Locus 2023

Sequence ID X_DroMel_CAF1
Location 5,543,118 – 5,543,434
Length 316
Max. P 0.989692
window3288 window3289 window3290 window3291 window3292 window3293 window3294

overview

Window 8

Location 5,543,118 – 5,543,234
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.64
Mean single sequence MFE -25.50
Consensus MFE -18.77
Energy contribution -19.43
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.74
SVM decision value 0.30
SVM RNA-class probability 0.678520
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5543118 116 + 22224390
CUUCACUUUGAAGAGUAAAAUUUUGAUUUCGAACAUGAUGUUACCAAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAA----UUUCUAGUUGAAAUAUAA
((((.....))))............(((((((....((.(((.........((((......))))....(((((((((.....)))))))))....))----).))...))))))).... ( -25.20)
>DroSec_CAF1 5031 116 + 1
CUCCA----AAAGAGUCCAAUUUUGAUUUCGAAAACGAUGUUACCGAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAAUAAAUAUCAAGUAGAAAAAUAA
...((----(((........))))).((((......((((((.........((((......))))....(((((((((.....)))))))))........)))))).....))))..... ( -23.70)
>DroSim_CAF1 4788 116 + 1
CUUCACUUUGAAGAGUCCAAUUAUGGUUUCGAAAACGAUGUUACCGAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAA----UUUCAAGUAGAAAAGUAA
.(((((((.((((..........((((((((....))).(..((((....))))..)....)))))...(((((((((.....)))))))))......----)))))))).)))...... ( -27.60)
>consensus
CUUCACUUUGAAGAGUCCAAUUUUGAUUUCGAAAACGAUGUUACCGAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAA____UUUCAAGUAGAAAAAUAA
((((.....)))).............((((.....................((((......))))....(((((((((.....)))))))))...................))))..... (-18.77 = -19.43 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,543,118 – 5,543,234
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 87.64
Mean single sequence MFE -25.30
Consensus MFE -19.81
Energy contribution -21.03
Covariance contribution 1.23
Combinations/Pair 1.07
Mean z-score -2.28
Structure conservation index 0.78
SVM decision value 0.46
SVM RNA-class probability 0.745429
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5543118 116 - 22224390
UUAUAUUUCAACUAGAAA----UUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUUGGUAACAUCAUGUUCGAAAUCAAAAUUUUACUCUUCAAAGUGAAG
....(((((.((((((((----(...((((((..((((..(((.....)))...))))..))))))...)))))))))(((.....))).)))))......((((((......)))))). ( -24.20)
>DroSec_CAF1 5031 116 - 1
UUAUUUUUCUACUUGAUAUUUAUUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUCGGUAACAUCGUUUUCGAAAUCAAAAUUGGACUCUUU----UGGAG
.......((((...((........((..(((((((((.....)))))))))...))(((((.....((((....))))....(((....))).........)))))))...----)))). ( -24.50)
>DroSim_CAF1 4788 116 - 1
UUACUUUUCUACUUGAAA----UUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUCGGUAACAUCGUUUUCGAAACCAUAAUUGGACUCUUCAAAGUGAAG
......(((.(((((((.----......(((((((((.....)))))))))....((((((.....((((....))))....(((....))).........)))))).))).))))))). ( -27.20)
>consensus
UUAUUUUUCUACUUGAAA____UUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUCGGUAACAUCGUUUUCGAAAUCAAAAUUGGACUCUUCAAAGUGAAG
......................(((((((((((((((.....)))))))))....((((((.....((((....))))....(((....))).........))))))......)))))). (-19.81 = -21.03 +   1.23)

alignment

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secondary structure

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Window 0

Location 5,543,158 – 5,543,274
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.01
Mean single sequence MFE -26.13
Consensus MFE -21.69
Energy contribution -21.80
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.72
Structure conservation index 0.83
SVM decision value 0.91
SVM RNA-class probability 0.879006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5543158 116 + 22224390
UUACCAAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAA----UUUCUAGUUGAAAUAUAAAUAAAAGGAAAGCAAAGAAAGCCUCCAGCUAAUGGGUUUU
......((((((((((((.....((....(((((((((.....))))))))).....(----((((.....)))))..........)).......)).))))).(((.....)))))))) ( -25.60)
>DroSec_CAF1 5067 120 + 1
UUACCGAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAAUAAAUAUCAAGUAGAAAAAUAAACAAAAGGAAAGGAAAGAAAGCCUCCAGCAAAUGGGUCUU
..((((....))))......(((((..(((((((((((.....)))))))....................................(((..((........)))))))))....))))). ( -25.90)
>DroSim_CAF1 4828 116 + 1
UUACCGAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAA----UUUCAAGUAGAAAAGUAAAUAAAGGGAAAGGAAAGAAAGCCUCCUGCAAAUGGGUCUU
..((((....))))......(((((....(((((((((.....)))))))))......----((((.....))))..........((((..((........)))))).......))))). ( -26.90)
>consensus
UUACCGAAAACGGUUUCUGUAGACCAAUGCUGUUAACCAAAAUGGUUAACAGAAUGAA____UUUCAAGUAGAAAAAUAAAUAAAAGGAAAGGAAAGAAAGCCUCCAGCAAAUGGGUCUU
..(((......)))......(((((....(((((((((.....)))))))))..................................(((..((........)))))........))))). (-21.69 = -21.80 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,543,158 – 5,543,274
Length 116
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.01
Mean single sequence MFE -27.17
Consensus MFE -22.25
Energy contribution -22.37
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -3.31
Structure conservation index 0.82
SVM decision value 1.21
SVM RNA-class probability 0.930909
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5543158 116 - 22224390
AAAACCCAUUAGCUGGAGGCUUUCUUUGCUUUCCUUUUAUUUAUAUUUCAACUAGAAA----UUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUUGGUAA
.....(((..(((.((((((.......))))))............((((...((((..----.(((..(((((((((.....)))))))))...)))))))..))))..)))..)))... ( -26.90)
>DroSec_CAF1 5067 120 - 1
AAGACCCAUUUGCUGGAGGCUUUCUUUCCUUUCCUUUUGUUUAUUUUUCUACUUGAUAUUUAUUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUCGGUAA
.(((((....(((((((((.....))))).........................................(((((((.....)))))))))))..)))))......((((....)))).. ( -26.60)
>DroSim_CAF1 4828 116 - 1
AAGACCCAUUUGCAGGAGGCUUUCUUUCCUUUCCCUUUAUUUACUUUUCUACUUGAAA----UUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUCGGUAA
.(((((....(((((((((.....))))))...............((((.....))))----.......((((((((.....)))))))))))..)))))......((((....)))).. ( -28.00)
>consensus
AAGACCCAUUUGCUGGAGGCUUUCUUUCCUUUCCUUUUAUUUAUUUUUCUACUUGAAA____UUCAUUCUGUUAACCAUUUUGGUUAACAGCAUUGGUCUACAGAAACCGUUUUCGGUAA
.(((((........(((((..........)))))..................................(((((((((.....)))))))))....)))))......((((....)))).. (-22.25 = -22.37 +   0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,543,274 – 5,543,394
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -42.97
Consensus MFE -40.99
Energy contribution -41.77
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -2.66
Structure conservation index 0.95
SVM decision value 1.66
SVM RNA-class probability 0.970518
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5543274 120 + 22224390
GGGCUAUCCAAACACUUUUUGGCCAGCUGAUUGGCCAAGGACACAUGCGCUUUAUUUUCACUGUUAACGCGAAGAGCGCUCUGUAUUGGCCAAGCCAACUUCGACAUCGAACCGGGCUCG
.((((..(((((.....)))))..))))..((((((((..(((...((((((....(((.(.......).)))))))))..))).))))))))(((...((((....))))...)))... ( -40.70)
>DroSec_CAF1 5187 120 + 1
GGGCUAUCCAAACUCUUUUUGGCCAGCUGAUUGGCCAAGGACACAUGCGCUUUAUUUUCACUGUUAACGCGAAGAGCGCUCUGUCUUGGCCAAGCCAAGUUCGACAUCGAACCGGGCUCG
.((((..(((((.....)))))..))))..(((((((((.(((...((((((....(((.(.......).)))))))))..))))))))))))(((..(((((....)))))..)))... ( -46.90)
>DroSim_CAF1 4944 120 + 1
GAUCUAUCCAAACUCUUUUUGGCCAGCUGAUUGGCCAAGGACACAUGCGCUUUAAUUUCACUGUUAACGCGAAGAGCGCUCUGUCUUGGCCAAGCCAAGUUCGACAUCGAACCGGGCUCG
...((..(((((.....)))))..))....(((((((((.(((...((((((....(((.(.......).)))))))))..))))))))))))(((..(((((....)))))..)))... ( -41.30)
>consensus
GGGCUAUCCAAACUCUUUUUGGCCAGCUGAUUGGCCAAGGACACAUGCGCUUUAUUUUCACUGUUAACGCGAAGAGCGCUCUGUCUUGGCCAAGCCAAGUUCGACAUCGAACCGGGCUCG
.((((..(((((.....)))))..))))..(((((((((.(((...((((((....(((.(.......).)))))))))..))))))))))))(((..(((((....)))))..)))... (-40.99 = -41.77 +   0.78)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,543,274 – 5,543,394
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -48.47
Consensus MFE -46.53
Energy contribution -47.53
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.63
Structure conservation index 0.96
SVM decision value 2.18
SVM RNA-class probability 0.989692
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5543274 120 - 22224390
CGAGCCCGGUUCGAUGUCGAAGUUGGCUUGGCCAAUACAGAGCGCUCUUCGCGUUAACAGUGAAAAUAAAGCGCAUGUGUCCUUGGCCAAUCAGCUGGCCAAAAAGUGUUUGGAUAGCCC
.(((((.(.((((....)))).).)))))((((((((((..(((((.(((((.......))))).....))))).)))))...))))).....((((.(((((.....))))).)))).. ( -44.30)
>DroSec_CAF1 5187 120 - 1
CGAGCCCGGUUCGAUGUCGAACUUGGCUUGGCCAAGACAGAGCGCUCUUCGCGUUAACAGUGAAAAUAAAGCGCAUGUGUCCUUGGCCAAUCAGCUGGCCAAAAAGAGUUUGGAUAGCCC
.(((((.((((((....)))))).)))))((((((((((.((((((.(((((.......))))).....))))).).))).))))))).....((((.(((((.....))))).)))).. ( -52.10)
>DroSim_CAF1 4944 120 - 1
CGAGCCCGGUUCGAUGUCGAACUUGGCUUGGCCAAGACAGAGCGCUCUUCGCGUUAACAGUGAAAUUAAAGCGCAUGUGUCCUUGGCCAAUCAGCUGGCCAAAAAGAGUUUGGAUAGAUC
.(((((.((((((....)))))).)))))((((((((((.((((((.(((((.......))))).....))))).).))).)))))))......(((.(((((.....))))).)))... ( -49.00)
>consensus
CGAGCCCGGUUCGAUGUCGAACUUGGCUUGGCCAAGACAGAGCGCUCUUCGCGUUAACAGUGAAAAUAAAGCGCAUGUGUCCUUGGCCAAUCAGCUGGCCAAAAAGAGUUUGGAUAGCCC
.(((((.((((((....)))))).)))))((((((((((.((((((.(((((.......))))).....))))).).))).))))))).....((((.(((((.....))))).)))).. (-46.53 = -47.53 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,543,314 – 5,543,434
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -41.87
Consensus MFE -39.80
Energy contribution -40.47
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.95
SVM decision value 0.47
SVM RNA-class probability 0.749677
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5543314 120 - 22224390
AGCACUUGCUCAGCACUGGCUUGAUCUCUUGCAACCGGUUCGAGCCCGGUUCGAUGUCGAAGUUGGCUUGGCCAAUACAGAGCGCUCUUCGCGUUAACAGUGAAAAUAAAGCGCAUGUGU
.((((.(((...((.(((((..(....)..))....(((.((((((.(.((((....)))).).)))))))))....))).))(((.(((((.......))))).....)))))).)))) ( -40.30)
>DroSec_CAF1 5227 120 - 1
AGCACUUGCUCAGCACUGGCUUGAUCUCUCGCAACAGGUUCGAGCCCGGUUCGAUGUCGAACUUGGCUUGGCCAAGACAGAGCGCUCUUCGCGUUAACAGUGAAAAUAAAGCGCAUGUGU
.((((.(((...((.(((((..(....)..))....(((.((((((.((((((....)))))).)))))))))....))).))(((.(((((.......))))).....)))))).)))) ( -43.20)
>DroSim_CAF1 4984 120 - 1
AGCACUUGCUCAGCACUGACUUGAUCUCUUGCAACAGGUUCGAGCCCGGUUCGAUGUCGAACUUGGCUUGGCCAAGACAGAGCGCUCUUCGCGUUAACAGUGAAAUUAAAGCGCAUGUGU
.((((.(((...((.(((.((((....((((...)))).(((((((.((((((....)))))).))))))).)))).))).))(((.(((((.......))))).....)))))).)))) ( -42.10)
>consensus
AGCACUUGCUCAGCACUGGCUUGAUCUCUUGCAACAGGUUCGAGCCCGGUUCGAUGUCGAACUUGGCUUGGCCAAGACAGAGCGCUCUUCGCGUUAACAGUGAAAAUAAAGCGCAUGUGU
.((((.(((...((.(((((..(....)..))....(((.((((((.((((((....)))))).)))))))))....))).))(((.(((((.......))))).....)))))).)))) (-39.80 = -40.47 +   0.67)

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 10:24:26 2006