Locus 3554

Sequence ID 2R_DroMel_CAF1
Location 11,870,616 – 11,870,786
Length 170
Max. P 0.994975
window5783 window5784 window5785 window5786 window5787

overview

Window 3

Location 11,870,616 – 11,870,719
Length 103
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 84.13
Mean single sequence MFE -27.37
Consensus MFE -24.04
Energy contribution -24.43
Covariance contribution 0.39
Combinations/Pair 1.04
Mean z-score -1.46
Structure conservation index 0.88
SVM decision value 0.39
SVM RNA-class probability 0.717353
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11870616 103 + 20766785
UCGUUGCCAUGUUGCCACGUUGCAUGCAAACAAGUGCAGCAAAUACACA----CACACGUACAUGCAGCGGCAACACAAAGACACGGACGCUGACACGCUGGUGCCC
..((((((..(((((...(((((((........)))))))...(((...----.....)))...)))))))))))..........((.((((........)))))). ( -30.00)
>DroEre_CAF1 13181 87 + 1
UCGUUGCCAUGUUGCCACGUUGCAUGCAAACAAGUGCAGCACACACACA--------------------GGCAACACAAAGACACGGACGCUGACACGCUGGUGCCC
..((((((.(((......(((((((........)))))))......)))--------------------))))))..........((.((((........)))))). ( -25.50)
>DroYak_CAF1 11031 105 + 1
UCGUUGCCAUGUUGCCACGUUGCAUGCAAACAAGUGCAGCACACAAACACACACACACUUACAGAC--UGGCAACACAAAGACACGGACGCUGACACGCUGGUGCCC
..(((....((((((((.(((((((........))))))).................(.....)..--))))))))....)))..((.((((........)))))). ( -26.60)
>consensus
UCGUUGCCAUGUUGCCACGUUGCAUGCAAACAAGUGCAGCACACACACA____CACAC_UACA__C___GGCAACACAAAGACACGGACGCUGACACGCUGGUGCCC
..(((....(((((((..(((((((........)))))))..................((....))...)))))))....)))..((.((((........)))))). (-24.04 = -24.43 +   0.39)

alignment

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secondary structure

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Window 4

Location 11,870,616 – 11,870,719
Length 103
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 84.13
Mean single sequence MFE -37.77
Consensus MFE -31.13
Energy contribution -31.13
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.82
SVM decision value 0.71
SVM RNA-class probability 0.830347
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11870616 103 - 20766785
GGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCCGCUGCAUGUACGUGUG----UGUGUAUUUGCUGCACUUGUUUGCAUGCAACGUGGCAACAUGGCAACGA
((((((..((((....))))..))))))..((((((((((((((((((((.(((----((.((....))))))).)))..)))))))..))))))))))(....).. ( -42.40)
>DroEre_CAF1 13181 87 - 1
GGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCC--------------------UGUGUGUGUGCUGCACUUGUUUGCAUGCAACGUGGCAACAUGGCAACGA
((((((..((((....))))..))))))..((((((((--------------------(((.(((((((.((....))..)))))))))).))))))))(....).. ( -34.50)
>DroYak_CAF1 11031 105 - 1
GGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCCA--GUCUGUAAGUGUGUGUGUGUUUGUGUGCUGCACUUGUUUGCAUGCAACGUGGCAACAUGGCAACGA
((((((..((((....))))..))))))...(((((((.--((.(((((..(.(((((..(....)..).)))).)..))))).))...(((....)))))))))). ( -36.40)
>consensus
GGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCC___G__UGUA_GUGUG____UGUGUGUGUGCUGCACUUGUUUGCAUGCAACGUGGCAACAUGGCAACGA
((((((..((((....))))..))))))...(((((((............................(((((((......)))).)))..(((....)))))))))). (-31.13 = -31.13 +   0.00)

alignment

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secondary structure

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Window 5

Location 11,870,653 – 11,870,755
Length 102
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 83.97
Mean single sequence MFE -32.83
Consensus MFE -29.90
Energy contribution -29.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.91
SVM decision value 1.64
SVM RNA-class probability 0.969503
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11870653 102 + 20766785
AGCAAAUACACA----CACACGUACAUGCAGCGGCAACACAAAGACACGGACGCUGACACGCUGGUGCCCGCACGUCAGCGCUCGUGCGUUUAUUUGCCGUUUCCG
.(((..(((...----.....)))..)))((((((((......(.((((..(((((((..((.(....).))..)))))))..)))))......)))))))).... ( -37.80)
>DroEre_CAF1 13218 86 + 1
AGCACACACACA--------------------GGCAACACAAAGACACGGACGCUGACACGCUGGUGCCCGCACGUCAGCGCUCGUGCGUUUAUUUGCCGUUUCCG
............--------------------(((((......(.((((..(((((((..((.(....).))..)))))))..)))))......)))))....... ( -30.00)
>DroYak_CAF1 11068 104 + 1
AGCACACAAACACACACACACUUACAGAC--UGGCAACACAAAGACACGGACGCUGACACGCUGGUGCCCGCACGUCAGCGCUCGUGCGUUUAUUUGCCGUUUCCG
.........................((((--.(((((......(.((((..(((((((..((.(....).))..)))))))..)))))......)))))))))... ( -30.70)
>consensus
AGCACACACACA____CACAC_UACA__C___GGCAACACAAAGACACGGACGCUGACACGCUGGUGCCCGCACGUCAGCGCUCGUGCGUUUAUUUGCCGUUUCCG
................................(((((......(.((((..(((((((..((.(....).))..)))))))..)))))......)))))....... (-29.90 = -29.90 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,870,653 – 11,870,755
Length 102
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 83.97
Mean single sequence MFE -43.43
Consensus MFE -40.13
Energy contribution -40.13
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.07
Structure conservation index 0.92
SVM decision value 2.53
SVM RNA-class probability 0.994975
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11870653 102 - 20766785
CGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCCGCUGCAUGUACGUGUG----UGUGUAUUUGCU
.(....)((((((((((.(((((..(((((((((((.(....).)))))))))))..))))).))))).)))))...(((.(((((....----..))))).))). ( -47.00)
>DroEre_CAF1 13218 86 - 1
CGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCC--------------------UGUGUGUGUGCU
.(....)((((((((((.(((((..(((((((((((.(....).)))))))))))..))))).))))).)))))--------------------............ ( -40.20)
>DroYak_CAF1 11068 104 - 1
CGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCCA--GUCUGUAAGUGUGUGUGUGUUUGUGUGCU
((((...((((((((((.(((((..(((((((((((.(....).)))))))))))..))))).))))).))))).--.))))..((((..((......))..)))) ( -43.10)
>consensus
CGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCC___G__UGUA_GUGUG____UGUGUGUGUGCU
.(....)((((((((((.(((((..(((((((((((.(....).)))))))))))..))))).))))).)))))................................ (-40.13 = -40.13 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,870,679 – 11,870,786
Length 107
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 83.04
Mean single sequence MFE -43.25
Consensus MFE -30.17
Energy contribution -31.50
Covariance contribution 1.33
Combinations/Pair 1.04
Mean z-score -2.11
Structure conservation index 0.70
SVM decision value 0.33
SVM RNA-class probability 0.690524
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11870679 107 - 20766785
CGGCGAUGACG---------GCCACGACGACAGACGGAAGCGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCCGC
(((((((....---------(((.........(.(....))(....))))..(((((.(((((..(((((((((((.(....).)))))))))))..))))).)))))))))))). ( -48.70)
>DroPse_CAF1 9032 106 - 1
AAGCGUUGAGGACGACGACGUGGACGAGGACAGACGGAA------ACGGAAAAUAAACGCAAGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUGCUUGUCUCUGUGUUG----
..((((((.......)))))).....((.(((((((...------.))..........(((((.((((((((((((.(....).)))))))))))).))))).))))).)).---- ( -40.70)
>DroEre_CAF1 13230 105 - 1
CAGCGAUGACG---------GCCACGACGACAGACGGAAGCGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCC--
..(((((....---------(((.........(.(....))(....))))..(((((.(((((..(((((((((((.(....).)))))))))))..))))).)))))))))).-- ( -43.60)
>DroYak_CAF1 11097 106 - 1
CAGCGAUGACG---------GCCACGACGACAGACGGAAGCGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCCA-
..((.....((---------....)).((.....))...))(....)((((((((((.(((((..(((((((((((.(....).)))))))))))..))))).))))).))))).- ( -43.80)
>DroAna_CAF1 9249 107 - 1
AAGCGAUGACG---------CUGACGACGACAGCCGGAAACGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCUUGUCUUUGUGUUGCCGC
..(((..((((---------(.(((((.(((.((((....)(....))))........((....))((((((((((.(....).))))))))))))).)))))...)))))..))) ( -46.50)
>DroPer_CAF1 10696 106 - 1
AAGCGUUGAGGACGACGACGUGGACGAGGACAGACGGAA------ACGGAAAAUAAACGCAAGAGCGGUGACGUGCGGUCACCAGCGUGUCAGCGUGCUUGUCUCUGUGUUG----
...(((((....)))))(((.(((((((.((...((...------.))..........(((...((((((((.....)))))).)).)))....)).))))))).)))....---- ( -36.20)
>consensus
AAGCGAUGACG_________GCCACGACGACAGACGGAAGCGGAAACGGCAAAUAAACGCACGAGCGCUGACGUGCGGGCACCAGCGUGUCAGCGUCCGUGUCUUUGUGUUGCC__
...............................................((((((((((.(((((..(((((((((((........)))))))))))..))))).))))).))))).. (-30.17 = -31.50 +   1.33)

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 10:58:21 2006