Locus 4867

Sequence ID 3L_DroMel_CAF1
Location 13,606,740 – 13,606,899
Length 159
Max. P 0.998601
window7682 window7683 window7684 window7685

overview

Window 2

Location 13,606,740 – 13,606,859
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.82
Mean single sequence MFE -23.77
Consensus MFE -20.36
Energy contribution -20.28
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -1.47
Structure conservation index 0.86
SVM decision value 0.00
SVM RNA-class probability 0.533704
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13606740 119 + 23771897
AC-UCGUAACUAUUACCAUAACAUUUAUGAUUAUUAACCUACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCAACU
..-((((((...............))))))..............(((.((((......((((((((..((((....))))..))))))))((((...........)))))))).)))... ( -23.86)
>DroSec_CAF1 13925 119 + 1
AC-UCGUAACUAUUACCAUAACAUUUAUGAUUAUUAACCUACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCAACU
..-((((((...............))))))..............(((.((((......((((((((..((((....))))..))))))))((((...........)))))))).)))... ( -23.86)
>DroSim_CAF1 22898 119 + 1
AC-UCGUAACUAUUACCAUAACAUUUAUGAUUAUUAACCUACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCUACU
..-..(((........((((.....))))................((.((((......((((((((..((((....))))..))))))))((((...........)))))))).))))). ( -22.90)
>DroEre_CAF1 16526 119 + 1
AC-UCGUAACUAUUACCAUAACAUUUAUGAUUAUUAACCCACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCCACU
..-((((((...............))))))...............((.((((......((((((((..((((....))))..))))))))((((...........)))))))).)).... ( -21.96)
>DroYak_CAF1 20719 119 + 1
AC-UCGUAACUAUUACCAUAACAUUUAUGAUUAUUAACCUACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGGAGCCUGGCAACU
.(-(((((.........((((((....)).))))..........))))))((((...(((((((((..((((....))))..)))))))))...))))(((....((....)).)))... ( -23.91)
>DroAna_CAF1 49715 120 + 1
GCCCCGUAACUAUUACCGUAGCAUUUAUGAUUAUUAACCCACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUACAUUUUCUGUGUUGCAAAAAGAAACCUGGCAACU
((((((((.((((....))))((....))...............))))))))((...(((((.(((..((((....))))..))).)))))...))(((((....((....)).))))). ( -26.10)
>consensus
AC_UCGUAACUAUUACCAUAACAUUUAUGAUUAUUAACCUACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCAACU
................(((((...)))))................((.((((......((((((((..((((....))))..))))))))((((...........)))))))).)).... (-20.36 = -20.28 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,606,740 – 13,606,859
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.82
Mean single sequence MFE -27.20
Consensus MFE -24.92
Energy contribution -25.17
Covariance contribution 0.25
Combinations/Pair 1.08
Mean z-score -1.20
Structure conservation index 0.92
SVM decision value 0.60
SVM RNA-class probability 0.793912
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13606740 119 - 23771897
AGUUGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGUAGGUUAAUAAUCAUAAAUGUUAUGGUAAUAGUUACGA-GU
.((((((((((((((.((((.....))))(((((((((..((((....))))..))))))))))))).)))..(((((...(((.....)))...)))))..)))))))........-.. ( -26.80)
>DroSec_CAF1 13925 119 - 1
AGUUGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGUAGGUUAAUAAUCAUAAAUGUUAUGGUAAUAGUUACGA-GU
.((((((((((((((.((((.....))))(((((((((..((((....))))..))))))))))))).)))..(((((...(((.....)))...)))))..)))))))........-.. ( -26.80)
>DroSim_CAF1 22898 119 - 1
AGUAGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGUAGGUUAAUAAUCAUAAAUGUUAUGGUAAUAGUUACGA-GU
....((..(((((((.((((.....))))(((((((((..((((....))))..))))))))))))).)))..)).((((((.(.....((((((.....))))))...).))))))-.. ( -25.40)
>DroEre_CAF1 16526 119 - 1
AGUGGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGUGGGUUAAUAAUCAUAAAUGUUAUGGUAAUAGUUACGA-GU
.((((...(((((((.((((.....))))(((((((((..((((....))))..))))))))))))).))))))).((((((.(.....((((((.....))))))...).))))))-.. ( -27.00)
>DroYak_CAF1 20719 119 - 1
AGUUGCCAGGCUCCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGUAGGUUAAUAAUCAUAAAUGUUAUGGUAAUAGUUACGA-GU
.((((((((((.(((.((((.....))))(((((((((..((((....))))..))))))))))).).)))..(((((...(((.....)))...)))))..)))))))........-.. ( -25.30)
>DroAna_CAF1 49715 120 - 1
AGUUGCCAGGUUUCUUUUUGCAACACAGAAAAUGUAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGUGGGUUAAUAAUCAUAAAUGCUACGGUAAUAGUUACGGGGC
.(((((.(((.....))).))))).....(((((((((..((((....))))..))))))))).....((((((..((((((........)))))).(((....))).......)))))) ( -31.90)
>consensus
AGUUGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGUAGGUUAAUAAUCAUAAAUGUUAUGGUAAUAGUUACGA_GU
.((((((((((((((.((((.....))))(((((((((..((((....))))..))))))))))))).)))..(((((...(((.....)))...)))))..)))))))........... (-24.92 = -25.17 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,606,779 – 13,606,899
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 96.44
Mean single sequence MFE -28.33
Consensus MFE -25.77
Energy contribution -25.72
Covariance contribution -0.05
Combinations/Pair 1.13
Mean z-score -2.47
Structure conservation index 0.91
SVM decision value 3.16
SVM RNA-class probability 0.998601
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13606779 120 + 23771897
ACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCAACUCUGCCACGACAAACAAUUAAAAACAAUGCGCCUCCAUCUU
...(((.(((((((...(((((((((..((((....))))..)))))))))...))(((((........)).(((((....))))).)))...................))))))))... ( -28.90)
>DroSec_CAF1 13964 120 + 1
ACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCAACUCUGCCACGACAAACAAUUAAAAACAAUGCGCCUCCAUCUU
...(((.(((((((...(((((((((..((((....))))..)))))))))...))(((((........)).(((((....))))).)))...................))))))))... ( -28.90)
>DroSim_CAF1 22937 120 + 1
ACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCUACUCUGCCACGACAAACAAUUAAAAACAAUGCGCCUCCAUCUU
...(((.(((((((...(((((((((..((((....))))..)))))))))...))(((((........)).((((......)))).)))...................))))))))... ( -28.50)
>DroEre_CAF1 16565 120 + 1
ACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCCACUCUGCCACGACAAACAAUUAAAAACAAUGCGCCUCCAUCUU
...(((.(((((((...(((((((((..((((....))))..)))))))))...))(((((........)).((((......)))).)))...................))))))))... ( -27.30)
>DroYak_CAF1 20758 120 + 1
ACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGGAGCCUGGCAACUCUGCCACGACAAACAAUUAAAAACAAUGCGCCUCCAUCUU
...(((.(((((((...(((((((((..((((....))))..)))))))))...))...(((...((....))((((....)))).....................)))))))))))... ( -30.30)
>DroAna_CAF1 49755 120 + 1
ACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUACAUUUUCUGUGUUGCAAAAAGAAACCUGGCAACUCUGCUACGACAAACAAUUAAAAACAAUGCACUCCCGCAGU
....((((((((((...(((((.(((..((((....))))..))).)))))...))))((((...((....))((((....)))).....................))))..)))))).. ( -26.10)
>consensus
ACAAUGCGGGGCACUCUAAAUGCAAUUAAGAUUACGAUCUAUAUUGCAUUUUCUGUGUUGCAAAAAGAAGCCUGGCAACUCUGCCACGACAAACAAUUAAAAACAAUGCGCCUCCAUCUU
...(((.(((((((...(((((((((..((((....))))..)))))))))...))...(((...((....))(((......))).....................)))))))))))... (-25.77 = -25.72 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,606,779 – 13,606,899
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.44
Mean single sequence MFE -33.45
Consensus MFE -30.44
Energy contribution -30.05
Covariance contribution -0.39
Combinations/Pair 1.11
Mean z-score -1.76
Structure conservation index 0.91
SVM decision value 1.81
SVM RNA-class probability 0.978254
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13606779 120 - 23771897
AAGAUGGAGGCGCAUUGUUUUUAAUUGUUUGUCGUGGCAGAGUUGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGU
..(.(((.(((((..((((...((..(...(((.((((......)))))))..)..))...))))....(((((((((..((((....))))..)))))))))...)))))))))..... ( -33.10)
>DroSec_CAF1 13964 120 - 1
AAGAUGGAGGCGCAUUGUUUUUAAUUGUUUGUCGUGGCAGAGUUGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGU
..(.(((.(((((..((((...((..(...(((.((((......)))))))..)..))...))))....(((((((((..((((....))))..)))))))))...)))))))))..... ( -33.10)
>DroSim_CAF1 22937 120 - 1
AAGAUGGAGGCGCAUUGUUUUUAAUUGUUUGUCGUGGCAGAGUAGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGU
..(.(((.(((((..............(((((.((.((((((.(((...)))...)))))).)))))))(((((((((..((((....))))..)))))))))...)))))))))..... ( -34.20)
>DroEre_CAF1 16565 120 - 1
AAGAUGGAGGCGCAUUGUUUUUAAUUGUUUGUCGUGGCAGAGUGGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGU
..(.(((.(((((..............(((((.((.((((((.(((...)))...)))))).)))))))(((((((((..((((....))))..)))))))))...)))))))))..... ( -34.20)
>DroYak_CAF1 20758 120 - 1
AAGAUGGAGGCGCAUUGUUUUUAAUUGUUUGUCGUGGCAGAGUUGCCAGGCUCCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGU
..(.(((.(((((.((((.........(((((....)))))(((((.((....))....))))))))).(((((((((..((((....))))..)))))))))...)))))))))..... ( -32.80)
>DroAna_CAF1 49755 120 - 1
ACUGCGGGAGUGCAUUGUUUUUAAUUGUUUGUCGUAGCAGAGUUGCCAGGUUUCUUUUUGCAACACAGAAAAUGUAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGU
..((((((.(..(.((((......(((((......))))).(((((.(((.....))).))))))))).(((((((((..((((....))))..)))))))))...)..))))))).... ( -33.30)
>consensus
AAGAUGGAGGCGCAUUGUUUUUAAUUGUUUGUCGUGGCAGAGUUGCCAGGCUUCUUUUUGCAACACAGAAAAUGCAAUAUAGAUCGUAAUCUUAAUUGCAUUUAGAGUGCCCCGCAUUGU
....(((.(((((..............(((((.((.((((((..((...))....)))))).)))))))(((((((((..((((....))))..)))))))))...))))))))...... (-30.44 = -30.05 +  -0.39)

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 11:35:41 2006