Locus 2363

Sequence ID 3R_DroMel_CAF1
Location 6,725,158 – 6,725,292
Length 134
Max. P 0.998220
window3810 window3811 window3812 window3813

overview

Window 0

Location 6,725,158 – 6,725,278
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.17
Mean single sequence MFE -33.98
Consensus MFE -27.17
Energy contribution -26.61
Covariance contribution -0.56
Combinations/Pair 1.13
Mean z-score -2.91
Structure conservation index 0.80
SVM decision value 2.15
SVM RNA-class probability 0.989195
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725158 120 + 27905053
GUUUAUCCACUGGCCGAUUGGCAAAAGAAGCCACAGCAAAAGCUUGCGGUGUGUGUGUGUGUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAAGGAGGAAAUAGCCAACAA
(((..(((..((((((..((((.......)))).......(((((((((((((((((((....)))))......))))))).)))))))......)))))).)))((......))))).. ( -38.00)
>DroEre_CAF1 9764 109 + 1
GUUUAUCCACUGGCCGAUUGGCAAAAGAAGCCACAGCAAAAGCUUGCGGUGU--------GUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAGGAAAGAAAUCCUC---AA
.........(((((((..((((.......)))).......((((((((((((--------((.((.......))))))))).)))))))......))))))).............---.. ( -36.20)
>DroYak_CAF1 9712 109 + 1
GUUUAUCCACUGGCCGAUUGGCAAAAGAAGCCACAGCAAAAGCUUGCGGUGU--------GUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAAGAAAGAAAUCCCC---AA
..........((((((..((((.......)))).......((((((((((((--------((.((.......))))))))).)))))))......))))))..............---.. ( -32.70)
>DroAna_CAF1 9575 102 + 1
GUC------CGGGUCGAUUGGCAAAAGAAGCCACAGCAAAAGCUUGCGGUGU--------GUGCAUAUAAUUUGAUAUGCCAGUGAGCUAAAAA-UGGCCAAGAAAGAAAUCCGU---AA
...------((((((..(((((......((((((.((((....))))(((((--------((.((.......))))))))).))).))).....-..)))))....))..)))).---.. ( -29.02)
>consensus
GUUUAUCCACUGGCCGAUUGGCAAAAGAAGCCACAGCAAAAGCUUGCGGUGU________GUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAAGAAAGAAAUCCCC___AA
...........(((((..((((.......)))).......(((((((.(.............((((((......))))))).)))))))......))))).................... (-27.17 = -26.61 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,725,158 – 6,725,278
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.17
Mean single sequence MFE -30.32
Consensus MFE -23.89
Energy contribution -25.33
Covariance contribution 1.44
Combinations/Pair 1.08
Mean z-score -2.47
Structure conservation index 0.79
SVM decision value 1.58
SVM RNA-class probability 0.965360
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725158 120 - 27905053
UUGUUGGCUAUUUCCUCCUUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCACACACACACACACCGCAAGCUUUUGCUGUGGCUUCUUUUGCCAAUCGGCCAGUGGAUAAAC
(..(((((((((........((((((.....(((((((..((((((......))))))...............)))))))......)))))).........))).))))))..)...... ( -32.56)
>DroEre_CAF1 9764 109 - 1
UU---GAGGAUUUCUUUCCUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCAC--------ACACCGCAAGCUUUUGCUGUGGCUUCUUUUGCCAAUCGGCCAGUGGAUAAAC
..---.((((......))))..(((((....(((((((..((((((......))))))..--------.....)))))))...((((((((.......))))..)))).)))))...... ( -33.30)
>DroYak_CAF1 9712 109 - 1
UU---GGGGAUUUCUUUCUUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCAC--------ACACCGCAAGCUUUUGCUGUGGCUUCUUUUGCCAAUCGGCCAGUGGAUAAAC
(.---.((((.....))))..)(((((....(((((((..((((((......))))))..--------.....)))))))...((((((((.......))))..)))).)))))...... ( -32.50)
>DroAna_CAF1 9575 102 - 1
UU---ACGGAUUUCUUUCUUGGCCA-UUUUUAGCUCACUGGCAUAUCAAAUUAUAUGCAC--------ACACCGCAAGCUUUUGCUGUGGCUUCUUUUGCCAAUCGACCCG------GAC
..---.(((...((....(((((..-.....(((......((((((......))))))..--------.(((.((((....)))).))))))......)))))..)).)))------... ( -22.92)
>consensus
UU___GGGGAUUUCUUUCUUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCAC________ACACCGCAAGCUUUUGCUGUGGCUUCUUUUGCCAAUCGGCCAGUGGAUAAAC
...............(((((((((.......(((((((..((((((......))))))...............))))))).......((((.......))))...)))))).)))..... (-23.89 = -25.33 +   1.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,725,198 – 6,725,292
Length 94
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 70.34
Mean single sequence MFE -25.55
Consensus MFE -15.95
Energy contribution -15.82
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -2.27
Structure conservation index 0.62
SVM decision value 3.04
SVM RNA-class probability 0.998220
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725198 94 + 27905053
AGCUUGCGGUGUGUGUGUGUGUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAAGGAGGAAAUAGCCAACAACA---CGGCCAAUUU-------CC----------------
(((((((((((((((((((....)))))......))))))).)))))))................((((((.(((.......---.)))..))))-------))---------------- ( -27.70)
>DroEre_CAF1 9804 97 + 1
AGCUUGCGGUGU--------GUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAGGAAAGAAAUCCUC---AAUA---CAGCCAAUUUCCAAUUUCCAAUUUCC---------
((((((((((((--------((.((.......))))))))).)))))))......((((.((((......)))).---....---..))))....................--------- ( -24.00)
>DroYak_CAF1 9752 96 + 1
AGCUUGCGGUGU--------GUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAAGAAAGAAAUCCCC---AACA---CAGCCAAUUU-------CCAAA---CUGGCCAAUA
((((((((((((--------((.((.......))))))))).)))))))......((((((.....(((((...(---....---..)...))))-------)....---.))))))... ( -28.20)
>DroAna_CAF1 9609 78 + 1
AGCUUGCGGUGU--------GUGCAUAUAAUUUGAUAUGCCAGUGAGCUAAAAA-UGGCCAAGAAAGAAAUCCGU---AAGCCACCAGCC------------------------------
.((((((((..(--------(.((((((......)))))))).((.((((....-))))))..........))))---))))........------------------------------ ( -22.30)
>consensus
AGCUUGCGGUGU________GUGCAUAUAAUUUGAUAUGCCGGCAAGCUAAAAAGUGGCCAAGAAAGAAAUCCCC___AACA___CAGCCAAUUU_______CC________________
(((((((.(.............((((((......))))))).)))))))......((((............................))))............................. (-15.95 = -15.82 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,725,198 – 6,725,292
Length 94
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 70.34
Mean single sequence MFE -25.16
Consensus MFE -14.49
Energy contribution -14.80
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -2.07
Structure conservation index 0.58
SVM decision value 2.00
SVM RNA-class probability 0.985312
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725198 94 - 27905053
----------------GG-------AAAUUGGCCG---UGUUGUUGGCUAUUUCCUCCUUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCACACACACACACACCGCAAGCU
----------------((-------((((.(((((---......)))))))))))................(((((((..((((((......))))))...............))))))) ( -25.23)
>DroEre_CAF1 9804 97 - 1
---------GGAAAUUGGAAAUUGGAAAUUGGCUG---UAUU---GAGGAUUUCUUUCCUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCAC--------ACACCGCAAGCU
---------.............((((((.(((((.---....---.((((......))))))))).))))))((((((..((((((......))))))..--------.....)))))). ( -25.50)
>DroYak_CAF1 9752 96 - 1
UAUUGGCCAG---UUUGG-------AAAUUGGCUG---UGUU---GGGGAUUUCUUUCUUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCAC--------ACACCGCAAGCU
...(((((((---...((-------(((((..(..---....---)..)))))))...)))))))......(((((((..((((((......))))))..--------.....))))))) ( -30.00)
>DroAna_CAF1 9609 78 - 1
------------------------------GGCUGGUGGCUU---ACGGAUUUCUUUCUUGGCCA-UUUUUAGCUCACUGGCAUAUCAAAUUAUAUGCAC--------ACACCGCAAGCU
------------------------------(((((((((((.---..(((......))).)))))-))....((....((((((((......)))))).)--------)....)).)))) ( -19.90)
>consensus
________________GG_______AAAUUGGCUG___UGUU___GGGGAUUUCUUUCUUGGCCACUUUUUAGCUUGCCGGCAUAUCAAAUUAUAUGCAC________ACACCGCAAGCU
..............................((((..........................)))).......(((((((..((((((......))))))...............))))))) (-14.49 = -14.80 +   0.31)

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 10:33:29 2006