Locus 7017

Sequence ID X_DroMel_CAF1
Location 17,578,188 – 17,578,373
Length 185
Max. P 0.928934
window11465 window11466 window11467 window11468

overview

Window 5

Location 17,578,188 – 17,578,307
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.38
Mean single sequence MFE -32.77
Consensus MFE -28.94
Energy contribution -29.17
Covariance contribution 0.23
Combinations/Pair 1.10
Mean z-score -2.21
Structure conservation index 0.88
SVM decision value 0.51
SVM RNA-class probability 0.763754
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17578188 119 + 22224390
CGUAGGUCCGGUCAUCUGGCCAAAAAUUACCAAAUUAUUACACACUCGCCGGAGAUUUGGUGUAAUAUACUAGACCUGAUCUCUGCUGACUUCAUCGCACUAUAUAUGCG-AUUGGCCCA
....((.((((((....))))........................(((.((((((((.(((.((......)).))).)))))))).)))....((((((.......))))-)).)).)). ( -32.60)
>DroSim_CAF1 18150 120 + 1
CGUAGGUCCGGUCAUCUGGCCAAAAAUUACCAAAUUAUUACACACUCACCUGAGAUUUGGUGUAAUAUACUAGACCUGAUCUCUGCUGACUUCAUCGCACUAUAUAUGCGGAUUGGCCCA
....((.((((....))))))........((((............(((.(.((((((.(((.((......)).))).)))))).).))).....(((((.......))))).)))).... ( -28.50)
>DroYak_CAF1 7862 119 + 1
CGGAGGUCCGGUCAUCUGGCCAAAAAUUACCAAAUUAUUACACACUCUCCGGGGAUUUGGUGUAAUAUACUAGACCUGAUCUCCGCUGACUUCAUCGCACUAUAUAUGCG-AUUGGCCCA
.(((((((.((((...(((..........)))...((((((((..(((....)))....)))))))).....)))).)))))))((..(.....(((((.......))))-))..))... ( -37.20)
>consensus
CGUAGGUCCGGUCAUCUGGCCAAAAAUUACCAAAUUAUUACACACUCACCGGAGAUUUGGUGUAAUAUACUAGACCUGAUCUCUGCUGACUUCAUCGCACUAUAUAUGCG_AUUGGCCCA
....((.((((....))))))........((((............(((.((((((((.(((.((......)).))).)))))))).)))......((((.......))))..)))).... (-28.94 = -29.17 +   0.23)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,578,188 – 17,578,307
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.38
Mean single sequence MFE -38.20
Consensus MFE -32.53
Energy contribution -32.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.85
SVM decision value 0.45
SVM RNA-class probability 0.740597
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17578188 119 - 22224390
UGGGCCAAU-CGCAUAUAUAGUGCGAUGAAGUCAGCAGAGAUCAGGUCUAGUAUAUUACACCAAAUCUCCGGCGAGUGUGUAAUAAUUUGGUAAUUUUUGGCCAGAUGACCGGACCUACG
..(((..((-(((((.....)))))))...)))..........(((((..((.((((((((.....(((....))).))))))))(((((((........))))))).))..)))))... ( -36.30)
>DroSim_CAF1 18150 120 - 1
UGGGCCAAUCCGCAUAUAUAGUGCGAUGAAGUCAGCAGAGAUCAGGUCUAGUAUAUUACACCAAAUCUCAGGUGAGUGUGUAAUAAUUUGGUAAUUUUUGGCCAGAUGACCGGACCUACG
((((((....(((((.....))))).(((..((....))..)))((((.....((((((((.....(((....))).))))))))(((((((........))))))))))))).)))).. ( -35.10)
>DroYak_CAF1 7862 119 - 1
UGGGCCAAU-CGCAUAUAUAGUGCGAUGAAGUCAGCGGAGAUCAGGUCUAGUAUAUUACACCAAAUCCCCGGAGAGUGUGUAAUAAUUUGGUAAUUUUUGGCCAGAUGACCGGACCUCCG
..(((..((-(((((.....)))))))...)))..(((((.((.((((.....((((((((....((....))....))))))))(((((((........))))))))))).)).))))) ( -43.20)
>consensus
UGGGCCAAU_CGCAUAUAUAGUGCGAUGAAGUCAGCAGAGAUCAGGUCUAGUAUAUUACACCAAAUCUCCGGAGAGUGUGUAAUAAUUUGGUAAUUUUUGGCCAGAUGACCGGACCUACG
.(((((....(((((.....))))).(((..((....))..)))((((.....((((((((....((......))..))))))))(((((((........))))))))))))).)))... (-32.53 = -32.53 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,578,228 – 17,578,347
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 88.86
Mean single sequence MFE -29.76
Consensus MFE -24.94
Energy contribution -25.50
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -2.25
Structure conservation index 0.84
SVM decision value 0.62
SVM RNA-class probability 0.801128
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17578228 119 + 22224390
CACACUCGCCGGAGAUUUGGUGUAAUAUACUAGACCUGAUCUCUGCUGACUUCAUCGCACUAUAUAUGCG-AUUGGCCCACCUUUUUUAUUUUUUUUUUGCCCGAAAUGGUGUUUGCCAU
.....(((.((((((((.(((.((......)).))).)))))))).)))....((((((.......))))-))((((.((((.((((................)))).))))...)))). ( -31.39)
>DroSim_CAF1 18190 111 + 1
CACACUCACCUGAGAUUUGGUGUAAUAUACUAGACCUGAUCUCUGCUGACUUCAUCGCACUAUAUAUGCGGAUUGGCCCACCUUU---------UUUUUGCCCGAAAUGGUGUUUGCCAU
.....(((.(.((((((.(((.((......)).))).)))))).).))).....(((((.......)))))..((((.((((.((---------((.......)))).))))...)))). ( -28.00)
>DroYak_CAF1 7902 108 + 1
CACACUCUCCGGGGAUUUGGUGUAAUAUACUAGACCUGAUCUCCGCUGACUUCAUCGCACUAUAUAUGCG-AUUGGCCCACCUUU-----------AUUGCCCCAAAUGGCGUUUGCCAU
.....((..((((((((.(((.((......)).))).))))))))..))....((((((.......))))-)).(((........-----------...)))....(((((....))))) ( -29.90)
>consensus
CACACUCACCGGAGAUUUGGUGUAAUAUACUAGACCUGAUCUCUGCUGACUUCAUCGCACUAUAUAUGCG_AUUGGCCCACCUUU_________UUUUUGCCCGAAAUGGUGUUUGCCAU
.....(((.((((((((.(((.((......)).))).)))))))).)))......((((.......))))...((((.((((..........................))))...)))). (-24.94 = -25.50 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,578,268 – 17,578,373
Length 105
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.36
Mean single sequence MFE -24.22
Consensus MFE -17.76
Energy contribution -17.54
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.10
Structure conservation index 0.73
SVM decision value 1.19
SVM RNA-class probability 0.928934
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17578268 105 - 22224390
AUUUC-----------AAAAUCCAAUGAAAUCCAA---UGAUGGCAAACACCAUUUCGGGCAAAAAAAAAAUAAAAAAGGUGGGCCAAU-CGCAUAUAUAGUGCGAUGAAGUCAGCAGAG
.((((-----------(........)))))((...---(((((((...((((..........................)))).))).((-(((((.....)))))))...))))...)). ( -22.27)
>DroSim_CAF1 18230 97 - 1
AUUUC-----------AAAAUCCAAUGAAACCCAA---UGAUGGCAAACACCAUUUCGGGCAAAAA---------AAAGGUGGGCCAAUCCGCAUAUAUAGUGCGAUGAAGUCAGCAGAG
(((((-----------(..................---...((((...((((.(((.........)---------)).)))).))))...(((((.....))))).))))))........ ( -19.60)
>DroYak_CAF1 7942 108 - 1
AUUUCUACAUCUCCACAAAAUCCAAUGAAACCCAAAUCCAAUGGCAAACGCCAUUUGGGGCAAU-----------AAAGGUGGGCCAAU-CGCAUAUAUAGUGCGAUGAAGUCAGCGGAG
..........((((...........((...(((((.....(((((....)))))))))).))..-----------....((.(((..((-(((((.....)))))))...))).)))))) ( -30.80)
>consensus
AUUUC___________AAAAUCCAAUGAAACCCAA___UGAUGGCAAACACCAUUUCGGGCAAAAA_________AAAGGUGGGCCAAU_CGCAUAUAUAGUGCGAUGAAGUCAGCAGAG
....................((...(((.............((((...((((..........................)))).))))...(((((.....)))))......)))...)). (-17.76 = -17.54 +  -0.22)

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 12:28:13 2006