Locus 1553

Sequence ID X_DroMel_CAF1
Location 4,462,704 – 4,462,936
Length 232
Max. P 0.998549
window2547 window2548 window2549 window2550 window2551

overview

Window 7

Location 4,462,704 – 4,462,824
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.89
Mean single sequence MFE -39.62
Consensus MFE -29.04
Energy contribution -29.60
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -3.58
Structure conservation index 0.73
SVM decision value 2.76
SVM RNA-class probability 0.996841
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462704 120 + 22224390
AUUUCAAAUUUUACGCUCUCGCUCUCGCGGACAGCGACGCCGCCGGCGGCAGCGCAGCGCAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCG
..............(((..((((.((((.....)))).((((....)))))))).)))((((..((((((((((((((......))))))))))))))(((....)))......)))).. ( -38.40)
>DroSec_CAF1 64267 120 + 1
ACUUCAAAUUUUACGCUCUCGCUCUCGCGGGCAGCGACGCCGCCGGCGGCAGCGCAGCACAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCG
.............(((((((((....))))).))))..(((...)))(((((.((......)).((((((((((((((......))))))))))))))................))))). ( -39.70)
>DroEre_CAF1 67969 102 + 1
---------------C---CGCUCUCGCGGACAGCGACGCCGACGGCGGCAGCGCAGCGCAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCG
---------------(---(((....))))...(((..((((....))))..))).(.((((..((((((((((((((......))))))))))))))(((....)))......))))). ( -36.20)
>DroYak_CAF1 65106 109 + 1
GCGUCGA---CUGCGC---UGCAUGCGCGAACAGCGACGCCGACGGCGGCAGCG---CGCAGC--GUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCG
..(((((---((((((---(((.(((((.....))...((((....)))).)))---.)))))--)((((((((((((......))))))))))))....))))))))............ ( -44.20)
>consensus
ACUUCAA___UUACGC___CGCUCUCGCGGACAGCGACGCCGACGGCGGCAGCGCAGCGCAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCG
..........................(((((...((((((((....)))).((........)).((((((((((((((......))))))))))))))....)))).......))))).. (-29.04 = -29.60 +   0.56)

alignment

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secondary structure

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Window 8

Location 4,462,704 – 4,462,824
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.89
Mean single sequence MFE -45.85
Consensus MFE -36.72
Energy contribution -38.10
Covariance contribution 1.38
Combinations/Pair 1.05
Mean z-score -3.82
Structure conservation index 0.80
SVM decision value 3.14
SVM RNA-class probability 0.998549
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462704 120 - 22224390
CGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGCGCUGCGCUGCCGCCGGCGGCGUCGCUGUCCGCGAGAGCGAGAGCGUAAAAUUUGAAAU
(((..(((....)))..))).(((((((((((((((......)))))))))))))))..((((((.((((..(((.((((((...)))))).)))..))))..))))))........... ( -48.10)
>DroSec_CAF1 64267 120 - 1
CGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGUGCUGCGCUGCCGCCGGCGGCGUCGCUGCCCGCGAGAGCGAGAGCGUAAAAUUUGAAGU
(((..(((....)))..)))..((((((((((((((......))))))))))))))(((...((.((((((((...)))))))).)).)))(((....)))................... ( -47.70)
>DroEre_CAF1 67969 102 - 1
CGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGCGCUGCGCUGCCGCCGUCGGCGUCGCUGUCCGCGAGAGCG---G---------------
((((.(((....)))(((....((((((((((((((......))))))))))))))(((.(((...))).)))(((...)))))))))).((((....)))---)--------------- ( -44.40)
>DroYak_CAF1 65106 109 - 1
CGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAC--GCUGCG---CGCUGCCGCCGUCGGCGUCGCUGUUCGCGCAUGCA---GCGCAG---UCGACGC
..((.(((....)))(((((....((((((((((((......))))))))))))(--((((((---((.(((((....))))).)))(((....))).)))---))))))---))...)) ( -43.20)
>consensus
CGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGCGCUGCGCUGCCGCCGGCGGCGUCGCUGUCCGCGAGAGCG___GCGUAA___UUGAAGU
(((..(((....)))..)))..((((((((((((((......))))))))))))))(((.(((..((((((((...))))))))))).)))(((....)))................... (-36.72 = -38.10 +   1.38)

alignment

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secondary structure

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Window 9

Location 4,462,744 – 4,462,858
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.31
Mean single sequence MFE -50.65
Consensus MFE -46.69
Energy contribution -48.25
Covariance contribution 1.56
Combinations/Pair 1.00
Mean z-score -6.23
Structure conservation index 0.92
SVM decision value 1.16
SVM RNA-class probability 0.924449
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462744 114 + 22224390
CGCCGGCGGCAGCGCAGCGCAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCGAAUCGGUUGCGCUGCGGCUGCGCUGAGA------AUAAGA
...(((((.(((((((((((((((((((((((((((((......)))))))))))))).((.((.(((....))).)).))...))))))))))).)))))))))...------...... ( -55.20)
>DroSec_CAF1 64307 114 + 1
CGCCGGCGGCAGCGCAGCACAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCGAAUCGGUUGCGCUGCGGCUGCGCUGAGA------ACAAAA
...(((((.(((((((((.(((((((((((((((((((......)))))))))))))).((.((.(((....))).)).))...))))).))))).)))))))))...------...... ( -49.80)
>DroEre_CAF1 67991 114 + 1
CGACGGCGGCAGCGCAGCGCAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCGAAUCGGUUGCGCUGCGGCUGCGCUGAGA------ACAAGA
...(((((.(((((((((((((((((((((((((((((......)))))))))))))).((.((.(((....))).)).))...))))))))))).)))))))))...------...... ( -55.40)
>DroYak_CAF1 65140 113 + 1
CGACGGCGGCAGCG---CGCAGC--GUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCGAAU--GUUGCGUUGCGGCUGCGCUGAUAGAAAAUACAAGA
...(((((.((((.---((((((--(((((((((((((......)))))))))))((((((.((.(((....))).)).).))--))))))))))))))))))))............... ( -42.20)
>consensus
CGACGGCGGCAGCGCAGCGCAGCCGUUGUAUUUAUAAAUACAACUUUAUAAAUACAACAUCAGUCGAUUUUCAUCUGCCGAAUCGGUUGCGCUGCGGCUGCGCUGAGA______ACAAGA
...(((((.(((((((((((((((((((((((((((((......)))))))))))))).((.((.(((....))).)).))...))))))))))).)))))))))............... (-46.69 = -48.25 +   1.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,462,744 – 4,462,858
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.31
Mean single sequence MFE -48.98
Consensus MFE -45.88
Energy contribution -47.00
Covariance contribution 1.12
Combinations/Pair 1.03
Mean z-score -5.55
Structure conservation index 0.94
SVM decision value 1.60
SVM RNA-class probability 0.966565
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462744 114 - 22224390
UCUUAU------UCUCAGCGCAGCCGCAGCGCAACCGAUUCGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGCGCUGCGCUGCCGCCGGCG
......------..((.(((((((.((((((((.((...((((..(((....)))..)))).((((((((((((((......)))))))))))))))).)))))))))))).))).)).. ( -53.20)
>DroSec_CAF1 64307 114 - 1
UUUUGU------UCUCAGCGCAGCCGCAGCGCAACCGAUUCGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGUGCUGCGCUGCCGCCGGCG
......------..((.(((((((.((((((((.((...((((..(((....)))..)))).((((((((((((((......)))))))))))))))).)))))))))))).))).)).. ( -51.30)
>DroEre_CAF1 67991 114 - 1
UCUUGU------UCUCAGCGCAGCCGCAGCGCAACCGAUUCGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGCGCUGCGCUGCCGCCGUCG
......------.....(((((((.((((((((.((...((((..(((....)))..)))).((((((((((((((......)))))))))))))))).)))))))))))).)))..... ( -53.00)
>DroYak_CAF1 65140 113 - 1
UCUUGUAUUUUCUAUCAGCGCAGCCGCAACGCAAC--AUUCGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAC--GCUGCG---CGCUGCCGCCGUCG
.................(((((((((((.((.(((--((.(((..(((....)))..))))))))(((((((((((......))))))))))).)--).))))---.)))).)))..... ( -38.40)
>consensus
UCUUGU______UCUCAGCGCAGCCGCAGCGCAACCGAUUCGGCAGAUGAAAAUCGACUGAUGUUGUAUUUAUAAAGUUGUAUUUAUAAAUACAACGGCUGCGCUGCGCUGCCGCCGGCG
.................(((((((.((((((((.((...((((..(((....)))..)))).((((((((((((((......)))))))))))))))).)))))))))))).)))..... (-45.88 = -47.00 +   1.12)

alignment

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secondary structure

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Window 1

Location 4,462,824 – 4,462,936
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.73
Mean single sequence MFE -24.98
Consensus MFE -21.31
Energy contribution -21.88
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.66
Structure conservation index 0.85
SVM decision value 0.56
SVM RNA-class probability 0.781234
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462824 112 + 22224390
AAUCGGUUGCGCUGCGGCUGCGCUGAGA------AUAAGAUACAAAACUCGUGCGCGGCGCUUCAAGAAACCAACUCAAAAGCAGACAAAUCAAAUAACUAA--CUUGUAGAAAAUAAAA
....((((...((((.(((((((((((.------.............)))).))))))).......((.......))....))))...))))..........--................ ( -25.34)
>DroSec_CAF1 64387 112 + 1
AAUCGGUUGCGCUGCGGCUGCGCUGAGA------ACAAAAUACAAAACUCGUGCGCGGCGCUUCAAGAAACCAACUCAAAAGCAGACAAAUCAAAUAACUAA--CUUGUAGAAAAUAAAA
....((((...((((.(((((((((((.------.............)))).))))))).......((.......))....))))...))))..........--................ ( -25.34)
>DroEre_CAF1 68071 108 + 1
AAUCGGUUGCGCUGCGGCUGCGCUGAGA------ACAAGAUACAAAACUCGUGCGCGGCGCUUCAAGUAACCAACUCAUAAGCAGACAAAUCAAAUAAUUAA--CUUGUCGAAAAA----
..((((((((...(((.((((((((((.------.............)))).))))))))).....))))))............(((((.............--.)))))))....---- ( -30.48)
>DroYak_CAF1 65215 114 + 1
AAU--GUUGCGUUGCGGCUGCGCUGAUAGAAAAUACAAGAUACAAAACUCGUGCGCGGCGCUUCAAGAAACCAACUCAAAAGCAGACAAAUCAAAUAUCUAAUUCUUGUGGAAAAU----
..(--((((((..(((.(((((((((......................))).)))))))))..)..((.......))....))).))).........((((.......))))....---- ( -18.75)
>consensus
AAUCGGUUGCGCUGCGGCUGCGCUGAGA______ACAAGAUACAAAACUCGUGCGCGGCGCUUCAAGAAACCAACUCAAAAGCAGACAAAUCAAAUAACUAA__CUUGUAGAAAAU____
....((((...((((.(((((((((((....................)))).))))))).......((.......))....))))...))))............................ (-21.31 = -21.88 +   0.56)

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 10:13:19 2006