Locus 169

Sequence ID	pao.193
Location	356,552 – 356,680
Length	128
Max. P	0.986795

overview

Window 7

Location	356,552 – 356,664
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	60.25
Mean single sequence MFE	-38.62
Consensus MFE	-17.66
Energy contribution	-18.14
Covariance contribution	0.47
Combinations/Pair	1.29
Mean z-score	-2.52
Structure conservation index	0.46
SVM decision value	2.05
SVM RNA-class probability	0.986795
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.193 356552 112 + 6264404
GCACCCGCAACUCGGCGCCCAGAGGCAC-UAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCUU-------UUCCUUGCCCGGUUGCGACCUGAGUUGUUCUCAGGACGACCAUGAAUC
.....(((((((.((((((....)))..-.(((...((((((..((((....))))..)))))).-------...)))))).))))))).((((((.....))))))............. ( -43.60)
>pf5.3563 353482 113 - 7074893
GACACCGCAG--AAAGGCCCUUGGGCACUCUCCUGCGGGGGCGGUAUGCUAGCAUACGCGCCCCGCUAAACACUCAUUCC-----UGCGACGUGAAGCGUUCUCAGGAUGACCAUGAAUU
.....(((((--..(((((....))).))...)))))(((((((((((....))))).)))))).........((((.((-----((.((((.....)).)).))))))))......... ( -46.20)
>pst.3151 377007 84 - 6397126
-----------------------------GACUCGCGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC-CUCAUUCC------AGAACGUGAACCGUUCUCAGGAUGCCCAUGAAUU
-----------------------------...((((((((..((((((....))))))..))))))))...-..(((((.------((((((.....))))))..))))).......... ( -34.10)
>psp.2850 373732 74 - 5928787
-----------------------------GACUCACGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC-CUCAUCCC-------GAACGUGAACCGUUCUCAGGAUGC---------
-----------------------------...((.(((((..((((((....))))))..))))).))...-..(((((.-------(((((.....)))))...))))).--------- ( -29.80)
>pss.2949 334632 76 - 6093698
-----------------------------GACUCGCGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC-CUCAUCCC-------GAACGUGAACCGUUCUCAGGAUGCCC-------
-----------------------------...((((((((..((((((....))))))..))))))))...-..(((((.-------(((((.....)))))...)))))...------- ( -35.20)
>pfo.3182 388121 106 - 6438405
GUCACCGCAG--AACCGGCCUUGGGCACUGGCCUGCGGGGUCGGUAUGCUAGCAUAGCCACCCCGCUAAACACUCAUUCC-----UGCGACGUGAAGCGUUCUCAGGAUGACC-------
((((((((((--....((((.........)))).(((((((.((((((....))).)))))))))).............)-----)))((((.....))))....)).)))).------- ( -42.80)
>consensus
_____________________________GACUCGCGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC_CUCAUUCC______GCAACGUGAACCGUUCUCAGGAUGACC_______
..................................((((((..((((((....))))))..))))))........(((((.........((((.....))))....))))).......... (-17.66 = -18.14 +   0.47)

alignment

secondary structure

dotplot

Window 8

Location	356,552 – 356,664
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	60.25
Mean single sequence MFE	-39.42
Consensus MFE	-13.36
Energy contribution	-13.78
Covariance contribution	0.42
Combinations/Pair	1.14
Mean z-score	-2.08
Structure conservation index	0.34
SVM decision value	0.85
SVM RNA-class probability	0.865138
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.193 356552 112 - 6264404
GAUUCAUGGUCGUCCUGAGAACAACUCAGGUCGCAACCGGGCAAGGAA-------AAGGGAGAACAUGCUAGCAUACGCCCCCCGCGCUUA-GUGCCUCUGGGCGCCGAGUUGCGGGUGC
.......(((((.((((((.....)))))).))..)))((((......-------..(......)(((....)))..))))((((((((..-(((((....)))))..)).))))))... ( -45.60)
>pf5.3563 353482 113 + 7074893
AAUUCAUGGUCAUCCUGAGAACGCUUCACGUCGCA-----GGAAUGAGUGUUUAGCGGGGCGCGUAUGCUAGCAUACCGCCCCCGCAGGAGAGUGCCCAAGGGCCUUU--CUGCGGUGUC
.....(((.((((((((.((.((.....)))).))-----)).)))).)))...((((((((.(((((....)))))))))))(((((.((((.(((....)))))))--)))))))... ( -49.50)
>pst.3151 377007 84 + 6397126
AAUUCAUGGGCAUCCUGAGAACGGUUCACGUUCU------GGAAUGAG-GUUUCGCGGGGCUCAUAUGCUAGCAUACGCCCCCCGCGAGUC-----------------------------
..(((((.....(((..((((((.....))))))------))))))))-..(((((((((..(.((((....)))).)..)))))))))..----------------------------- ( -31.60)
>psp.2850 373732 74 + 5928787
---------GCAUCCUGAGAACGGUUCACGUUC-------GGGAUGAG-GUUUCGCGGGGCUCAUAUGCUAGCAUACGCCCCCCGUGAGUC-----------------------------
---------.((((((((..(((.....)))))-------))))))..-..(((((((((..(.((((....)))).)..)))))))))..----------------------------- ( -32.40)
>pss.2949 334632 76 + 6093698
-------GGGCAUCCUGAGAACGGUUCACGUUC-------GGGAUGAG-GUUUCGCGGGGCUCAUAUGCUAGCAUACGCCCCCCGCGAGUC-----------------------------
-------...((((((((..(((.....)))))-------))))))..-..(((((((((..(.((((....)))).)..)))))))))..----------------------------- ( -34.30)
>pfo.3182 388121 106 + 6438405
-------GGUCAUCCUGAGAACGCUUCACGUCGCA-----GGAAUGAGUGUUUAGCGGGGUGGCUAUGCUAGCAUACCGACCCCGCAGGCCAGUGCCCAAGGCCGGUU--CUGCGGUGAC
-------.((((((....((.((.....))))(((-----(((...........(((((((((.((((....)))))).))))))).((((.........))))..))--)))))))))) ( -43.10)
>consensus
_______GGGCAUCCUGAGAACGGUUCACGUCCC______GGAAUGAG_GUUUCGCGGGGCGCAUAUGCUAGCAUACGCCCCCCGCGAGUC_____________________________
...............((((.....))))..........................((((((....((((....))))....)))))).................................. (-13.36 = -13.78 +   0.42)

alignment

secondary structure

dotplot

Window 9

Location	356,568 – 356,680
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	61.14
Mean single sequence MFE	-37.17
Consensus MFE	-17.66
Energy contribution	-18.14
Covariance contribution	0.47
Combinations/Pair	1.29
Mean z-score	-2.21
Structure conservation index	0.48
SVM decision value	1.80
SVM RNA-class probability	0.977935
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.193 356568 112 + 6264404
GCCCAGAGGCAC-UAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCUU-------UUCCUUGCCCGGUUGCGACCUGAGUUGUUCUCAGGACGACCAUGAAUCAUUUGAGAGUUCCCGA
...((((((((.-.......((((((..((((....))))..)))))).-------.....)))).(((((...((((((.....)))))).)))))........))))........... ( -34.14)
>pf5.3563 353496 111 - 7074893
GCCCUUGGGCACUCUCCUGCGGGGGCGGUAUGCUAGCAUACGCGCCCCGCUAAACACUCAUUCC-----UGCGACGUGAAGCGUUCUCAGGAUGACCAUGAAUUGUUCGAGAGUUC----
(((....)))((((((..((((((((((((((....))))).)))))).........((((.((-----((.((((.....)).)).))))))))........)))..))))))..---- ( -47.20)
>pst.3151 377007 95 - 6397126
-------------GACUCGCGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC-CUCAUUCC------AGAACGUGAACCGUUCUCAGGAUGCCCAUGAAUUGUCCGAGAGUU-----
-------------...((((((((..((((((....))))))..))))))))(((-(((.....------((((((.....))))))..((((...........))))))).)))----- ( -37.90)
>psp.2850 373732 74 - 5928787
-------------GACUCACGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC-CUCAUCCC-------GAACGUGAACCGUUCUCAGGAUGC-------------------------
-------------...((.(((((..((((((....))))))..))))).))...-..(((((.-------(((((.....)))))...))))).------------------------- ( -29.80)
>pss.2949 334632 76 - 6093698
-------------GACUCGCGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC-CUCAUCCC-------GAACGUGAACCGUUCUCAGGAUGCCC-----------------------
-------------...((((((((..((((((....))))))..))))))))...-..(((((.-------(((((.....)))))...)))))...----------------------- ( -35.20)
>pfo.3182 388135 92 - 6438405
GGCCUUGGGCACUGGCCUGCGGGGUCGGUAUGCUAGCAUAGCCACCCCGCUAAACACUCAUUCC-----UGCGACGUGAAGCGUUCUCAGGAUGACC-----------------------
((((.........)))).(((((((.((((((....))).)))))))))).......((((.((-----((.((((.....)).)).))))))))..----------------------- ( -38.80)
>consensus
_____________GACUCGCGGGGGGCGUAUGCUAGCAUAUGAGCCCCGCGAAAC_CUCAUUCC______GCAACGUGAACCGUUCUCAGGAUGACC_______________________
..................((((((..((((((....))))))..))))))........(((((.........((((.....))))....))))).......................... (-17.66 = -18.14 +   0.47)

alignment

secondary structure

dotplot

Window 0

Location	356,568 – 356,680
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	61.14
Mean single sequence MFE	-37.13
Consensus MFE	-13.36
Energy contribution	-13.78
Covariance contribution	0.42
Combinations/Pair	1.14
Mean z-score	-2.06
Structure conservation index	0.36
SVM decision value	0.99
SVM RNA-class probability	0.896976
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.193 356568 112 - 6264404
UCGGGAACUCUCAAAUGAUUCAUGGUCGUCCUGAGAACAACUCAGGUCGCAACCGGGCAAGGAA-------AAGGGAGAACAUGCUAGCAUACGCCCCCCGCGCUUA-GUGCCUCUGGGC
.((((..................(((((.((((((.....)))))).))..)))((((......-------..(......)(((....)))..)))))))).(((((-(.....)))))) ( -34.00)
>pf5.3563 353496 111 + 7074893
----GAACUCUCGAACAAUUCAUGGUCAUCCUGAGAACGCUUCACGUCGCA-----GGAAUGAGUGUUUAGCGGGGCGCGUAUGCUAGCAUACCGCCCCCGCAGGAGAGUGCCCAAGGGC
----..(((((((((((.(((((.....(((((.((.((.....)))).))-----))))))))))))).((((((((.(((((....))))))).))))))..))))))(((....))) ( -49.90)
>pst.3151 377007 95 + 6397126
-----AACUCUCGGACAAUUCAUGGGCAUCCUGAGAACGGUUCACGUUCU------GGAAUGAG-GUUUCGCGGGGCUCAUAUGCUAGCAUACGCCCCCCGCGAGUC-------------
-----(((.((((..((..(((.((....)))))(((((.....))))))------)...))))-)))((((((((..(.((((....)))).)..))))))))...------------- ( -33.70)
>psp.2850 373732 74 + 5928787
-------------------------GCAUCCUGAGAACGGUUCACGUUC-------GGGAUGAG-GUUUCGCGGGGCUCAUAUGCUAGCAUACGCCCCCCGUGAGUC-------------
-------------------------.((((((((..(((.....)))))-------))))))..-..(((((((((..(.((((....)))).)..)))))))))..------------- ( -32.40)
>pss.2949 334632 76 + 6093698
-----------------------GGGCAUCCUGAGAACGGUUCACGUUC-------GGGAUGAG-GUUUCGCGGGGCUCAUAUGCUAGCAUACGCCCCCCGCGAGUC-------------
-----------------------...((((((((..(((.....)))))-------))))))..-..(((((((((..(.((((....)))).)..)))))))))..------------- ( -34.30)
>pfo.3182 388135 92 + 6438405
-----------------------GGUCAUCCUGAGAACGCUUCACGUCGCA-----GGAAUGAGUGUUUAGCGGGGUGGCUAUGCUAGCAUACCGACCCCGCAGGCCAGUGCCCAAGGCC
-----------------------((((.(((((.((.((.....)))).))-----)))...........(((((((((.((((....)))))).))))))).))))...(((...))). ( -38.50)
>consensus
_______________________GGGCAUCCUGAGAACGGUUCACGUCCC______GGAAUGAG_GUUUCGCGGGGCGCAUAUGCUAGCAUACGCCCCCCGCGAGUC_____________
...............................((((.....))))..........................((((((....((((....))))....)))))).................. (-13.36 = -13.78 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:16:27 2007