Locus 198

Sequence ID pao.1712
Location 3,207,166 – 3,207,289
Length 123
Max. P 0.971767
window783 window784 window785 window786

overview

Window 3

Location 3,207,166 – 3,207,278
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 43.02
Mean single sequence MFE -54.10
Consensus MFE -24.70
Energy contribution -29.32
Covariance contribution 4.62
Combinations/Pair 1.66
Mean z-score -5.48
Structure conservation index 0.46
SVM decision value 1.14
SVM RNA-class probability 0.921885
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.1712 3207166 112 + 6264404
UAGGUCUCACGACCUGUUGAAAACCGGUCCCUCG----GGGCCGGUUUUUUUA-UGCCUGCG---UUUCGCCGGGCAUGAAAAAACCCGCGUCCCUUGCGGGUACGCGGGCCUCUGCCUC
((((((....))))))..((((((((((((....----))))))))))))(((-((((((((---...)).))))))))).....((((((((((....))).))))))).......... ( -57.90)
>pau.1282 4175432 112 - 6537648
CGCAAUUUACUCGAACAUUUCCCGCUUGGCAAAU----AUUUUUUUAACUUUU-UCAUCGGC---UUAGGUCGUCGGAGGAAAGUCCGCGGGGUGCCUUGGUAGACUGCCGGGCACGAAG
..........((........(((((..((((((.----.....)))...((((-((..((((---....))))..))))))..))).)))))((((((.(((.....))))))))))).. ( -32.40)
>pf5.2596 4971749 112 + 7074893
UAGUCCCUCGGGAUUGUUAUCGAGCCGAUCCAUUUUUUGGAUCGGCUUUUUUAUUGCCCGGAGUUCUUCACCGGCAAUAAAAAACCCGCCGCUACCAGCAGGUAUCGGCGGG--------
((((((....)))))).....(((((((((((.....)))))))))))((((((((((.((.(.....).))))))))))))..(((((((.((((....)))).)))))))-------- ( -58.20)
>pfo.2361 4537202 109 + 6438405
UAGUCCUUCGGGAUUGUUAUCAAGCCGACCCGUUUUUCGGGUCGGCUUUUUUG-UGCCUGCAGUUUUCUGCGGGCAAUAAAAAACCCGCCACGGC--GCAAGCCUCGGCGGG--------
((((((....)))))).....(((((((((((.....)))))))))))(((((-(((((((((....)))))))).))))))..((((((..(((--....)))..))))))-------- ( -67.90)
>consensus
UAGUCCUUACGGAUUGUUAUCAAGCCGACCCAUU____GGGUCGGCUUUUUUA_UGCCCGCA___UUUCGCCGGCAAUAAAAAACCCGCCGCGACC_GCAGGUAUCGGCGGG________
((((((....)))))).......(((((((((.....)))))))))(((((((.((((.((((....)))).)))).)))))))(((((((.((((....)))).)))))))........ (-24.70 = -29.32 +   4.62)

alignment

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secondary structure

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Window 4

Location 3,207,166 – 3,207,278
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 43.02
Mean single sequence MFE -49.12
Consensus MFE -17.90
Energy contribution -23.77
Covariance contribution 5.88
Combinations/Pair 1.54
Mean z-score -4.62
Structure conservation index 0.36
SVM decision value 1.68
SVM RNA-class probability 0.971767
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.1712 3207166 112 - 6264404
GAGGCAGAGGCCCGCGUACCCGCAAGGGACGCGGGUUUUUUCAUGCCCGGCGAAA---CGCAGGCA-UAAAAAAACCGGCCC----CGAGGGACCGGUUUUCAACAGGUCGUGAGACCUA
..((.((((((((((((.(((....)))))))))))))))))(((((..(((...---))).))))-)...(((((((((((----...))).))))))))....(((((....))))). ( -61.50)
>pau.1282 4175432 112 + 6537648
CUUCGUGCCCGGCAGUCUACCAAGGCACCCCGCGGACUUUCCUCCGACGACCUAA---GCCGAUGA-AAAAGUUAAAAAAAU----AUUUGCCAAGCGGGAAAUGUUCGAGUAAAUUGCG
.((((....((((.((((....))))....((((((......)))).))......---))))....-............(((----((((.((....)).)))))))))))......... ( -25.00)
>pf5.2596 4971749 112 - 7074893
--------CCCGCCGAUACCUGCUGGUAGCGGCGGGUUUUUUAUUGCCGGUGAAGAACUCCGGGCAAUAAAAAAGCCGAUCCAAAAAAUGGAUCGGCUCGAUAACAAUCCCGAGGGACUA
--------(((((((.((((....)))).)))))))((((((((((((.(.((.....))).))))))))))))(((((((((.....)))))))))..........(((....)))... ( -55.90)
>pfo.2361 4537202 109 - 6438405
--------CCCGCCGAGGCUUGC--GCCGUGGCGGGUUUUUUAUUGCCCGCAGAAAACUGCAGGCA-CAAAAAAGCCGACCCGAAAAACGGGUCGGCUUGAUAACAAUCCCGAAGGACUA
--------.((((((.(((....--))).))))))(((((((..((((.((((....)))).))))-.....(((((((((((.....)))))))))))............))))))).. ( -54.10)
>consensus
________CCCGCCGAUACCCGC_GGACGCGGCGGGUUUUUCAUUGCCGGCGAAA___UCCAGGCA_UAAAAAAACCGACCC____AAUGGGUCGGCUUGAUAACAAUCCCGAAGGACUA
........(((((((.((((....)))).)))))))..(((((.((((.(((......))).)))).)))))(((((((((((.....)))))))))))......(((((....))))). (-17.90 = -23.77 +   5.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,207,177 – 3,207,289
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 40.17
Mean single sequence MFE -50.03
Consensus MFE -22.60
Energy contribution -25.60
Covariance contribution 3.00
Combinations/Pair 1.69
Mean z-score -4.92
Structure conservation index 0.45
SVM decision value 1.23
SVM RNA-class probability 0.934057
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.1712 3207177 112 + 6264404
ACCUGUUGAAAACCGGUCCCUCG----GGGCCGGUUUUUUUA-UGCCUGCG---UUUCGCCGGGCAUGAAAAAACCCGCGUCCCUUGCGGGUACGCGGGCCUCUGCCUCGACGCUCUCCG
....(((((..((((((((....----))))))))(((((((-((((((((---...)).))))))))))))).((((((((((....))).)))))))........)))))........ ( -55.10)
>pau.1282 4175443 110 - 6537648
CGAACAUUUCCCGCUUGGCAAAU----AUUUUUUUAACUUUU-UCAUCGGC---UUAGGUCGUCGGAGGAAAGUCCGCGGGGUGCCUUGGUAGACUGCCGGGCACGAAGAGGAGAGGC--
.........(((((..((((((.----.....)))...((((-((..((((---....))))..))))))..))).)))))((((((.(((.....))))))))).............-- ( -32.20)
>pf5.2596 4971760 101 + 7074893
GAUUGUUAUCGAGCCGAUCCAUUUUUUGGAUCGGCUUUUUUAUUGCCCGGAGUUCUUCACCGGCAAUAAAAAACCCGCCGCUACCAGCAGGUAUCGGCGGG-------------------
(((....)))(((((((((((.....)))))))))))((((((((((.((.(.....).))))))))))))..(((((((.((((....)))).)))))))------------------- ( -52.50)
>pfo.2361 4537213 98 + 6438405
GAUUGUUAUCAAGCCGACCCGUUUUUCGGGUCGGCUUUUUUG-UGCCUGCAGUUUUCUGCGGGCAAUAAAAAACCCGCCACGGC--GCAAGCCUCGGCGGG-------------------
(((....)))(((((((((((.....)))))))))))(((((-(((((((((....)))))))).))))))..((((((..(((--....)))..))))))------------------- ( -60.30)
>consensus
GAUUGUUAUCAAGCCGACCCAUU____GGGUCGGCUUUUUUA_UGCCCGCA___UUUCGCCGGCAAUAAAAAACCCGCCGCGACC_GCAGGUAUCGGCGGG___________________
............(((((((((.....)))))))))(((((((.((((.((((....)))).)))).)))))))(((((((.((((....)))).)))))))................... (-22.60 = -25.60 +   3.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,207,177 – 3,207,289
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 40.17
Mean single sequence MFE -46.25
Consensus MFE -15.88
Energy contribution -21.50
Covariance contribution 5.62
Combinations/Pair 1.50
Mean z-score -4.47
Structure conservation index 0.34
SVM decision value 1.42
SVM RNA-class probability 0.952255
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.1712 3207177 112 - 6264404
CGGAGAGCGUCGAGGCAGAGGCCCGCGUACCCGCAAGGGACGCGGGUUUUUUCAUGCCCGGCGAAA---CGCAGGCA-UAAAAAAACCGGCCC----CGAGGGACCGGUUUUCAACAGGU
((.....(((((.(((((((((((((((.(((....))))))))))))))....)))))))))...---))......-....(((((((((((----...))).))))))))........ ( -55.20)
>pau.1282 4175443 110 + 6537648
--GCCUCUCCUCUUCGUGCCCGGCAGUCUACCAAGGCACCCCGCGGACUUUCCUCCGACGACCUAA---GCCGAUGA-AAAAGUUAAAAAAAU----AUUUGCCAAGCGGGAAAUGUUCG
--..........(((((...((((.((((....))))....((((((......)))).))......---))))))))-)...........(((----((((.((....)).))))))).. ( -24.70)
>pf5.2596 4971760 101 - 7074893
-------------------CCCGCCGAUACCUGCUGGUAGCGGCGGGUUUUUUAUUGCCGGUGAAGAACUCCGGGCAAUAAAAAAGCCGAUCCAAAAAAUGGAUCGGCUCGAUAACAAUC
-------------------(((((((.((((....)))).)))))))((((((((((((.(.((.....))).))))))))))))(((((((((.....)))))))))............ ( -52.60)
>pfo.2361 4537213 98 - 6438405
-------------------CCCGCCGAGGCUUGC--GCCGUGGCGGGUUUUUUAUUGCCCGCAGAAAACUGCAGGCA-CAAAAAAGCCGACCCGAAAAACGGGUCGGCUUGAUAACAAUC
-------------------(((((((.(((....--))).)))))))........((((.((((....)))).))))-.....(((((((((((.....))))))))))).......... ( -52.50)
>consensus
___________________CCCGCCGAUACCCGC_GGACGCGGCGGGUUUUUCAUUGCCGGCGAAA___UCCAGGCA_UAAAAAAACCGACCC____AAUGGGUCGGCUUGAUAACAAUC
...................(((((((.((((....)))).)))))))..(((((.((((.(((......))).)))).)))))(((((((((((.....))))))))))).......... (-15.88 = -21.50 +   5.62)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:17:28 2007