Locus 8180

Sequence ID X_DroMel_CAF1
Location 20,344,296 – 20,344,443
Length 147
Max. P 0.998519
window13436 window13437 window13438 window13439

overview

Window 6

Location 20,344,296 – 20,344,405
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.83
Mean single sequence MFE -30.38
Consensus MFE -14.23
Energy contribution -13.87
Covariance contribution -0.36
Combinations/Pair 1.13
Mean z-score -3.20
Structure conservation index 0.47
SVM decision value 1.69
SVM RNA-class probability 0.972391
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20344296 109 + 22224390
AUUCGCGUAGUUUUUCAGUUUUGACACAUGUCACUCAAAACAGACAC--ACACAAAUGCAC--GUACACACAGGUGUCCGUGUGUGUG--UACACUCGAAAGAAUCUUAUUACUU-----
......(((((..(((.(((((((..........)))))))..((((--(((((...((((--.(......).))))...))))))))--)..........)))....)))))..----- ( -27.80)
>DroSec_CAF1 12040 91 + 1
AUUCGCGUAGUUUUUCAGUUUUGACACAUGUCACUCAAAACAGACAC--A------------------CACAGGUGUCU--GUGUGUG--UACACUCGAAGAAAUCGUAUUACUU-----
....(((...((((((.(((((((..........)))))))..((((--(------------------(((((....))--)))))))--)......))))))..))).......----- ( -28.20)
>DroSim_CAF1 13813 107 + 1
AUUCGCGUAGUUUUUCAGUUUUGACACAUGUCACUCAAAACAGACAC--ACACAAAUGCAC--GUACACACAGGUGUCU--GUGUGUG--UACACUUGAAGAAAUCCUAUUACUU-----
......((((..((((.....((((....)))).((((.....((((--(((((...((((--.(......).)))).)--)))))))--)....)))).))))..)))).....----- ( -27.90)
>DroEre_CAF1 8706 113 + 1
AUUCGCGUAGUUUUUCAGUUUUGACACAUGUCACUCAAAACAGACACGCACACAAGUGCACGCACACACACAGGUGUCC--GUGUGUG--UGCACUUGAAAGAAUUUUCAGGCUUAU---
((((((((.((((....(((((((..........)))))))))))))))...((((((((((((((((((....)))..--)))))))--))))))))...))))............--- ( -40.80)
>DroYak_CAF1 12684 114 + 1
AUUCGCGUAGUUUUUCAGUUUUGACACAUGUCACUCAAAACAGACAC--ACACAAAUGCAC--AUACACACAGGUGUCC--GUGUGUGCGUACACUUGAAAUAAUCCUGAGGCGCAUAAC
....((((.....(((((..(((.....((((..........)))).--......((((((--(((((((....)))..--))))))))))..........)))..)))))))))..... ( -27.20)
>consensus
AUUCGCGUAGUUUUUCAGUUUUGACACAUGUCACUCAAAACAGACAC__ACACAAAUGCAC__AUACACACAGGUGUCC__GUGUGUG__UACACUUGAAAAAAUCCUAUUACUU_____
..........((((((.(((((((..........))))))).(((((..........................)))))...(((((....)))))..))))))................. (-14.23 = -13.87 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,344,296 – 20,344,405
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.83
Mean single sequence MFE -33.84
Consensus MFE -18.04
Energy contribution -19.64
Covariance contribution 1.60
Combinations/Pair 1.13
Mean z-score -3.02
Structure conservation index 0.53
SVM decision value 1.72
SVM RNA-class probability 0.973775
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20344296 109 - 22224390
-----AAGUAAUAAGAUUCUUUCGAGUGUA--CACACACACGGACACCUGUGUGUAC--GUGCAUUUGUGU--GUGUCUGUUUUGAGUGACAUGUGUCAAAACUGAAAAACUACGCGAAU
-----..........((((...((((((((--(..((((((((....))))))))..--)))))))))...--((((...((((.((((((....)))...))).))))...)))))))) ( -32.20)
>DroSec_CAF1 12040 91 - 1
-----AAGUAAUACGAUUUCUUCGAGUGUA--CACACAC--AGACACCUGUG------------------U--GUGUCUGUUUUGAGUGACAUGUGUCAAAACUGAAAAACUACGCGAAU
-----........(((.....))).(((((--(((((((--((....)))))------------------)--)))((.(((((((..........))))))).)).....))))).... ( -26.40)
>DroSim_CAF1 13813 107 - 1
-----AAGUAAUAGGAUUUCUUCAAGUGUA--CACACAC--AGACACCUGUGUGUAC--GUGCAUUUGUGU--GUGUCUGUUUUGAGUGACAUGUGUCAAAACUGAAAAACUACGCGAAU
-----............(((..((((((((--(((((((--((....))))))))..--)))))))))...--((((...((((.((((((....)))...))).))))...))))))). ( -31.60)
>DroEre_CAF1 8706 113 - 1
---AUAAGCCUGAAAAUUCUUUCAAGUGCA--CACACAC--GGACACCUGUGUGUGUGCGUGCACUUGUGUGCGUGUCUGUUUUGAGUGACAUGUGUCAAAACUGAAAAACUACGCGAAU
---....((.(((((....))))).))(((--(((((((--((....))))))))))))..((((....))))((((...((((.((((((....)))...))).))))...)))).... ( -40.90)
>DroYak_CAF1 12684 114 - 1
GUUAUGCGCCUCAGGAUUAUUUCAAGUGUACGCACACAC--GGACACCUGUGUGUAU--GUGCAUUUGUGU--GUGUCUGUUUUGAGUGACAUGUGUCAAAACUGAAAAACUACGCGAAU
....((((.(((((((((((..((((((((((.((((((--((....)))))))).)--)))))))))...--)))...))))))))((((....))))..............))))... ( -38.10)
>consensus
_____AAGUAAUAAGAUUCUUUCAAGUGUA__CACACAC__GGACACCUGUGUGUAC__GUGCAUUUGUGU__GUGUCUGUUUUGAGUGACAUGUGUCAAAACUGAAAAACUACGCGAAU
......................((((((((...((((((..((....)))))))).....)))))))).....((((...((((.((((((....)))...))).))))...)))).... (-18.04 = -19.64 +   1.60)

alignment

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secondary structure

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Window 8

Location 20,344,336 – 20,344,443
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 69.20
Mean single sequence MFE -28.74
Consensus MFE -7.67
Energy contribution -7.99
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -3.04
Structure conservation index 0.27
SVM decision value 3.13
SVM RNA-class probability 0.998519
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20344336 107 + 22224390
CAGACAC--ACACAAAUGCAC--GUACACACAGGUGUCCGUGUGUGUG--UACACUCGAAAGAAUCUUAUUACUU-------AUGGUCCCAUAUAUAUGCGAAUGCUUUCGAGGAAGUUA
..(((((--((((....((((--(.((((....)))).))))))))))--)...((((((((..((.(((....(-------(((....))))...))).))...))))))))...))). ( -34.50)
>DroSec_CAF1 12080 87 + 1
CAGACAC--A------------------CACAGGUGUCU--GUGUGUG--UACACUCGAAGAAAUCGUAUUACUU-------AUUGUUCAAU--AAACGCAAAUGCUUUCGAGGAAGUUA
...((((--(------------------(((((....))--)))))))--)...(((((((((...(((.....)-------))..)))...--....((....)).))))))....... ( -25.30)
>DroSim_CAF1 13853 103 + 1
CAGACAC--ACACAAAUGCAC--GUACACACAGGUGUCU--GUGUGUG--UACACUUGAAGAAAUCCUAUUACUU-------AUUGUUCAAU--AAACGCAAAUGCUUUCGAGUAAGUUA
...((((--(((((...((((--.(......).)))).)--)))))))--)..((((((((............((-------(((....)))--))..((....))))))))))...... ( -24.90)
>DroEre_CAF1 8746 101 + 1
CAGACACGCACACAAGUGCACGCACACACACAGGUGUCC--GUGUGUG--UGCACUUGAAAGAAUUUUCAGGCUUAU-----AUUGGCUAAU--AAAUGCGAAUACUUUCGA--------
......((((..((((((((((((((((((....)))..--)))))))--))))))))............((((...-----...))))...--...))))...........-------- ( -36.80)
>DroYak_CAF1 12724 106 + 1
CAGACAC--ACACAAAUGCAC--AUACACACAGGUGUCC--GUGUGUGCGUACACUUGAAAUAAUCCUGAGGCGCAUAACCUAUUGACAAAC--AAA------UACUUUCGAGUAAUAUG
.......--......((((((--(((((((....)))..--))))))))))..((((((((........(((.......))).(((.....)--)).------...))))))))...... ( -22.20)
>consensus
CAGACAC__ACACAAAUGCAC__AUACACACAGGUGUCC__GUGUGUG__UACACUUGAAAAAAUCCUAUUACUU_______AUUGUCCAAU__AAACGCAAAUGCUUUCGAGGAAGUUA
((.((((..((((....................))))....)))).))......(((((((.............................................)))))))....... ( -7.67 =  -7.99 +   0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,344,336 – 20,344,443
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 69.20
Mean single sequence MFE -30.18
Consensus MFE -10.02
Energy contribution -9.94
Covariance contribution -0.08
Combinations/Pair 1.20
Mean z-score -2.77
Structure conservation index 0.33
SVM decision value 2.97
SVM RNA-class probability 0.997937
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20344336 107 - 22224390
UAACUUCCUCGAAAGCAUUCGCAUAUAUAUGGGACCAU-------AAGUAAUAAGAUUCUUUCGAGUGUA--CACACACACGGACACCUGUGUGUAC--GUGCAUUUGUGU--GUGUCUG
.......((((((((...((...(((.((((....)))-------).)))....))..))))))))..((--((((((((((.((((....)))).)--)))....)))))--))).... ( -32.10)
>DroSec_CAF1 12080 87 - 1
UAACUUCCUCGAAAGCAUUUGCGUUU--AUUGAACAAU-------AAGUAAUACGAUUUCUUCGAGUGUA--CACACAC--AGACACCUGUG------------------U--GUGUCUG
.......((((((.((....))((((--(((.......-------.))))).))......))))))...(--(((((((--((....)))))------------------)--))))... ( -24.70)
>DroSim_CAF1 13853 103 - 1
UAACUUACUCGAAAGCAUUUGCGUUU--AUUGAACAAU-------AAGUAAUAGGAUUUCUUCAAGUGUA--CACACAC--AGACACCUGUGUGUAC--GUGCAUUUGUGU--GUGUCUG
..(((((.((((((((......))))--.))))....)-------))))....((((.....((((((((--(((((((--((....))))))))..--)))))))))...--..)))). ( -29.60)
>DroEre_CAF1 8746 101 - 1
--------UCGAAAGUAUUCGCAUUU--AUUAGCCAAU-----AUAAGCCUGAAAAUUCUUUCAAGUGCA--CACACAC--GGACACCUGUGUGUGUGCGUGCACUUGUGUGCGUGUCUG
--------..(((((..((((..(((--((........-----)))))..))))....)))))....(((--(((((((--((....))))))))))))..((((....))))....... ( -34.40)
>DroYak_CAF1 12724 106 - 1
CAUAUUACUCGAAAGUA------UUU--GUUUGUCAAUAGGUUAUGCGCCUCAGGAUUAUUUCAAGUGUACGCACACAC--GGACACCUGUGUGUAU--GUGCAUUUGUGU--GUGUCUG
((...((((....))))------..)--).........((((.....))))..((((.....((((((((((.((((((--((....)))))))).)--)))))))))...--..)))). ( -30.10)
>consensus
UAACUUACUCGAAAGCAUUCGCAUUU__AUUGGACAAU_______AAGUAAUAAGAUUCUUUCAAGUGUA__CACACAC__GGACACCUGUGUGUAC__GUGCAUUUGUGU__GUGUCUG
.........(....)..................................................(((......)))....((((((....(((((....)))))........)))))). (-10.02 =  -9.94 +  -0.08)

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 12:57:42 2006