Locus 172

Sequence ID	pao.3052
Location	5,780,854 – 5,780,962
Length	108
Max. P	0.883107

overview

Window 7

Location	5,780,854 – 5,780,962
Length	108
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	65.49
Mean single sequence MFE	-40.42
Consensus MFE	-22.30
Energy contribution	-25.55
Covariance contribution	3.25
Combinations/Pair	1.16
Mean z-score	-1.54
Structure conservation index	0.55
SVM decision value	0.93
SVM RNA-class probability	0.883107
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3052 5780854 108 + 6264404
CCGGCUGAAAUACGUGGA---------AGCGCCCCACAGCGCGCGGUGCGGGGCGUUUUUUUUAACGGCGGCCACGGGCAUACUAGGCCGGUCCAAUUCCCAGGUGCCCGCCACCCC
..(((((.....((((((---------((((((((.((.(....).)).)))))))))))....))).))))).(((((((.((.((...........)).)))))))))....... ( -44.50)
>pau.3190 6053017 106 + 6537648
CCGGCUGAAAUACGUGGA---------AGCGCCCCACAGCGCGCGGUGCGGGGCGUUUUUUUUAACGGCGGCCACGGGCAUACUAGGCCGGUCCAAUUCCCAGGUGCCCGCCACC--
..(((((.....((((((---------((((((((.((.(....).)).)))))))))))....))).))))).(((((((.((.((...........)).))))))))).....-- ( -44.50)
>pel.192 5485902 106 - 5888780
C-CGGCAAAACACAUGAAUUCCAGACCAACGCCCCGCCGCACACGCUGCGGGGCGUUUUUUUUACAGGCCCGCGCGGGCAUACUAGGCCAGUCUCCAUCCCCGGUAC----------
(-(((.........((.....))(((.((((((((((.((....)).))))))))))..........((((....))))...........))).......))))...---------- ( -38.20)
>ppk.2938 5762511 94 + 6181863
-------------AUGAAUUCCAGACAAACGCCCCCCUGCAUCCGCAGCGAGGCGUUUUUUUUGCCUGCCCAGGCGGGCAUACUAGGCCAGUCUCCAUCCUUGGUAC----------
-------------.........(((((((((((.(.((((....)))).).)))))))....(((((((....)))))))..........))))(((....)))...---------- ( -34.50)
>consensus
C_GGCUGAAAUACAUGAA_________AACGCCCCACAGCACGCGCUGCGGGGCGUUUUUUUUAACGGCCCCCACGGGCAUACUAGGCCAGUCCAAAUCCCAGGUAC__________
...........................((((((((.((((....)))).)))))))).........(((((.(((.(((.......)))((........))..))).)))))..... (-22.30 = -25.55 +   3.25)

alignment

secondary structure

dotplot

Window 8

Location	5,780,854 – 5,780,962
Length	108
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	65.49
Mean single sequence MFE	-43.85
Consensus MFE	-27.20
Energy contribution	-32.20
Covariance contribution	5.00
Combinations/Pair	1.17
Mean z-score	-1.16
Structure conservation index	0.62
SVM decision value	0.42
SVM RNA-class probability	0.729903
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3052 5780854 108 - 6264404
GGGGUGGCGGGCACCUGGGAAUUGGACCGGCCUAGUAUGCCCGUGGCCGCCGUUAAAAAAAACGCCCCGCACCGCGCGCUGUGGGGCGCU---------UCCACGUAUUUCAGCCGG
(((((.(((((((.(((((...........)))))..))))))).))).))...........(((((((((.(....).)))))))))..---------.................. ( -45.50)
>pau.3190 6053017 106 - 6537648
--GGUGGCGGGCACCUGGGAAUUGGACCGGCCUAGUAUGCCCGUGGCCGCCGUUAAAAAAAACGCCCCGCACCGCGCGCUGUGGGGCGCU---------UCCACGUAUUUCAGCCGG
--..(((((((((.(((((...........)))))..)))))((((..((.(((......)))((((((((.(....).)))))))))).---------.))))........)))). ( -45.00)
>pel.192 5485902 106 + 5888780
----------GUACCGGGGAUGGAGACUGGCCUAGUAUGCCCGCGCGGGCCUGUAAAAAAAACGCCCCGCAGCGUGUGCGGCGGGGCGUUGGUCUGGAAUUCAUGUGUUUUGCCG-G
----------...((((.((((((..(..(((......((((....))))..........((((((((((.((....)).)))))))))))).)..)..))))......)).)))-) ( -44.90)
>ppk.2938 5762511 94 - 6181863
----------GUACCAAGGAUGGAGACUGGCCUAGUAUGCCCGCCUGGGCAGGCAAAAAAAACGCCUCGCUGCGGAUGCAGGGGGGCGUUUGUCUGGAAUUCAU-------------
----------.......((((..((((..((((.....((((....)))))))).....(((((((((.((((....)))).)))))))))))))...))))..------------- ( -40.00)
>consensus
__________GCACCUGGGAAGGAGACCGGCCUAGUAUGCCCGCGGCCGCCGGUAAAAAAAACGCCCCGCACCGCGCGCUGUGGGGCGCU_________UCCACGUAUUUCAGCC_G
..(((.(((((((.(((((..(....)...)))))..))))))).)))............(((((((((((((....)))))))))))))........................... (-27.20 = -32.20 +   5.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:16:36 2007