Locus 3256

Sequence ID 2L_DroMel_CAF1
Location 9,401,984 – 9,402,120
Length 136
Max. P 0.999258
window5170 window5171 window5172

overview

Window 0

Location 9,401,984 – 9,402,083
Length 99
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 92.56
Mean single sequence MFE -17.57
Consensus MFE -13.80
Energy contribution -14.00
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.79
SVM decision value 0.48
SVM RNA-class probability 0.754450
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9401984 99 + 22407834
ACGAGCAUUUGCAUUUUACUUCUGCCUUCACUUAUUUUU-UUUCACAGCUGACUUUCU---UUGCUUUUUUUAUUGUGCUGCAGCAAAUGCCGCAGAAUGCUU
..(((((((((((.......((.((..............-.......)).))......---.)))...........(((.(((.....))).))))))))))) ( -16.74)
>DroSec_CAF1 30684 97 + 1
ACGAGCAUUUGCAUUUCACUUCUGCCUUCACUUAUUCUU-UUUCACAACUGACUUUCU---UGC--UUUUUUAUUGUGCUGCAGCAAAUGCCGCAGAAUGCUU
..((((((((((((((.....((((...(((........-..................---...--.........)))..)))).))))))....)))))))) ( -15.26)
>DroSim_CAF1 32848 97 + 1
ACGAGCAUUUGCAUUUCACUUCUGCCUUCACUUAUUCUU-UUUCACAGCUGACUUUUU---UAG--UUUUUUAUUGUGCUGCAGCAAAUGCCGCAGAAUGCUU
..(((((((..............................-...(((((..((((....---.))--)).....)))))((((.((....)).))))))))))) ( -18.10)
>DroEre_CAF1 31201 101 + 1
ACGAGCAUUUGCAUUUUACUUCUGCCUUCACUUAUUCUUUUUUCACAACCGACUUUUUGUGUUU--UUUUUUAUUGUGCUGCAGCAAAUGCCGCAGAAUGCUU
..((((((((((((((.....((((...(((............(((((........)))))...--.........)))..)))).))))))....)))))))) ( -21.05)
>DroYak_CAF1 32695 97 + 1
ACGAACAUUUGCAUUUCACUUCUGCCUUCACUUAUUCUU-UUUCACAACUGAGUUUCU---UGC--UUUUUUAUUGUGCUGCAGCAAAUGCCGCAGAAUGCUU
..........(((((........................-...(((((..((((....---.))--)).....)))))((((.((....)).))))))))).. ( -16.70)
>consensus
ACGAGCAUUUGCAUUUCACUUCUGCCUUCACUUAUUCUU_UUUCACAACUGACUUUCU___UGC__UUUUUUAUUGUGCUGCAGCAAAUGCCGCAGAAUGCUU
..((((((((((((((.....((((...(((............................................)))..)))).))))))....)))))))) (-13.80 = -14.00 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,401,984 – 9,402,083
Length 99
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 92.56
Mean single sequence MFE -22.78
Consensus MFE -19.28
Energy contribution -19.36
Covariance contribution 0.08
Combinations/Pair 1.09
Mean z-score -2.91
Structure conservation index 0.85
SVM decision value 3.47
SVM RNA-class probability 0.999258
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9401984 99 - 22407834
AAGCAUUCUGCGGCAUUUGCUGCAGCACAAUAAAAAAAGCAA---AGAAAGUCAGCUGUGAAA-AAAAAUAAGUGAAGGCAGAAGUAAAAUGCAAAUGCUCGU
.(((((((((((((....))))))).............(((.---......((.(((......-.............))).)).......))).))))))... ( -20.65)
>DroSec_CAF1 30684 97 - 1
AAGCAUUCUGCGGCAUUUGCUGCAGCACAAUAAAAAA--GCA---AGAAAGUCAGUUGUGAAA-AAGAAUAAGUGAAGGCAGAAGUGAAAUGCAAAUGCUCGU
.((((((.((((.(((((.((((.((...........--)).---......(((.((((....-....)))).)))..)))))))))...))))))))))... ( -25.30)
>DroSim_CAF1 32848 97 - 1
AAGCAUUCUGCGGCAUUUGCUGCAGCACAAUAAAAAA--CUA---AAAAAGUCAGCUGUGAAA-AAGAAUAAGUGAAGGCAGAAGUGAAAUGCAAAUGCUCGU
.((((((.((((.(((((.((((..(((........(--((.---....)))...((......-.)).....)))...)))))))))...))))))))))... ( -23.00)
>DroEre_CAF1 31201 101 - 1
AAGCAUUCUGCGGCAUUUGCUGCAGCACAAUAAAAAA--AAACACAAAAAGUCGGUUGUGAAAAAAGAAUAAGUGAAGGCAGAAGUAAAAUGCAAAUGCUCGU
.((((((.....((((((.((((..(((.........--...(((((........)))))............)))...)))).....)))))).))))))... ( -22.15)
>DroYak_CAF1 32695 97 - 1
AAGCAUUCUGCGGCAUUUGCUGCAGCACAAUAAAAAA--GCA---AGAAACUCAGUUGUGAAA-AAGAAUAAGUGAAGGCAGAAGUGAAAUGCAAAUGUUCGU
.((((((.((((.(((((.((((.((...........--)).---......(((.((((....-....)))).)))..)))))))))...))))))))))... ( -22.80)
>consensus
AAGCAUUCUGCGGCAUUUGCUGCAGCACAAUAAAAAA__CAA___AGAAAGUCAGUUGUGAAA_AAGAAUAAGUGAAGGCAGAAGUGAAAUGCAAAUGCUCGU
.(((((((((((((....)))))))..........................(((.((((.........)))).)))..(((.........))).))))))... (-19.28 = -19.36 +   0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,402,021 – 9,402,120
Length 99
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 82.98
Mean single sequence MFE -23.46
Consensus MFE -17.62
Energy contribution -17.82
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -1.98
Structure conservation index 0.75
SVM decision value 0.44
SVM RNA-class probability 0.735613
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9402021 99 - 22407834
AGUGGAAG--GGCGCUGUGGUGGAUGACAAAUUGCUGACAAGCAUUCUGCGGCAUUUGCUGCAGCACA--AUAAAAAAAGCAA----AGAAAGUCA--GCUGUGAAA-AA
......(.--(((((((..(..((((.((...((((....))))...))...))))..)..))))...--.............----.(.....).--))).)....-.. ( -25.70)
>DroSec_CAF1 30721 97 - 1
AGGGGAAG--GGCGCUGUGGAGGAUGACAAAAUGCUGACAAGCAUUCUGCGGCAUUUGCUGCAGCACA--AUAAAAAA--GCA----AGAAAGUCA--GUUGUGAAA-AA
........--...((((..(..((((.((.((((((....)))))).))...))))..)..))))(((--((......--...----.........--)))))....-.. ( -23.47)
>DroSim_CAF1 32885 97 - 1
AGUGGAAG--GGCGCUGUGGAGGAUGACAAAUUGCUGACAAGCAUUCUGCGGCAUUUGCUGCAGCACA--AUAAAAAA--CUA----AAAAAGUCA--GCUGUGAAA-AA
((((....--..))))(..(....((((....((((....))))..(((((((....)))))))....--........--...----.....))))--.)..)....-.. ( -22.80)
>DroEre_CAF1 31238 103 - 1
AGUGGAGGAUGACGCUGUGGAGGAUGACAAAUUGCUGACAAGCAUUCUGCGGCAUUUGCUGCAGCACA--AUAAAAAA--AAA-CACAAAAAGUCG--GUUGUGAAAAAA
((((........))))(((.............((((....))))..(((((((....)))))))))).--........--...-(((((.......--.)))))...... ( -24.40)
>DroYak_CAF1 32732 97 - 1
AGUGGAAG--GACGCUGUGGAGGAUGACAAAUUGCUGACAAGCAUUCUGCGGCAUUUGCUGCAGCACA--AUAAAAAA--GCA----AGAAACUCA--GUUGUGAAA-AA
........--..(((....(((..........((((....))))..(((((((....)))))))....--........--...----.....))).--...)))...-.. ( -21.60)
>DroAna_CAF1 33068 97 - 1
-------G--GACUUUGGUGAGGUUGACAAAUUGCUGACAAGCAUUCUGCGGCAUUUACUGCAGCAAACAAAAAAAAA--GAAACA-UGAAACCGAAACCAGAAAAA-AA
-------.--...((((((..((((..((...((((....))))..((((((......))))))..............--......-)).))))...))))))....-.. ( -22.80)
>consensus
AGUGGAAG__GACGCUGUGGAGGAUGACAAAUUGCUGACAAGCAUUCUGCGGCAUUUGCUGCAGCACA__AUAAAAAA__GAA____AGAAAGUCA__GCUGUGAAA_AA
.............((((..(..((((.((...((((....))))...))...))))..)..))))............................................. (-17.62 = -17.82 +   0.20)

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 10:48:09 2006