Locus 49

Sequence ID	pao_1
Location	3,650,816 – 3,650,894
Length	78
Max. P	0.999848

overview

Window 5

Location	3,650,816 – 3,650,894
Length	78
Sequences	6
Columns	78
Reading direction	forward
Mean pairwise identity	94.85
Mean single sequence MFE	-30.17
Consensus MFE	-28.90
Energy contribution	-28.73
Covariance contribution	-0.16
Combinations/Pair	1.09
Mean z-score	-1.93
Structure conservation index	0.96
SVM decision value	3.24
SVM RNA-class probability	0.998825
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 3650816 78 + 1
UGGUGGGUGAUGACGGGAUCGAACCGCCGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAUCACCCUU
....(((((((...(((.(((......))))))((((((.....)))))).((((........))))..))))))).. ( -31.30)
>pel_1 1 76 + 1
UGGUGGGUGAUGACGGGAUCGAACCGCCGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCGGCUGAGCUAAUCACCC--
....(((((((...(((.(((......))))))((((((.....)))))).((((........))))..)))))))-- ( -30.10)
>pf5_1 1 78 + 1
UGGUGGGUGAUGACGGGAUCGAACCGCCGACAUUCUGCUUGUAAGGCAGACGCUCUCCCGGCUGAGCUAAUCACCCUU
....((((((((.(((.......))).).....((((((.....)))))).((((........))))..))))))).. ( -27.70)
>pfo_1 1 76 + 1
UGGUGGGUGAUGACGGGAUCGAACCGCCGACAUUCUGCUUGUAAGGCAGACGCUCUCCCAGCUGAGCUAAUCACCC--
....((((((((.(((.......))).).....((((((.....)))))).((((........))))..)))))))-- ( -26.50)
>ppk_1 1 77 + 1
UGGUGGGUGAUGACGGGAUCGAACCGCCGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCGGCUGAGCUAAUCACCCU-
....(((((((...(((.(((......))))))((((((.....)))))).((((........))))..))))))).- ( -31.30)
>pst_1 1 78 + 1
UGGUGGGUGAUGACGGGAUCGAACCGCCGACCCGCUGCUUGUAAGGCAGCUGCUCUCCCAGCUGAGCUAAUCACCCUU
....(((((((...(((.(((......))))))((((((.....)))))).((((........))))..))))))).. ( -34.10)
>consensus
UGGUGGGUGAUGACGGGAUCGAACCGCCGACCCUCUGCUUGUAAGGCAGAUGCUCUCCCAGCUGAGCUAAUCACCCU_
....(((((((...(((.(((......))))))((((((.....)))))).((((........))))..))))))).. (-28.90 = -28.73 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	3,650,816 – 3,650,894
Length	78
Sequences	6
Columns	78
Reading direction	reverse
Mean pairwise identity	94.85
Mean single sequence MFE	-30.57
Consensus MFE	-29.96
Energy contribution	-29.68
Covariance contribution	-0.28
Combinations/Pair	1.05
Mean z-score	-2.17
Structure conservation index	0.98
SVM decision value	4.24
SVM RNA-class probability	0.999848
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 3650816 78 - 1
AAGGGUGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA
..(((((((..((((........)))).(((((.......)))))(((((((....)))))))....))))))).... ( -30.70)
>pel_1 1 76 - 1
--GGGUGAUUAGCUCAGCCGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA
--(((((((..((((........)))).(((((.......)))))(((((((....)))))))....))))))).... ( -30.50)
>pf5_1 1 78 - 1
AAGGGUGAUUAGCUCAGCCGGGAGAGCGUCUGCCUUACAAGCAGAAUGUCGGCGGUUCGAUCCCGUCAUCACCCACCA
..(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).... ( -29.30)
>pfo_1 1 76 - 1
--GGGUGAUUAGCUCAGCUGGGAGAGCGUCUGCCUUACAAGCAGAAUGUCGGCGGUUCGAUCCCGUCAUCACCCACCA
--(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).... ( -29.10)
>ppk_1 1 77 - 1
-AGGGUGAUUAGCUCAGCCGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA
-.(((((((..((((........)))).(((((.......)))))(((((((....)))))))....))))))).... ( -30.70)
>pst_1 1 78 - 1
AAGGGUGAUUAGCUCAGCUGGGAGAGCAGCUGCCUUACAAGCAGCGGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA
..(((((((..((((........)))).(((((.......)))))(((((((....)))))))....))))))).... ( -33.10)
>consensus
_AGGGUGAUUAGCUCAGCCGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA
..(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).... (-29.96 = -29.68 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:48:26 2007