Locus 2957

Sequence ID 3R_DroMel_CAF1
Location 7,904,366 – 7,904,500
Length 134
Max. P 0.791502
window4755 window4756 window4757 window4758

overview

Window 5

Location 7,904,366 – 7,904,460
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 88.83
Mean single sequence MFE -28.75
Consensus MFE -23.11
Energy contribution -24.18
Covariance contribution 1.06
Combinations/Pair 1.15
Mean z-score -1.78
Structure conservation index 0.80
SVM decision value 0.59
SVM RNA-class probability 0.791502
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7904366 94 + 27905053
UAAGCAAGUCGCUCUGGCGUCACAAAGCUUCUACUGGGUGAGUGUGUGUGCGUGUGUGUAAGCAUUUUACACAUUCAACAAGUGGCCUUUAUUU
.......(.(((....))).)..((((...(((((...((((((((((...((((......))))..))))))))))...))))).)))).... ( -27.00)
>DroSec_CAF1 35764 92 + 1
UAAGCAAGUCGCUCUGACGUCACAAUGCUGCCACUGAGUGAGUGUGUGUGCGUG--UGUAAGCAUUUCACACAUUCAACAAGUGGCCUUUAUUU
..((((.((.((......)).))..))))((((((...((((((((((...(((--(....))))..))))))))))...))))))........ ( -32.70)
>DroSim_CAF1 37503 94 + 1
UAAGCAAGUCGCUCUGACGUCACAAAGCUGCCACUGAGUGAGUGUGUGUGCGUGUGUGUAAGCAUUUCACACAUUCAACAAGUGGCCUUUAUUU
..........(((.((......)).))).((((((...((((((((((...((((......))))..))))))))))...))))))........ ( -32.10)
>DroYak_CAF1 36377 92 + 1
UAAGCAAGUCGCUCUGACGUCACUAAGCUGCCACAGAGAGUGUGUGCGUGCGUGUGAGUGAGCAUUCC--GCAUUCAACAGGUGGUCUUUAUUU
..........((((..((.((((...(((((((((.....)))).))).))..))))))))))...((--((.........))))......... ( -23.20)
>consensus
UAAGCAAGUCGCUCUGACGUCACAAAGCUGCCACUGAGUGAGUGUGUGUGCGUGUGUGUAAGCAUUUCACACAUUCAACAAGUGGCCUUUAUUU
..(((..((.((......)).))...)))((((((...((((((((((...((((......))))..))))))))))...))))))........ (-23.11 = -24.18 +   1.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,904,366 – 7,904,460
Length 94
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 88.83
Mean single sequence MFE -23.95
Consensus MFE -16.99
Energy contribution -19.80
Covariance contribution 2.81
Combinations/Pair 1.04
Mean z-score -1.51
Structure conservation index 0.71
SVM decision value -0.04
SVM RNA-class probability 0.514612
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7904366 94 - 27905053
AAAUAAAGGCCACUUGUUGAAUGUGUAAAAUGCUUACACACACGCACACACACUCACCCAGUAGAAGCUUUGUGACGCCAGAGCGACUUGCUUA
......((((.(((.(.(((.(((((....(((..........))).))))).))).).)))((..((((((......))))))..)).)))). ( -19.70)
>DroSec_CAF1 35764 92 - 1
AAAUAAAGGCCACUUGUUGAAUGUGUGAAAUGCUUACA--CACGCACACACACUCACUCAGUGGCAGCAUUGUGACGUCAGAGCGACUUGCUUA
........((((((.(.(((.((((((...(((.....--...))))))))).))).).))))))......(..(.(((.....))))..)... ( -26.40)
>DroSim_CAF1 37503 94 - 1
AAAUAAAGGCCACUUGUUGAAUGUGUGAAAUGCUUACACACACGCACACACACUCACUCAGUGGCAGCUUUGUGACGUCAGAGCGACUUGCUUA
.....(((((((((.(.(((.((((((...(((..........))))))))).))).).)))))).((((((......))))))..)))..... ( -29.80)
>DroYak_CAF1 36377 92 - 1
AAAUAAAGACCACCUGUUGAAUGC--GGAAUGCUCACUCACACGCACGCACACACUCUCUGUGGCAGCUUAGUGACGUCAGAGCGACUUGCUUA
......................((--((..(((((((((((..((..((.((((.....)))))).))...)))).))..)))))..))))... ( -19.90)
>consensus
AAAUAAAGGCCACUUGUUGAAUGUGUGAAAUGCUUACACACACGCACACACACUCACUCAGUGGCAGCUUUGUGACGUCAGAGCGACUUGCUUA
.....(((((((((.(.(((.((((((...(((..........))))))))).))).).)))))).((((((......))))))..)))..... (-16.99 = -19.80 +   2.81)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,904,397 – 7,904,500
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 90.29
Mean single sequence MFE -27.88
Consensus MFE -23.83
Energy contribution -24.57
Covariance contribution 0.75
Combinations/Pair 1.14
Mean z-score -1.60
Structure conservation index 0.85
SVM decision value 0.45
SVM RNA-class probability 0.739410
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7904397 103 + 27905053
UACUGGGUGAGUGUGUGUGCGUGUGUGUAAGCAUUUUACACAUUCAACAAGUGGCCUUUAUUUGGGCAACAAAGAAAAGGAAGCUGCAGCAAACUAAAGUUCG
..((((.((((((((((...((((......))))..)))))))))).).(((..(((((.((((.....))))..)))))..))).))).............. ( -27.90)
>DroSec_CAF1 35795 101 + 1
CACUGAGUGAGUGUGUGUGCGUG--UGUAAGCAUUUCACACAUUCAACAAGUGGCCUUUAUUUGGGCAACAAAGAAAAGGAAGCUGCAGCAAAAUAAAGUUCU
((((...((((((((((...(((--(....))))..))))))))))...)))).(((((.((((.....))))..)))))..((....))............. ( -30.70)
>DroSim_CAF1 37534 103 + 1
CACUGAGUGAGUGUGUGUGCGUGUGUGUAAGCAUUUCACACAUUCAACAAGUGGCCUUUAUUUGGGCAACAAAGAAAAGGAAGCUGCAGCAAAAUAAAGUUCU
((((...((((((((((...((((......))))..))))))))))...)))).(((((.((((.....))))..)))))..((....))............. ( -30.90)
>DroYak_CAF1 36408 101 + 1
CACAGAGAGUGUGUGCGUGCGUGUGAGUGAGCAUUCC--GCAUUCAACAGGUGGUCUUUAUUUGGGCAACAAAGAAAAGGAAGCUGCAGCGAAAUAAAGUUCU
(((...(((((((.(.((((..........)))).))--)))))).....)))..((((((((.(....)............((....)).)))))))).... ( -22.00)
>consensus
CACUGAGUGAGUGUGUGUGCGUGUGUGUAAGCAUUUCACACAUUCAACAAGUGGCCUUUAUUUGGGCAACAAAGAAAAGGAAGCUGCAGCAAAAUAAAGUUCU
((((...((((((((((...((((......))))..))))))))))...)))).(((((.((((.....))))..)))))..((....))............. (-23.83 = -24.57 +   0.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,904,397 – 7,904,500
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 90.29
Mean single sequence MFE -22.21
Consensus MFE -16.11
Energy contribution -18.18
Covariance contribution 2.06
Combinations/Pair 1.03
Mean z-score -1.70
Structure conservation index 0.73
SVM decision value 0.05
SVM RNA-class probability 0.559958
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7904397 103 - 27905053
CGAACUUUAGUUUGCUGCAGCUUCCUUUUCUUUGUUGCCCAAAUAAAGGCCACUUGUUGAAUGUGUAAAAUGCUUACACACACGCACACACACUCACCCAGUA
.(..(((((.((((..(((((............))))).)))))))))..)(((.(.(((.(((((....(((..........))).))))).))).).))). ( -20.60)
>DroSec_CAF1 35795 101 - 1
AGAACUUUAUUUUGCUGCAGCUUCCUUUUCUUUGUUGCCCAAAUAAAGGCCACUUGUUGAAUGUGUGAAAUGCUUACA--CACGCACACACACUCACUCAGUG
....((((((((....(((((............)))))..))))))))..((((.(.(((.((((((...(((.....--...))))))))).))).).)))) ( -24.50)
>DroSim_CAF1 37534 103 - 1
AGAACUUUAUUUUGCUGCAGCUUCCUUUUCUUUGUUGCCCAAAUAAAGGCCACUUGUUGAAUGUGUGAAAUGCUUACACACACGCACACACACUCACUCAGUG
....((((((((....(((((............)))))..))))))))..((((.(.(((.((((((...(((..........))))))))).))).).)))) ( -23.60)
>DroYak_CAF1 36408 101 - 1
AGAACUUUAUUUCGCUGCAGCUUCCUUUUCUUUGUUGCCCAAAUAAAGACCACCUGUUGAAUGC--GGAAUGCUCACUCACACGCACGCACACACUCUCUGUG
.......((((((((..((((.......((((((((.....))))))))......))))...))--))))))..................((((.....)))) ( -20.12)
>consensus
AGAACUUUAUUUUGCUGCAGCUUCCUUUUCUUUGUUGCCCAAAUAAAGGCCACUUGUUGAAUGUGUGAAAUGCUUACACACACGCACACACACUCACUCAGUG
....((((((((....(((((............)))))..))))))))..((((.(.(((.((((((...(((..........))))))))).))).).)))) (-16.11 = -18.18 +   2.06)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:42 2006