAG_____AAAACAG
..(((......)))...(.(((((((......))))))).)((((.......((((((((....)).))))))....)))).............. (-18.65 = -19.22 +   0.57)

alignment

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secondary structure

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Window 9

Location 22,620,555 – 22,620,659
Length 104
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 77.32
Mean single sequence MFE -32.90
Consensus MFE -21.83
Energy contribution -22.68
Covariance contribution 0.85
Combinations/Pair 1.12
Mean z-score -2.01
Structure conservation index 0.66
SVM decision value 1.41
SVM RNA-class probability 0.951403
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22620555 104 + 27905053
UGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUUAAAUCCGCUUCUGGAUAUACCCAGAUCACGCGCU--CGCAAUGGCUAGU-CCCCAUG--
.(((((((((....)))((((.............(((((((((......))))))))).(((((......)))))....)))).--)))))).......-.......-- ( -33.30)
>DroSec_CAF1 68816 105 + 1
UGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUCUGGGUAUCCCCAGAUCACGCGCU--CACAAUGGCUAGUGCCCCCUG--
......((((.((((((((((.............(((((((((......))))))))).((((((....))))))....)))).--))).)))....))))......-- ( -39.60)
>DroSim_CAF1 70607 105 + 1
UGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUCUGGGUAUCUCCAGAUCACGCGCU--CACAAUGGCUAGUGCCCCAUG--
......((((.((((((((((.............(((((((((......))))))))).((((((....))))))....)))).--))).)))....))))......-- ( -37.10)
>DroEre_CAF1 76988 89 + 1
UGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUUUGGGGAU------AUCACGCGCU--CACAAUGGCCA------------
...((.((.((..((((((((.....(((((..((((((((((......)))))))))....)..)))------))...)))).--)))).))))))------------ ( -28.40)
>DroYak_CAF1 71936 82 + 1
UGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUC-------------------CACU--CACAAUGGCCCA----UCAAG--
..((((((.((....)))))))).....((((..(((((...(((((......))))).))-------------------))).--.....))))...----.....-- ( -25.40)
>DroPer_CAF1 80384 109 + 1
UGUUGCUCACACAUGCGGCGCAAAUUAUGUCAACGUGGAUUUGUGAAGUCAACUCCGCACUCGGGGAUAUCCGUGGCACACACACACACACGGACACAUGCCACAGACA
.(((((........)))))........((((...((((...((((.......(((((....)))))...((((((.............))))))))))..)))).)))) ( -33.62)
>consensus
UGUUGCGCACACAUGUGGCGCAAAUUAUGUCAACGUGGAUUUGUGGAGUCAAAUCCGCUUCUGGGUAU__CCAGAUCACGCGCU__CACAAUGGCUAGU_CCCCAUG__
..((((((.((....)))))))).....((((..(((((((((......)))))))))...(((......)))..................)))).............. (-21.83 = -22.68 +   0.85)

alignment

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secondary structure

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dotplot

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Window 0

Location 22,620,555 – 22,620,659
Length 104
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 77.32
Mean single sequence MFE -32.18
Consensus MFE -17.39
Energy contribution -18.48
Covariance contribution 1.10
Combinations/Pair 1.11
Mean z-score -1.63
Structure conservation index 0.54
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22620555 104 - 27905053
--CAUGGGG-ACUAGCCAUUGCG--AGCGCGUGAUCUGGGUAUAUCCAGAAGCGGAUUUAACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACA
--..(((..-.....)))(((((--.(((((((.((((((....)))))).(((((((....((.((........)).))...)))))))....))))))).))))).. ( -30.80)
>DroSec_CAF1 68816 105 - 1
--CAGGGGGCACUAGCCAUUGUG--AGCGCGUGAUCUGGGGAUACCCAGAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACA
--.....(((....)))..(((.--((((.((..((((((....)))))).))(((((((......))))))).)))).)))....((((((((....)).)))))).. ( -41.40)
>DroSim_CAF1 70607 105 - 1
--CAUGGGGCACUAGCCAUUGUG--AGCGCGUGAUCUGGAGAUACCCAGAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACA
--.....(((....)))..(((.--((((.((..(((((......))))).))(((((((......))))))).)))).)))....((((((((....)).)))))).. ( -37.40)
>DroEre_CAF1 76988 89 - 1
------------UGGCCAUUGUG--AGCGCGUGAU------AUCCCCAAAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACA
------------.......(((.--(((((.((..------.....))...))(((((((......)))))))..))).)))....((((((((....)).)))))).. ( -25.70)
>DroYak_CAF1 71936 82 - 1
--CUUGA----UGGGCCAUUGUG--AGUG-------------------GAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACA
--.(..(----((..((((....--.)))-------------------)....(((((((......))))))).)))..)......((((((((....)).)))))).. ( -24.40)
>DroPer_CAF1 80384 109 - 1
UGUCUGUGGCAUGUGUCCGUGUGUGUGUGUGUGCCACGGAUAUCCCCGAGUGCGGAGUUGACUUCACAAAUCCACGUUGACAUAAUUUGCGCCGCAUGUGUGAGCAACA
(((((((((((..((..((....))..))..)))))))))))...(((....))).((((.((.((((......((.((.((.....)))).))....)))))))))). ( -33.40)
>consensus
__CAUGGGG_ACUAGCCAUUGUG__AGCGCGUGAUCUGG__AUACCCAGAAGCGGAUUUGACUCCACAAAUCCACGUUGACAUAAUUUGCGCCACAUGUGUGCGCAACA
.................((((((...(((.......(((......))).....(((((((......))))))).)))...))))))((((((((....)).)))))).. (-17.39 = -18.48 +   1.10)

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 13:12:18 2006