Locus 24

Sequence ID	pao.2980
Location	5,635,975 – 5,636,131
Length	156
Max. P	0.995955

overview

Window 7

Location	5,635,975 – 5,636,091
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	70.99
Mean single sequence MFE	-36.40
Consensus MFE	-24.61
Energy contribution	-24.87
Covariance contribution	0.26
Combinations/Pair	1.38
Mean z-score	-3.13
Structure conservation index	0.68
SVM decision value	2.64
SVM RNA-class probability	0.995955
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2980 5635975 116 + 6264404
UGUAGUUUUACUACUAAAAAUUGUAUCCAGAGGGCUGUUUCUCAGACUGAUCUGUAGUAAAACUACAAGUCGCCGGGUA--CACCC-CCGGAGAACAUCCAAGAAUUAGCU-GCGGUCGC
((((((((((((((...............(((((....)))))(((....)))))))))))))))))..((.(((((..--....)-)))).)).(..((.((......))-..))..). ( -32.80)
>pss.318 5514594 115 - 6093698
UGUAGUUUUACUACUGGGUCCGAUACUCGGAGGGCUGAAAUCGUCGUCGAUUUGUAGUAAAACUACACGCCGCCGGAUCCCACCCU-CCGGAA---AUCCAAGAAUUUAUG-UCGUCUGC
((((((((((((((..(((((..........))))).((((((....)))))))))))))))))))).....(((((........)-))))..---...............-........ ( -35.60)
>pel.2957 5464775 113 + 5888780
UGUAGUUUUACUACUACCCCGUAGGUGCAAAAGCAUGAAAUGCGAAAGCAUUUGUAGUAAAACUACACCGCGCCGGAUG--ACUGU-CCGGUA---AUCCAAGAAUUCACG-ACGUCUGC
((((((((((((((..........((((....)))).((((((....))))))))))))))))))))....(((((((.--...))-))))).---...............-........ ( -41.20)
>ppk.199 5771025 113 - 6181863
UGUAGUUUUACUACUACUCGUGUCGUGUAAAAGCAUGAAAUGCGAAAGCAAAUGUAGUAAAACUACAACGCGCCGGAAG--ACACC-CCGGUA---AUCCAAGAAUUCACG-ACGUCUGC
((((((((((((((........((((((....))))))..(((....)))...))))))))))))))....(((((...--.....-))))).---...............-........ ( -37.40)
>pf5.303 6480924 114 - 7074893
UGUAGUUUUACUACUCGUAUAUACAUUCGAAAGGCUGAAAUGGCCGACGAUUUGUAGUAAAACUACACGCCGCUGGAUC--AACCU-CCGGCA---AUCCAAGAAUUUAUAAUCGUCUGC
((((((((((((((..((....))..(((...((((.....))))..)))...)))))))))))))).((((..((...--..)).-.)))).---........................ ( -34.80)
>pfo.254 5902164 115 - 6438405
UGUAGUUUUACUACUCGUCUAUACAUUCGAAAGGCUGAAAUGCCGGAUGAUUUGUAGUAAAACUACACGCCGCCGGAAC--AACCUGUCGGCA---AUCCAAGAAUUUUAAAUCGUCUGC
((((((((((((((((((((...(....)...(((......)))))))))...)))))))))))))).((((.(((...--...))).)))).---........................ ( -36.60)
>consensus
UGUAGUUUUACUACUAGUCCAUACAUUCAAAAGGCUGAAAUGCCAAACGAUUUGUAGUAAAACUACACGCCGCCGGAUC__AACCU_CCGGAA___AUCCAAGAAUUUACG_UCGUCUGC
((((((((((((((.........((.((....)).))((((((....))))))))))))))))))))....(((((...........)))))............................ (-24.61 = -24.87 +   0.26)

alignment

secondary structure

dotplot

Window 8

Location	5,635,975 – 5,636,091
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	70.99
Mean single sequence MFE	-35.75
Consensus MFE	-17.55
Energy contribution	-18.41
Covariance contribution	0.86
Combinations/Pair	1.05
Mean z-score	-2.23
Structure conservation index	0.49
SVM decision value	1.91
SVM RNA-class probability	0.982265
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2980 5635975 116 - 6264404
GCGACCGC-AGCUAAUUCUUGGAUGUUCUCCGG-GGGUG--UACCCGGCGACUUGUAGUUUUACUACAGAUCAGUCUGAGAAACAGCCCUCUGGAUACAAUUUUUAGUAGUAAAACUACA
.((.(((.-.....(((((((((.....)))))-)))).--....)))))...(((((((((((((((((...(((((((........))).))))......))).)))))))))))))) ( -35.00)
>pss.318 5514594 115 + 6093698
GCAGACGA-CAUAAAUUCUUGGAU---UUCCGG-AGGGUGGGAUCCGGCGGCGUGUAGUUUUACUACAAAUCGACGACGAUUUCAGCCCUCCGAGUAUCGGACCCAGUAGUAAAACUACA
........-.........((.(((---...(((-((((((..(((((.(((..(((((.....)))))..))).))..)))..)).)))))))...))).))....((((.....)))). ( -37.80)
>pel.2957 5464775 113 - 5888780
GCAGACGU-CGUGAAUUCUUGGAU---UACCGG-ACAGU--CAUCCGGCGCGGUGUAGUUUUACUACAAAUGCUUUCGCAUUUCAUGCUUUUGCACCUACGGGGUAGUAGUAAAACUACA
.......(-((((((((....)))---).((((-(....--..))))))))))((((((((((((((((((((....))))))..(((....)))((....))...)))))))))))))) ( -40.20)
>ppk.199 5771025 113 + 6181863
GCAGACGU-CGUGAAUUCUUGGAU---UACCGG-GGUGU--CUUCCGGCGCGUUGUAGUUUUACUACAUUUGCUUUCGCAUUUCAUGCUUUUACACGACACGAGUAGUAGUAAAACUACA
...(.(((-((.(((.((((((..---..))))-))...--.)))))))))..((((((((((((((...(((....))).....(((((...........))))))))))))))))))) ( -34.70)
>pf5.303 6480924 114 + 7074893
GCAGACGAUUAUAAAUUCUUGGAU---UGCCGG-AGGUU--GAUCCAGCGGCGUGUAGUUUUACUACAAAUCGUCGGCCAUUUCAGCCUUUCGAAUGUAUAUACGAGUAGUAAAACUACA
....((.......((((....)))---)((((.-.((..--...))..))))))(((((((((((((...(((..(((.......)))...))).(((....))).))))))))))))). ( -32.40)
>pfo.254 5902164 115 + 6438405
GCAGACGAUUUAAAAUUCUUGGAU---UGCCGACAGGUU--GUUCCGGCGGCGUGUAGUUUUACUACAAAUCAUCCGGCAUUUCAGCCUUUCGAAUGUAUAGACGAGUAGUAAAACUACA
....(((((((((.....))))))---)((((...((..--...))..))))))(((((((((((((.........(((......)))..(((..........)))))))))))))))). ( -34.40)
>consensus
GCAGACGA_CGUAAAUUCUUGGAU___UACCGG_AGGGU__GAUCCGGCGGCGUGUAGUUUUACUACAAAUCAUCCCGCAUUUCAGCCUUUCGAAUGUAAAGACUAGUAGUAAAACUACA
..................((((((.....((....)).....)))))).....((((((((((((((.......................................)))))))))))))) (-17.55 = -18.41 +   0.86)

alignment

secondary structure

dotplot

Window 9

Location	5,636,015 – 5,636,131
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.74
Mean single sequence MFE	-33.40
Consensus MFE	-21.27
Energy contribution	-20.80
Covariance contribution	-0.47
Combinations/Pair	1.19
Mean z-score	-1.64
Structure conservation index	0.64
SVM decision value	0.81
SVM RNA-class probability	0.857095
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2980 5636015 116 + 6264404
CUCAGACUGAUCUGUAGUAAAACUACAAGUCGCCGGGUA--CACCC-CCGGAGAACAUCCAAGAAUUAGCU-GCGGUCGCCCACGAGGCCGGCCGCUCACCUAUGGCAUCCGAUUCUGGA
.(((((..((..(((((.....)))))..))((((((..--....)-))(((.....)))......(((..-(((((((.((....)).)))))))....))).))).......))))). ( -40.50)
>pss.318 5514634 114 - 6093698
UCGUCGUCGAUUUGUAGUAAAACUACACGCCGCCGGAUCCCACCCU-CCGGAA---AUCCAAGAAUUUAUG-UCGUCUGCCCACAAGGCCAGUCGCAAACUCA-GGCAACCGAUUCUGGA
(((..((((...(((((.....))))).(((.(((((........)-))))..---.............((-.((.(((.((....)).))).))))......-)))...))))..))). ( -29.70)
>pel.2957 5464815 112 + 5888780
UGCGAAAGCAUUUGUAGUAAAACUACACCGCGCCGGAUG--ACUGU-CCGGUA---AUCCAAGAAUUCACG-ACGUCUGCCCAUAAGGCCAGUCGCAAACUCA-GGCCAUCGAUUCUGGU
(((....)))..(((((.....)))))....(((((((.--...))-))))).---..(((.(((((...(-((....(((.....)))..)))((.......-.))....)))))))). ( -32.80)
>ppk.199 5771065 112 - 6181863
UGCGAAAGCAAAUGUAGUAAAACUACAACGCGCCGGAAG--ACACC-CCGGUA---AUCCAAGAAUUCACG-ACGUCUGCCCAUAAGGCCAGUCGCAAUCUCA-GGCAAUCGAUUCUGGU
(((....)))..(((((.....)))))....(((((...--.....-))))).---..(((.(((((...(-((....(((.....)))..)))((.......-.))....)))))))). ( -31.30)
>pf5.303 6480964 113 - 7074893
UGGCCGACGAUUUGUAGUAAAACUACACGCCGCUGGAUC--AACCU-CCGGCA---AUCCAAGAAUUUAUAAUCGUCUGCCCAAAAGGCCAGUCGCAAACUCA-GGCAACCGAUUCUGGA
.(((.((((((((((((.....))))).((((..((...--..)).-.)))).---..............))))))).)))......((((((.....)))..-)))..(((....))). ( -32.70)
>pfo.254 5902204 114 - 6438405
UGCCGGAUGAUUUGUAGUAAAACUACACGCCGCCGGAAC--AACCUGUCGGCA---AUCCAAGAAUUUUAAAUCGUCUGCCCACAAGGCCAGUCGCAAACUCA-GGCAACCGAUUCUGGA
((((((((....(((((.....))))).((((.(((...--...))).)))).---)))).............((.(((.((....)).))).))........-)))).(((....))). ( -33.40)
>consensus
UGCCAAACGAUUUGUAGUAAAACUACACGCCGCCGGAUC__AACCU_CCGGAA___AUCCAAGAAUUUACG_UCGUCUGCCCACAAGGCCAGUCGCAAACUCA_GGCAACCGAUUCUGGA
............(((((.....)))))....(((((...........)))))......(((.(((((.......(.(((.((....)).))).)((.........))....)))))))). (-21.27 = -20.80 +  -0.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:05:35 2007