Locus 7081

Sequence ID 2L_DroMel_CAF1
Location 19,809,985 – 19,810,265
Length 280
Max. P 0.795868
window11303 window11304 window11305 window11306 window11307

overview

Window 3

Location 19,809,985 – 19,810,105
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -38.77
Consensus MFE -35.74
Energy contribution -35.63
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.80
Structure conservation index 0.92
SVM decision value 0.33
SVM RNA-class probability 0.690151
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19809985 120 + 22407834
AGUGCUAACGCCCAGUAAACCCAGCAGGCUCAUUCCAAUCACCUGGGAUUCAGGUGCCGAUUGACUCAGCUCGCUGUUGAGUCCCUCGAAUACCUGUUGCAGUUCGUAGAUAUAGUUAUA
.(.((....)).).(..(((.(((((((...........((((((.....)))))).(((..((((((((.....))))))))..)))....)))))))..)))..)............. ( -36.10)
>DroSec_CAF1 76858 120 + 1
ACUGCUGACGGCCAGUAAGCCCAACAGGCUCAUUCCAAUCACCUGGGCUUCAGGUGCCGAUUGACUCAGCUUGCUGUUGAGUCCCUCGAACACCUGUUGCAGUUCGAAGAUGUAGUUAUA
(((((....(((......)))(((((((...........((((((.....)))))).(((..((((((((.....))))))))..)))....)))))))............))))).... ( -40.10)
>DroSim_CAF1 78446 120 + 1
ACUGCUGACGGCCAGUAAGCCCAACAGGCUCAUUCCAAUCACCUGGGAUUCAGGUGCCGAUUGACUCAGCUUGCUGUUGAGUCCCUCGAACACCUGUUGCAGUUCGAAGAUGUAGUUAUA
(((((....(((......)))(((((((...........((((((.....)))))).(((..((((((((.....))))))))..)))....)))))))............))))).... ( -40.10)
>consensus
ACUGCUGACGGCCAGUAAGCCCAACAGGCUCAUUCCAAUCACCUGGGAUUCAGGUGCCGAUUGACUCAGCUUGCUGUUGAGUCCCUCGAACACCUGUUGCAGUUCGAAGAUGUAGUUAUA
..(((((.....)))))(((.(((((((...........((((((.....)))))).(((..((((((((.....))))))))..)))....)))))))..)))................ (-35.74 = -35.63 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,809,985 – 19,810,105
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -41.33
Consensus MFE -37.91
Energy contribution -38.47
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.98
Structure conservation index 0.92
SVM decision value 0.56
SVM RNA-class probability 0.782581
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19809985 120 - 22407834
UAUAACUAUAUCUACGAACUGCAACAGGUAUUCGAGGGACUCAACAGCGAGCUGAGUCAAUCGGCACCUGAAUCCCAGGUGAUUGGAAUGAGCCUGCUGGGUUUACUGGGCGUUAGCACU
...................((((((((((..((((..((((((.(.....).))))))..))))((((((.....))))))..........))))(((.((....)).)))))).))).. ( -36.40)
>DroSec_CAF1 76858 120 - 1
UAUAACUACAUCUUCGAACUGCAACAGGUGUUCGAGGGACUCAACAGCAAGCUGAGUCAAUCGGCACCUGAAGCCCAGGUGAUUGGAAUGAGCCUGUUGGGCUUACUGGCCGUCAGCAGU
.................((((((((((((((((((..((((((.(.....).))))))..))..((((((.....))))))....))))..))))))).((((....))))....))))) ( -43.80)
>DroSim_CAF1 78446 120 - 1
UAUAACUACAUCUUCGAACUGCAACAGGUGUUCGAGGGACUCAACAGCAAGCUGAGUCAAUCGGCACCUGAAUCCCAGGUGAUUGGAAUGAGCCUGUUGGGCUUACUGGCCGUCAGCAGU
.................((((((((((((((((((..((((((.(.....).))))))..))..((((((.....))))))....))))..))))))).((((....))))....))))) ( -43.80)
>consensus
UAUAACUACAUCUUCGAACUGCAACAGGUGUUCGAGGGACUCAACAGCAAGCUGAGUCAAUCGGCACCUGAAUCCCAGGUGAUUGGAAUGAGCCUGUUGGGCUUACUGGCCGUCAGCAGU
.................((((((((((((((((((..((((((.(.....).))))))..))..((((((.....))))))....))))..))))))).((((....))))....))))) (-37.91 = -38.47 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,810,025 – 19,810,145
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -42.23
Consensus MFE -39.27
Energy contribution -39.50
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.93
SVM decision value 0.29
SVM RNA-class probability 0.670559
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19810025 120 + 22407834
ACCUGGGAUUCAGGUGCCGAUUGACUCAGCUCGCUGUUGAGUCCCUCGAAUACCUGUUGCAGUUCGUAGAUAUAGUUAUAUUUCUCGCCAGUUGUGCCUCGCUGUUUGAGACUCUUGCCC
..(((((...((((((.(((..((((((((.....))))))))..)))..))))))...)....((.(((.(((....))).)))))))))......((((.....)))).......... ( -32.40)
>DroSec_CAF1 76898 120 + 1
ACCUGGGCUUCAGGUGCCGAUUGACUCAGCUUGCUGUUGAGUCCCUCGAACACCUGUUGCAGUUCGAAGAUGUAGUUAUAUUUCUCGCCAGUGGUGCCUCGCUGGCGGAGACUCUUGCCC
....((((..((((((.(((..((((((((.....))))))))..)))..))))))(((((.........))))).....((((.(((((((((....))))))))))))).....)))) ( -48.80)
>DroSim_CAF1 78486 120 + 1
ACCUGGGAUUCAGGUGCCGAUUGACUCAGCUUGCUGUUGAGUCCCUCGAACACCUGUUGCAGUUCGAAGAUGUAGUUAUAUUUCUCGCCAGUGGUGCCUCGCUGGCGGAGACUCUUGCCC
....(((...((((((.(((..((((((((.....))))))))..)))..))))))(((((.........))))).....((((.(((((((((....)))))))))))))......))) ( -45.50)
>consensus
ACCUGGGAUUCAGGUGCCGAUUGACUCAGCUUGCUGUUGAGUCCCUCGAACACCUGUUGCAGUUCGAAGAUGUAGUUAUAUUUCUCGCCAGUGGUGCCUCGCUGGCGGAGACUCUUGCCC
....(((...((((((.(((..((((((((.....))))))))..)))..))))))..........................((((((((((((....)))))))).))))......))) (-39.27 = -39.50 +   0.23)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,810,025 – 19,810,145
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -41.67
Consensus MFE -35.33
Energy contribution -36.67
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.85
SVM decision value 0.60
SVM RNA-class probability 0.795868
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19810025 120 - 22407834
GGGCAAGAGUCUCAAACAGCGAGGCACAACUGGCGAGAAAUAUAACUAUAUCUACGAACUGCAACAGGUAUUCGAGGGACUCAACAGCGAGCUGAGUCAAUCGGCACCUGAAUCCCAGGU
(((...(((((((.....((.((......)).)).(((.(((....))).))).((((.(((.....))))))).)))))))..(((.(.(((((.....))))).))))...))).... ( -35.20)
>DroSec_CAF1 76898 120 - 1
GGGCAAGAGUCUCCGCCAGCGAGGCACCACUGGCGAGAAAUAUAACUACAUCUUCGAACUGCAACAGGUGUUCGAGGGACUCAACAGCAAGCUGAGUCAAUCGGCACCUGAAGCCCAGGU
((((..(((((((((((((.(......).)))))).)).............((((((((.((.....)))))))))))))))..(((...(((((.....)))))..)))..)))).... ( -47.30)
>DroSim_CAF1 78486 120 - 1
GGGCAAGAGUCUCCGCCAGCGAGGCACCACUGGCGAGAAAUAUAACUACAUCUUCGAACUGCAACAGGUGUUCGAGGGACUCAACAGCAAGCUGAGUCAAUCGGCACCUGAAUCCCAGGU
(((...(((((((((((((.(......).)))))).)).............((((((((.((.....)))))))))))))))..(((...(((((.....)))))..)))...))).... ( -42.50)
>consensus
GGGCAAGAGUCUCCGCCAGCGAGGCACCACUGGCGAGAAAUAUAACUACAUCUUCGAACUGCAACAGGUGUUCGAGGGACUCAACAGCAAGCUGAGUCAAUCGGCACCUGAAUCCCAGGU
(((......((((.(((((.(......).)))))))))..........................(((((((.(((..((((((.(.....).))))))..))))))))))...))).... (-35.33 = -36.67 +   1.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,810,145 – 19,810,265
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.72
Mean single sequence MFE -35.11
Consensus MFE -32.31
Energy contribution -31.87
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.76
Structure conservation index 0.92
SVM decision value 0.23
SVM RNA-class probability 0.645638
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19810145 120 - 22407834
UGGCAUUCAAAUCCAUAAUAUGAUGUCACUCACCAUCAAAUUCGUGCAACAAGUUGUGGACACAGUUCCGCUUGAACAACGUGGACCGGGAACGGCUGCCCUCCAGGCCUAUGCCAACAA
((((((.....((((((((.((.((.(((..............))))).)).)))))))).........(((((......(..(.(((....))))..)....)))))..)))))).... ( -33.94)
>DroSec_CAF1 77018 120 - 1
UGGCAUUCAAAUCCAUAAUAUGAUGUCACUCACCAUCAAAUUCGUGCAGCAAGUUGUGGAUAGCGUUCCGGUUGAACAACGUGGACCGGGAACGGCUACCCUCCAGGCCUAUGCCGACAA
.(((((....(((((((((.((.((.(((..............))))).)).)))))))))...(((((((((.(......).)))).)))))((((........)))).)))))..... ( -37.04)
>DroSim_CAF1 78606 120 - 1
UGGCAUUCAAAUCCAUAAUAUGAUGUCACUCACCCUCAAAUUCGUGCAGCAAGUUGUGGACAGCGUUCCGAUUGAACAACGUGGACCGGGAACGGCUACCCUACAGGCCUAUGCCAACAA
((((((.....((((((((.((.((.(((..............))))).)).))))))))..((((((.....))))...((((.(((....))))))).......))..)))))).... ( -34.34)
>consensus
UGGCAUUCAAAUCCAUAAUAUGAUGUCACUCACCAUCAAAUUCGUGCAGCAAGUUGUGGACAGCGUUCCGAUUGAACAACGUGGACCGGGAACGGCUACCCUCCAGGCCUAUGCCAACAA
((((((.....((((((((.((.((.(((..............))))).)).))))))))....((((.....))))...((((.(((....)))))))...........)))))).... (-32.31 = -31.87 +  -0.44)

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 12:27:03 2006