Locus 1087

Sequence ID 2R_DroMel_CAF1
Location 4,380,241 – 4,380,401
Length 160
Max. P 0.622340
window1922 window1923 window1924

overview

Window 2

Location 4,380,241 – 4,380,361
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.50
Mean single sequence MFE -40.22
Consensus MFE -31.24
Energy contribution -29.33
Covariance contribution -1.91
Combinations/Pair 1.50
Mean z-score -1.76
Structure conservation index 0.78
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4380241 120 + 20766785
AGGGCGUGCUCAAUCUGAUCCUGGAGGCCAUUGACAAGAUCAACAUAAUCACCUCGCAGGGCUUCCUAGCCAGCUUCCUGGCCGGCGACGAGACCGGCCAGAGCUGGGAUCUCAUCUCCA
.(((.(((........(((((.(((((((..(((...(((.......)))...)))...)))))))....(((((..(((((((((.....).)))))))))))))))))).))).))). ( -47.00)
>DroVir_CAF1 60515 120 + 1
AGGGCGUGCUCAAUCUCAUACUGGAAGCCAUUGACAAGAUAAACAUUAUAACCUCGCAAGGCUUUUUAGCCAGUUUUCUGGCCGGCGACGAGACCGGCCAGAGUUGGGAUUUAAUCUCCA
.(((.((....(((((((.((((((((((.(((.(.((..............)).))))))))).....))))).(((((((((((.....).)))))))))).)))))))..)).))). ( -39.54)
>DroGri_CAF1 7358 120 + 1
AGGGUGUGCUCAAUCUAAUACUGGAGGCCAUUGACAAGAUCAACAUAAUCACCUCGCAGGGUUUUCUGGCCAGUUUUCUGGCCGGCGACGAGACCGGCCAGAGUUGGGAUCUGAUCUCGA
.(((....)))..((((....))))(((((..(((..(((.......))).((.....)))))...)))))....(((((((((((.....).))))))))))(((((((...))))))) ( -38.30)
>DroWil_CAF1 8121 120 + 1
AGGGCGUUCUUAAUCUCAUUUUAGAGGCCAUUGACAAGAUCAAUAUAAUCACUUCACAGGGAUUUUUGGCCAGUUUUCUGGCUGGCGACGAGACUGGCCAGAGUUGGGAUCUCAUUUCCA
..(((.((((.((......)).)))))))(((((.....)))))..............(((((((((((((((((((.(.(....).).))))))))))))).....))))))....... ( -33.10)
>DroMoj_CAF1 2679 120 + 1
AGGGCGUGCUCAAUCUCAUUUUGGAGGCCAUUGACAAAAUUAAUAUAAUUACAUCGCAGGGCUUCUUGGCCAGCUUCCUGGCCGGCGACGAGACUGGUCAGAGCUGGGAUCUAAUCUCAA
..(((.((..((.((((.....(((((((..(((...(((((...)))))...)))...)))))))(((((((....))))))).....)))).))..))..)))(((((...))))).. ( -35.80)
>DroAna_CAF1 6978 120 + 1
AGGGAGUUCUCAACCUCAUCCUGGAGGCUAUUGACAAGAUCAAUAUAAUUACAUCUCAGGGCUUCCUGGCCAGCUUCCUGGCCGGAGACGAGACUGGCCAAAGCUGGGACCUCAUCUCCA
((((((((((...((((......)))).((((((.....))))))............))))))))))((((((....))))))(((((.(((.(..((....))..)...))).))))). ( -47.60)
>consensus
AGGGCGUGCUCAAUCUCAUACUGGAGGCCAUUGACAAGAUCAACAUAAUCACCUCGCAGGGCUUCCUGGCCAGCUUCCUGGCCGGCGACGAGACCGGCCAGAGCUGGGAUCUCAUCUCCA
.(((....)))...........(((((((..(((...(((.......)))...)))...)))))))...((((((..((((((((........))))))))))))))............. (-31.24 = -29.33 +  -1.91)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,380,281 – 4,380,401
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.72
Mean single sequence MFE -37.37
Consensus MFE -30.78
Energy contribution -30.53
Covariance contribution -0.25
Combinations/Pair 1.33
Mean z-score -1.67
Structure conservation index 0.82
SVM decision value 0.18
SVM RNA-class probability 0.622340
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4380281 120 + 20766785
CAACAUAAUCACCUCGCAGGGCUUCCUAGCCAGCUUCCUGGCCGGCGACGAGACCGGCCAGAGCUGGGAUCUCAUCUCCACCUAUUUGUACCAACUCUUGGCCGCCAUCAUCAAGGGCAA
...........(((.(...(((.......((((((..(((((((((.....).)))))))))))))).......................(((.....)))..))).....).))).... ( -35.80)
>DroVir_CAF1 60555 120 + 1
AAACAUUAUAACCUCGCAAGGCUUUUUAGCCAGUUUUCUGGCCGGCGACGAGACCGGCCAGAGUUGGGAUUUAAUCUCCACGUACCUGUACCAACUGCUGGCCGCCAUCAUCAAGGGCAA
.............((....)).......((((((..((((((((((.....).)))))))))(((((((.......)))..(((....))))))).)))))).(((.........))).. ( -39.40)
>DroGri_CAF1 7398 120 + 1
CAACAUAAUCACCUCGCAGGGUUUUCUGGCCAGUUUUCUGGCCGGCGACGAGACCGGCCAGAGUUGGGAUCUGAUCUCGACGUAUUUGUAUCAACUGCUCGCCGCCAUCAUCAAAGGCAA
..........((((....)))).....((((((((.((((((((((.....).)))))))))((((((((...))))))))...........)))))...)))(((.........))).. ( -40.40)
>DroWil_CAF1 8161 120 + 1
CAAUAUAAUCACUUCACAGGGAUUUUUGGCCAGUUUUCUGGCUGGCGACGAGACUGGCCAGAGUUGGGAUCUCAUUUCCACAUAUUUGUAUCAACUACUCGCCGCCAUUAUCAAGGGAAA
............(((.(...(((....((((((....))))))((((.((((.((....))((((((((.......)))(((....)))..))))).)))).))))...)))...)))). ( -32.60)
>DroMoj_CAF1 2719 120 + 1
UAAUAUAAUUACAUCGCAGGGCUUCUUGGCCAGCUUCCUGGCCGGCGACGAGACUGGUCAGAGCUGGGAUCUAAUCUCAACUUAUCUCUACCAGCUACUGGCCGCCAUCAUCAAGGGCAA
...........(.(((((((....)))((((((....)))))).)))).).....((((((((((((.......................)))))).))))))(((.........))).. ( -39.10)
>DroAna_CAF1 7018 120 + 1
CAAUAUAAUUACAUCUCAGGGCUUCCUGGCCAGCUUCCUGGCCGGAGACGAGACUGGCCAAAGCUGGGACCUCAUCUCCACCUACCUGUACCAACUACUGGCCGCCAUCAUCAAGGGAAA
.............(((((((.......((((((....))))))(((((.(((.(..((....))..)...))).))))).))).((.(((.....))).)).............)))).. ( -36.90)
>consensus
CAACAUAAUCACCUCGCAGGGCUUCCUGGCCAGCUUCCUGGCCGGCGACGAGACCGGCCAGAGCUGGGAUCUCAUCUCCACCUAUCUGUACCAACUACUGGCCGCCAUCAUCAAGGGCAA
...............((........((((((((....)))))))).((.((...(((((((((((((.......................)))))).)))))))...)).))....)).. (-30.78 = -30.53 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,380,281 – 4,380,401
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.72
Mean single sequence MFE -42.48
Consensus MFE -32.90
Energy contribution -33.52
Covariance contribution 0.61
Combinations/Pair 1.17
Mean z-score -1.64
Structure conservation index 0.77
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4380281 120 - 20766785
UUGCCCUUGAUGAUGGCGGCCAAGAGUUGGUACAAAUAGGUGGAGAUGAGAUCCCAGCUCUGGCCGGUCUCGUCGCCGGCCAGGAAGCUGGCUAGGAAGCCCUGCGAGGUGAUUAUGUUG
(..(((..(((((.(.((((((.((((((((((......)))((.......))))))))))))))).).)))))((.((((((....))))))(((....)))))).))..)........ ( -46.60)
>DroVir_CAF1 60555 120 - 1
UUGCCCUUGAUGAUGGCGGCCAGCAGUUGGUACAGGUACGUGGAGAUUAAAUCCCAACUCUGGCCGGUCUCGUCGCCGGCCAGAAAACUGGCUAAAAAGCCUUGCGAGGUUAUAAUGUUU
....(((((.....(((((((((..(((((((....)))..(((.......)))))))((((((((((......))))))))))...)))))).....)))...)))))........... ( -45.30)
>DroGri_CAF1 7398 120 - 1
UUGCCUUUGAUGAUGGCGGCGAGCAGUUGAUACAAAUACGUCGAGAUCAGAUCCCAACUCUGGCCGGUCUCGUCGCCGGCCAGAAAACUGGCCAGAAAACCCUGCGAGGUGAUUAUGUUG
(..((((.......((((((((((..(((((........)))))(..((((.......))))..).).)))))))))((((((....))))))............))))..)........ ( -42.30)
>DroWil_CAF1 8161 120 - 1
UUUCCCUUGAUAAUGGCGGCGAGUAGUUGAUACAAAUAUGUGGAAAUGAGAUCCCAACUCUGGCCAGUCUCGUCGCCAGCCAGAAAACUGGCCAAAAAUCCCUGUGAAGUGAUUAUAUUG
..((.(((.(((.((((((((((..((....)).......(((....(((.......)))...)))..))))))))))(((((....)))))..........))).))).))........ ( -34.00)
>DroMoj_CAF1 2719 120 - 1
UUGCCCUUGAUGAUGGCGGCCAGUAGCUGGUAGAGAUAAGUUGAGAUUAGAUCCCAGCUCUGACCAGUCUCGUCGCCGGCCAGGAAGCUGGCCAAGAAGCCCUGCGAUGUAAUUAUAUUA
((((....(((((.(((((.(((.((((((..((..(((.......)))..))))))))))).)).))))))))...((((((....))))))..........))))............. ( -41.50)
>DroAna_CAF1 7018 120 - 1
UUUCCCUUGAUGAUGGCGGCCAGUAGUUGGUACAGGUAGGUGGAGAUGAGGUCCCAGCUUUGGCCAGUCUCGUCUCCGGCCAGGAAGCUGGCCAGGAAGCCCUGAGAUGUAAUUAUAUUG
.........(((((.((((((((.((((((.((...((........))..)).)))))))))))).((((((..(((((((((....)))))).)))..)...))))))).))))).... ( -45.20)
>consensus
UUGCCCUUGAUGAUGGCGGCCAGUAGUUGGUACAAAUACGUGGAGAUGAGAUCCCAACUCUGGCCAGUCUCGUCGCCGGCCAGAAAACUGGCCAAAAAGCCCUGCGAGGUGAUUAUAUUG
((((....(((((.(((((((((.((((((.......................)))))))))))).))))))))...((((((....))))))..........))))............. (-32.90 = -33.52 +   0.61)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:10 2006