Locus 886

Sequence ID 3L_DroMel_CAF1
Location 2,686,838 – 2,686,942
Length 104
Max. P 0.967922
window1361 window1362

overview

Window 1

Location 2,686,838 – 2,686,942
Length 104
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 80.90
Mean single sequence MFE -35.77
Consensus MFE -19.63
Energy contribution -22.07
Covariance contribution 2.45
Combinations/Pair 1.08
Mean z-score -3.66
Structure conservation index 0.55
SVM decision value 1.62
SVM RNA-class probability 0.967922
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2686838 104 + 23771897
CUGACAAGCUUCACUUUCCCACGCAGCUCGCAGCGAUAUUUUUAGAAAUGCUAAUAAUUCACUCGAAAAGUGUGAGCUGCGUG-GGCUCCC-------GAUGCCAUACAUUU
.......((.((.....(((((((((((((((.(((.(((.((((.....)))).)))....))).....)))))))))))))-)).....-------)).))......... ( -35.70)
>DroSec_CAF1 47907 103 + 1
CUGACAAGCUUCACUUUCCCACGCAGCUCGCAGCGGUAUUUUUAGAAAUGCUAAUAAUUCACUCGAAAAGUGUGAGCUGCGUG-GGCUC-C-------GAUGCCAUACAUUU
.......((.((.....(((((((((((((((..(((((((....))))))).....(((....)))...)))))))))))))-))...-.-------)).))......... ( -37.20)
>DroSim_CAF1 46514 103 + 1
CUGACAAGCUUCACUUUCCCACGCAGCUCGCAGCGGUAUUUUUAGAAAUGCUAAUAAUUCACUCGAAAAGUGUGAGCUGCGUG-GGCUC-C-------GAUGCCAUACAUUU
.......((.((.....(((((((((((((((..(((((((....))))))).....(((....)))...)))))))))))))-))...-.-------)).))......... ( -37.20)
>DroEre_CAF1 52729 110 + 1
CUGACAAGCUUCGCUUUCCCACGCAGCUCGUCGCCGUAUUUUUAGAAAUGCUAAUAAUUCACUCGAAAAGUGUGAGCUGCGUG-GGCGU-AUGUAUGGGCUGCCAUACAUUU
...((((((...)))).(((((((((((((.(((.((((((....))))))......(((....)))..))))))))))))))-)).))-((((((((....)))))))).. ( -41.90)
>DroYak_CAF1 48372 103 + 1
CUGACAAGCUUCACUUUCCCACGCAGCUCGCCGCGGUAUUUUUAGAAAUGCUAAUAAUUCACUCGAAAAGUGUGAGCUGCGUG-GGCGU-C-------GCAGCCACACAUUU
.......(((.(((...((((((((((((((.(((((((((....))))))).....(((....)))..))))))))))))))-)).))-.-------).)))......... ( -37.00)
>DroAna_CAF1 46172 90 + 1
CUGGCAGGCUUCGU-----------------CUAGAUAUUUUUGGAAAAGCUAAUAACUCACUCGAAAUGUGUGGGCUUCCUUGGGGGU-CCUU----CUCCCCACACAUUU
......(((((..(-----------------(((((....)))))).))))).............(((((((((((((((....)))).-....----...))))))))))) ( -25.60)
>consensus
CUGACAAGCUUCACUUUCCCACGCAGCUCGCAGCGGUAUUUUUAGAAAUGCUAAUAAUUCACUCGAAAAGUGUGAGCUGCGUG_GGCGC_C_______GAUGCCAUACAUUU
...................((((((((((((...(((((((....))))))).....(((....)))....)))))))))))).(((..............)))........ (-19.63 = -22.07 +   2.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,686,838 – 2,686,942
Length 104
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 80.90
Mean single sequence MFE -35.03
Consensus MFE -20.26
Energy contribution -22.54
Covariance contribution 2.28
Combinations/Pair 1.10
Mean z-score -2.89
Structure conservation index 0.58
SVM decision value 1.12
SVM RNA-class probability 0.918257
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2686838 104 - 23771897
AAAUGUAUGGCAUC-------GGGAGCC-CACGCAGCUCACACUUUUCGAGUGAAUUAUUAGCAUUUCUAAAAAUAUCGCUGCGAGCUGCGUGGGAAAGUGAAGCUUGUCAG
...((...(((.((-------(....((-((((((((((.(((((...)))))......((((...............)))).))))))))))))....))).)))...)). ( -38.26)
>DroSec_CAF1 47907 103 - 1
AAAUGUAUGGCAUC-------G-GAGCC-CACGCAGCUCACACUUUUCGAGUGAAUUAUUAGCAUUUCUAAAAAUACCGCUGCGAGCUGCGUGGGAAAGUGAAGCUUGUCAG
...((...(((.((-------(-...((-((((((((((.(((((...)))))......((((...............)))).))))))))))))....))).)))...)). ( -37.86)
>DroSim_CAF1 46514 103 - 1
AAAUGUAUGGCAUC-------G-GAGCC-CACGCAGCUCACACUUUUCGAGUGAAUUAUUAGCAUUUCUAAAAAUACCGCUGCGAGCUGCGUGGGAAAGUGAAGCUUGUCAG
...((...(((.((-------(-...((-((((((((((.(((((...)))))......((((...............)))).))))))))))))....))).)))...)). ( -37.86)
>DroEre_CAF1 52729 110 - 1
AAAUGUAUGGCAGCCCAUACAU-ACGCC-CACGCAGCUCACACUUUUCGAGUGAAUUAUUAGCAUUUCUAAAAAUACGGCGACGAGCUGCGUGGGAAAGCGAAGCUUGUCAG
..((((((((....))))))))-...((-((((((((((.(((((...)))))........................(....))))))))))))).((((...))))..... ( -40.90)
>DroYak_CAF1 48372 103 - 1
AAAUGUGUGGCUGC-------G-ACGCC-CACGCAGCUCACACUUUUCGAGUGAAUUAUUAGCAUUUCUAAAAAUACCGCGGCGAGCUGCGUGGGAAAGUGAAGCUUGUCAG
.......((((.((-------.-((.((-((((((((((.(((((...))))).(((.((((.....)))).)))........))))))))))))...))...))..)))). ( -37.50)
>DroAna_CAF1 46172 90 - 1
AAAUGUGUGGGGAG----AAGG-ACCCCCAAGGAAGCCCACACAUUUCGAGUGAGUUAUUAGCUUUUCCAAAAAUAUCUAG-----------------ACGAAGCCUGCCAG
((((((((((((..----....-..))))..((....))))))))))..............(((((((............)-----------------).)))))....... ( -17.80)
>consensus
AAAUGUAUGGCAUC_______G_AAGCC_CACGCAGCUCACACUUUUCGAGUGAAUUAUUAGCAUUUCUAAAAAUACCGCGGCGAGCUGCGUGGGAAAGUGAAGCUUGUCAG
.......(((((..............((.((((((((((.(((((...))))).(((.((((.....)))).)))........))))))))))))...........))))). (-20.26 = -22.54 +   2.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:35 2006