Locus 54

Sequence ID	pao_1
Location	4,780,759 – 4,780,835
Length	76
Max. P	0.988671

overview

Window 4

Location	4,780,759 – 4,780,835
Length	76
Sequences	6
Columns	76
Reading direction	forward
Mean pairwise identity	82.59
Mean single sequence MFE	-29.83
Consensus MFE	-27.39
Energy contribution	-27.50
Covariance contribution	0.11
Combinations/Pair	1.12
Mean z-score	-3.28
Structure conservation index	0.92
SVM decision value	2.13
SVM RNA-class probability	0.988671
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4780759 76 + 1
AACGGAAAAAGGCCGGUGGCAAAAGCCACCAGCCAUCAGCCUUUCGCUUGACGCUCGGGCUGUAGACGCAAGGUCG
..........(((.((((((....)))))).)))..((((((...((.....))..))))))..(((.....))). ( -30.80)
>pel_1 1 76 + 1
AACGGAAAAAGGCCGGUGGCAUAAGCCACCAGCCAUCAGCCCUUCGCUUAACGCUCGGACUGGAGUCGCAAAGUCG
...((.....(((.((((((....)))))).))).....))....((((..(((((......))).))..)))).. ( -25.70)
>pf5_1 1 76 + 1
AACGGAAAAAGGCCGGUGGCAAAAGCCACCAGCCAUCAGCCGUUCGCUUAACGCUUGGGCUGGAGACACAAAGUCG
..........(((.((((((....)))))).))).((((((....((.....))...)))))).(((.....))). ( -30.30)
>pfo_1 1 62 + 1
AACGGAAAAAGGCCGGUGGCAAGAGCCACCAGCCAUCAGCCUGUCGCUUGACGCUCGGGCUG--------------
..........(((.((((((....)))))).)))..(((((((..((.....)).)))))))-------------- ( -30.40)
>pfs_1 1 76 + 1
AACGGAAAAAGGCCGGUGGCAAGAGCCACCAGCCAUCAGCCUUCAGCUUAACGCUUGGGCUGGAGACGCAAGGUCG
..........(((.((((((....)))))).))).(((((((..(((.....))).))))))).(((.....))). ( -34.10)
>ppk_1 1 62 + 1
AACGGAAAAAGGCCGGUGGCAUAAGCCACCAGCCAUCAGCCUUUCGCUCAACGCUCAGGCUG--------------
..........(((.((((((....)))))).)))..((((((...((.....))..))))))-------------- ( -27.70)
>consensus
AACGGAAAAAGGCCGGUGGCAAAAGCCACCAGCCAUCAGCCUUUCGCUUAACGCUCGGGCUGGAGACGCAA_GUCG
..........(((.((((((....)))))).)))..((((((...((.....))..)))))).............. (-27.39 = -27.50 +   0.11)

alignment

secondary structure

dotplot

Window 5

Location	4,780,759 – 4,780,835
Length	76
Sequences	6
Columns	76
Reading direction	reverse
Mean pairwise identity	82.59
Mean single sequence MFE	-35.00
Consensus MFE	-32.24
Energy contribution	-32.10
Covariance contribution	-0.14
Combinations/Pair	1.06
Mean z-score	-4.35
Structure conservation index	0.92
SVM decision value	2.13
SVM RNA-class probability	0.988602
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4780759 76 - 1
CGACCUUGCGUCUACAGCCCGAGCGUCAAGCGAAAGGCUGAUGGCUGGUGGCUUUUGCCACCGGCCUUUUUCCGUU
.(((.....)))..(((((...((.....))....)))))..((((((((((....)))))))))).......... ( -34.40)
>pel_1 1 76 - 1
CGACUUUGCGACUCCAGUCCGAGCGUUAAGCGAAGGGCUGAUGGCUGGUGGCUUAUGCCACCGGCCUUUUUCCGUU
.......(((....((((((..((.....))...))))))..((((((((((....))))))))))......))). ( -36.40)
>pf5_1 1 76 - 1
CGACUUUGUGUCUCCAGCCCAAGCGUUAAGCGAACGGCUGAUGGCUGGUGGCUUUUGCCACCGGCCUUUUUCCGUU
.(((.....)))..(((((...((.....))....)))))..((((((((((....)))))))))).......... ( -35.30)
>pfo_1 1 62 - 1
--------------CAGCCCGAGCGUCAAGCGACAGGCUGAUGGCUGGUGGCUCUUGCCACCGGCCUUUUUCCGUU
--------------(((((.(.((.....))..).)))))..((((((((((....)))))))))).......... ( -32.50)
>pfs_1 1 76 - 1
CGACCUUGCGUCUCCAGCCCAAGCGUUAAGCUGAAGGCUGAUGGCUGGUGGCUCUUGCCACCGGCCUUUUUCCGUU
.(((.....)))..(((((..(((.....)))...)))))..((((((((((....)))))))))).......... ( -36.00)
>ppk_1 1 62 - 1
--------------CAGCCUGAGCGUUGAGCGAAAGGCUGAUGGCUGGUGGCUUAUGCCACCGGCCUUUUUCCGUU
--------------((((((..((.....))...))))))..((((((((((....)))))))))).......... ( -35.40)
>consensus
CGAC_UUGCGUCUCCAGCCCGAGCGUUAAGCGAAAGGCUGAUGGCUGGUGGCUUUUGCCACCGGCCUUUUUCCGUU
..............(((((...((.....))....)))))..((((((((((....)))))))))).......... (-32.24 = -32.10 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:48:37 2007