Locus 730

Sequence ID 3R_DroMel_CAF1
Location 2,607,194 – 2,607,474
Length 280
Max. P 0.976226
window1149 window1150 window1151 window1152

overview

Window 9

Location 2,607,194 – 2,607,314
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.31
Mean single sequence MFE -37.12
Consensus MFE -34.22
Energy contribution -34.23
Covariance contribution 0.00
Combinations/Pair 1.13
Mean z-score -2.34
Structure conservation index 0.92
SVM decision value 1.76
SVM RNA-class probability 0.975858
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2607194 120 - 27905053
UUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUAGGGGAUUGUAUUUGUGGAAAGUUCGGGGAUGGUUUCCGACGUGACAUUUGUCCUGUGUGACGGGGAGUUUCACUAAAGUAAA
...(((((((((.....)))))))))((((((((((((((........))))))))))))))..((.(((.((((..(((.((((.......)))).))).))))..)))))........ ( -38.30)
>DroSim_CAF1 71200 120 - 1
UUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUGGGGGAUUGUAUUUGUGGAAAGUUCGGGGAUGGUUUUCGACGUGACAUGUGCCCUGUGUGACGGGGAGUUUCACUAAAGUAAA
...(((((((((.....)))))))))(((((((((((..(........)..)))))))))))(..((......))..)((((.((...(((((.....))))).)).))))......... ( -38.80)
>DroEre_CAF1 76080 120 - 1
UUAUUAGCAGCUUAGGCAGCUGUUAAGAGCUUUUCAUAGGGGAUUGUAUUUGUGGAAAGUUUGGGGAUGGUUUCCGACGUGACAUUUGUCCUCUGUGACGGGGAGUUUCAAUAAAGUAAA
...(((((((((.....)))))))))(((((((((((((((((((((...((((((((.(........).))))).)))..)))...)))))))))))...)))))))............ ( -37.00)
>DroYak_CAF1 74666 120 - 1
UUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUAGGGGAUUCUAUUUGUAGAAAGUUCGGGGAUGGUUUCCGACGUGACAUUUGCCCUCUGGAAUGGGGAGUUUCACUAAAGUAAA
...(((((((((.....)))))))))((((((..((((((((.(((((....))))).(((((.(((.....)))..)).)))......)))))...)))..))))))............ ( -34.40)
>consensus
UUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUAGGGGAUUGUAUUUGUGGAAAGUUCGGGGAUGGUUUCCGACGUGACAUUUGCCCUCUGUGACGGGGAGUUUCACUAAAGUAAA
...(((((((((.....)))))))))((((((((((((((........)))))))))))))).((((....))))...((((.((...(((((.....))))).)).))))......... (-34.22 = -34.23 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,607,234 – 2,607,354
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -42.35
Consensus MFE -41.40
Energy contribution -41.40
Covariance contribution -0.00
Combinations/Pair 1.10
Mean z-score -2.32
Structure conservation index 0.98
SVM decision value 1.77
SVM RNA-class probability 0.976226
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2607234 120 - 27905053
CCACAUCCGCACUGACCAAUUCCUGGCCUGUGUCCAUUCGUUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUAGGGGAUUGUAUUUGUGGAAAGUUCGGGGAUGGUUUCCGACGU
...(((((((((.(.(((.....))).).))))((........(((((((((.....)))))))))((((((((((((((........)))))))))))))))))))))........... ( -41.30)
>DroSim_CAF1 71240 120 - 1
CCACAUCCGCACUGACCAAUUCCUGGCCUGUGUCCAUUCGUUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUGGGGGAUUGUAUUUGUGGAAAGUUCGGGGAUGGUUUUCGACGU
...(((((((((.(.(((.....))).).))))((........(((((((((.....)))))))))(((((((((((..(........)..))))))))))))))))))........... ( -40.80)
>DroEre_CAF1 76120 120 - 1
CCACAUCCACACUGACCAAUUCCUGGCCGGUGUCCAUUCGUUAUUAGCAGCUUAGGCAGCUGUUAAGAGCUUUUCAUAGGGGAUUGUAUUUGUGGAAAGUUUGGGGAUGGUUUCCGACGU
...(((((((((((.(((.....))).))))))((........(((((((((.....)))))))))((((((((((((((........)))))))))))))))))))))........... ( -42.00)
>DroYak_CAF1 74706 120 - 1
CCACAUCCGCACUGACCAAUUCCUGGUCGGUGUCCAUUCGUUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUAGGGGAUUCUAUUUGUAGAAAGUUCGGGGAUGGUUUCCGACGU
...(((((((((((((((.....))))))))))((........(((((((((.....)))))))))(((((((..(((((........)))))..))))))))))))))........... ( -45.30)
>consensus
CCACAUCCGCACUGACCAAUUCCUGGCCGGUGUCCAUUCGUUAUUAGCAGCUUAGGCAGCUGUUGAGAGCUUUUCAUAGGGGAUUGUAUUUGUGGAAAGUUCGGGGAUGGUUUCCGACGU
...(((((((((((.(((.....))).))))))((........(((((((((.....)))))))))((((((((((((((........)))))))))))))))))))))........... (-41.40 = -41.40 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,607,314 – 2,607,434
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.52
Mean single sequence MFE -34.45
Consensus MFE -31.12
Energy contribution -32.25
Covariance contribution 1.12
Combinations/Pair 1.06
Mean z-score -1.45
Structure conservation index 0.90
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2607314 120 + 27905053
CGAAUGGACACAGGCCAGGAAUUGGUCAGUGCGGAUGUGGGUGUCUCCUUUACCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUG
.....((((((.((((((...))))))(((((((((.((((((.......)))))).))))........................((((.....)))))))))..........)))))). ( -35.20)
>DroSim_CAF1 71320 118 + 1
CGAAUGGACACAGGCCAGGAAUUGGUCAGUGCGGAUGUGGGUGU--CCUUUACCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUG
.....((((((.((((((...))))))(((((((((.((((((.--....)))))).))))........................((((.....)))))))))..........)))))). ( -35.50)
>DroEre_CAF1 76200 118 + 1
CGAAUGGACACCGGCCAGGAAUUGGUCAGUGUGGAUGUGGGUGU--CCUUUUCCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUG
.....(((((((((((((...))))))((((.((((.((((...--......)))).)))).......................(((((.....))))))))).........))))))). ( -33.40)
>DroYak_CAF1 74786 117 + 1
CGAAUGGACACCGACCAGGAAUUGGUCAGUGCGGAUGUGGAUGU--CCUUUUCCCAAGUCCA-UUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCUCUAUUCAUUAAGGUGUCUG
.....(((((((((((((...))))))((((..(((((((....--)).....((((((...-.......)))))).)))))..))))........................))))))). ( -33.70)
>consensus
CGAAUGGACACAGGCCAGGAAUUGGUCAGUGCGGAUGUGGGUGU__CCUUUACCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUG
.....(((((((((((((...))))))(((((((((.((((((.......)))))).))))........................((((.....))))))))).........))))))). (-31.12 = -32.25 +   1.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,607,354 – 2,607,474
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.28
Mean single sequence MFE -31.30
Consensus MFE -30.88
Energy contribution -29.75
Covariance contribution -1.12
Combinations/Pair 1.21
Mean z-score -1.23
Structure conservation index 0.99
SVM decision value -0.01
SVM RNA-class probability 0.528035
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2607354 120 + 27905053
GUGUCUCCUUUACCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUGUGGGUGGCUUUUCGAAUAGGGUGGCCAUUAGCCCACACCG
(((..........((((((...........))))))........(((((.....))))))))..........(((((..((..((((((.(((.....))).))))))..))..))))). ( -30.20)
>DroSim_CAF1 71360 118 + 1
GUGU--CCUUUACCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUGUGGGUGGCUUCUCGAAUGGGGUGGCCAUUAGCCCACACCG
(((.--.((((..((((((...........)))))).....(((....)))..))))..)))..........(((((..((..((((((.(((.....))).))))))..))..))))). ( -32.70)
>DroEre_CAF1 76240 118 + 1
GUGU--CCUUUUCCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUGCGGAUGGCUUCUCGAAUGGGGUGGUCAUUAGCCCACACCC
(((.--.((((..((((((...........)))))).....(((....)))..))))..)))..........(((((..((.(((((((.(((.....))).))))))).))..))))). ( -30.00)
>DroYak_CAF1 74826 117 + 1
AUGU--CCUUUUCCCAAGUCCA-UUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCUCUAUUCAUUAAGGUGUCUGUGGGUGGCUUCUCGAAUAGAGUGGCCAUCAGCCCACACCC
....--.......((((((...-.......))))))........(((((.....))))).............(((((..((.(((((((.(((.....))).))))))).))..))))). ( -32.30)
>consensus
GUGU__CCUUUACCCAAGUCCCUUUUAAUUACUUGGAAUAUCAACACUUUGUCAAAGUGCGCUAUUCAUUAAGGUGUCUGUGGGUGGCUUCUCGAAUAGGGUGGCCAUUAGCCCACACCC
.............((((((...........))))))........(((((.....))))).............(((((..((.(((((((.(((.....))).))))))).))..))))). (-30.88 = -29.75 +  -1.12)

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 09:50:27 2006