Locus 8837

Sequence ID 3R_DroMel_CAF1
Location 23,659,064 – 23,659,158
Length 94
Max. P 0.871235
window14189 window14190

overview

Window 9

Location 23,659,064 – 23,659,158
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.99
Mean single sequence MFE -22.83
Consensus MFE -14.09
Energy contribution -13.57
Covariance contribution -0.52
Combinations/Pair 1.20
Mean z-score -1.86
Structure conservation index 0.62
SVM decision value 0.87
SVM RNA-class probability 0.871235
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23659064 94 + 27905053
AAACGUGGCGAAGAAAAGCAAUUAGCGAAAUUAAUUGCUCAAGUUUCGC--UUUGAAAUAUUCAUCC------GUGAGAUUAAUUCGCCGGCCG----------------ACAA--AGCU
...(((((((((....(((((((((.....)))))))))..((((((((--..(((.....)))...------))))))))..)))))))..))----------------....--.... ( -24.90)
>DroVir_CAF1 166492 94 + 1
AAACGUUGCGAAGAAAAGCAAUUAGCGAAAUUAAUUGCUUAAGUUUCGC-UUUUGAAAUAUUUAUCUGCCCGAGUGAGAUUAAUUCAAC-----------------------AA--GGAU
.......((((((..((((((((((.....))))))))))...))))))-(((((....(((.((((((....)).)))).)))....)-----------------------))--)).. ( -19.20)
>DroGri_CAF1 156976 94 + 1
AAACGUUGCAAAGAAAAGCAAUUAGCGAAAUUAAUUGCUGAAGUUUCGC-UUUUGAAAUAUUUAUCUGCCCGAAUGAGAUUAAUUCAAC-----------------------AA--GCAU
((((.((((........))))(((((((......))))))).)))).((-(((((((.((...((((.........)))))).))))).-----------------------))--)).. ( -16.60)
>DroSec_CAF1 121000 94 + 1
AAACGUGGCGAAGAAAAGCAAUUAGCGAAAUUAAUUGCUCAAGUUUCGC--UUUGAAAUAUUCAUCA------GUGAGAUUAAUUCGCCGGCCG----------------ACAA--AGCU
...(((((((((....(((((((((.....)))))))))..((((((((--(.(((.....)))..)------))))))))..)))))))..))----------------....--.... ( -26.10)
>DroWil_CAF1 138689 114 + 1
AAACGGAGCGAAGAAAAGCAAUUAGCGAAAUUAAUUGCUUAAGUUUCGU--UUUGAAAUAUUCAUCU----GAGUGGGAUUAAUUCAACAGUCGGGGUCGGGGCCAACUGAAGAAGGGCU
...((((((((((..((((((((((.....))))))))))...))))))--))))...(((((....----))))).......(((..((((...(((....))).))))..)))..... ( -31.00)
>DroMoj_CAF1 179747 95 + 1
AAACGUUGCGAAGAAAAGCAAUUAGCGAAAUUAAUUGCUUAAGUUUCGCCCUUUGAAAUAUUUAUCUGCUCGACUGACAUUAAUUCAAC-----------------------AA--GGAU
.......((((((..((((((((((.....))))))))))...))))))((((((((.((....((.........))...)).))))..-----------------------))--)).. ( -19.20)
>consensus
AAACGUUGCGAAGAAAAGCAAUUAGCGAAAUUAAUUGCUUAAGUUUCGC__UUUGAAAUAUUCAUCU____GAGUGAGAUUAAUUCAAC_______________________AA__GGAU
.......((((((...(((((((((.....)))))))))....))))))....((((.((.((((........))))...)).))))................................. (-14.09 = -13.57 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,659,064 – 23,659,158
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.99
Mean single sequence MFE -20.41
Consensus MFE -13.04
Energy contribution -13.07
Covariance contribution 0.03
Combinations/Pair 1.14
Mean z-score -1.64
Structure conservation index 0.64
SVM decision value 0.65
SVM RNA-class probability 0.812178
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23659064 94 - 27905053
AGCU--UUGU----------------CGGCCGGCGAAUUAAUCUCAC------GGAUGAAUAUUUCAAA--GCGAAACUUGAGCAAUUAAUUUCGCUAAUUGCUUUUCUUCGCCACGUUU
.(((--....----------------.))).((((((...(((....------.)))(((........(--((((((.((((....)))))))))))........)))))))))...... ( -21.59)
>DroVir_CAF1 166492 94 - 1
AUCC--UU-----------------------GUUGAAUUAAUCUCACUCGGGCAGAUAAAUAUUUCAAAA-GCGAAACUUAAGCAAUUAAUUUCGCUAAUUGCUUUUCUUCGCAACGUUU
....--..-----------------------.(((((.(((((((......).))))...)).)))))..-(((((....(((((((((.......)))))))))...)))))....... ( -17.80)
>DroGri_CAF1 156976 94 - 1
AUGC--UU-----------------------GUUGAAUUAAUCUCAUUCGGGCAGAUAAAUAUUUCAAAA-GCGAAACUUCAGCAAUUAAUUUCGCUAAUUGCUUUUCUUUGCAACGUUU
.(((--((-----------------------(.(((.......)))..))))))................-(((((.....((((((((.......))))))))....)))))....... ( -18.20)
>DroSec_CAF1 121000 94 - 1
AGCU--UUGU----------------CGGCCGGCGAAUUAAUCUCAC------UGAUGAAUAUUUCAAA--GCGAAACUUGAGCAAUUAAUUUCGCUAAUUGCUUUUCUUCGCCACGUUU
.(((--....----------------.))).((((((...(((....------.)))(((........(--((((((.((((....)))))))))))........)))))))))...... ( -21.79)
>DroWil_CAF1 138689 114 - 1
AGCCCUUCUUCAGUUGGCCCCGACCCCGACUGUUGAAUUAAUCCCACUC----AGAUGAAUAUUUCAAA--ACGAAACUUAAGCAAUUAAUUUCGCUAAUUGCUUUUCUUCGCUCCGUUU
(((..(((..(((((((........)))))))..)))............----.((.(((..((((...--..))))...(((((((((.......)))))))))))).)))))...... ( -21.70)
>DroMoj_CAF1 179747 95 - 1
AUCC--UU-----------------------GUUGAAUUAAUGUCAGUCGAGCAGAUAAAUAUUUCAAAGGGCGAAACUUAAGCAAUUAAUUUCGCUAAUUGCUUUUCUUCGCAACGUUU
..((--((-----------------------..((((...((((..(((.....)))..))))))))))))(((((....(((((((((.......)))))))))...)))))....... ( -21.40)
>consensus
AGCC__UU_______________________GUUGAAUUAAUCUCACUC____AGAUAAAUAUUUCAAA__GCGAAACUUAAGCAAUUAAUUUCGCUAAUUGCUUUUCUUCGCAACGUUU
.......................................................................(((((....(((((((((.......)))))))))...)))))....... (-13.04 = -13.07 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:56 2006