Locus 4687

Sequence ID 3R_DroMel_CAF1
Location 12,337,858 – 12,337,999
Length 141
Max. P 0.995841
window7697 window7698 window7699 window7700

overview

Window 7

Location 12,337,858 – 12,337,961
Length 103
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 89.26
Mean single sequence MFE -22.02
Consensus MFE -17.08
Energy contribution -17.48
Covariance contribution 0.40
Combinations/Pair 1.09
Mean z-score -3.31
Structure conservation index 0.78
SVM decision value 2.62
SVM RNA-class probability 0.995841
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12337858 103 + 27905053
AUUAU-CCCACCUUUGCUAUAGCACUUAUGUAUCAUUAAGAAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAUGGGCUA
.....-((((....(((....)))...........((((((((...........))))))))((...(((((((.........)))))))...))..))))... ( -16.80)
>DroSec_CAF1 6749 104 + 1
AUUUUCCCCACCUCUGCUAUAUCACUUAUAUGUCAUUAAGAAAUUCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAGGGGUCA
.........((((((((..(((.(((((...((.(((((((.....))))))).))...))))).)))((((((.........))))))....).))))))).. ( -19.80)
>DroSim_CAF1 5881 103 + 1
AUUAU-CCCACCUCUGCUAUAUCACUUACAUGUCAUUAAGAAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCGGCCAGGGGCCA
.....-....((((((((.(((.(((((...((.(((((((.....))))))).))...))))).)))((((((.........))))))...)).))))))... ( -19.30)
>DroEre_CAF1 6208 103 + 1
AUUAU-GCCGCCCCUGCAAUAGCACUUAUGUAUCAUUAAGAAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAGGGGCUA
.....-...((((((((((((((((....))....((((((((...........)))))))))))))(((((((.........)))))))..)).))))))).. ( -27.70)
>DroYak_CAF1 2242 103 + 1
AUAAU-CCCACCCCGGCAAUAGCACUUAUGAAUCAUAAAGAAUUCCUUUUAAUUAUUCUUGAGCUAUAGUUUUCAACUUUUCUGAAAACUUCCGCCAGGGGCUA
.....-....(((((((.(((((...((((...))))((((((...........))))))..)))))((((((((.......))))))))...))).))))... ( -26.50)
>consensus
AUUAU_CCCACCUCUGCUAUAGCACUUAUGUAUCAUUAAGAAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAGGGGCUA
..........((((((...................((((((((...........))))))))((...(((((((.........)))))))...))))))))... (-17.08 = -17.48 +   0.40)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,337,858 – 12,337,961
Length 103
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 89.26
Mean single sequence MFE -23.10
Consensus MFE -15.34
Energy contribution -15.18
Covariance contribution -0.16
Combinations/Pair 1.14
Mean z-score -2.26
Structure conservation index 0.66
SVM decision value -0.05
SVM RNA-class probability 0.506536
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12337858 103 - 27905053
UAGCCCAUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUUCUUAAUGAUACAUAAGUGCUAUAGCAAAGGUGGG-AUAAU
...(((((((((..(((((((((.....))))))))).......((((((...........)))))).............)))))).((....)))))-..... ( -19.00)
>DroSec_CAF1 6749 104 - 1
UGACCCCUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGAAUUUCUUAAUGACAUAUAAGUGAUAUAGCAGAGGUGGGGAAAAU
...((((.......(((((((((.....)))))))))....((((((((.............)))))..((..((((.....))))..)))))..))))..... ( -20.62)
>DroSim_CAF1 5881 103 - 1
UGGCCCCUGGCCGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUUCUUAAUGACAUGUAAGUGAUAUAGCAGAGGUGGG-AUAAU
.((((...))))..(((((((((.....)))))))))....(((((((((...........))))))..((..((((.....))))..))))).....-..... ( -19.20)
>DroEre_CAF1 6208 103 - 1
UAGCCCCUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUUCUUAAUGAUACAUAAGUGCUAUUGCAGGGGCGGC-AUAAU
..(((((((.(((.(((((((((.....))))))))).......((((((...........))))))..................))))))))))...-..... ( -26.80)
>DroYak_CAF1 2242 103 - 1
UAGCCCCUGGCGGAAGUUUUCAGAAAAGUUGAAAACUAUAGCUCAAGAAUAAUUAAAAGGAAUUCUUUAUGAUUCAUAAGUGCUAUUGCCGGGGUGGG-AUUAU
..(((((.(((((.(((((((((.....))))))))).((((........(((((.((((....)))).))))).......))))))))))))))...-..... ( -29.86)
>consensus
UAGCCCCUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUUCUUAAUGAUACAUAAGUGCUAUAGCAGAGGUGGG_AUAAU
...(((((.((...(((((((((.....))))))))).......((((((...........))))))....................))..))).))....... (-15.34 = -15.18 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,337,897 – 12,337,999
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -21.10
Consensus MFE -19.18
Energy contribution -19.06
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -1.65
Structure conservation index 0.91
SVM decision value 1.80
SVM RNA-class probability 0.977600
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12337897 102 + 27905053
AAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAUGGGCUACCAUAUUGGUCAACUUUGGCAUACUUUUAAGGCUGUUG
................(((((((....(((((((.........)))))))..(((((.((...(((.....)))...)).)))))....)))))))...... ( -19.20)
>DroSec_CAF1 6789 102 + 1
AAAUUCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAGGGGUCACCAUAUUGGUCAACUUUGGCAUACUUUUAAAGCGGUUG
.(((..((((((...............(((((((.........)))))))..((((((((...(((.....)))...)))))))).....))))))..))). ( -21.10)
>DroSim_CAF1 5920 102 + 1
AAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCGGCCAGGGGCCACCAUAUUGGUCAACUUUGGCAUACUUUUAAAGCGGUUG
....((((((((...............(((((((.........)))))))...(((((((...(((.....)))...)))))))......)))))).))... ( -20.70)
>DroEre_CAF1 6247 102 + 1
AAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAGGGGCUACCAUAUUGGUCAACUUUGGCAUACUUUUAAAGCUGUUG
.....................((((..(((((((.........)))))))..((((((((...(((.....)))...)))))))).........)))).... ( -20.40)
>DroYak_CAF1 2281 102 + 1
AAUUCCUUUUAAUUAUUCUUGAGCUAUAGUUUUCAACUUUUCUGAAAACUUCCGCCAGGGGCUACCAUAUUGGUCAACUUUGGCAUACUUUUAAAGCUGUUG
.....................((((..((((((((.......))))))))...(((((((...(((.....)))...)))))))..........)))).... ( -24.10)
>consensus
AAUUCCUUUUAAUUAUUCUUGAGUUAUAGUUUUCAACUUUUUCGAAAACUUCUGCCAGGGGCUACCAUAUUGGUCAACUUUGGCAUACUUUUAAAGCUGUUG
......................(((..(((((((.........)))))))...(((((((...(((.....)))...)))))))..........)))..... (-19.18 = -19.06 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,337,897 – 12,337,999
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -20.38
Consensus MFE -18.42
Energy contribution -17.82
Covariance contribution -0.60
Combinations/Pair 1.25
Mean z-score -1.89
Structure conservation index 0.90
SVM decision value 2.44
SVM RNA-class probability 0.993960
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12337897 102 - 27905053
CAACAGCCUUAAAAGUAUGCCAAAGUUGACCAAUAUGGUAGCCCAUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUU
......((((.......(((((..((((.((.....))))))...)))))..(((((((((.....)))))))))...................)))).... ( -21.60)
>DroSec_CAF1 6789 102 - 1
CAACCGCUUUAAAAGUAUGCCAAAGUUGACCAAUAUGGUGACCCCUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGAAUUU
......((((.......(((((..(((.(((.....))))))...)))))..(((((((((.....)))))))))..................))))..... ( -19.30)
>DroSim_CAF1 5920 102 - 1
CAACCGCUUUAAAAGUAUGCCAAAGUUGACCAAUAUGGUGGCCCCUGGCCGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUU
...((..(((((...(((.....((((((((.....)))((((...))))..(((((((((.....))))))))).))))).....))).))))).)).... ( -21.50)
>DroEre_CAF1 6247 102 - 1
CAACAGCUUUAAAAGUAUGCCAAAGUUGACCAAUAUGGUAGCCCCUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUU
......((((.......(((((..((((.((.....))))))...)))))..(((((((((.....)))))))))..................))))..... ( -19.40)
>DroYak_CAF1 2281 102 - 1
CAACAGCUUUAAAAGUAUGCCAAAGUUGACCAAUAUGGUAGCCCCUGGCGGAAGUUUUCAGAAAAGUUGAAAACUAUAGCUCAAGAAUAAUUAAAAGGAAUU
....((((.........(((((..((((.((.....))))))...)))))..(((((((((.....)))))))))..))))..................... ( -20.10)
>consensus
CAACAGCUUUAAAAGUAUGCCAAAGUUGACCAAUAUGGUAGCCCCUGGCAGAAGUUUUCGAAAAAGUUGAAAACUAUAACUCAAGAAUAAUUAAAAGGAAUU
......((((.......(((((..(((.(((.....))))))...)))))..(((((((((.....)))))))))...................)))).... (-18.42 = -17.82 +  -0.60)

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 11:36:30 2006