Locus 9173

Sequence ID 3R_DroMel_CAF1
Location 24,469,151 – 24,469,304
Length 153
Max. P 0.976775
window14671 window14672 window14673 window14674 window14675

overview

Window 1

Location 24,469,151 – 24,469,247
Length 96
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 85.14
Mean single sequence MFE -32.16
Consensus MFE -23.38
Energy contribution -23.70
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -1.71
Structure conservation index 0.73
SVM decision value 0.19
SVM RNA-class probability 0.627549
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24469151 96 + 27905053
--------GUCCAGUGGGCAAGAACAACUCGUUUUGCGGCUGAGAUUG--UGUUUGUUGCCCCAUCUAUAUGGCUGCAUGGCUGGAGGUAUAGCUGUAGCUCUAAC
--------.....(.(((((((((((.(((((......)).)))....--))))).))))))).....((.(((((((..((((......))))))))))).)).. ( -27.70)
>DroSec_CAF1 12293 94 + 1
----------CCAGUAGGCAACAACAACUCGUGUUGUGGCCGAGAUUG--UGUUUGUUGCCUCAUCUAUAUGGCUGCAUGGCUGGAGCUAUAGCUGUAGCUAUAAC
----------...(.((((((((((((((((.((....)))))).)))--)...))))))))).....((((((((((..((((......)))))))))))))).. ( -35.80)
>DroSim_CAF1 24102 96 + 1
--------GUCCAGUGGGCAACAACAACUCGUGUUGUGGCUGAGAUUG--UGUUUGUUGCCUCAUCUAUAUGGGUGCAUGGCUGGAGCUAUAGCUGUAGCUAUAAC
--------.((((((((((((((((((((((.((....)))))).)))--)...))))))))(((((....)))))....))))))..((((((....)))))).. ( -34.10)
>DroEre_CAF1 15733 99 + 1
-------CUACCAGUGGGCAACAACAAGUUGUGUUGUGGCUGAGAUUGAGUGUUUGUUGCCCCAUCUGAAUGGCUGCAUGGCCGAAGCUAUAGCUUUAGCUAUAAC
-------....(((.(((((((((((....((.((......)).))....)).)))))))))...)))..(((((....)))))....((((((....)))))).. ( -30.40)
>DroYak_CAF1 21935 104 + 1
ACGUCUACGUCCAGUGGGCAACAACAAGUUGUGUUGUGGCCGAGAUUG--UGUUUGUUGGCCCAUCUGAAUGGCUGCAUGGCAGAAGCUAGAGCUGUUGCUAUAAC
..((((((.....)))))).......(((..(..((.((((((.(...--....).)))))))).....)..)))..(((((((.(((....))).)))))))... ( -32.80)
>consensus
________GUCCAGUGGGCAACAACAACUCGUGUUGUGGCUGAGAUUG__UGUUUGUUGCCCCAUCUAUAUGGCUGCAUGGCUGGAGCUAUAGCUGUAGCUAUAAC
...........(((((((((((((((....((.(((....))).))....)).)))))))))(((....))))))).(((((((.(((....))).)))))))... (-23.38 = -23.70 +   0.32)

alignment

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secondary structure

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Window 2

Location 24,469,151 – 24,469,247
Length 96
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 85.14
Mean single sequence MFE -27.67
Consensus MFE -19.16
Energy contribution -20.20
Covariance contribution 1.04
Combinations/Pair 1.14
Mean z-score -2.38
Structure conservation index 0.69
SVM decision value 0.95
SVM RNA-class probability 0.889020
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24469151 96 - 27905053
GUUAGAGCUACAGCUAUACCUCCAGCCAUGCAGCCAUAUAGAUGGGGCAACAAACA--CAAUCUCAGCCGCAAAACGAGUUGUUCUUGCCCACUGGAC--------
((...(((....)))..)).(((((.........(((....)))((((((.....(--(((.(((...........)))))))..)))))).))))).-------- ( -21.40)
>DroSec_CAF1 12293 94 - 1
GUUAUAGCUACAGCUAUAGCUCCAGCCAUGCAGCCAUAUAGAUGAGGCAACAAACA--CAAUCUCGGCCACAACACGAGUUGUUGUUGCCUACUGG----------
((((((((....)))))))).((((.........(((....)))((((((((...(--(((.((((.........)))))))))))))))).))))---------- ( -32.10)
>DroSim_CAF1 24102 96 - 1
GUUAUAGCUACAGCUAUAGCUCCAGCCAUGCACCCAUAUAGAUGAGGCAACAAACA--CAAUCUCAGCCACAACACGAGUUGUUGUUGCCCACUGGAC--------
((((((((....))))))))(((((..(((....))).....((.(((((((...(--(((.(((...........))))))))))))))))))))).-------- ( -29.40)
>DroEre_CAF1 15733 99 - 1
GUUAUAGCUAAAGCUAUAGCUUCGGCCAUGCAGCCAUUCAGAUGGGGCAACAAACACUCAAUCUCAGCCACAACACAACUUGUUGUUGCCCACUGGUAG-------
((((((((....))))))))...(((......)))..((((...(((((((((.((........................))))))))))).))))...------- ( -29.76)
>DroYak_CAF1 21935 104 - 1
GUUAUAGCAACAGCUCUAGCUUCUGCCAUGCAGCCAUUCAGAUGGGCCAACAAACA--CAAUCUCGGCCACAACACAACUUGUUGUUGCCCACUGGACGUAGACGU
((((.(((....))).)))).(((((..(.(((((((....))))...........--.......(((.((((((.....)))))).)))..))).).)))))... ( -25.70)
>consensus
GUUAUAGCUACAGCUAUAGCUCCAGCCAUGCAGCCAUAUAGAUGGGGCAACAAACA__CAAUCUCAGCCACAACACGAGUUGUUGUUGCCCACUGGAC________
((((((((....))))))))(((((.........(((....)))((((((((.................((((......)))))))))))).)))))......... (-19.16 = -20.20 +   1.04)

alignment

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secondary structure

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Window 3

Location 24,469,169 – 24,469,280
Length 111
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 90.07
Mean single sequence MFE -25.50
Consensus MFE -18.56
Energy contribution -20.04
Covariance contribution 1.48
Combinations/Pair 1.08
Mean z-score -2.18
Structure conservation index 0.73
SVM decision value 0.58
SVM RNA-class probability 0.789078
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24469169 111 - 27905053
AAACAAACCAAAAGAUCACACCGUUUUGGCUUGGUUAGAGCUACAGCUAUACCUCCAGCCAUGCAGCCAUAUAGAUGGGGCAACAAACA--CAAUCUCAGCCGCAAAACGAGU
...................((((((((((((.(((...(((....)))..)))...)))))(((..((((....))))(((........--........))))))))))).)) ( -26.29)
>DroSec_CAF1 12309 111 - 1
AAACAAACCAGAAAAUCACACCGUUUUGGCCUGGUUAUAGCUACAGCUAUAGCUCCAGCCAUGCAGCCAUAUAGAUGAGGCAACAAACA--CAAUCUCGGCCACAACACGAGU
......................(((.(((((.(((((((((....)))))))))...(((...((..........)).)))........--.......))))).)))...... ( -26.40)
>DroSim_CAF1 24120 111 - 1
AAACAAACCAGAAAAUCACACCGUUUUGGCCUGGUUAUAGCUACAGCUAUAGCUCCAGCCAUGCACCCAUAUAGAUGAGGCAACAAACA--CAAUCUCAGCCACAACACGAGU
......................(((.(((((((((((((((....)))))))..))))...(((.(.(((....))).)))).......--........)))).)))...... ( -22.90)
>DroEre_CAF1 15752 113 - 1
AAACAAACCAGAAAAUCAGACCGUUUUGGCCUGGUUAUAGCUAAAGCUAUAGCUUCGGCCAUGCAGCCAUUCAGAUGGGGCAACAAACACUCAAUCUCAGCCACAACACAACU
..................((..(((((((((.(((((((((....)))))))))..)))))(((..((((....)))).)))..))))..))..................... ( -28.60)
>DroYak_CAF1 21961 111 - 1
AAACAAACCAGAAAAUCAGACCGUUUUGGCCUGGUUAUAGCAACAGCUCUAGCUUCUGCCAUGCAGCCAUUCAGAUGGGCCAACAAACA--CAAUCUCGGCCACAACACAACU
......................(((.(((((.(((((.(((....))).))))).((((...))))((((....))))...........--.......))))).)))...... ( -23.30)
>consensus
AAACAAACCAGAAAAUCACACCGUUUUGGCCUGGUUAUAGCUACAGCUAUAGCUCCAGCCAUGCAGCCAUAUAGAUGGGGCAACAAACA__CAAUCUCAGCCACAACACGAGU
......................(((.(((((.(((((((((....)))))))))...(((......((((....))))))).................))))).)))...... (-18.56 = -20.04 +   1.48)

alignment

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secondary structure

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Window 4

Location 24,469,207 – 24,469,304
Length 97
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 88.24
Mean single sequence MFE -31.64
Consensus MFE -23.00
Energy contribution -23.48
Covariance contribution 0.48
Combinations/Pair 1.09
Mean z-score -2.12
Structure conservation index 0.73
SVM decision value 0.64
SVM RNA-class probability 0.807648
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24469207 97 + 27905053
UAUAUGGCUGCAUGGCUGGAGGUAUAGCUGUAGCUCUAACCAAGCCAAAACGGUGUGAUCUUUUGGUUUGUUUGCGGAAAGGUGCAAUAGCAGUAGC------
......(((((.(((((...(((..(((....)))...))).)))))......(((.(((((((.((......)).))))))))))...)))))...------ ( -29.90)
>DroSec_CAF1 12347 97 + 1
UAUAUGGCUGCAUGGCUGGAGCUAUAGCUGUAGCUAUAACCAGGCCAAAACGGUGUGAUUUUCUGGUUUGUUUGCGGAAAGGUGCAAUAGCAGUAGC------
......((((((((((((.(((....))).)))))))(((((((((.....)))........))))))...(((((......)))))..)))))...------ ( -30.70)
>DroSim_CAF1 24158 97 + 1
UAUAUGGGUGCAUGGCUGGAGCUAUAGCUGUAGCUAUAACCAGGCCAAAACGGUGUGAUUUUCUGGUUUGUUUGUGGAAAGGUGCACUAGCAGUAGC------
..(((.((((((((((((.(((....))).))))))).(((...(((((((((...(.....)....)))))).)))...))))))))....)))..------ ( -28.90)
>DroEre_CAF1 15792 103 + 1
UGAAUGGCUGCAUGGCCGAAGCUAUAGCUUUAGCUAUAACCAGGCCAAAACGGUCUGAUUUUCUGGUUUGUUUGCGGAAAGGUGCACUAGCAAUAGCAAUAGC
....(((((....)))))..(((((.(((...((((..((((((((.....)))))...((((((.........)))))))))....))))...))).))))) ( -31.70)
>DroYak_CAF1 21999 103 + 1
UGAAUGGCUGCAUGGCAGAAGCUAGAGCUGUUGCUAUAACCAGGCCAAAACGGUCUGAUUUUCUGGUUUGUUUGCGGAAAGGUGCAAUAGCAAUAGCAAUAGC
.......((((...))))..((((..(((((((((((.((((((((.....)))))...((((((.........)))))))))...)))))))))))..)))) ( -37.00)
>consensus
UAUAUGGCUGCAUGGCUGGAGCUAUAGCUGUAGCUAUAACCAGGCCAAAACGGUGUGAUUUUCUGGUUUGUUUGCGGAAAGGUGCAAUAGCAGUAGC______
......((((((((((((.(((....))).)))))))(((((((((.....)))........))))))((((((((......))))..)))))))))...... (-23.00 = -23.48 +   0.48)

alignment

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secondary structure

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Window 5

Location 24,469,207 – 24,469,304
Length 97
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 88.24
Mean single sequence MFE -25.20
Consensus MFE -19.10
Energy contribution -19.90
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.72
Structure conservation index 0.76
SVM decision value 1.78
SVM RNA-class probability 0.976775
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24469207 97 - 27905053
------GCUACUGCUAUUGCACCUUUCCGCAAACAAACCAAAAGAUCACACCGUUUUGGCUUGGUUAGAGCUACAGCUAUACCUCCAGCCAUGCAGCCAUAUA
------....((((..((((........))))........................(((((.(((...(((....)))..)))...))))).))))....... ( -21.70)
>DroSec_CAF1 12347 97 - 1
------GCUACUGCUAUUGCACCUUUCCGCAAACAAACCAGAAAAUCACACCGUUUUGGCCUGGUUAUAGCUACAGCUAUAGCUCCAGCCAUGCAGCCAUAUA
------....((((..((((........))))........................((((..(((((((((....)))))))))...)))).))))....... ( -24.60)
>DroSim_CAF1 24158 97 - 1
------GCUACUGCUAGUGCACCUUUCCACAAACAAACCAGAAAAUCACACCGUUUUGGCCUGGUUAUAGCUACAGCUAUAGCUCCAGCCAUGCACCCAUAUA
------((....))..(((((..((((.............))))............((((..(((((((((....)))))))))...)))))))))....... ( -22.92)
>DroEre_CAF1 15792 103 - 1
GCUAUUGCUAUUGCUAGUGCACCUUUCCGCAAACAAACCAGAAAAUCAGACCGUUUUGGCCUGGUUAUAGCUAAAGCUAUAGCUUCGGCCAUGCAGCCAUUCA
(((.((((...(((....))).......))))....................((..(((((.(((((((((....)))))))))..))))).)))))...... ( -27.80)
>DroYak_CAF1 21999 103 - 1
GCUAUUGCUAUUGCUAUUGCACCUUUCCGCAAACAAACCAGAAAAUCAGACCGUUUUGGCCUGGUUAUAGCAACAGCUCUAGCUUCUGCCAUGCAGCCAUUCA
((((..(((.((((((((((........))))...((((((....(((((....))))).)))))).)))))).)))..))))..((((...))))....... ( -29.00)
>consensus
______GCUACUGCUAUUGCACCUUUCCGCAAACAAACCAGAAAAUCACACCGUUUUGGCCUGGUUAUAGCUACAGCUAUAGCUCCAGCCAUGCAGCCAUAUA
......(((..(((....)))...............................((..((((..(((((((((....)))))))))...)))).)))))...... (-19.10 = -19.90 +   0.80)

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 13:28:12 2006