Locus 4133

Sequence ID 2R_DroMel_CAF1
Location 13,579,690 – 13,579,861
Length 171
Max. P 0.996693
window6654 window6655 window6656 window6657

overview

Window 4

Location 13,579,690 – 13,579,799
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 87.92
Mean single sequence MFE -28.27
Consensus MFE -25.76
Energy contribution -25.82
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.91
Structure conservation index 0.91
SVM decision value 2.73
SVM RNA-class probability 0.996693
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13579690 109 + 20766785
AUGGCAAGUGCAGCUUCCGCUGGAACUAAAACGGAAACAAAAAUGAAAAUGAAAAUGCAACUGAAACUGAAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAAC
...(((..(((((((((.((((..........(....)..................................(((.........))))))).)))))))))..)))... ( -27.90)
>DroSec_CAF1 132746 109 + 1
AUGGCAAGUGCAGCUUCCGCUGGAACUAAAACGGAAACAAAAAUGAAAAGGAAAAUGCAACUGAAACUGUAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAAC
...(((..(((((((((.((((..........(....).................((((........))))................)))).)))))))))..)))... ( -28.60)
>DroSim_CAF1 131124 109 + 1
AUGGCAAGUGCAGCUUCCGCUGGAACUAAAACGGAAACAAAAAUGAAAAUGAAAAUGCAACUGAAACUGUAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAAC
...(((..(((((((((.((((..........(....).................((((........))))................)))).)))))))))..)))... ( -28.60)
>DroEre_CAF1 128402 91 + 1
AUGGCAAGUGCAGCUUCCGCUGCAACUAAAACGGAAACAGA------------AAUG------AAAAUGGAAGUGCAACUCAAACGGCAGCCGAAGCUGUGACUGUAAC
...(((..(((((((((.(((((.........(....)...------------..((------(...((......))..)))....))))).)))))))))..)))... ( -28.00)
>consensus
AUGGCAAGUGCAGCUUCCGCUGGAACUAAAACGGAAACAAAAAUGAAAAUGAAAAUGCAACUGAAACUGUAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAAC
...(((..(((((((((.((((..........(....)..................................(((.........))))))).)))))))))..)))... (-25.76 = -25.82 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,579,721 – 13,579,838
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 89.17
Mean single sequence MFE -29.18
Consensus MFE -24.91
Energy contribution -25.72
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.59
Structure conservation index 0.85
SVM decision value 1.94
SVM RNA-class probability 0.983433
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13579721 117 + 20766785
CGGAAACAAAAAUGAAAAUGAAAAUGCAACUGAAACUGAAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAU
((((((..((((..(..((((((.(((............................(((((....)))))((((((.....))))))))))))))).)..))))......)))))).. ( -28.50)
>DroSec_CAF1 132777 117 + 1
CGGAAACAAAAAUGAAAAGGAAAAUGCAACUGAAACUGUAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAU
.(....)......((((..((....((((((((((.(((................(((((....)))))((((((.....)))))))))))))).))))).....))..)))).... ( -29.20)
>DroSim_CAF1 131155 117 + 1
CGGAAACAAAAAUGAAAAUGAAAAUGCAACUGAAACUGUAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAU
.(....)......((((.(((....((((((((((.(((................(((((....)))))((((((.....)))))))))))))).))))).....))).)))).... ( -30.10)
>DroEre_CAF1 128433 99 + 1
CGGAAACAGA------------AAUG------AAAAUGGAAGUGCAACUCAAACGGCAGCCGAAGCUGUGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAU
((((((((..------------..))------......(((((((..........(((((....)))))((((((.....)))))))))))))................)))))).. ( -28.90)
>consensus
CGGAAACAAAAAUGAAAAUGAAAAUGCAACUGAAACUGUAACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAU
((((((..................((((........))))..........((((((((...((((.(((((((((.....))))))))))))).)))))))).......)))))).. (-24.91 = -25.72 +   0.81)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,579,721 – 13,579,838
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 89.17
Mean single sequence MFE -29.57
Consensus MFE -22.24
Energy contribution -23.55
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -2.14
Structure conservation index 0.75
SVM decision value 0.75
SVM RNA-class probability 0.842084
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13579721 117 - 20766785
AUCAGAAAGUAAUUAAAACAACAUGAAAUGCGACUGUGAGUUACAGUCGCAGCUUCGGCUGCCGUUUGAGUUCCAGUUUCAGUUUCAGUUGCAUUUUCAUUUUCAUUUUUGUUUCCG
....((((((........((((.((((((..(((((.((..(.(((..(((((....)))))...))))..)))))))...)))))))))).......))))))............. ( -31.46)
>DroSec_CAF1 132777 117 - 1
AUCAGAAAGUAAUUAAAACAACAUGAAAUGCGACUGUGAGUUACAGUCGCAGCUUCGGCUGCCGUUUGAGUUCCAGUUACAGUUUCAGUUGCAUUUUCCUUUUCAUUUUUGUUUCCG
....(((((.........((((.(((((((..((((.((..(.(((..(((((....)))))...))))..))))))..)).)))))))))........)))))............. ( -30.13)
>DroSim_CAF1 131155 117 - 1
AUCAGAAAGUAAUUAAAACAACAUGAAAUGCGACUGUGAGUUACAGUCGCAGCUUCGGCUGCCGUUUGAGUUCCAGUUACAGUUUCAGUUGCAUUUUCAUUUUCAUUUUUGUUUCCG
....((((((........((((.(((((((..((((.((..(.(((..(((((....)))))...))))..))))))..)).))))))))).......))))))............. ( -31.66)
>DroEre_CAF1 128433 99 - 1
AUCAGAAAGUAAUUAAAACAACAUGAAAUGCGACUGUGAGUUACAGUCACAGCUUCGGCUGCCGUUUGAGUUGCACUUCCAUUUU------CAUU------------UCUGUUUCCG
..((((((((((((.((((............(((((((...))))))).((((....))))..)))).))))))...........------..))------------))))...... ( -25.01)
>consensus
AUCAGAAAGUAAUUAAAACAACAUGAAAUGCGACUGUGAGUUACAGUCGCAGCUUCGGCUGCCGUUUGAGUUCCAGUUACAGUUUCAGUUGCAUUUUCAUUUUCAUUUUUGUUUCCG
..((((((((.......)).....((((((((((((((...)))))))(((((....)))))............................)))))))........))))))...... (-22.24 = -23.55 +   1.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,579,760 – 13,579,861
Length 101
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 83.20
Mean single sequence MFE -28.13
Consensus MFE -19.50
Energy contribution -20.78
Covariance contribution 1.28
Combinations/Pair 1.20
Mean z-score -1.81
Structure conservation index 0.69
SVM decision value 0.08
SVM RNA-class probability 0.574486
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13579760 101 + 20766785
AACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAUUUAUUUAGAGUGGUGCCAAGG---GG
........(((((((((((...((((.(((((((((.....))))))))))))).))))))))....((((((((((.....)))))).))))....))---). ( -31.00)
>DroSec_CAF1 132816 101 + 1
AACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAUUUAUUUAGAAUGGUGUCAAGG---GG
........(((((((((((...((((.(((((((((.....))))))))))))).))))))))....((((((((((.....)))))).))))....))---). ( -31.50)
>DroSim_CAF1 131194 101 + 1
AACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAUUUAUUUAGAAUGGUGCCAAGG---GG
........(((((((((((...((((.(((((((((.....))))))))))))).))))))))....((((((((((.....)))))).))))....))---). ( -31.40)
>DroEre_CAF1 128454 101 + 1
AAGUGCAACUCAAACGGCAGCCGAAGCUGUGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAUUUAUUUAGAGUGGUGCCAAGG---AG
........(((....((((.((((((.(((((((((.....))))))))))))).................((((((.....)))))).))))))...)---)) ( -29.40)
>DroYak_CAF1 132623 101 + 1
AAGUGCGACUCCAACGACAGCCGAAGCUGUGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAUUUAUUUAGAGUGGUGGCAAGG---GG
...(((.((..((((((((...((((.(((((((((.....))))))))))))).)))))))..........(((((.....))))))..)).)))...---.. ( -31.80)
>DroAna_CAF1 125367 88 + 1
----------------GGGGCCAAAACUGCGACCGUAAUUCACUAACAAAUUUCGUGUUGUUUUAAUUACUUUCUGAUUUAUUUAACGGAGCGACUCGGUGGUC
----------------(.((......)).)((((((((((....(((((........)))))..))))))...............((.(((...))).)))))) ( -13.70)
>consensus
AACUGGAACUCAAACGGCAGCCGAAGCUGCGACUGUAACUCACAGUCGCAUUUCAUGUUGUUUUAAUUACUUUCUGAUUUAUUUAGAGUGGUGCCAAGG___GG
...............((((.((((((.(((((((((.....))))))))))))).................((((((.....)))))).))))))......... (-19.50 = -20.78 +   1.28)

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 11:12:38 2006