Locus 2136

Sequence ID 2L_DroMel_CAF1
Location 5,778,195 – 5,778,373
Length 178
Max. P 0.970880
window3454 window3455 window3456

overview

Window 4

Location 5,778,195 – 5,778,301
Length 106
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 90.65
Mean single sequence MFE -41.10
Consensus MFE -35.69
Energy contribution -37.70
Covariance contribution 2.01
Combinations/Pair 1.14
Mean z-score -3.51
Structure conservation index 0.87
SVM decision value 1.67
SVM RNA-class probability 0.970880
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5778195 106 - 22407834
AUAGUCGAGCCACUAGUC-UCAUAUCUUGCUCGUUCGCAUUUUUCGUGCGGUUCAGCGAGAAGAAGAAGACGGCUGGCAUACGGAAAAGCUGUAUACGUAUACGGCG
...((((.((((...(((-((...(((((((...((((((.....))))))...)))))))....).))))...))))((((((.....)))))).......)))). ( -35.90)
>DroSec_CAF1 15298 102 - 1
AUAGUCGAGCUACUCGUCUUCAUCUCUUGUUCGUUCGCAUUUUGCG-----UUCAGCGAGAAGGAGAAGACGACUGGCAUACGGAAAAGCUGUAUACGUAUACGGCG
...((((.((((.((((((((..((((((((.(..(((.....)))-----..))))))).))..)))))))).))))((((((.....)))))).......)))). ( -41.00)
>DroSim_CAF1 16062 107 - 1
AUAGCCGAGCUACUCGUCUUCAUCUCUUGCUCGUUCGCAUUUUCCGUGCGGUUCAGCGAGAAGGAGAAGACGUCUGGCAUACGGAAAAGCUGUAUACGUAUACGGCG
...((((.((((..(((((((..((((((((...((((((.....))))))...)))))).))..)))))))..))))((((((.....)))))).......)))). ( -46.40)
>consensus
AUAGUCGAGCUACUCGUCUUCAUCUCUUGCUCGUUCGCAUUUUCCGUGCGGUUCAGCGAGAAGGAGAAGACGACUGGCAUACGGAAAAGCUGUAUACGUAUACGGCG
...((((.((((.((((((((.(((((((((...((((((.....))))))...)))))).))).)))))))).))))((((((.....)))))).......)))). (-35.69 = -37.70 +   2.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 5,778,234 – 5,778,341
Length 107
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 80.45
Mean single sequence MFE -30.87
Consensus MFE -19.18
Energy contribution -21.30
Covariance contribution 2.12
Combinations/Pair 1.13
Mean z-score -1.80
Structure conservation index 0.62
SVM decision value 0.02
SVM RNA-class probability 0.542349
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5778234 107 - 22407834
UAGUGGAACUGUUGCUCAAAGUGCGAGCAAUGAGUAUCUGAUAGUCGAGCCACUAGUC-UCAUAUCUUGCUCGUUCGCAUUUUUCGUGCGGUUCAGCGAGAAGAAGAA
..((.(((((((.....(((((((((((...(((((...((((...(((.(....).)-)).)))).))))))))))))))))....))))))).))........... ( -33.70)
>DroSec_CAF1 15337 91 - 1
------------UGCUCAAAUUGCGAGUAGUGGGUAUCUGAUAGUCGAGCUACUCGUCUUCAUCUCUUGUUCGUUCGCAUUUUGCG-----UUCAGCGAGAAGGAGAA
------------..........(((((((((((.(((...))).))..))))))))).....((((((.(((((((((.....)))-----...)))))).)))))). ( -27.40)
>DroSim_CAF1 16101 96 - 1
------------UGCUAAAAUUGCGAGUAAUGGGUAUCUGAUAGCCGAGCUACUCGUCUUCAUCUCUUGCUCGUUCGCAUUUUCCGUGCGGUUCAGCGAGAAGGAGAA
------------..........(((((((.(.(((........))).)..))))))).....((((((.(((((((((((.....))))))....))))).)))))). ( -31.50)
>consensus
____________UGCUCAAAUUGCGAGUAAUGGGUAUCUGAUAGUCGAGCUACUCGUCUUCAUCUCUUGCUCGUUCGCAUUUUCCGUGCGGUUCAGCGAGAAGGAGAA
............(((((.......))))).((((((.((........)).))))))(((((...(((((((...((((((.....))))))...))))))).))))). (-19.18 = -21.30 +   2.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 5,778,262 – 5,778,373
Length 111
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 80.56
Mean single sequence MFE -26.90
Consensus MFE -17.31
Energy contribution -18.10
Covariance contribution 0.79
Combinations/Pair 1.15
Mean z-score -1.77
Structure conservation index 0.64
SVM decision value 0.13
SVM RNA-class probability 0.596774
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5778262 111 - 22407834
AAAAUUUGGUGUCCAAUUAAGGUAUACUCCUCUAGUGGAACUGUUGCUCAAAGUGCGAGCAAUGAGUAUCUGAUAGUCGAGCCACUAGUC-UCAUAUCUUGCUCGUUCGCAU
.......(((.((((....(((......)))....)))))))..........((((((((...(((((...((((...(((.(....).)-)).)))).))))))))))))) ( -28.40)
>DroSec_CAF1 15360 95 - 1
A-AAUUUGGUGAGCAAUUAAGAUAUACU----------------UGCUCAAAUUGCGAGUAGUGGGUAUCUGAUAGUCGAGCUACUCGUCUUCAUCUCUUGUUCGUUCGCAU
.-......((((((...(((((..((((----------------(((.......))))))).........(((.((.((((...)))).)))))..)))))...)))))).. ( -25.30)
>DroSim_CAF1 16129 95 - 1
A-AAUUUGGUGAGCAAUUAAGAUAUACU----------------UGCUAAAAUUGCGAGUAAUGGGUAUCUGAUAGCCGAGCUACUCGUCUUCAUCUCUUGCUCGUUCGCAU
.-......((((((..........((((----------------(((.......)))))))..(((((...(((((.((((...)))).))..)))...))))))))))).. ( -27.00)
>consensus
A_AAUUUGGUGAGCAAUUAAGAUAUACU________________UGCUCAAAUUGCGAGUAAUGGGUAUCUGAUAGUCGAGCUACUCGUCUUCAUCUCUUGCUCGUUCGCAU
........((((((...............................((.......))((((((.(((....(((.((.((((...)))).))))).))))))))))))))).. (-17.31 = -18.10 +   0.79)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:36 2006