Locus 8275

Sequence ID X_DroMel_CAF1
Location 20,583,555 – 20,583,693
Length 138
Max. P 0.999894
window13587 window13588 window13589

overview

Window 7

Location 20,583,555 – 20,583,653
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.20
Mean single sequence MFE -31.77
Consensus MFE -22.37
Energy contribution -22.93
Covariance contribution 0.56
Combinations/Pair 1.32
Mean z-score -2.97
Structure conservation index 0.70
SVM decision value 3.45
SVM RNA-class probability 0.999225
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20583555 98 + 22224390
GU-GUCACGGAAAAAUCUAAGGCUUAAAUUUCACAUAGGGCUCUACGAAGUAUGUAGUGAAAAAAAAA---------------------UUGUUUUGGCUACAUACUUCUAGGCACCUAC
..-(((..(((....)))..)))............((((((.(((.((((((((((((.((((.....---------------------...)))).))))))))))))))))).)))). ( -31.50)
>DroSec_CAF1 153353 115 + 1
GU-GUCACAGAAAAAUCUAAGGCUUCAAUUUCACCUAGGGGUCUACGAAGUAUGCAGAAUAAAACGAACACGAAUGCGAAAUAUAUAUUUUGUUUUGGCUGCAUACUUCUAGGCAC----
((-(((.............(((((((...........)))))))..(((((((((((..(((((((((....................))))))))).)))))))))))..)))))---- ( -32.35)
>DroSim_CAF1 167327 115 + 1
GU-GUCACAGAAAAAUCUAAGGCUUCAAUUUCACCUAGGGGUCUACGAAGUAUGCAGUGAAAAACGAACUCGAAUGCGAAAUAUAUAUUUUGUUUUGGCUGCAUACUUCUAGGCAC----
((-(((.............(((((((...........)))))))..((((((((((((.(((..((....))...(((((((....)))))))))).))))))))))))..)))))---- ( -36.30)
>DroEre_CAF1 147543 114 + 1
GUGGCACCAGAAAGAGCUAAGGUUUCAAAUUCACAUAGGGGUCUACAAGGUAUGCAGUGAAAAACGAACACGAAUGCGAACUAGAUA--GUAUUUUUGCUGCAUACCACUAGACAC----
.(((.(((............))).))).............(((((...(((((((((..((((.......((....)).(((....)--)).))))..)))))))))..)))))..---- ( -29.00)
>DroYak_CAF1 150515 112 + 1
GU-GCCACAGCAAGAGCUAAGGUUUCAAAUUCGCAUAG-GGUCUACAAAGUAUGCAGUGAAAGACGAACUCGAGUGCGAACUAGUAU--AUGUUUAUGCUGCAUACUUCUAGACAC----
..-(((..(((....)))..)))...............-.(((((..(((((((((((...(((((......(((....))).....--.)))))..))))))))))).)))))..---- ( -29.70)
>consensus
GU_GUCACAGAAAAAUCUAAGGCUUCAAUUUCACAUAGGGGUCUACGAAGUAUGCAGUGAAAAACGAACACGAAUGCGAAAUAGAUA__UUGUUUUGGCUGCAUACUUCUAGGCAC____
...(((..(((....)))..))).................(((((.((((((((((((.((((((((......................)))))))))))))))))))))))))...... (-22.37 = -22.93 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,583,594 – 20,583,693
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 76.99
Mean single sequence MFE -33.02
Consensus MFE -26.28
Energy contribution -26.62
Covariance contribution 0.34
Combinations/Pair 1.07
Mean z-score -4.20
Structure conservation index 0.80
SVM decision value 4.42
SVM RNA-class probability 0.999894
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20583594 99 + 22224390
CUCUACGAAGUAUGUAGUGAAAAAAAAA---------------------UUGUUUUGGCUACAUACUUCUAGGCACCUACCUAUACGAGUAUAGGGAUUUUUGUGGAACCCACAUACAUA
.((((.((((((((((((.((((.....---------------------...)))).))))))))))))))))......((((((....))))))......(((((...)))))...... ( -32.40)
>DroSec_CAF1 153392 111 + 1
GUCUACGAAGUAUGCAGAAUAAAACGAACACGAAUGCGAAAUAUAUAUUUUGUUUUGGCUGCAUACUUCUAGGCAC----CUAUACGAGUAUAUUGAUU-UUGUGGAACCCACA----UA
(((((.(((((((((((..(((((((((....................))))))))).))))))))))))))))..----...................-.(((((...)))))----.. ( -31.35)
>DroSim_CAF1 167366 112 + 1
GUCUACGAAGUAUGCAGUGAAAAACGAACUCGAAUGCGAAAUAUAUAUUUUGUUUUGGCUGCAUACUUCUAGGCAC----CUAUACGAGUAUAUUGAUUUUUGUGGAACCCACA----UA
(((((.((((((((((((.(((..((....))...(((((((....)))))))))).)))))))))))))))))..----.....................(((((...)))))----.. ( -35.30)
>consensus
GUCUACGAAGUAUGCAGUGAAAAACGAAC_CGAAUGCGAAAUAUAUAUUUUGUUUUGGCUGCAUACUUCUAGGCAC____CUAUACGAGUAUAUUGAUUUUUGUGGAACCCACA____UA
(((((.(((((((((((...((((((((....................))))))))..))))))))))))))))...........................(((((...)))))...... (-26.28 = -26.62 +   0.34)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,583,594 – 20,583,693
Length 99
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.99
Mean single sequence MFE -26.08
Consensus MFE -22.08
Energy contribution -21.97
Covariance contribution -0.11
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.85
SVM decision value 3.07
SVM RNA-class probability 0.998338
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20583594 99 - 22224390
UAUGUAUGUGGGUUCCACAAAAAUCCCUAUACUCGUAUAGGUAGGUGCCUAGAAGUAUGUAGCCAAAACAA---------------------UUUUUUUUUCACUACAUACUUCGUAGAG
...((((((((...)))).......((((((....))))))...))))((((((((((((((..((((...---------------------.....))))..))))))))))).))).. ( -27.40)
>DroSec_CAF1 153392 111 - 1
UA----UGUGGGUUCCACAA-AAUCAAUAUACUCGUAUAG----GUGCCUAGAAGUAUGCAGCCAAAACAAAAUAUAUAUUUCGCAUUCGUGUUCGUUUUAUUCUGCAUACUUCGUAGAC
..----(((((...))))).-........(((.....(((----....)))(((((((((((..(((((.((((....))))(((....)))...)))))...))))))))))))))... ( -26.00)
>DroSim_CAF1 167366 112 - 1
UA----UGUGGGUUCCACAAAAAUCAAUAUACUCGUAUAG----GUGCCUAGAAGUAUGCAGCCAAAACAAAAUAUAUAUUUCGCAUUCGAGUUCGUUUUUCACUGCAUACUUCGUAGAC
..----(((((...)))))..........(((.....(((----....)))(((((((((((..(((((...........((((....))))...)))))...))))))))))))))... ( -24.84)
>consensus
UA____UGUGGGUUCCACAAAAAUCAAUAUACUCGUAUAG____GUGCCUAGAAGUAUGCAGCCAAAACAAAAUAUAUAUUUCGCAUUCG_GUUCGUUUUUCACUGCAUACUUCGUAGAC
......(((((...)))))...............((((......))))((((((((((((((..(((((..........................)))))...))))))))))).))).. (-22.08 = -21.97 +  -0.11)

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 12:59:55 2006