Locus 36

Sequence ID	pao_1
Location	3,133,430 – 3,133,531
Length	101
Max. P	0.882741

overview

Window 4

Location	3,133,430 – 3,133,531
Length	101
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	83.88
Mean single sequence MFE	-31.25
Consensus MFE	-29.60
Energy contribution	-29.60
Covariance contribution	0.00
Combinations/Pair	1.09
Mean z-score	-1.65
Structure conservation index	0.95
SVM decision value	0.92
SVM RNA-class probability	0.882741
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 3133430 101 + 1
CCAGCAGCGCGGGAUUUGUUUGGUAGGCACGAUUGGAUUCGAACCAACGACCCCCACCAUGUCAAGGUGGUGCUCUAACCAACUGAGCUACGUGCCUGCUG
.((((((((((((.(((..(((((((((((....((..(((......)))..))((((.......)))))))).)).)))))..))))).)))).)))))) ( -36.80)
>pau_1 1 101 + 1
CCAGCAGUGCGGGAUUUGUUUGGUAGGCACGAUUGGAUUCGAACCAACGACCCCCACCAUGUCAAGGUGGUGCUCUAACCAACUGAGCUACGUGCCUGCUG
.((((((..((((.(((..(((((((((((....((..(((......)))..))((((.......)))))))).)).)))))..))))).))..).))))) ( -34.40)
>pel_1 1 80 + 1
------------------UUUGGUAGGCACAAUUGGACUCGAACCAACGACCCCCACCAUGUCAAGGUGGUGCUCUAACCAACUGAGCUAUGUGCCUG---
------------------.....((((((((.((((.......))))......(((((.......))))).((((.........))))..))))))))--- ( -25.40)
>ppk_1 1 80 + 1
------------------UUUGGUAGGCACAAUUGGACUCGAACCAACGACCCCCACCAUGUCAAGGUGGUGCUCUAACCAACUGAGCUAUGUGCCUG---
------------------.....((((((((.((((.......))))......(((((.......))))).((((.........))))..))))))))--- ( -25.40)
>psp_1 1 81 + 1
--------------------UGGUAGGCGCGAUUGGACUCGAACCAACGACCCCCACCAUGUCAAGGUGGUGCUCUAACCAACUGAGCUACGUGCCUGCUG
--------------------.((((((((((.((((.......))))......(((((.......))))).((((.........))))..)))))))))). ( -31.60)
>pss_1 1 101 + 1
CCAGCAGAGCGGAUUUUGUUUGGUAGGCGCGAUUGGACUCGAACCAACGACCCCCACCAUGUCAAGGUGGUGCUCUAACCAACUGAGCUACGUGCCUGCUG
.((((((.(((...(((..(((((((((((....((..(((......)))..))((((.......)))))))).)).)))))..)))...)))..)))))) ( -33.90)
>consensus
__________________UUUGGUAGGCACGAUUGGACUCGAACCAACGACCCCCACCAUGUCAAGGUGGUGCUCUAACCAACUGAGCUACGUGCCUGCUG
.....................((((((((((.((((.......))))......(((((.......))))).((((.........))))..)))))))))). (-29.60 = -29.60 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	3,133,430 – 3,133,531
Length	101
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	83.88
Mean single sequence MFE	-33.28
Consensus MFE	-28.84
Energy contribution	-28.73
Covariance contribution	-0.11
Combinations/Pair	1.05
Mean z-score	-1.79
Structure conservation index	0.87
SVM decision value	0.62
SVM RNA-class probability	0.803571
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 3133430 101 - 1
CAGCAGGCACGUAGCUCAGUUGGUUAGAGCACCACCUUGACAUGGUGGGGGUCGUUGGUUCGAAUCCAAUCGUGCCUACCAAACAAAUCCCGCGCUGCUGG
((((((((.....((((.........)))).(((((.......)))))(((...(((((.(((......))).....)))))......))))).)))))). ( -37.10)
>pau_1 1 101 - 1
CAGCAGGCACGUAGCUCAGUUGGUUAGAGCACCACCUUGACAUGGUGGGGGUCGUUGGUUCGAAUCCAAUCGUGCCUACCAAACAAAUCCCGCACUGCUGG
((((((((.....((((.........)))).(((((.......)))))(((...(((((.(((......))).....)))))......))))).)))))). ( -37.10)
>pel_1 1 80 - 1
---CAGGCACAUAGCUCAGUUGGUUAGAGCACCACCUUGACAUGGUGGGGGUCGUUGGUUCGAGUCCAAUUGUGCCUACCAAA------------------
---.(((((((..((((.........)))).(((((.......)))))((((((......))).)))...)))))))......------------------ ( -29.70)
>ppk_1 1 80 - 1
---CAGGCACAUAGCUCAGUUGGUUAGAGCACCACCUUGACAUGGUGGGGGUCGUUGGUUCGAGUCCAAUUGUGCCUACCAAA------------------
---.(((((((..((((.........)))).(((((.......)))))((((((......))).)))...)))))))......------------------ ( -29.70)
>psp_1 1 81 - 1
CAGCAGGCACGUAGCUCAGUUGGUUAGAGCACCACCUUGACAUGGUGGGGGUCGUUGGUUCGAGUCCAAUCGCGCCUACCA--------------------
..(((((...((.((((.........))))))...)))).).(((((((.((.(((((.......))))).)).)))))))-------------------- ( -27.40)
>pss_1 1 101 - 1
CAGCAGGCACGUAGCUCAGUUGGUUAGAGCACCACCUUGACAUGGUGGGGGUCGUUGGUUCGAGUCCAAUCGCGCCUACCAAACAAAAUCCGCUCUGCUGG
((((((((.....((((.........))))............(((((((.((.(((((.......))))).)).)))))))..........)).)))))). ( -38.70)
>consensus
CAGCAGGCACGUAGCUCAGUUGGUUAGAGCACCACCUUGACAUGGUGGGGGUCGUUGGUUCGAGUCCAAUCGUGCCUACCAAA__________________
....(((((((..((((.........)))).(((((.......)))))((((((......))).)))...)))))))........................ (-28.84 = -28.73 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:47:46 2007