Locus 9

Sequence ID	pao.3201
Location	6,041,924 – 6,042,163
Length	239
Max. P	0.999716

overview

Window 6

Location	6,041,924 – 6,042,044
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.78
Mean single sequence MFE	-37.50
Consensus MFE	-33.38
Energy contribution	-32.77
Covariance contribution	-0.61
Combinations/Pair	1.10
Mean z-score	-1.24
Structure conservation index	0.89
SVM decision value	0.18
SVM RNA-class probability	0.623057
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3201 6041924 120 - 6264404
GAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCCCGUUGAAAAGGUAGGGGAUGACUUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGAUAGCUGGUUCUCCUCGAAAGC
...((((((......))))))((((((((.....((((((.(((.(.(((...........))).).))).))))))...(((((.((.......))..))))))))))))).(....). ( -38.10)
>pau.3340 6314843 120 - 6537648
GAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCCCGUUGAAAAGGUAGGGGAUGACUUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGAUAGCUGGUUCUCCUCGAAAGC
...((((((......))))))((((((((.....((((((.(((.(.(((...........))).).))).))))))...(((((.((.......))..))))))))))))).(....). ( -38.10)
>pss.1919 3849792 120 - 6093698
GAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGAUAGCUGGUUCUCCUCGAAAGC
...((((((......))))))((((((((...((((((((.(((((....)))))((....)).)))).)))).......(((((.((.......))..))))))))))))).(....). ( -37.10)
>psp.1833 3633796 120 - 5928787
GAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGAUAGCUGGUUCUCCUCGAAAGC
...((((((......))))))((((((((...((((((((.(((((....)))))((....)).)))).)))).......(((((.((.......))..))))))))))))).(....). ( -37.10)
>pfo.3002 5728701 120 - 6438405
GAAGGUUAGGUAACACUGACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGAUAGCUGGUUCUCCUCGAAAGC
...((((((......))))))((((((((...((((((((.(((((....)))))((....)).)))).)))).......(((((.((.......))..))))))))))))).(....). ( -37.50)
>pst.2031 3871793 120 - 6397126
GAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGAUAGCUGGUUCUCCUCGAAAGC
...((((((......))))))((((((((...((((((((.(((((....)))))((....)).)))).)))).......(((((.((.......))..))))))))))))).(....). ( -37.10)
>consensus
GAAGGUUAGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAAGGCUAAUCAAGCUCGGAGAUAGCUGGUUCUCCUCGAAAGC
...((((((......))))))(((((((((..(((.(((.(........).)))))).......((...((.((((..............)))).))....))))))))))).(....). (-33.38 = -32.77 +  -0.61)

alignment

secondary structure

dotplot

Window 7

Location	6,041,964 – 6,042,084
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.83
Mean single sequence MFE	-40.17
Consensus MFE	-39.02
Energy contribution	-37.97
Covariance contribution	-1.05
Combinations/Pair	1.11
Mean z-score	-2.10
Structure conservation index	0.97
SVM decision value	3.94
SVM RNA-class probability	0.999716
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3201 6041964 120 - 6264404
GUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCCCGUUGAAAAGGUAGGGGAUGACUUGUGGAUCGGAGUGAAA
.....(.((((....)))))..((((((((..((((((((...((((((......))))))....))))...(((.((.((........)).))))).)).))..))))).)))...... ( -39.90)
>pau.3340 6314883 120 - 6537648
GUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCCCGUUGAAAAGGUAGGGGAUGACUUGUGGAUCGGAGUGAAA
.....(.((((....)))))..((((((((..((((((((...((((((......))))))....))))...(((.((.((........)).))))).)).))..))))).)))...... ( -39.90)
>pss.1919 3849832 120 - 6093698
GAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAA
.....(.((((....)))))..((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).)))...... ( -40.20)
>pel.69 5770496 120 + 5888780
GUAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAA
.....(.((((....)))))..((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).)))...... ( -40.60)
>psp.1833 3633836 120 - 5928787
GAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAA
.....(.((((....)))))..((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).)))...... ( -40.20)
>pst.2031 3871833 120 - 6397126
GAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAA
.....(.((((....)))))..((((((((((((((((((...((((((......))))))....))))..........(((((((....))))))).)).))))))))).)))...... ( -40.20)
>consensus
GAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUAACUGGAGGACCGAACCGACUACCGUUGAAAAGUUAGCGGAUGACCUGUGGAUCGGAGUGAAA
.....(.((((....)))))..((((((((((((((((((...((((((......))))))....))))...(((.(((.(........).)))))).)).))))))))).)))...... (-39.02 = -37.97 +  -1.05)

alignment

secondary structure

dotplot

Window 8

Location	6,042,004 – 6,042,123
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.37
Mean single sequence MFE	-39.43
Consensus MFE	-37.60
Energy contribution	-37.55
Covariance contribution	-0.05
Combinations/Pair	1.09
Mean z-score	-1.14
Structure conservation index	0.95
SVM decision value	1.11
SVM RNA-class probability	0.916670
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3201 6042004 119 - 6264404
GUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCC
...((....))((((((....))((.(-((..((((((.((.(((((((((....))))...)))))))...)))........((((((......))))))....)))..))))))))). ( -38.30)
>pau.3340 6314923 119 - 6537648
GUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCCACUCC
...((....))((((((....))((.(-((..((((((.((.(((((((((....))))...)))))))...)))........((((((......))))))....)))..))))))))). ( -38.30)
>pss.1919 3849872 119 - 6093698
GUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAC
...((....))((((((.....)))).-))((((((((.(((.((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....))))). ( -39.90)
>pel.69 5770536 120 + 5888780
GUAGCGAAAGCGAGUCUUAAUAGGGCGCUUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUGACUGGAGGACCGAACCGACUAC
.(((((((((((..(((....))).)))))...))))))((.(((((((((....))))...))))))).(((...((((...((((((......))))))....))))...)))..... ( -40.30)
>psp.1833 3633876 119 - 5928787
GUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAC
...((....))((((((.....)))).-))((((((((.(((.((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....))))). ( -39.90)
>pst.2031 3871873 119 - 6397126
GUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAC
...((....))((((((.....)))).-))((((((((.(((.((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....))))). ( -39.90)
>consensus
GUAGCGAAAGCGAGUCUUAAUAGGGCG_UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUUGAAGGUUAGGUAACACUAACUGGAGGACCGAACCGACUAC
...((....))..((((.....))))....((((((((.((.(((((((((....))))...)))))))...))).((((...((((((......))))))....)))).....))))). (-37.60 = -37.55 +  -0.05)

alignment

secondary structure

dotplot

Window 9

Location	6,042,044 – 6,042,163
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.37
Mean single sequence MFE	-42.78
Consensus MFE	-40.38
Energy contribution	-40.22
Covariance contribution	-0.17
Combinations/Pair	1.03
Mean z-score	-2.20
Structure conservation index	0.94
SVM decision value	3.53
SVM RNA-class probability	0.999341
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.3201 6042044 119 - 6264404
GACUUAUAUUCAGUGGCAAGCUUAACCGUAUAGGGUAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUU
(.(((((...(((((((..(((((.((.....)).)))))...((....))..((((.....)))).-....)))))))((.(((((((((....))))...)))))))))))))..... ( -40.80)
>pau.3340 6314963 119 - 6537648
GACUUAUAUUCAGUGGCAAGCUUAACCGUAUAGGGUAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGAGCAGGUU
(.(((((...(((((((..(((((.((.....)).)))))...((....))..((((.....)))).-....)))))))((.(((((((((....))))...)))))))))))))..... ( -40.80)
>pel.69 5770576 120 + 5888780
GACUUAUAUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCGCUUUAGUCGCUGGGUAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUU
....(((((((((((((..((((..((.....))..))))((.((....))..((((.....))))))....)))))))))))))(.((((....)))))(((((..(....)..))))) ( -44.00)
>pf5.3378 6385201 119 - 7074893
GACUUAUUUUCAGUGGCAAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUU
....((((..(((((((..((((..((.....))..))))...((....))((((((.....)))).-))..)))))))..))))(.((((....)))))(((((..(....)..))))) ( -43.70)
>pfo.3002 5728821 119 - 6438405
GACUUAUUUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUU
....((((..(((((((..((((..((.....))..))))...((....))((((((.....)))).-))..)))))))..))))(.((((....)))))(((((..(....)..))))) ( -43.70)
>pst.2031 3871913 119 - 6397126
GACUUAUUUUCAGUGGCGAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG-UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUU
....((((..(((((((..((((..((.....))..))))...((....))((((((.....)))).-))..)))))))..))))(.((((....)))))(((((..(....)..))))) ( -43.70)
>consensus
GACUUAUAUUCAGUGGCAAGCUUAACCGAAUAGGGGAGGCGUAGCGAAAGCGAGUCUUAAUAGGGCG_UCUAGUCGCUGGGAAUAGACCCGAAACCGGGCGAUCUAUCCAUGGGCAGGUU
....(((((((((((((..((((..((.....))..))))...((....))..((((.....))))......)))))))))))))(.((((....)))))(((((.((....)).))))) (-40.38 = -40.22 +  -0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:04:19 2007