Locus 6628

Sequence ID 3R_DroMel_CAF1
Location 17,430,306 – 17,430,502
Length 196
Max. P 0.995396
window10789 window10790 window10791

overview

Window 9

Location 17,430,306 – 17,430,404
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 98.64
Mean single sequence MFE -18.84
Consensus MFE -18.73
Energy contribution -18.51
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -1.48
Structure conservation index 0.99
SVM decision value 0.18
SVM RNA-class probability 0.623647
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17430306 98 + 27905053
ACUUAAUGGGCAUGAAAACCGUCUGCGCCAGAAACAACAACAAAAGCAAGAAAAACAAGCGCAGUUCAAGCAUCAAAAAGCUGCCGUCACGCCCCUCU
.......((((.(((.....(.((((((..............................))))))..).(((........)))....))).)))).... ( -19.51)
>DroSec_CAF1 34194 98 + 1
ACCUAAUGGGUAUGAAAACCGUCUGCGCCAGAAACAACAACAAAAGCAAGAAAAACAAGCGCAGUUCAAGCAUCAAAAAGCUGCCGUCACGCCCCUCU
.......(((..(((.....(.((((((..............................))))))..).(((........)))....)))..))).... ( -18.51)
>DroSim_CAF1 31334 98 + 1
ACUUAAUGGGUAUGAAAACCGUCUGCGCCAGAAACAACAACAAAAGCAAGAAAAACAAGCGCAGUUCAAGCAUCAAAAAGCUGCCGUCACGCCCCUCU
.......(((..(((.....(.((((((..............................))))))..).(((........)))....)))..))).... ( -18.51)
>consensus
ACUUAAUGGGUAUGAAAACCGUCUGCGCCAGAAACAACAACAAAAGCAAGAAAAACAAGCGCAGUUCAAGCAUCAAAAAGCUGCCGUCACGCCCCUCU
.......((((.(((.....(.((((((..............................))))))..).(((........)))....))).)))).... (-18.73 = -18.51 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 17,430,338 – 17,430,441
Length 103
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 94.73
Mean single sequence MFE -39.64
Consensus MFE -32.66
Energy contribution -33.10
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -2.76
Structure conservation index 0.82
SVM decision value 2.57
SVM RNA-class probability 0.995396
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17430338 103 - 27905053
GCAGGGAAGGCAGGGGGUGGUGAGCGGCAAG--CACUCAAGAGGGGCGUGACGGCAGCUUUUUGAUGCUUGAACUGCGCUUGUUUUUCUUGCUUUUGUUGUUGUU
((((.(((((((((..(.((..((((.((((--((.((((((((.((......))..)))))))))))))).....))))..)))..))))))))).)))).... ( -43.20)
>DroSec_CAF1 34226 104 - 1
GCAGGGAAGGCAGG-GGUGGUGAGCGGCAAGCGCACUCAAGAGGGGCGUGACGGCAGCUUUUUGAUGCUUGAACUGCGCUUGUUUUUCUUGCUUUUGUUGUUGUU
((((.(((((((((-((..(..((((.((((((...((((((((.((......))..)))))))))))))).....))))..)..))))))))))).)))).... ( -41.60)
>DroSim_CAF1 31366 104 - 1
GCAGGGAGGGCAGG-GGUGGUGAGCGGCAAGCGCACUCAAGAGGGGCGUGACGGCAGCUUUUUGAUGCUUGAACUGCGCUUGUUUUUCUUGCUUUUGUUGUUGUU
((((.(((((((((-((..(..((((.((((((...((((((((.((......))..)))))))))))))).....))))..)..))))))))))).)))).... ( -41.20)
>DroEre_CAF1 33969 104 - 1
GCAGAGGAGGCAGG-GGUGGUGAGCGGCAAGCUCACUCAAGAGGGGCGUGACGGCAGCUUUUUGAUGCUUGAACUGCGCUUGUUUUUCUUGCUUUUGUUGUUGUU
((((..((((((((-((..(..((((.(((((....((((((((.((......))..)))))))).))))).....))))..)..))))))))))..)))).... ( -39.30)
>DroYak_CAF1 34602 104 - 1
GCAGAGGAGGCAGG-GGUAGUGCGCGGCAAGCGCACUCAAGAGGGGCGUGAUGGCAGCUUUUUGAUGCUUGAACUUCGCUUGUUUUUCUUGGUUUUGUUGUUAUU
((((..(((.((((-((.(((((((.....))))))))((((.(((((....((((.(.....).)))).......))))).))))))))).)))..)))).... ( -32.90)
>consensus
GCAGGGAAGGCAGG_GGUGGUGAGCGGCAAGCGCACUCAAGAGGGGCGUGACGGCAGCUUUUUGAUGCUUGAACUGCGCUUGUUUUUCUUGCUUUUGUUGUUGUU
((((.(((((((((....((..((((.((((((...((((((((.((......))..)))))))))))))).....))))..))...))))))))).)))).... (-32.66 = -33.10 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 17,430,404 – 17,430,502
Length 98
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 87.02
Mean single sequence MFE -36.90
Consensus MFE -29.02
Energy contribution -28.66
Covariance contribution -0.36
Combinations/Pair 1.26
Mean z-score -1.65
Structure conservation index 0.79
SVM decision value 0.33
SVM RNA-class probability 0.692523
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17430404 98 - 27905053
GCGGGCUGCGGUGGAGCGGUAAAGCG--------AGAGAGACGCUGUAUGUCUGGCCCCGUUUGAUGGGGCAGGGAAGGCAGGGGGUGGUGAGCGGCAAG--CACUCA
((..(((((......)))))...))(--------((.....((((.(.(((((.(((((((...))))))).....))))).).))))....((.....)--).))). ( -38.00)
>DroSec_CAF1 34292 107 - 1
GCGGGCUGCGGUGGAGCGGUAGAGCGAGAGAGCGAGAGAGACGCUGUAUGUCUGGCCUCGUUUGAUGGGGCAGGGAAGGCAGG-GGUGGUGAGCGGCAAGCGCACUCA
((..(((((......)))))...))..(((.(((.......(.((((...(((.(((((((...)))))))..)))..)))).-)((.(....).))...))).))). ( -39.30)
>DroSim_CAF1 31432 99 - 1
GCGGGCUGCGUUGGAGCGGUAGAGCG--------AGAGAGACGCUGUAUGUCUGGCCUCGUUUGAUGGGGCAGGGAGGGCAGG-GGUGGUGAGCGGCAAGCGCACUCA
((..(((((......)))))...))(--------((.....(((..(.(((((.(((((((...))))))).....)))))..-.)..))).(((.....))).))). ( -36.80)
>DroEre_CAF1 34035 98 - 1
GUGGG-AGCGGGGGAGCGGUAGAGCG--------AGAGAGACGCUGUAGGUCUGGCCUCGUUUGAUGGGGCAGAGGAGGCAGG-GGUGGUGAGCGGCAAGCUCACUCA
...((-(.(...(.((((......(.--------...)...)))).).).))).(((((.((((......)))).)))))...-...(((((((.....))))))).. ( -34.60)
>DroYak_CAF1 34668 98 - 1
GUGGG-AGCUGUGGAGCAGCAAAGCG--------AGAGAGACGCUGUAGGUCUGGCCUCGUAUGGUGGGGCAGAGGAGGCAGG-GGUAGUGCGCGGCAAGCGCACUCA
.....-.((((.....))))......--------.......(.((((...(((.((((((.....))))))..)))..)))).-)(.(((((((.....)))))))). ( -35.80)
>consensus
GCGGGCUGCGGUGGAGCGGUAGAGCG________AGAGAGACGCUGUAUGUCUGGCCUCGUUUGAUGGGGCAGGGAAGGCAGG_GGUGGUGAGCGGCAAGCGCACUCA
((..(((((......)))))...))..................((((...(((.(((((((...)))))))..)))..)))).....((((.((.....)).)))).. (-29.02 = -28.66 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:17 2006