Locus 33

Sequence ID	pao.2783
Location	5,275,768 – 5,275,965
Length	197
Max. P	0.592409

overview

Window 2

Location	5,275,768 – 5,275,886
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.52
Mean single sequence MFE	-37.65
Consensus MFE	-24.35
Energy contribution	-25.48
Covariance contribution	1.13
Combinations/Pair	1.34
Mean z-score	-1.32
Structure conservation index	0.65
SVM decision value	0.12
SVM RNA-class probability	0.592409
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2783 5275768 118 - 6264404
UGGAAGAGCUCCGUAACAC-CAGGCGCCCUUCCAA-GUUUGCUCAAUCGGCAGUUGACGUAGCCGGUGACUACCGUCACCCAUGCUCUGCCGGGCAGCCAACCGAAUUUCGGUCGCCCGC
((((((.((.((.......-..)).)).)))))).-....((......(((((.....(((...((((((....))))))..))).)))))((((.....((((.....)))).)))))) ( -44.50)
>psp.505 4886577 117 + 5928787
UGGGAAUGUUCCGCAACAC-UCAGGGACCUCCCAAUACUUGCUCAGUCAGU-GCUGACGUAGUCGGCGACCACCGUCGCUCAUGCUCUGCUG-GCAGUAAACCUAUUAAGACCCGUCCCG
.((((..(((.........-...(((....)))..((((.((.(((.(((.-(((((((....))(((((....)))))))).)).))))))-))))))..........)))...)))). ( -37.00)
>pfo.2844 5404857 118 - 6438405
UGGGAAAGGCCCGCAACAC-UUGGGACGAUCCCAAUACUUGCUCAGUCAGU-GCUGACGUAGUCGGCGACCACCGUCGCUCAUGCUCUGCCGAGAAGUAAACCUAUUAAGACCCGUUCGC
.(((.....)))(((((..-(((((.....)))))(((((.(((.(.(((.-(((((((....))(((((....)))))))).)).)))).))))))))...............))).)) ( -35.40)
>pf5.3193 6020698 119 - 7074893
UGGGAAAACCCCGCAACACUUUGGGGCGCUCCCAAUACUUGCUCAGUCAGU-GCUGACGUAGUCGGCGACCACCGUCGCUCAUGCUCUGCUGAGAAGUAAACCUAUUAAGACCCGCUCCC
(((((...(((((........)))))...))))).(((((.(((((.(((.-(((((((....))(((((....)))))))).)).)))))))))))))..................... ( -41.80)
>ppk.2709 5319407 104 - 6181863
UGGGAAACCCCCGCAACACUCUGGGGAUCUCCCAAUACUUGCUCAGUCAGU-GCUGACGU---------------UCGCUCAUGCUCUGCUUGGCAGUAAACCUAUUAAGACCCGUCCAG
(((((...(((((........)))))...))))).((((.(((.((.(((.-(((((.(.---------------...)))).)).))))).)))))))..................... ( -30.20)
>pss.492 5135564 117 + 6093698
UGGGAAUGUUCCGCAACAC-UCAGGGACCUCCCAAUACUUGCUCAGUCAGU-GCUGACGUAGUCGGCGACCACCGUCGCUCAUGCUCUGCUG-GCAGUAAACCUAUUAAGACCCGUCCCG
.((((..(((.........-...(((....)))..((((.((.(((.(((.-(((((((....))(((((....)))))))).)).))))))-))))))..........)))...)))). ( -37.00)
>consensus
UGGGAAAGCCCCGCAACAC_UUGGGGACCUCCCAAUACUUGCUCAGUCAGU_GCUGACGUAGUCGGCGACCACCGUCGCUCAUGCUCUGCUG_GCAGUAAACCUAUUAAGACCCGUCCCC
(((((...(((((........)))))...))))).((((.((((.(((((...)))))(((...((((((....))))))..)))......))))))))..................... (-24.35 = -25.48 +   1.13)

alignment

secondary structure

dotplot

Window 3

Location	5,275,808 – 5,275,925
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.24
Mean single sequence MFE	-45.45
Consensus MFE	-30.58
Energy contribution	-32.28
Covariance contribution	1.70
Combinations/Pair	1.27
Mean z-score	-1.10
Structure conservation index	0.67
SVM decision value	-0.06
SVM RNA-class probability	0.505258
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2783 5275808 117 + 6264404
GGUGACGGUAGUCACCGGCUACGUCAACUGCCGAUUGAGCAAAC-UUGGAAGGGCGCCUG-GUGUUACGGAGCUCUUCCACCCAGCGCGAGGUAACGCGAAGCAGGGUGUAAC-UUUCGG
((((((....))))))(((..........)))((..(.......-..((((((((..(((-......))).))))))))((((..((((......)))).....))))....)-..)).. ( -43.90)
>pst.577 5331612 117 - 6397126
AGCGACGGUGGUCGCCGACUACGUCAGC-ACUGACUGAGCAAGUAUUGGGAAGUCCCUGA-GUGUUGCGGAACAUUCCCACCCAGCGCGAGGUAACGCGUUGC-GGGUGUUACAGGUCGG
.((((((.(((((...))))))))).))-.((((((.((((.....((((((.((((...-.....).)))...))))))(((((((((......))))))).-)).))))...)))))) ( -46.80)
>pfo.2844 5404897 117 + 6438405
AGCGACGGUGGUCGCCGACUACGUCAGC-ACUGACUGAGCAAGUAUUGGGAUCGUCCCAA-GUGUUGCGGGCCUUUCCCACCCAGCGCGAGGUAACGCGUUGC-GGGUGUAACAGGUCGA
.(((((....)))))......((.((((-(((.(((.....)))..((((.....)))))-))))))))(((((.(..(((((((((((......))))))..-)))))..).))))).. ( -48.70)
>pf5.3193 6020738 118 + 7074893
AGCGACGGUGGUCGCCGACUACGUCAGC-ACUGACUGAGCAAGUAUUGGGAGCGCCCCAAAGUGUUGCGGGGUUUUCCCACCCAGCGCGAGGUAACGCGUUGC-GGGUGUAGCACUUCGG
......((((.((.((((.(((.((((.-.....))))....))))))))).))))((.(((((((((((((....))).(((((((((......))))))).-)).)))))))))).)) ( -49.00)
>ppk.2709 5319447 104 + 6181863
AGCGA---------------ACGUCAGC-ACUGACUGAGCAAGUAUUGGGAGAUCCCCAGAGUGUUGCGGGGGUUUCCCACCCAGCGCGAGGUAACGCGUUGCGGGGUGUAACAGGUCGG
.((..---------------......))-.((((((..(((.....((((((((((((..........))))))))))))(((((((((......))))))).))..)))....)))))) ( -44.50)
>pel.2708 5010528 103 + 5888780
AGCGA---------------ACGUCAGC-ACUGACUGAGCAAGUAUUGGGACUGCCCUGGUGUGUUGCGGGC-CUUCCCACCCAGCGCGAGGUAACGCGUUGCGGGGUGUUACAAGUCGG
.((..---------------......))-.((((((.((((.....(((((..((((...........))))-..)))))(((((((((......))))))).))..))))...)))))) ( -39.80)
>consensus
AGCGACGGUGGUCGCCGACUACGUCAGC_ACUGACUGAGCAAGUAUUGGGAGCGCCCCAA_GUGUUGCGGGGCUUUCCCACCCAGCGCGAGGUAACGCGUUGC_GGGUGUAACAGGUCGG
.((((((.(((((...))))))))).))..((((((.........(((((.....)))))..(((((((((.....)))((((((((((......))))))...)))))))))))))))) (-30.58 = -32.28 +   1.70)

alignment

secondary structure

dotplot

Window 4

Location	5,275,848 – 5,275,965
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.45
Mean single sequence MFE	-38.80
Consensus MFE	-27.86
Energy contribution	-28.12
Covariance contribution	0.25
Combinations/Pair	1.17
Mean z-score	-1.02
Structure conservation index	0.72
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>pao.2783 5275848 117 - 6264404
CCAGUCCCCUCUCCGGCAGACCAUGAGGUGCCUACCCGCGCCGAAA-GUUACACCCUGCUUCGCGUUACCUCGCGCUGGGUGGAAGAGCUCCGUAACAC-CAGGCGCCCUUCCAA-GUUU
..((.(.((((...((....))..)))).).))....(((((....-(((((((((.((...(((......))))).))))(((.....))))))))..-..)))))........-.... ( -36.40)
>pau.2921 5547780 117 - 6537648
CCAGUCCCCUCUCCGGCAGACCAUGAGGUGCCUACCCGCGCCGAAA-GUUACACCCUGCUUCGCGUUACCUCGCGCUGGGUGGAAGAGCUCCGUAACAC-CAGGCGCCCUUCCAA-GUUU
..((.(.((((...((....))..)))).).))....(((((....-(((((((((.((...(((......))))).))))(((.....))))))))..-..)))))........-.... ( -36.40)
>pfo.2844 5404936 115 - 6438405
CAGACCCUCUC---GGCAGAUCAUGAGGCGCAUAUCCGCGUCGACCUGUUACACCC-GCAACGCGUUACCUCGCGCUGGGUGGGAAAGGCCCGCAACAC-UUGGGACGAUCCCAAUACUU
..(..(((.((---(((((.((....(((((......))))))).))))).(((((-(...((((......)))).)))))).)).)))..).......-(((((.....)))))..... ( -36.80)
>pf5.3193 6020777 116 - 7074893
CAGACCCACUC---AGCAGAUCAUGAGGCGCACAUCCGCGCCGAAGUGCUACACCC-GCAACGCGUUACCUCGCGCUGGGUGGGAAAACCCCGCAACACUUUGGGGCGCUCCCAAUACUU
....(((((((---(((....(((..(((((......)))))...)))........-.....(((......)))))))))))))....(((((........))))).............. ( -43.60)
>ppk.2709 5319471 117 - 6181863
CAGACCCGCUA---AGCAGAUCAUGAGGUGCACACCCGCGCCGACCUGUUACACCCCGCAACGCGUUACCUCGCGCUGGGUGGGAAACCCCCGCAACACUCUGGGGAUCUCCCAAUACUU
((((.......---(((((.((....(((((......))))))).))))).......((..((((......))))..(((.((....))))))).....))))(((....)))....... ( -39.30)
>pel.2708 5010552 116 - 5888780
CAGACCCGCUA---AGCAGAUCAUGAGGCGCACACCCGCGCCGACUUGUAACACCCCGCAACGCGUUACCUCGCGCUGGGUGGGAAG-GCCCGCAACACACCAGGGCAGUCCCAAUACUU
...((((((..---.......((...(((((......)))))....)).........))..((((......))))..))))((((..-((((...........))))..))))....... ( -40.27)
>consensus
CAGACCCCCUC___AGCAGAUCAUGAGGCGCACACCCGCGCCGAAAUGUUACACCC_GCAACGCGUUACCUCGCGCUGGGUGGGAAAGCCCCGCAACAC_CUGGGGCCCUCCCAAUACUU
..........................(((((......)))))..........((((.((...(((......))))).))))((((...(((((........)))))...))))....... (-27.86 = -28.12 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:06:23 2007