Locus 7252

Sequence ID X_DroMel_CAF1
Location 18,092,704 – 18,092,861
Length 157
Max. P 0.954786
window11870 window11871 window11872 window11873

overview

Window 0

Location 18,092,704 – 18,092,821
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.13
Mean single sequence MFE -40.73
Consensus MFE -29.14
Energy contribution -29.96
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -4.75
Structure conservation index 0.72
SVM decision value 0.28
SVM RNA-class probability 0.664135
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18092704 117 + 22224390
GUGGGAUAUAAAUUCAGUCGUUUCUGGGCUAUUUCCACAGAGACAUC---UCAAAGAGAACCCUACCAAGCCUUGCACUGAUCUAUCUAUACAUAUCGUAGAUCUCUGCCAGGCUUGGUA
..(((..............(((((((((......)).))))))).((---((...)))).)))((((((((((.(((..(((((((...........)))))))..))).)))))))))) ( -45.20)
>DroSec_CAF1 1421 113 + 1
GUGGUAUAUAAAUUCAGUCGUUGCUGGGCUAUUUCCACAGAGACAUC---UCAAAGAGAACUCUACCAAGCCUUGCACCGAUC----UAUACAUAUCGUAGAUCUCUGCCAGGCUUGGUA
((((...(((..((((((....)))))).)))..))))((((...((---((...)))).))))(((((((((.(((..((((----(((.......)))))))..))).))))))))). ( -41.80)
>DroSim_CAF1 1414 113 + 1
GUGGGAUAUAAAUUCAGUCGUUGCUGGGCUAUUUCCACAGAGACAUC---UCAAAGAGAACUCUACCAAGCCUUGCACCGAUC----UAUACAAAUCGUAGAUCUCUGCCAGGCUUGGUA
((((((......((((((....))))))....))))))((((...((---((...)))).))))(((((((((.(((..((((----(((.......)))))))..))).))))))))). ( -43.40)
>DroYak_CAF1 147 116 + 1
GUGGGAUAUAAAUUCAGUCGUUGCUGGGCGAUUUCCACAGAGACAUCCUCCUAAAGAUAACUCUCUCAAGCCUUGCACAGAUC----UAUACAUAUCAUAGAUCUCUGCCAGACUUGGUA
((((((......((((((....))))))....))))))(((((.(((........)))...)))))((((.((.(((.(((((----(((.......)))))))).))).)).))))... ( -32.50)
>consensus
GUGGGAUAUAAAUUCAGUCGUUGCUGGGCUAUUUCCACAGAGACAUC___UCAAAGAGAACUCUACCAAGCCUUGCACCGAUC____UAUACAUAUCGUAGAUCUCUGCCAGGCUUGGUA
((((((......(((((......)))))....))))))((((...((........))...))))(((((((((.(((..((((.................))))..))).))))))))). (-29.14 = -29.96 +   0.81)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,092,704 – 18,092,821
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.13
Mean single sequence MFE -39.15
Consensus MFE -27.70
Energy contribution -28.08
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -3.32
Structure conservation index 0.71
SVM decision value 0.51
SVM RNA-class probability 0.764022
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18092704 117 - 22224390
UACCAAGCCUGGCAGAGAUCUACGAUAUGUAUAGAUAGAUCAGUGCAAGGCUUGGUAGGGUUCUCUUUGA---GAUGUCUCUGUGGAAAUAGCCCAGAAACGACUGAAUUUAUAUCCCAC
((((((((((.(((..(((((((..........).))))))..))).))))))))))(((......((.(---(.(((.((((.((......)))))).))).)).)).......))).. ( -42.92)
>DroSec_CAF1 1421 113 - 1
UACCAAGCCUGGCAGAGAUCUACGAUAUGUAUA----GAUCGGUGCAAGGCUUGGUAGAGUUCUCUUUGA---GAUGUCUCUGUGGAAAUAGCCCAGCAACGACUGAAUUUAUAUACCAC
((((((((((.(((..((((((.........))----))))..))).))))))))))(((.((((...))---))...))).((((..((((..(((......)))...))))...)))) ( -37.70)
>DroSim_CAF1 1414 113 - 1
UACCAAGCCUGGCAGAGAUCUACGAUUUGUAUA----GAUCGGUGCAAGGCUUGGUAGAGUUCUCUUUGA---GAUGUCUCUGUGGAAAUAGCCCAGCAACGACUGAAUUUAUAUCCCAC
((((((((((.(((..((((((.........))----))))..))).))))))))))(((.((((...))---))...)))((.(((.((((..(((......)))...)))).))))). ( -38.80)
>DroYak_CAF1 147 116 - 1
UACCAAGUCUGGCAGAGAUCUAUGAUAUGUAUA----GAUCUGUGCAAGGCUUGAGAGAGUUAUCUUUAGGAGGAUGUCUCUGUGGAAAUCGCCCAGCAACGACUGAAUUUAUAUCCCAC
...(((((((.(((.(((((((((.....))))----))))).))).)))))))..((((.((((((....)))))).))))((((........(((......)))..........)))) ( -37.17)
>consensus
UACCAAGCCUGGCAGAGAUCUACGAUAUGUAUA____GAUCGGUGCAAGGCUUGGUAGAGUUCUCUUUGA___GAUGUCUCUGUGGAAAUAGCCCAGCAACGACUGAAUUUAUAUCCCAC
((((((((((.(((..((((.................))))..))).))))))))))((((((((........))(((..(((.((......)))))..)))...))))))......... (-27.70 = -28.08 +   0.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,092,744 – 18,092,861
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.70
Mean single sequence MFE -39.58
Consensus MFE -27.70
Energy contribution -27.96
Covariance contribution 0.25
Combinations/Pair 1.13
Mean z-score -5.70
Structure conservation index 0.70
SVM decision value 0.80
SVM RNA-class probability 0.854035
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18092744 117 + 22224390
AGACAUC---UCAAAGAGAACCCUACCAAGCCUUGCACUGAUCUAUCUAUACAUAUCGUAGAUCUCUGCCAGGCUUGGUAGUGUAUCUCUACAGGAUAUCAUGCCUAACUACUUUGACUG
.((.(((---(...(((((((.(((((((((((.(((..(((((((...........)))))))..))).))))))))))).)).)))))...)))).)).................... ( -43.10)
>DroSec_CAF1 1461 113 + 1
AGACAUC---UCAAAGAGAACUCUACCAAGCCUUGCACCGAUC----UAUACAUAUCGUAGAUCUCUGCCAGGCUUGGUAGUGUAUCUCUACAGGAUCUCAUGCAUAACUACUUUGGCUG
.((.(((---(...(((((((.(((((((((((.(((..((((----(((.......)))))))..))).))))))))))).)).)))))...)))).)).................... ( -43.90)
>DroSim_CAF1 1454 113 + 1
AGACAUC---UCAAAGAGAACUCUACCAAGCCUUGCACCGAUC----UAUACAAAUCGUAGAUCUCUGCCAGGCUUGGUAGUGUAUCUCUACAGGAUCUCAUGCCUAACUACUUUGGCUG
.((.(((---(...(((((((.(((((((((((.(((..((((----(((.......)))))))..))).))))))))))).)).)))))...)))).))..(((..........))).. ( -47.30)
>DroYak_CAF1 187 116 + 1
AGACAUCCUCCUAAAGAUAACUCUCUCAAGCCUUGCACAGAUC----UAUACAUAUCAUAGAUCUCUGCCAGACUUGGUAGCGCAUCUCCUCGGCAUCUCAUUCCUAACCACUUUGGCUG
..........((((((......((..((((.((.(((.(((((----(((.......)))))))).))).)).))))..)).((.........))................))))))... ( -24.00)
>consensus
AGACAUC___UCAAAGAGAACUCUACCAAGCCUUGCACCGAUC____UAUACAUAUCGUAGAUCUCUGCCAGGCUUGGUAGUGUAUCUCUACAGGAUCUCAUGCCUAACUACUUUGGCUG
..........((((((...((.(((((((((((.(((..((((.................))))..))).))))))))))).))((((.....))))..............))))))... (-27.70 = -27.96 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,092,744 – 18,092,861
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.70
Mean single sequence MFE -44.27
Consensus MFE -32.38
Energy contribution -33.13
Covariance contribution 0.75
Combinations/Pair 1.12
Mean z-score -4.77
Structure conservation index 0.73
SVM decision value 1.45
SVM RNA-class probability 0.954786
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18092744 117 - 22224390
CAGUCAAAGUAGUUAGGCAUGAUAUCCUGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUAUGUAUAGAUAGAUCAGUGCAAGGCUUGGUAGGGUUCUCUUUGA---GAUGUCU
..(((..........)))..(((((((...(((((.((.(((((((((((.(((..(((((((..........).))))))..))).))))))))))).)))))))..).---)))))). ( -45.50)
>DroSec_CAF1 1461 113 - 1
CAGCCAAAGUAGUUAUGCAUGAGAUCCUGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUAUGUAUA----GAUCGGUGCAAGGCUUGGUAGAGUUCUCUUUGA---GAUGUCU
........(((....)))..((.((((...(((((.((.(((((((((((.(((..((((((.........))----))))..))).))))))))))).)))))))..).---))).)). ( -44.10)
>DroSim_CAF1 1454 113 - 1
CAGCCAAAGUAGUUAGGCAUGAGAUCCUGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUUUGUAUA----GAUCGGUGCAAGGCUUGGUAGAGUUCUCUUUGA---GAUGUCU
..(((..........)))..((.((((...(((((.((.(((((((((((.(((..((((((.........))----))))..))).))))))))))).)))))))..).---))).)). ( -46.80)
>DroYak_CAF1 187 116 - 1
CAGCCAAAGUGGUUAGGAAUGAGAUGCCGAGGAGAUGCGCUACCAAGUCUGGCAGAGAUCUAUGAUAUGUAUA----GAUCUGUGCAAGGCUUGAGAGAGUUAUCUUUAGGAGGAUGUCU
.((((.....)))).......(((((((..((((((((.((..(((((((.(((.(((((((((.....))))----))))).))).)))))))..)).).)))))))....)).))))) ( -40.70)
>consensus
CAGCCAAAGUAGUUAGGCAUGAGAUCCUGUAGAGAUACACUACCAAGCCUGGCAGAGAUCUACGAUAUGUAUA____GAUCGGUGCAAGGCUUGGUAGAGUUCUCUUUGA___GAUGUCU
..............((((((....((....(((((.((.(((((((((((.(((..((((.................))))..))).))))))))))).)))))))..))....)))))) (-32.38 = -33.13 +   0.75)

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 12:34:14 2006