Locus 167

Sequence ID	pao.2936
Location	5,537,738 – 5,537,866
Length	128
Max. P	0.984686

overview

Window 2

Location	5,537,738 – 5,537,850
Length	112
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	78.07
Mean single sequence MFE	-48.63
Consensus MFE	-30.44
Energy contribution	-30.17
Covariance contribution	-0.28
Combinations/Pair	1.22
Mean z-score	-2.31
Structure conservation index	0.63
SVM decision value	1.49
SVM RNA-class probability	0.958827
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2936 5537738 112 + 6264404
AAAUGCUCCUUACGGGUU-GCAGCCUGCCGC---AGAACGGUCAGGCAAGGAGUGAAUG--UUUUCUU-GGCUUGCCUGGUGGAGAGGCGAACGAACGCCUGCCCACGCGGCAAGGGGC
....(((((((..((((.-...))))(((((---........((((((((....(((..--..)))..-..))))))))((((..(((((......)))))..)))))))))))))))) ( -53.80)
>pfo.288 5816639 113 - 6438405
--AUGCUCCUUACGGGUU-GUAGCCUGCCGCUCAAAAACGGUCAGACAAGGAGUGAAUGACACUUAUG-GACUUGC-UGG-CGCGGGGCACAUGCAUGCCCGCCGCCACAGCAAGGGGC
--..(((((((....(((-(((((((((((........))).))).(...(((((.....)))))...-)....))-)((-((.((((((......))))).))))))))))))))))) ( -41.90)
>ppk.2829 5544859 115 + 6181863
--AUGCUCCUUACGGGUUAGUAGUCUGCCAGUGAA-UCUGGUCAGACAAGGAGUGAAUGACACUGUAU-GUCUUGCACGGAGGGGAGGCACAUGAGCGCCUGCCAGCUCGGCAAGGGGC
--..(((((((.((((((....(((((((((....-.)))).))))).....(((...((((.....)-)))...)))....((.((((.(....).)))).))))))))..))))))) ( -48.50)
>psp.340 5251467 114 - 5928787
--AUGCUCCUUACGGGUU-GUAGCCUGCCGCUCAAAAGCGGUCAGACAAGGAGUGAAUGACACUGUUG-GUCUUGCUCAG-GGACAGGCACAUGCGCGCCUGCCGUGACAGCAAGGGGC
--..(((((((.(((((.-...)))))(((((....)))))..((((.((.((((.....)))).)).-)))).(((((.-((.(((((.(....).))))))).)))..))))))))) ( -46.00)
>pf5.339 6399905 115 - 7074893
--AUGCUCCUUACGGGUU-GUAGCCUGCCGCCUAUAAGCGGUCAGACAAGGAGUGAAUGACACUGGUGUGUCUUGCCUGG-UAGUAGGCACAUAUGCGCCUGCCGUCACGGCAAGGGGC
--..(((((((.(((((.-...)))))((((......))))......)))))))....(((((....)))))((((((((-..((((((.(....).))))))..))).)))))..... ( -48.20)
>pau.3075 5809116 110 + 6537648
--AUGCUCCUUACGGGUU-GCAGCCUGCCGC---AGAACGGUCAGGCAAGGAGUGAAUG--UUUUCUU-GGCUUGCCUGGUGGAGAGGCGAACGAACGCCUGCCCGCGCGGCAAGGGGC
--..(((((((..((((.-...))))(((((---........((((((((....(((..--..)))..-..))))))))((((..(((((......)))))..)))))))))))))))) ( -53.40)
>consensus
__AUGCUCCUUACGGGUU_GUAGCCUGCCGCU_AAAAACGGUCAGACAAGGAGUGAAUGACACUGCUG_GUCUUGCCUGG_GGAGAGGCACAUGAACGCCUGCCGGCACGGCAAGGGGC
....(((((((.(((((.....)))))(((........)))......))))))).................((((((....((..((((........))))..))....)))))).... (-30.44 = -30.17 +  -0.28)

alignment

secondary structure

dotplot

Window 3

Location	5,537,738 – 5,537,850
Length	112
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	78.07
Mean single sequence MFE	-46.63
Consensus MFE	-37.74
Energy contribution	-36.08
Covariance contribution	-1.66
Combinations/Pair	1.42
Mean z-score	-3.21
Structure conservation index	0.81
SVM decision value	1.78
SVM RNA-class probability	0.976909
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2936 5537738 112 - 6264404
GCCCCUUGCCGCGUGGGCAGGCGUUCGUUCGCCUCUCCACCAGGCAAGCC-AAGAAAA--CAUUCACUCCUUGCCUGACCGUUCU---GCGGCAGGCUGC-AACCCGUAAGGAGCAUUU
((..(((((((((((((.(((((......))))).)))))((((((((..-..(((..--..)))....))))))))........---))))))))..))-...((....))....... ( -50.50)
>pfo.288 5816639 113 + 6438405
GCCCCUUGCUGUGGCGGCGGGCAUGCAUGUGCCCCGCG-CCA-GCAAGUC-CAUAAGUGUCAUUCACUCCUUGUCUGACCGUUUUUGAGCGGCAGGCUAC-AACCCGUAAGGAGCAU--
((.((((((((((((((.((((((....))))))).))-)))-.))....-....((((.....))))....(((((.(((((....))))))))))...-.....)))))).))..-- ( -45.70)
>ppk.2829 5544859 115 - 6181863
GCCCCUUGCCGAGCUGGCAGGCGCUCAUGUGCCUCCCCUCCGUGCAAGAC-AUACAGUGUCAUUCACUCCUUGUCUGACCAGA-UUCACUGGCAGACUACUAACCCGUAAGGAGCAU--
((.((((((.(((..((.((((((....)))))))).))).(((...(((-((...)))))...))).....(((((.((((.-....))))))))).........)))))).))..-- ( -43.40)
>psp.340 5251467 114 + 5928787
GCCCCUUGCUGUCACGGCAGGCGCGCAUGUGCCUGUCC-CUGAGCAAGAC-CAACAGUGUCAUUCACUCCUUGUCUGACCGCUUUUGAGCGGCAGGCUAC-AACCCGUAAGGAGCAU--
((.(((((((((((.(((((((((....))))))).))-.))).))....-....((((.....))))....(((((.(((((....))))))))))...-.....)))))).))..-- ( -45.90)
>pf5.339 6399905 115 + 7074893
GCCCCUUGCCGUGACGGCAGGCGCAUAUGUGCCUACUA-CCAGGCAAGACACACCAGUGUCAUUCACUCCUUGUCUGACCGCUUAUAGGCGGCAGGCUAC-AACCCGUAAGGAGCAU--
(((....((((...))))((((((....))))))....-...)))..(((((....))))).....(((((((((((.(((((....)))))))))).((-.....))))))))...-- ( -47.20)
>pau.3075 5809116 110 - 6537648
GCCCCUUGCCGCGCGGGCAGGCGUUCGUUCGCCUCUCCACCAGGCAAGCC-AAGAAAA--CAUUCACUCCUUGCCUGACCGUUCU---GCGGCAGGCUGC-AACCCGUAAGGAGCAU--
((..((((((((..(((.(((((......))))).)))..((((((((..-..(((..--..)))....))))))))........---))))))))..))-...((....)).....-- ( -47.10)
>consensus
GCCCCUUGCCGUGACGGCAGGCGCUCAUGUGCCUCUCC_CCAGGCAAGAC_AAAAAGUGUCAUUCACUCCUUGUCUGACCGUUUUU_AGCGGCAGGCUAC_AACCCGUAAGGAGCAU__
....((((((.....((.((((((....)))))).)).....))))))..................(((((((((((.((((......))))))))).((......))))))))..... (-37.74 = -36.08 +  -1.66)

alignment

secondary structure

dotplot

Window 4

Location	5,537,754 – 5,537,866
Length	112
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	77.23
Mean single sequence MFE	-44.57
Consensus MFE	-24.33
Energy contribution	-24.05
Covariance contribution	-0.28
Combinations/Pair	1.30
Mean z-score	-1.81
Structure conservation index	0.55
SVM decision value	0.40
SVM RNA-class probability	0.720584
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2936 5537754 112 + 6264404
UU-GCAGCCUGCCGC---AGAACGGUCAGGCAAGGAGUGAAUG--UUUUCUU-GGCUUGCCUGGUGGAGAGGCGAACGAACGCCUGCCCACGCGGCAAGGGGCGACAUUCUAGAGAAGG
((-((..((((((((---........((((((((....(((..--..)))..-..))))))))((((..(((((......)))))..))))))))).))).)))).............. ( -48.50)
>pfo.288 5816653 115 - 6438405
UU-GUAGCCUGCCGCUCAAAAACGGUCAGACAAGGAGUGAAUGACACUUAUG-GACUUGC-UGG-CGCGGGGCACAUGCAUGCCCGCCGCCACAGCAAGGGGCGCAAUUGUAGAGAAGG
((-((.((((((((........))))....(...(((((.....)))))...-).(((((-(((-((.((((((......))))).)))))..))))))))))))))............ ( -39.40)
>ppk.2829 5544873 117 + 6181863
UUAGUAGUCUGCCAGUGAA-UCUGGUCAGACAAGGAGUGAAUGACACUGUAU-GUCUUGCACGGAGGGGAGGCACAUGAGCGCCUGCCAGCUCGGCAAGGGGCGCAAUUGUAGAGAAGC
......(((((((((....-.)))).)))))....((((.....))))(..(-.((((((.(((..((.((((.(....).)))).))..).)))))))).)..).............. ( -41.10)
>psp.340 5251481 116 - 5928787
UU-GUAGCCUGCCGCUCAAAAGCGGUCAGACAAGGAGUGAAUGACACUGUUG-GUCUUGCUCAG-GGACAGGCACAUGCGCGCCUGCCGUGACAGCAAGGGGCGCAAUUGUAGAGAAGG
.(-((.((((((((((....)))(((.((((.((.((((.....)))).)).-)))).)))...-)).))))))))(((((.(((((.......)).))).)))))............. ( -43.00)
>pf5.339 6399919 117 - 7074893
UU-GUAGCCUGCCGCCUAUAAGCGGUCAGACAAGGAGUGAAUGACACUGGUGUGUCUUGCCUGG-UAGUAGGCACAUAUGCGCCUGCCGUCACGGCAAGGGGCGCAAUUGUAGAGAAGG
..-.....(((((((......)))).)))((((..((((.....)))).((((.((((((((((-..((((((.(....).))))))..))).))))))).))))..))))........ ( -47.30)
>pau.3075 5809130 112 + 6537648
UU-GCAGCCUGCCGC---AGAACGGUCAGGCAAGGAGUGAAUG--UUUUCUU-GGCUUGCCUGGUGGAGAGGCGAACGAACGCCUGCCCGCGCGGCAAGGGGCGACAUUCUAGAGAAGG
((-((..((((((((---........((((((((....(((..--..)))..-..))))))))((((..(((((......)))))..))))))))).))).)))).............. ( -48.10)
>consensus
UU_GUAGCCUGCCGCU_AAAAACGGUCAGACAAGGAGUGAAUGACACUGCUG_GUCUUGCCUGG_GGAGAGGCACAUGAACGCCUGCCGGCACGGCAAGGGGCGCAAUUGUAGAGAAGG
......((((((((........)))).............................((((((....((..((((........))))..))....))))))))))................ (-24.33 = -24.05 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	5,537,754 – 5,537,866
Length	112
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.23
Mean single sequence MFE	-42.65
Consensus MFE	-32.49
Energy contribution	-31.05
Covariance contribution	-1.44
Combinations/Pair	1.52
Mean z-score	-3.17
Structure conservation index	0.76
SVM decision value	1.98
SVM RNA-class probability	0.984686
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2936 5537754 112 - 6264404
CCUUCUCUAGAAUGUCGCCCCUUGCCGCGUGGGCAGGCGUUCGUUCGCCUCUCCACCAGGCAAGCC-AAGAAAA--CAUUCACUCCUUGCCUGACCGUUCU---GCGGCAGGCUGC-AA
............(((.(((...(((((((((((.(((((......))))).)))))((((((((..-..(((..--..)))....))))))))........---))))))))).))-). ( -47.70)
>pfo.288 5816653 115 + 6438405
CCUUCUCUACAAUUGCGCCCCUUGCUGUGGCGGCGGGCAUGCAUGUGCCCCGCG-CCA-GCAAGUC-CAUAAGUGUCAUUCACUCCUUGUCUGACCGUUUUUGAGCGGCAGGCUAC-AA
....................((((((..(((((.((((((....))))))).))-)))-)))))..-....((((.....))))....(((((.(((((....))))))))))...-.. ( -39.80)
>ppk.2829 5544873 117 - 6181863
GCUUCUCUACAAUUGCGCCCCUUGCCGAGCUGGCAGGCGCUCAUGUGCCUCCCCUCCGUGCAAGAC-AUACAGUGUCAUUCACUCCUUGUCUGACCAGA-UUCACUGGCAGACUACUAA
............((((((....((((.....))))(((((....)))))........))))))(((-((...)))))...........(((((.((((.-....)))))))))...... ( -37.00)
>psp.340 5251481 116 + 5928787
CCUUCUCUACAAUUGCGCCCCUUGCUGUCACGGCAGGCGCGCAUGUGCCUGUCC-CUGAGCAAGAC-CAACAGUGUCAUUCACUCCUUGUCUGACCGCUUUUGAGCGGCAGGCUAC-AA
.............(((((.(((.((((...))))))).)))))((((((((((.-((((((.((((-....((((.....))))....))))....))))...)).))))))).))-). ( -41.40)
>pf5.339 6399919 117 + 7074893
CCUUCUCUACAAUUGCGCCCCUUGCCGUGACGGCAGGCGCAUAUGUGCCUACUA-CCAGGCAAGACACACCAGUGUCAUUCACUCCUUGUCUGACCGCUUAUAGGCGGCAGGCUAC-AA
........(((..((((((...(((((...)))))))))))..)))((((....-..))))..(((((....)))))...........(((((.(((((....))))))))))...-.. ( -45.70)
>pau.3075 5809130 112 - 6537648
CCUUCUCUAGAAUGUCGCCCCUUGCCGCGCGGGCAGGCGUUCGUUCGCCUCUCCACCAGGCAAGCC-AAGAAAA--CAUUCACUCCUUGCCUGACCGUUCU---GCGGCAGGCUGC-AA
............(((.(((...((((((..(((.(((((......))))).)))..((((((((..-..(((..--..)))....))))))))........---))))))))).))-). ( -44.30)
>consensus
CCUUCUCUACAAUUGCGCCCCUUGCCGUGACGGCAGGCGCUCAUGUGCCUCUCC_CCAGGCAAGAC_AAAAAGUGUCAUUCACUCCUUGUCUGACCGUUUUU_AGCGGCAGGCUAC_AA
....................((((((.....((.((((((....)))))).)).....))))))........................(((((.((((......)))))))))...... (-32.49 = -31.05 +  -1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:16:23 2007