Locus 17

Sequence ID	pao.3145
Location	5,953,099 – 5,953,197
Length	98
Max. P	0.872977

overview

Window 4

Location	5,953,099 – 5,953,197
Length	98
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	47.42
Mean single sequence MFE	-32.38
Consensus MFE	-7.81
Energy contribution	-8.45
Covariance contribution	0.64
Combinations/Pair	1.22
Mean z-score	-1.87
Structure conservation index	0.24
SVM decision value	0.88
SVM RNA-class probability	0.872977
Prediction	RNA
WARNING	Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.3145 5953099 98 + 6264404
GCCGCCAACCCGGGGAUAGUGCGGAACGCCGGGCUCCGGGCGGCGCACCAAAUAGGCGCAGACGCGCUCCGACAGUUGCGCAAAAAGUGUGCA-AUGGC
((((((..(((((((...(.(((...))))...))))))).)))..........(((((....)))))......((((((((.....))))))-))))) ( -41.60)
>pss.121 202615 89 + 6093698
UUUGCACAACCUUGCAGGGU--------CUAUCAUGGAGCUAAUGCACAGCAAUGGUGCUCAUGUGCCCGUCACUGCGCUCCAUAAGCGUGCA-UUGC-
..(((((.((((....))))--------.....(((((((.......(((..((((.((......))))))..))).)))))))....)))))-....- ( -28.00)
>pel.3099 5693343 79 + 5888780
AUUGGCCAAUCG----------------CCAGCAGCGAAAAAGCGCACAAAAUCGGUGCGCGACCUUUGGCCGCCCUGCGCGAAAAGCGUGCA-GC---
...(((((((((----------------(.....))))....((((((.......)))))).....))))))...(((((((.....))))))-).--- ( -35.80)
>ppk.3053 5968290 79 + 6181863
AUUGGCCAGUCG----------------CCAGCACGGGAAACAUGCACAAUUUCGGUGCGCAGCAGCGGGGCAAGCUGCGCGAAAAAUGUGCA-AC---
.(((((.....)----------------))))....(....).((((((.(((...((((((((.((...))..)))))))).))).))))))-..--- ( -29.60)
>pfo.3253 6171995 82 + 6438405
GCCAUC-ACCCAAAUGGCAC--------UCGGGAU-------ACGCACAACAACGGUGCGUGGCCGUGCAUCCAGUUGCGCGAAAAGCGUGCAUCCGU-
(((((.-......)))))..--------.((((.(-------((((((.......)))))))((((((((......))))))....)).....)))).- ( -28.20)
>psp.2918 259261 89 - 5928787
UUUGCCGGGUCAAACCGGCU--------UCGCGACCAAGGUAAUGCACACUAAUGGUGCUCAUGUGUACGCCGCAGCGCUCCAUAAGCGUGCG-ACUC-
...(((((......))))).--------.....((....))..(((((.((.((((.((.(.((((.....))))).)).)))).)).)))))-....- ( -31.10)
>consensus
AUUGCCCAACCG____G__U________CCAGCAUCGAGAAAACGCACAAAAACGGUGCGCAGCCGCGCGCCAAGCUGCGCGAAAAGCGUGCA_ACG__
............................................((((.......))))..................(((((.....)))))....... ( -7.81 =  -8.45 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	5,953,099 – 5,953,197
Length	98
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	47.42
Mean single sequence MFE	-33.23
Consensus MFE	-7.03
Energy contribution	-6.53
Covariance contribution	-0.50
Combinations/Pair	1.38
Mean z-score	-1.60
Structure conservation index	0.21
SVM decision value	0.37
SVM RNA-class probability	0.708043
Prediction	RNA
WARNING	Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.3145 5953099 98 - 6264404
GCCAU-UGCACACUUUUUGCGCAACUGUCGGAGCGCGUCUGCGCCUAUUUGGUGCGCCGCCCGGAGCCCGGCGUUCCGCACUAUCCCCGGGUUGGCGGC
(((..-............((((..(....)..))))....(((((.....)))))(((((((((.(....(((...))).....).))))).))))))) ( -38.50)
>pss.121 202615 89 - 6093698
-GCAA-UGCACGCUUAUGGAGCGCAGUGACGGGCACAUGAGCACCAUUGCUGUGCAUUAGCUCCAUGAUAG--------ACCCUGCAAGGUUGUGCAAA
-....-(((((..(((((((((((((..(.((((......)).)).)..))))......)))))))))..(--------(((......))))))))).. ( -34.20)
>pel.3099 5693343 79 - 5888780
---GC-UGCACGCUUUUCGCGCAGGGCGGCCAAAGGUCGCGCACCGAUUUUGUGCGCUUUUUCGCUGCUGG----------------CGAUUGGCCAAU
---.(-(((.((.....)).))))...((((((.....((((((.......))))))....((((.....)----------------)))))))))... ( -32.40)
>ppk.3053 5968290 79 - 6181863
---GU-UGCACAUUUUUCGCGCAGCUUGCCCCGCUGCUGCGCACCGAAAUUGUGCAUGUUUCCCGUGCUGG----------------CGACUGGCCAAU
---..-((((((.((((.(((((((..((...)).)))))))...)))).))))))............(((----------------(.....)))).. ( -29.20)
>pfo.3253 6171995 82 - 6438405
-ACGGAUGCACGCUUUUCGCGCAACUGGAUGCACGGCCACGCACCGUUGUUGUGCGU-------AUCCCGA--------GUGCCAUUUGGGU-GAUGGC
-..((((((.(((.....))).........(((((((.(((...))).)))))))))-------))))...--------..((((((.....-)))))) ( -29.30)
>psp.2918 259261 89 + 5928787
-GAGU-CGCACGCUUAUGGAGCGCUGCGGCGUACACAUGAGCACCAUUAGUGUGCAUUACCUUGGUCGCGA--------AGCCGGUUUGACCCGGCAAA
-...(-(((..((((((((.((((....)))).).)))))))((((...(((.....)))..)))).))))--------.(((((......)))))... ( -35.80)
>consensus
__CGU_UGCACGCUUUUCGCGCAACGCGACGAACGCAUGCGCACCGAUAUUGUGCAUUACCUCGAUCCCGG________A__C____CGACUGGGCAAA
......(((.(.......).))).................((((.......))))............................................ ( -7.03 =  -6.53 +  -0.50)

alignment

secondary structure

dotplot

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