Locus 2610

Sequence ID X_DroMel_CAF1
Location 6,996,400 – 6,996,600
Length 200
Max. P 0.880558
window4273 window4274 window4275 window4276 window4277

overview

Window 3

Location 6,996,400 – 6,996,520
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -29.21
Consensus MFE -28.53
Energy contribution -28.53
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -1.50
Structure conservation index 0.98
SVM decision value 0.13
SVM RNA-class probability 0.596135
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6996400 120 + 22224390
CAGCAAUCGAAUGUGAAUAGUGAUUCCCAUGAGGGUCCAUAUAUGUAUAUGCUACUUUAUAUGUGUUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUG
..........((((((...(((((((((....)))..(((...(((((((((((..............)))))))))))....))))))))).......(((......)))..)))))). ( -27.44)
>DroSec_CAF1 18763 120 + 1
CAGCAAUCGAAUGUGAAAAGUGAUUCCCACGAGGGUCCAUAUAUGUAUGUGCUACUGUAUAUGUGUUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUG
..........((((((...(((((((.......((..((((....))))..)).(((((((((........))))))))).....))))))).......(((......)))..)))))). ( -28.50)
>DroSim_CAF1 3906 120 + 1
CAGCAAUCGAAUGUGAAAAGUGAUUCCCACGAGGGUCCAUAUAUGUAUGUGCUACUGUAUAUGUGCUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUG
..........((((((...(((((((((....)))..(((...(((((((((((..(((....)))..)))))))))))....))))))))).......(((......)))..)))))). ( -31.70)
>consensus
CAGCAAUCGAAUGUGAAAAGUGAUUCCCACGAGGGUCCAUAUAUGUAUGUGCUACUGUAUAUGUGUUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUG
..........((((((...(((((((((....)))..(((...(((((((((((..(((....)))..)))))))))))....))))))))).......(((......)))..)))))). (-28.53 = -28.53 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,996,440 – 6,996,560
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -27.30
Consensus MFE -26.73
Energy contribution -26.73
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -1.58
Structure conservation index 0.98
SVM decision value 0.26
SVM RNA-class probability 0.659142
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6996440 120 + 22224390
AUAUGUAUAUGCUACUUUAUAUGUGUUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAU
...(((((((((((..............)))))))))))...................(((((((..(((((.....((((...(((.....))).)))).....)))))...))))))) ( -25.64)
>DroSec_CAF1 18803 120 + 1
AUAUGUAUGUGCUACUGUAUAUGUGUUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAU
.(((((..(..((.(((((((((........)))))))))........((((....(((((...............)))))....))))))..)..))))).....(((((...))))). ( -26.36)
>DroSim_CAF1 3946 120 + 1
AUAUGUAUGUGCUACUGUAUAUGUGCUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAU
...(((((((((((..(((....)))..)))))))))))...................(((((((..(((((.....((((...(((.....))).)))).....)))))...))))))) ( -29.90)
>consensus
AUAUGUAUGUGCUACUGUAUAUGUGUUUUAGUAUAUGCAGCAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAU
...(((((((((((..(((....)))..)))))))))))...................(((((((..(((((.....((((...(((.....))).)))).....)))))...))))))) (-26.73 = -26.73 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,996,440 – 6,996,560
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -31.29
Consensus MFE -30.45
Energy contribution -30.23
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.98
Structure conservation index 0.97
SVM decision value 0.86
SVM RNA-class probability 0.869321
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6996440 120 - 22224390
AUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUGCUGCAUAUACUAAAACACAUAUAAAGUAGCAUAUACAUAU
.......((((........((((((.(((((((((..((.(....)))..))))).)))).(((((((((((.....))))).))))))......)))))).......))))........ ( -31.56)
>DroSec_CAF1 18803 120 - 1
AUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUGCUGCAUAUACUAAAACACAUAUACAGUAGCACAUACAUAU
.......(((.((.((...((((((.(((((((((..((.(....)))..))))).)))).(((((((((((.....))))).))))))......))))))....)).)).)))...... ( -31.20)
>DroSim_CAF1 3946 120 - 1
AUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUGCUGCAUAUACUAAAGCACAUAUACAGUAGCACAUACAUAU
.......(((.((......((((((((((..(((((..(((((((((((....))).))))))))..)))))......)))).)))))).....)).))).....(((.....))).... ( -31.10)
>consensus
AUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUGCUGCAUAUACUAAAACACAUAUACAGUAGCACAUACAUAU
.......(((.((.((...((((((.(((((((((..((.(....)))..))))).)))).(((((((((((.....))))).))))))......))))))....)).)).)))...... (-30.45 = -30.23 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,996,480 – 6,996,600
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 99.44
Mean single sequence MFE -30.00
Consensus MFE -29.57
Energy contribution -29.90
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.99
SVM decision value 0.75
SVM RNA-class probability 0.841525
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6996480 120 + 22224390
CAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAUGUAUUGGCUUACAUAAGCUUCAGUUUCUGCCCAGCAUGGU
..........(((...(((((((((..(((((.....((((...(((.....))).)))).....)))))...)))))))))...)))........(((.(((...)))...)))..... ( -28.20)
>DroSec_CAF1 18843 120 + 1
CAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAUGUAUUGGCUUACAUAAGCUUCAGUUUCUGCCCAGCUUGGU
..........(((...(((((((((..(((((.....((((...(((.....))).)))).....)))))...)))))))))...))).....((((((.(((...)))...)))))).. ( -30.90)
>DroSim_CAF1 3986 120 + 1
CAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAUGUAUUGGCUUACAUAAGCUUCAGUUUCUGCCCAGCUUGGU
..........(((...(((((((((..(((((.....((((...(((.....))).)))).....)))))...)))))))))...))).....((((((.(((...)))...)))))).. ( -30.90)
>consensus
CAAAUGAAUCGCCCACACAUGCACAUCCGCAAAUCACAUGUACAAGCGAAGUGCUCACAUAAAUAUUGCGCAUUGUGUAUGUAUUGGCUUACAUAAGCUUCAGUUUCUGCCCAGCUUGGU
..........(((...(((((((((..(((((.....((((...(((.....))).)))).....)))))...)))))))))...))).....((((((.(((...)))...)))))).. (-29.57 = -29.90 +   0.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,996,480 – 6,996,600
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -36.50
Consensus MFE -35.87
Energy contribution -36.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.98
SVM decision value 0.91
SVM RNA-class probability 0.880558
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6996480 120 - 22224390
ACCAUGCUGGGCAGAAACUGAAGCUUAUGUAAGCCAAUACAUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUG
....((((((((..........))))).))).(((.((((((.((((.(.(((((....(((((((((.....))))..)))))....))))).))))).)))))).))).......... ( -35.10)
>DroSec_CAF1 18843 120 - 1
ACCAAGCUGGGCAGAAACUGAAGCUUAUGUAAGCCAAUACAUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUG
...(((((...(((...))).)))))(((...(((.((((((.((((.(.(((((....(((((((((.....))))..)))))....))))).))))).)))))).)))....)))... ( -37.20)
>DroSim_CAF1 3986 120 - 1
ACCAAGCUGGGCAGAAACUGAAGCUUAUGUAAGCCAAUACAUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUG
...(((((...(((...))).)))))(((...(((.((((((.((((.(.(((((....(((((((((.....))))..)))))....))))).))))).)))))).)))....)))... ( -37.20)
>consensus
ACCAAGCUGGGCAGAAACUGAAGCUUAUGUAAGCCAAUACAUACACAAUGCGCAAUAUUUAUGUGAGCACUUCGCUUGUACAUGUGAUUUGCGGAUGUGCAUGUGUGGGCGAUUCAUUUG
...(((((...(((...))).)))))(((...(((.((((((.((((.(.(((((....(((((((((.....))))..)))))....))))).))))).)))))).)))....)))... (-35.87 = -36.20 +   0.33)

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 10:39:08 2006