Locus 6209

Sequence ID 3R_DroMel_CAF1
Location 16,198,785 – 16,198,985
Length 200
Max. P 0.955458
window10127 window10128 window10129 window10130

overview

Window 7

Location 16,198,785 – 16,198,905
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -26.60
Consensus MFE -26.60
Energy contribution -26.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.53
Structure conservation index 1.00
SVM decision value 1.45
SVM RNA-class probability 0.955458
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16198785 120 + 27905053
CUUUUGCUCUUUACUGGUCUGACUUUUUAGCAUAUUUCCCUUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAG
.............(((((..(((...........................((((..(((.((((((((......))))))))..)))..)))).((((.....))))...)))..))))) ( -26.50)
>DroSec_CAF1 27984 120 + 1
UUUUUGCUCUUUACUGGUCUGACUUUUUAGCAUAUUUCCCUUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAG
.............(((((..(((...........................((((..(((.((((((((......))))))))..)))..)))).((((.....))))...)))..))))) ( -26.50)
>DroEre_CAF1 28196 120 + 1
UUUUUGCUCUUUACUGGUCUGACUUUUUAGCAUAUUUCCCUUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAG
.............(((((..(((...........................((((..(((.((((((((......))))))))..)))..)))).((((.....))))...)))..))))) ( -26.50)
>DroYak_CAF1 30394 120 + 1
UUUUUGCACUUUACUGGUCUGACUUUUUAGCAUAUUUCCCUUAACAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCUCCGUCCAGCCAG
.............(((((..(((...........................((((..(((.((((((((......))))))))..)))..)))).((((.....))))...)))..))))) ( -26.90)
>consensus
UUUUUGCUCUUUACUGGUCUGACUUUUUAGCAUAUUUCCCUUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAG
.............(((((..(((...........................((((..(((.((((((((......))))))))..)))..)))).((((.....))))...)))..))))) (-26.60 = -26.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,198,825 – 16,198,945
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.75
Mean single sequence MFE -32.97
Consensus MFE -31.77
Energy contribution -31.65
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.36
Structure conservation index 0.96
SVM decision value 0.98
SVM RNA-class probability 0.894392
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16198825 120 + 27905053
UUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAGGAUUUUAUUCUGGUCUGGGAAUCAUCGAGGCUCAUUACGU
...((((....(((..(((.((((((((......))))))))..)))..)))))))........((((.((((((((((((((...))))))).)))))......)).))))........ ( -33.30)
>DroSec_CAF1 28024 120 + 1
UUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAGGAUUUUAUUCUGGUCUGGGAAUCAUCGAGGCUCAUUACGU
...((((....(((..(((.((((((((......))))))))..)))..)))))))........((((.((((((((((((((...))))))).)))))......)).))))........ ( -33.30)
>DroEre_CAF1 28236 120 + 1
UUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAGGAUUUUGUUCUGGUCUGGGAAUCAUCGAGGCUCAUUACGU
...((((....(((..(((.((((((((......))))))))..)))..)))))))........((((.((((((((((((((...))))))).)))))......)).))))........ ( -33.60)
>DroYak_CAF1 30434 120 + 1
UUAACAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCUCCGUCCAGCCAGGAUUUUAUUCUGGUCUGGGAAUCAUCGAGGCUCAUUACGU
..........((((..(((.((((((((......))))))))..)))..)))).((((.....))))..((((((((((((((...))))))).))))((..(.....)..))...))). ( -31.70)
>consensus
UUAGCAUAUUUUUAUUUGUAGCAUUUAUAAGUGAAUAAAUGCGCGCAUUUAAAUGCCACUUUCUGGCCCCGUCCAGCCAGGAUUUUAUUCUGGUCUGGGAAUCAUCGAGGCUCAUUACGU
...((((....(((..(((.((((((((......))))))))..)))..)))))))........((((.((((((((((((((...))))))).)))))......)).))))........ (-31.77 = -31.65 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,198,825 – 16,198,945
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.75
Mean single sequence MFE -31.77
Consensus MFE -31.35
Energy contribution -31.60
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.77
Structure conservation index 0.99
SVM decision value 1.42
SVM RNA-class probability 0.952098
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16198825 120 - 27905053
ACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGCAUUUAUUCACUUAUAAAUGCUACAAAUAAAAAUAUGCUAA
.((((.((.(((((((....))((((.((((.........))))))))..)))))))....((((((((((((((....))))..........)))))))))).........)))).... ( -32.90)
>DroSec_CAF1 28024 120 - 1
ACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGCAUUUAUUCACUUAUAAAUGCUACAAAUAAAAAUAUGCUAA
.((((.((.(((((((....))((((.((((.........))))))))..)))))))....((((((((((((((....))))..........)))))))))).........)))).... ( -32.90)
>DroEre_CAF1 28236 120 - 1
ACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAACAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGCAUUUAUUCACUUAUAAAUGCUACAAAUAAAAAUAUGCUAA
.((((.((.(((((((....))((((.((((.........))))))))..)))))))....((((((((((((((....))))..........)))))))))).........)))).... ( -32.90)
>DroYak_CAF1 30434 120 - 1
ACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGAGCCAGAAAGUGGCAUUUAAAUGCGCGCAUUUAUUCACUUAUAAAUGCUACAAAUAAAAAUAUGUUAA
(((((.((.((..(((....))((((.((((.........))))))))..)..))))....((((((((((((((....))))..........)))))))))).........)))))... ( -28.40)
>consensus
ACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGCAUUUAUUCACUUAUAAAUGCUACAAAUAAAAAUAUGCUAA
.((((.((.(((((((....))((((.((((.........))))))))..)))))))....((((((((((((((....))))..........)))))))))).........)))).... (-31.35 = -31.60 +   0.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,198,865 – 16,198,985
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 99.17
Mean single sequence MFE -36.21
Consensus MFE -35.96
Energy contribution -36.21
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.58
Structure conservation index 0.99
SVM decision value 1.18
SVM RNA-class probability 0.926703
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16198865 120 - 27905053
CGUGCAUAAAAUGCUGAGCACAAAAAAAUUUCCACUGCAUACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGC
(((((((.(((((((..(((...............)))..((....((.(((((((....))((((.((((.........))))))))..)))))))....)))))))))..))))))). ( -37.56)
>DroSec_CAF1 28064 120 - 1
CGUGCAUAAAAUGCUGAGCACAAAAAAAUUUCCACUGCAUACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGC
(((((((.(((((((..(((...............)))..((....((.(((((((....))((((.((((.........))))))))..)))))))....)))))))))..))))))). ( -37.56)
>DroEre_CAF1 28276 120 - 1
CGUGCAUAAAAUGCUGAGCACAAAAAAAUUUCCACUGCAUACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAACAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGC
(((((((.(((((((..(((...............)))..((....((.(((((((....))((((.((((.........))))))))..)))))))....)))))))))..))))))). ( -37.56)
>DroYak_CAF1 30474 120 - 1
CGUGCAUAAAAUGCUGAGCACAAAAAAAUUUCCACUGCAUACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGAGCCAGAAAGUGGCAUUUAAAUGCGCGC
(((((((.(((((((..(((...............)))..((....((.((..(((....))((((.((((.........))))))))..)..))))....)))))))))..))))))). ( -32.16)
>consensus
CGUGCAUAAAAUGCUGAGCACAAAAAAAUUUCCACUGCAUACGUAAUGAGCCUCGAUGAUUCCCAGACCAGAAUAAAAUCCUGGCUGGACGGGGCCAGAAAGUGGCAUUUAAAUGCGCGC
(((((((.(((((((..(((...............)))..((....((.(((((((....))((((.((((.........))))))))..)))))))....)))))))))..))))))). (-35.96 = -36.21 +   0.25)

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 12:15:40 2006