Locus 4188

Sequence ID 2L_DroMel_CAF1
Location 11,994,611 – 11,994,891
Length 280
Max. P 0.775037
window6619 window6620 window6621

overview

Window 9

Location 11,994,611 – 11,994,731
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.56
Mean single sequence MFE -36.23
Consensus MFE -31.05
Energy contribution -31.72
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.86
SVM decision value -0.03
SVM RNA-class probability 0.520072
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11994611 120 + 22407834
AGCUUGUGCAGCAGGCUGCAGCUGUUGCUGCUGUGGCUGUCCAAAGACACUUUGUGCACCUGUUGCCGCAGCUCCUACACCAAAAAUGCUAUUCCUUGCAUUGGCAUUGCUAAUCGUUCC
((((((.(((((((((..((((.......))))..))((..(((((...)))))..)).))))))))).))))...........(((((((..........)))))))............ ( -38.20)
>DroSec_CAF1 6291 111 + 1
AGCUUGAGCAGCAGGCUGCAGCU---------GUGGCUGUCCAAACACACUUGUUGCACCUGUUGCCGCAGCUCCUACACCAAAUAUGCUAUUCCCUGCAUUGGCAUUGCUCAUCGUUCC
((((((.((((((((.((((((.---------(((............)))..)))))))))))))))).))))......(((...((((........)))))))................ ( -34.70)
>DroSim_CAF1 6269 120 + 1
AGCUUGAGCAGCAGGCUGCAGCUGUUGCUGCUGUGGCUGUCCAAACACACUUGUUGCACCUGUUGCCGCAGCUCCCACACCAAAUAUGCUAUUCCCUGCAUUGGCAUUGCUCAUCGUUCC
((((((.((((((((..(((((....)))))((..((.((........))..))..)))))))))))).))))......(((...((((........)))))))................ ( -35.80)
>consensus
AGCUUGAGCAGCAGGCUGCAGCUGUUGCUGCUGUGGCUGUCCAAACACACUUGUUGCACCUGUUGCCGCAGCUCCUACACCAAAUAUGCUAUUCCCUGCAUUGGCAUUGCUCAUCGUUCC
((((((.((((((((.((((((...........(((....))).........)))))))))))))))).))))......(((...((((........)))))))................ (-31.05 = -31.72 +   0.67)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,994,651 – 11,994,771
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -34.70
Consensus MFE -33.47
Energy contribution -33.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.96
SVM decision value 0.41
SVM RNA-class probability 0.726375
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11994651 120 + 22407834
CCAAAGACACUUUGUGCACCUGUUGCCGCAGCUCCUACACCAAAAAUGCUAUUCCUUGCAUUGGCAUUGCUAAUCGUUCCGCCGAAAAUGCUAUUGGUGUUGCUGGCUUGGCUUGUGGCA
.(((((...))))).........((((((((((((.(((((((.(((((........)))))((((((.....(((......))).)))))).)))))))....))...))).))))))) ( -35.80)
>DroSec_CAF1 6322 120 + 1
CCAAACACACUUGUUGCACCUGUUGCCGCAGCUCCUACACCAAAUAUGCUAUUCCCUGCAUUGGCAUUGCUCAUCGUUCCUCCGAAAAUGCUAUUGGUGUUGCUGGCUUGGCUUGUGGCA
...((((....))))........((((((((((((.(((((((..((((........))))(((((((.....(((......))).))))))))))))))....))...))).))))))) ( -34.20)
>DroSim_CAF1 6309 120 + 1
CCAAACACACUUGUUGCACCUGUUGCCGCAGCUCCCACACCAAAUAUGCUAUUCCCUGCAUUGGCAUUGCUCAUCGUUCCUCCGAAAAUGCUAUUGGUGUUGCUGGCUUGGCUUGUGGCA
...........(((..((......((((.((((..((((((((..((((........))))(((((((.....(((......))).))))))))))))).))..)))))))).))..))) ( -34.10)
>consensus
CCAAACACACUUGUUGCACCUGUUGCCGCAGCUCCUACACCAAAUAUGCUAUUCCCUGCAUUGGCAUUGCUCAUCGUUCCUCCGAAAAUGCUAUUGGUGUUGCUGGCUUGGCUUGUGGCA
.......................((((((((((((.(((((((..((((........))))(((((((.....(((......))).))))))))))))))....))...))).))))))) (-33.47 = -33.47 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,994,771 – 11,994,891
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.22
Mean single sequence MFE -45.57
Consensus MFE -42.62
Energy contribution -43.40
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.94
SVM decision value 0.54
SVM RNA-class probability 0.775037
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11994771 120 + 22407834
UUCCCAAAUAUAUUUCCCGCACUCAGCGUGGGCUUUCCAAAAAUGGAUGCAGAUGUAUUGGCGGCAGCCGGAGCUGCUGCAGCGAAGGGAUUACUGGACUGCUGAGGGGCAGCCGACACA
.((((.((((((((((((((.....))).))((..((((....)))).))))))))))).((((((((....))))))))......))))....(((.(((((....))))))))..... ( -46.70)
>DroSec_CAF1 6442 120 + 1
UUCCCAAAUAUAUUUCCCGCACUCAGUGUGGGCUUUCCAAAAAUGGAUGCAGAUGUAUUGGCGGCGGACGGAGCUGCUGCAGCGAAGGGAUUACUGGGAUGCUGAGGGGCAGCCGACACA
.((((.(((((((((.((((((...))))))((..((((....)))).))))))))))).(((((((......)))))))......))))......((.((((....)))).))...... ( -41.70)
>DroSim_CAF1 6429 120 + 1
UUCCCAAAUAUAUUUCCCGCACUCAGUGUGGGCUUUCCAAAAAUGGAUGCAGAUGUAUUGGCGGCGGACGGAGCUGCUGCAGCGAAGGGAUUACUGGGCUGCUGAGGGGCAGCCGACACA
.((((.(((((((((.((((((...))))))((..((((....)))).))))))))))).(((((((......)))))))......))))......(((((((....)))))))...... ( -48.30)
>consensus
UUCCCAAAUAUAUUUCCCGCACUCAGUGUGGGCUUUCCAAAAAUGGAUGCAGAUGUAUUGGCGGCGGACGGAGCUGCUGCAGCGAAGGGAUUACUGGGCUGCUGAGGGGCAGCCGACACA
.((((.(((((((((.((((((...))))))((..((((....)))).))))))))))).(((((((......)))))))......))))......(((((((....)))))))...... (-42.62 = -43.40 +   0.78)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:58 2006