Locus 62

Sequence ID pao.2545
Location 4,791,766 – 4,791,996
Length 230
Max. P 0.996967
window342 window343 window344

overview

Window 2

Location 4,791,766 – 4,791,866
Length 100
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 77.67
Mean single sequence MFE -29.63
Consensus MFE -19.27
Energy contribution -16.78
Covariance contribution -2.49
Combinations/Pair 1.52
Mean z-score -2.05
Structure conservation index 0.65
SVM decision value 1.34
SVM RNA-class probability 0.944497
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4791766 100 - 6264404
AAUUCGGGUAUGUGAUAGAA--GUAAGACUGAAUGAUCUCUUUCACUGGUGAUCAUUCAAGUCAAGGUAAAAUUUGCGAGUUC-------------AA-GCGCGAAUUUUCGGCGA
...(((..............--....((((((((((((.((......)).)))))))).))))...(.((((((((((.....-------------..-.)))))))))))..))) ( -27.70)
>pau.414 5802597 100 + 6537648
AAUUCGGGUAUGUGAUAGAA--GUAAGACUGAAUGAUCUCUUUCACUGGUGAUCAUUCAAGUCAAGGUAAAAUUUGCGAGUUC-------------AA-GCGCGAAUUUUCGGCGA
...(((..............--....((((((((((((.((......)).)))))))).))))...(.((((((((((.....-------------..-.)))))))))))..))) ( -27.70)
>pel.2704 5001686 112 - 5888780
AAUUCGGAUAUGUGAUAGAA--AU-AGACUGAAC-ACCAGUUUCACUGCUGGUGGAUCAGGCUAAGGUAAAAUUUGUGAGUUCUGCUCGAAAGAGCGACGUGCGAAUUUUCGGCGA
...(((..............--.(-((.((((.(-((((((......)))))))..)))).)))..(.(((((((((..(((..((((....)))))))..))))))))))..))) ( -36.10)
>ppk.338 5482056 112 + 6181863
AAUUCGGAUAUGUGAUAGAU--AU-AGACUGAAC-ACCAGUUUCACUGCUGGUGGAUCAGGCUAAGGUAAAAUUUGUGAGUUCUGCUCGAAAGAGCAACGUACGAAUUUUCGGCGA
...(((..............--.(-((.((((.(-((((((......)))))))..)))).)))..(.((((((((((.((..(((((....))))))).)))))))))))..))) ( -37.30)
>pf5.74 6950066 112 + 7074893
AAUUUGGGUAUGUGAUAGAAAGAU-AGACUGAAC-GUUACUUUCACUGGUAACGGAUCAGGCUAAGGUAAAAUUUGUGAGUUCUCUUUUAAUUAAGAA--UGCAAAUUUUCGGCGA
((((((.((...((((.(((((((-((.((((.(-((((((......)))))))..)))).)))......((((....)))).)))))).))))...)--).))))))........ ( -23.10)
>pfo.66 6314935 111 + 6438405
AAUUUGGGUAUGUGAUAGAAAGAU-AGACUGAAC-GUUACUUUCACUGGUAACGGAUCAGGCUAAGGUAAAAUUUGUGAGUUCUCUU--AAUUGAGAA-AUUCGAAUUUUCGGCGA
..........(((..........(-((.((((.(-((((((......)))))))..)))).)))..(.((((((((....(((((..--....)))))-...))))))))).))). ( -25.90)
>consensus
AAUUCGGGUAUGUGAUAGAA__AU_AGACUGAAC_AUCACUUUCACUGGUGAUGGAUCAGGCUAAGGUAAAAUUUGUGAGUUCU__U__AA__A__AA_GUGCGAAUUUUCGGCGA
............................((((.(.((((((......)))))).).))))(((...(.((((((((((.....((((......))))...)))))))))))))).. (-19.27 = -16.78 +  -2.49)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,791,866 – 4,791,956
Length 90
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 67.27
Mean single sequence MFE -25.58
Consensus MFE -14.17
Energy contribution -12.98
Covariance contribution -1.19
Combinations/Pair 1.40
Mean z-score -2.86
Structure conservation index 0.55
SVM decision value 2.78
SVM RNA-class probability 0.996967
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4791866 90 - 6264404
CACCAUCU--AAAACAAUCGUCG--------AAAGCUCAGAAAUGAAUGUUC------------------GUGAAUGAACAUUGAUUUCUGGUC-UUUGCACCAGAACUGUUCUUUAAA
........--.........((((--------((..(.(((((((.(((((((------------------(....)))))))).))))))))..-)))).))................. ( -21.80)
>pss.3053 5951255 108 - 6093698
CACCACUU--ACUGCUUCUGUUU------UGAAAGCUUAGAAAUGAGCAUUCCAUUGAUCCUGAUGAUCAGUGCAUGAAUGUUGAUUUCUAGUC-UUUG-AUUAGAUC-GUUCUUUAAA
........--......((((...------(.((((.((((((((.(((((((((((((((.....))))))))...))))))).)))))))).)-))).-).))))..-.......... ( -29.70)
>pel.2704 5001798 97 - 5888780
CACCACUCUUUCAGGUUUCGCAGCACUGCUCAGAACUUAGAAAUGAGCAUUCGGUGA------------------UGAAUGUUGAUUUCUGACU-UUUG--UCAGAUC-GUUCUUUAAA
((((.(((((((((((((.(((....)))...)))))).)))).))).....)))).------------------.(((((......((((((.-...)--))))).)-))))...... ( -25.70)
>pf5.74 6950178 85 + 7074893
CACCAUAA--ACUGCUUCUGAA-----------AGCUUAGAAAUGAGCAUUC-----------AC--------CUUGAAUGUUGAUUUCUAGUCUUUUG-AUUAGAUC-GUUCUUUAAA
.....(((--(..((.((((((-----------((.((((((((.(((((((-----------..--------...))))))).)))))))).)))...-.)))))..-))..)))).. ( -21.70)
>pfo.66 6315046 97 + 6438405
CACCACUA---CUGCUUCUGAAG------UAAAAGCUUAGAAAUGAGCAUUCCAUCG---UUGAU--------GGUGAAUGUUGAUUUCUAGUCUUUUG-ACUGGUUC-GUUCUUUAAA
.((((..(---((........))------)(((((.((((((((.(((((((((((.---..)))--------))..)))))).)))))))).))))).-..))))..-.......... ( -24.40)
>psp.2973 5782417 107 - 5928787
CACCACUU--ACUGCUUCUG-UU------UGAAAGCUUAGAAAUGAGCAUUCCAUUGAUCCUGAUGAUCAGUGCAUGAAUGUUGAUUUCUAGUC-UUUG-AUUAGAUC-GUUCUUUAAA
........--......((((-.(------..((..((.((((((.(((((((((((((((.....))))))))...))))))).))))))))..-))..-).))))..-.......... ( -30.20)
>consensus
CACCACUU__ACUGCUUCUGAAG______U_AAAGCUUAGAAAUGAGCAUUCCAU_G______AU________CAUGAAUGUUGAUUUCUAGUC_UUUG_AUUAGAUC_GUUCUUUAAA
....................................((((((((.(((((((........................))))))).))))))))........................... (-14.17 = -12.98 +  -1.19)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,791,905 – 4,791,996
Length 91
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 71.60
Mean single sequence MFE -29.42
Consensus MFE -21.00
Energy contribution -20.53
Covariance contribution -0.47
Combinations/Pair 1.27
Mean z-score -1.17
Structure conservation index 0.71
SVM decision value 0.99
SVM RNA-class probability 0.895356
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2545 4791905 91 - 6264404
UUUGCACGCAGGAGGUCAGGAGUUCGAUCCUCCUUGGCUCCACCAUCU--AAAACAAUCGUCG--------AAAGCUCAGAAAUGAAUGUUC------------------GUGAAUGAA
..........((((.(.(((((.......))))).).)))).......--....((.(((.((--------((...(((....)))...)))------------------)))).)).. ( -23.90)
>pss.3053 5951292 111 - 6093698
CUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUUGGCUCCACCACUU--ACUGCUUCUGUUU------UGAAAGCUUAGAAAUGAGCAUUCCAUUGAUCCUGAUGAUCAGUGCAUGAA
..((((((((((((...(((((.......)))))(((.....)))...--....)))))))..------.(((.(((((....))))).)))...(((((.....)))))))))).... ( -34.70)
>pel.2704 5001834 101 - 5888780
CUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUUGGCUCCACCACUCUUUCAGGUUUCGCAGCACUGCUCAGAACUUAGAAAUGAGCAUUCGGUGA------------------UGAA
....(((((.((((.(.(((((.......))))).).))))....(((((((((((((.(((....)))...)))))).)))).)))......))).------------------)).. ( -29.10)
>pf5.74 6950216 87 + 7074893
CUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUUGGCUCCACCAUAA--ACUGCUUCUGAA-----------AGCUUAGAAAUGAGCAUUC-----------AC--------CUUGAA
..........((((.(.(((((.......))))).).)))).......--........((((-----------.(((((....))))).)))-----------).--------...... ( -25.00)
>pfo.66 6315084 99 + 6438405
CUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUUGGCUCCACCACUA---CUGCUUCUGAAG------UAAAAGCUUAGAAAUGAGCAUUCCAUCG---UUGAU--------GGUGAA
((((....)))).(((((((((.......)))).))))).(((((.((---((........))------))...(((((....))))).........---....)--------)))).. ( -29.10)
>psp.2973 5782454 110 - 5928787
CUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUUGGCUCCACCACUU--ACUGCUUCUG-UU------UGAAAGCUUAGAAAUGAGCAUUCCAUUGAUCCUGAUGAUCAGUGCAUGAA
..((((((((((((...(((((.......)))))(((.....)))...--....))))))-).------.(((.(((((....))))).)))...(((((.....)))))))))).... ( -34.70)
>consensus
CUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUUGGCUCCACCACUU__ACUGCUUCUGAAG______U_AAAGCUUAGAAAUGAGCAUUCCAU_G______AU________CAUGAA
..........((((.(.(((((.......))))).).)))).................................(((((....)))))............................... (-21.00 = -20.53 +  -0.47)

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 Thu Jan 18 21:09:30 2007