Locus 668

Sequence ID X_DroMel_CAF1
Location 1,866,822 – 1,867,079
Length 257
Max. P 0.998051
window1073 window1074 window1075 window1076 window1077 window1078

overview

Window 3

Location 1,866,822 – 1,866,941
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.85
Mean single sequence MFE -34.83
Consensus MFE -29.34
Energy contribution -30.15
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.98
Structure conservation index 0.84
SVM decision value 0.52
SVM RNA-class probability 0.766858
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1866822 119 - 22224390
UGUGUGUU-UUGUGUUGUGUGUGGCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAGCAAAGAAGAAGCAGCGAUAGGCGAAGUGAGCAAAGAGCAA
..(((.((-((((.((((.(((.((((((((...)))...(((....(((..((.....))..)))......)))...............))))).))).)))).....)))))).))). ( -31.40)
>DroSec_CAF1 4063 114 - 1
UGUGUGUU-UUGUGUUGU--GUGGCUGCGCCGAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAGCAAAG---AAGCAGCGAUAGGCGAAGUGCGCAAAGAGCAA
....((((-((.((((((--(((((...(((...)))..........(((..((.....))..))).....)))))))))))..)---)))))((.....(((.....))).....)).. ( -35.60)
>DroEre_CAF1 2653 119 - 1
UGUGUGUUUUUGUGUUGUGUGU-GCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCUGCAAAGAAGAAGCAGCGAUAGGCGAAGUGCGCAAAGAGCAA
.........((((....((((.-.((.((((...(((..((....))(((..((.....))..))).....))).((((((.........))))))...)))).))..))))....)))) ( -38.90)
>DroYak_CAF1 4536 120 - 1
UGUGUGUUUUUGUGUUGUGUGUGGCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAGCAAAGAAGAAGCAGCGAUAGGCAAAGUGCGCAAAGAGCAG
(((((((((((((....(((.((((((((((((......))))....)))...))))))))..))))))))(((.(((.((.........)).)))...))).....)))))........ ( -33.40)
>consensus
UGUGUGUU_UUGUGUUGUGUGUGGCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAGCAAAGAAGAAGCAGCGAUAGGCGAAGUGCGCAAAGAGCAA
(((((((((((((.((((...((((((((((((......))))....)))...))))))))).))))))))(((.(((.((.........)).)))...))).....)))))........ (-29.34 = -30.15 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,866,862 – 1,866,968
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.50
Mean single sequence MFE -35.86
Consensus MFE -31.41
Energy contribution -32.22
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.88
SVM decision value 0.94
SVM RNA-class probability 0.885301
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1866862 106 - 22224390
---U----------ACAUUGGCAGCCGCACACACACGCUUUGUGUGUU-UUGUGUUGUGUGUGGCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAG
---(----------((....(((((((((((((.((((..........-..)))))))))))))))))(((...)))...........))).((((((......)).....))))..... ( -36.50)
>DroSec_CAF1 4100 104 - 1
---U----------ACAUUGGCAGCCGCACACACACGCUUUGUGUGUU-UUGUGUUGU--GUGGCUGCGCCGAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAG
---(----------((....((((((((((((((((((.....)))).-..))).)))--))))))))(((...)))...........))).((((((......)).....))))..... ( -35.20)
>DroEre_CAF1 2693 119 - 1
AACCACACAUACACACUUUGGCAGCCGCACACACACGCUUUGUGUGUUUUUGUGUUGUGUGU-GCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCUG
...............(((((((.((.((((((((((((.............))).)))))))-)).)))))))))((...(((....(((..((.....))..)))......))).)).. ( -36.92)
>DroYak_CAF1 4576 110 - 1
AAAC----------ACAUUGGCUGCCGCACACACACGCUUUGUGUGUUUUUGUGUUGUGUGUGGCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAG
....----------...(((((.((((((((((.((((.............))))))))))))))...))))).(((..((....))(((..((.....))..))).....)))...... ( -34.82)
>consensus
___C__________ACAUUGGCAGCCGCACACACACGCUUUGUGUGUU_UUGUGUUGUGUGUGGCUGCGCCAAAGGCAAUUGGAAAACGUAAUGGCCGACAAAACGAAAACGCCACGCAG
.................((((((((((((((((.((((.............)))))))))))))))..))))).(((..((....))(((..((.....))..))).....)))...... (-31.41 = -32.22 +   0.81)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,866,902 – 1,867,007
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.92
Mean single sequence MFE -37.66
Consensus MFE -25.91
Energy contribution -27.54
Covariance contribution 1.63
Combinations/Pair 1.11
Mean z-score -3.56
Structure conservation index 0.69
SVM decision value 2.79
SVM RNA-class probability 0.997022
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1866902 105 + 22224390
AUUGCCUUUGGCGCAGCCACACACAACACAA-AACACACAAAGCGUGUGUGUGCGGCUGCCAAUGU----------A----GAUGUACAUGUUGAUGUGCGCCCGCAAAGAAAAAUCGUU
.((((....(((((((((.((((((.(((..-............))))))))).))))))......----------.----...((((((....))))))))).))))............ ( -37.34)
>DroSec_CAF1 4140 97 + 1
AUUGCCUUCGGCGCAGCCAC--ACAACACAA-AACACACAAAGCGUGUGUGUGCGGCUGCCAAUGU----------A----GAUGUGCAUGUAGAUG------CGCAAAGAAAAAUCGUU
...(((...)))((((((.(--((.......-.((((((.....))))))))).))))))......----------.----..(((((((....)))------))))............. ( -32.60)
>DroEre_CAF1 2733 119 + 1
AUUGCCUUUGGCGCAGC-ACACACAACACAAAAACACACAAAGCGUGUGUGUGCGGCUGCCAAAGUGUGUAUGUGUGGUUGUGUGUGCAUGUAAAUGUACAACCGCAAAGAAAAAUCGUU
...(((((((((((.((-(((((((.(.(.............).)))))))))).)).))))))).)).....((((((((((..(........)..))))))))))............. ( -44.72)
>DroYak_CAF1 4616 110 + 1
AUUGCCUUUGGCGCAGCCACACACAACACAAAAACACACAAAGCGUGUGUGUGCGGCAGCCAAUGU----------GUUUGUAUGUGCAUGUAAAUGUGCGCCAGCAAAGAAAAAUCGUU
.((((...(((((((..((((.((((((((...(((((((.....)))))))((....))...)))----------).)))).))))(((....))))))))))))))............ ( -36.00)
>consensus
AUUGCCUUUGGCGCAGCCACACACAACACAA_AACACACAAAGCGUGUGUGUGCGGCUGCCAAUGU__________A____GAUGUGCAUGUAAAUGUGCGCCCGCAAAGAAAAAUCGUU
.((((.....(.((((((.((((((.(((...............))))))))).)))))))......................(((((((....)))))))...))))............ (-25.91 = -27.54 +   1.63)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,866,902 – 1,867,007
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.92
Mean single sequence MFE -38.65
Consensus MFE -27.41
Energy contribution -28.22
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -3.72
Structure conservation index 0.71
SVM decision value 2.99
SVM RNA-class probability 0.998051
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1866902 105 - 22224390
AACGAUUUUUCUUUGCGGGCGCACAUCAACAUGUACAUC----U----------ACAUUGGCAGCCGCACACACACGCUUUGUGUGUU-UUGUGUUGUGUGUGGCUGCGCCAAAGGCAAU
............((((.(((.........((((((....----)----------))).))(((((((((((((.((((..........-..))))))))))))))))))))....)))). ( -39.10)
>DroSec_CAF1 4140 97 - 1
AACGAUUUUUCUUUGCG------CAUCUACAUGCACAUC----U----------ACAUUGGCAGCCGCACACACACGCUUUGUGUGUU-UUGUGUUGU--GUGGCUGCGCCGAAGGCAAU
..((((.......((.(------(((....)))).))..----.----------..))))((((((((((((((((((.....)))).-..))).)))--))))))))(((...)))... ( -35.60)
>DroEre_CAF1 2733 119 - 1
AACGAUUUUUCUUUGCGGUUGUACAUUUACAUGCACACACAACCACACAUACACACUUUGGCAGCCGCACACACACGCUUUGUGUGUUUUUGUGUUGUGUGU-GCUGCGCCAAAGGCAAU
............((((((((((................))))))...........(((((((.((.((((((((((((.............))).)))))))-)).))))))))))))). ( -41.81)
>DroYak_CAF1 4616 110 - 1
AACGAUUUUUCUUUGCUGGCGCACAUUUACAUGCACAUACAAAC----------ACAUUGGCUGCCGCACACACACGCUUUGUGUGUUUUUGUGUUGUGUGUGGCUGCGCCAAAGGCAAU
............((((((((((((((....)))(((((((((.(----------(((...((....))(((((((.....)))))))...)))))))))))))..))))))...))))). ( -38.10)
>consensus
AACGAUUUUUCUUUGCGGGCGCACAUCUACAUGCACAUA____C__________ACAUUGGCAGCCGCACACACACGCUUUGUGUGUU_UUGUGUUGUGUGUGGCUGCGCCAAAGGCAAU
.........(((((((.......(((....)))...........................(((((((((((((.((((.............)))))))))))))))))).)))))).... (-27.41 = -28.22 +   0.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,866,941 – 1,867,047
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.40
Mean single sequence MFE -33.23
Consensus MFE -28.21
Energy contribution -29.15
Covariance contribution 0.94
Combinations/Pair 1.14
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 1.02
SVM RNA-class probability 0.901488
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1866941 106 + 22224390
AAGCGUGUGUGUGCGGCUGCCAAUGU----------A----GAUGUACAUGUUGAUGUGCGCCCGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGUA
..(((((..((((((.((((....))----------)----).))))))..)..))))((((((((..((((((....))))))...((((....)))).))))))))..(((....))) ( -34.20)
>DroSec_CAF1 4177 100 + 1
AAGCGUGUGUGUGCGGCUGCCAAUGU----------A----GAUGUGCAUGUAGAUG------CGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGCA
..((.((..((..((.((((....))----------)----).))..))..))((((------(.((.((((((....))))))...((((....))))..)).)))))))((....)). ( -29.50)
>DroEre_CAF1 2772 120 + 1
AAGCGUGUGUGUGCGGCUGCCAAAGUGUGUAUGUGUGGUUGUGUGUGCAUGUAAAUGUACAACCGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGCA
..((.....((..((((.(((....((.(((..((((((((((..(........)..)))))))))).((((((....)))))).........))).))....)))))))..))...)). ( -38.60)
>DroYak_CAF1 4656 110 + 1
AAGCGUGUGUGUGCGGCAGCCAAUGU----------GUUUGUAUGUGCAUGUAAAUGUGCGCCAGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUUAAGUGGGCGUCGUGCGAAAGCA
..((.....((..((((.(((.....----------........(..(((....)))..).(((.(..((((((....)))))).).))).............)))))))..))...)). ( -30.60)
>consensus
AAGCGUGUGUGUGCGGCUGCCAAUGU__________A____GAUGUGCAUGUAAAUGUGCGCCCGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGCA
..((.....((..((((.(((......................(((((((....))))))).((((..((((((....))))))..)))).............)))))))..))...)). (-28.21 = -29.15 +   0.94)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,866,968 – 1,867,079
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.27
Mean single sequence MFE -32.38
Consensus MFE -21.29
Energy contribution -22.60
Covariance contribution 1.31
Combinations/Pair 1.18
Mean z-score -1.63
Structure conservation index 0.66
SVM decision value 0.06
SVM RNA-class probability 0.563384
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1866968 111 + 22224390
-GAUGUACAUGUUGAUGUGCGCCCGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGUAUUUCCGUGGCG-AAAACUAGUUUAAGAAUCGCG-------
-(((((((((....))))))((((((..((((((....))))))...((((....)))).)))))))))((((....)))).......(((-(...((......))..)))).------- ( -31.30)
>DroSec_CAF1 4204 106 + 1
-GAUGUGCAUGUAGAUG------CGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGCAUUUCCGUGGCGCAAAACUAGUUUAGGAAUCGCA-------
-..(((((((....)))------)))).((((((....))))))..((((..(((..(.(((..(((((((((....))))......)))))...))).)..)))...)))).------- ( -30.90)
>DroEre_CAF1 2812 120 + 1
GUGUGUGCAUGUAAAUGUACAACCGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGCAUUUCCCUGGCCCAAAACUAGUUUAAGAAUGGCGAGUGAUA
...(((((((....))))))).((((..((((((....))))))..)))).(((((((...((((((..((((....))))..)....)))))......(((.......)))))))))). ( -36.90)
>DroYak_CAF1 4686 120 + 1
GUAUGUGCAUGUAAAUGUGCGCCAGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUUAAGUGGGCGUCGUGCGAAAGCAUUUCCCUGGCCCAAAACUAGUUUAAGAAUGACGGUAAUGA
((..((((((......))))))..))........((((((((((.....((((((.((...((((((..((((....))))..)....))))).)).)))))).)))).))))))..... ( -30.40)
>consensus
_GAUGUGCAUGUAAAUGUGCGCCCGCAAAGAAAAAUCGUUUUCUAGGUGGAAUUAUUCAAGUGGGCGUCGUGCGAAAGCAUUUCCCUGGCCCAAAACUAGUUUAAGAAUCGCG_______
...(((((((....))))))).((((..((((((....))))))..))))..(((..(.(((..(((((((((....))))......)))))...))).)..)))............... (-21.29 = -22.60 +   1.31)

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 09:50:44 2006