Locus 68

Sequence ID pao.2544
Location 4,785,858 – 4,786,020
Length 162
Max. P 0.969353
window395 window396 window397 window398 window399

overview

Window 5

Location 4,785,858 – 4,785,961
Length 103
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 74.72
Mean single sequence MFE -27.52
Consensus MFE -9.48
Energy contribution -10.03
Covariance contribution 0.56
Combinations/Pair 1.21
Mean z-score -2.79
Structure conservation index 0.34
SVM decision value 1.64
SVM RNA-class probability 0.969353
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2544 4785858 103 + 6264404
CUCGGGAAUCCCUCCAAACUGGUGGGCGGCAUUCUCUACGUCUGCCACCUUGCUGUCAAGAGUUUUCUCU-UAAAAAACCUGAACUUAG--GUUUCAAC-----AGCAACU
...((....(((.((.....)).))).((((..(.....)..)))).))(((((((.(((((....))))-)...(((((((....)))--))))..))-----))))).. ( -31.80)
>pau.415 5796687 103 - 6537648
CUCGGGAAUCCCUCCAAACUGGUGGGCGGCAUUCUCUACGUCUGCCACCUUGCUGUCAAGAGUUUUCUCU-UAAAAAACCUGAACUUAG--GUUUCAAC-----AGCAACU
...((....(((.((.....)).))).((((..(.....)..)))).))(((((((.(((((....))))-)...(((((((....)))--))))..))-----))))).. ( -31.80)
>pf5.3377 6380851 102 + 7074893
CUCGGGAACCCCUCCUAA--GCGAGGCGACAUUCUACAU-CAUGCCACCCUUCUGUCAAGCAUUUUCUCA-AUAAAAUCUUGAGGUUAGCUGCGUUGAC-----CUCGCUU
...((((.....))))((--((((((((((.........-..((.((......)).))(((.(..(((((-(.......))))))..))))..)))).)-----))))))) ( -27.50)
>pfo.3001 5723911 103 + 6438405
CUCGGGAACCCCUCCUAA--UCAGGCCGGCAUUCUAUAC-CAUGCCAAACCUCUGUCAAGCAUUUUCUCAUUUAAAAACCUGAGGUUAGCUGCAUUGAC-----ACCACCC
...(((............--..(((..(((((.......-.)))))...))).(((((((((...(((((..........))))).....))).)))))-----)...))) ( -22.80)
>psp.2682 5244545 107 + 5928787
CUCGGGAACCCCUCCUAA--GCGAGGCAGCAUUCUCAACUCAUGCCACCCUUCUGUCAACCUUUUUCUCA-GUAAAAACCUGAGGUUACAUGCGUUGACUACU-ACCACCC
...(((....((((....--..))))..((((.........))))..)))....(((((((....(((((-(.......))))))......).))))))....-....... ( -23.40)
>pst.387 5722721 108 - 6397126
CUCGGGAACCCCUCCUAA--GCGAGGCAGCAUUCUCAACUUAUGCUACCCUUCUGUCAACCUUUUUCUCA-GUAAAAACCUGAGGUUACAUGCGUUGACUACUAACCGCUU
...((((.....))))((--(((.((.(((((.........))))).)).....(((((((....(((((-(.......))))))......).)))))).......))))) ( -27.80)
>consensus
CUCGGGAACCCCUCCUAA__GCGAGGCGGCAUUCUCUAC_CAUGCCACCCUUCUGUCAAGCAUUUUCUCA_UUAAAAACCUGAGGUUAG_UGCGUUGAC_____ACCACCU
((((((....(((..........))).(((((.........)))))................................))))))........................... ( -9.48 = -10.03 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,785,858 – 4,785,961
Length 103
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 74.72
Mean single sequence MFE -33.75
Consensus MFE -15.82
Energy contribution -14.88
Covariance contribution -0.94
Combinations/Pair 1.37
Mean z-score -2.15
Structure conservation index 0.47
SVM decision value 1.05
SVM RNA-class probability 0.906205
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2544 4785858 103 - 6264404
AGUUGCU-----GUUGAAAC--CUAAGUUCAGGUUUUUUA-AGAGAAAACUCUUGACAGCAAGGUGGCAGACGUAGAGAAUGCCGCCCACCAGUUUGGAGGGAUUCCCGAG
..(((((-----((((((((--((......)))))))..(-((((....)))))))))))))(((((((..(.....)..)))))))..((.....)).(((...)))... ( -35.80)
>pau.415 5796687 103 + 6537648
AGUUGCU-----GUUGAAAC--CUAAGUUCAGGUUUUUUA-AGAGAAAACUCUUGACAGCAAGGUGGCAGACGUAGAGAAUGCCGCCCACCAGUUUGGAGGGAUUCCCGAG
..(((((-----((((((((--((......)))))))..(-((((....)))))))))))))(((((((..(.....)..)))))))..((.....)).(((...)))... ( -35.80)
>pf5.3377 6380851 102 - 7074893
AAGCGAG-----GUCAACGCAGCUAACCUCAAGAUUUUAU-UGAGAAAAUGCUUGACAGAAGGGUGGCAUG-AUGUAGAAUGUCGCCUCGC--UUAGGAGGGGUUCCCGAG
((((((.-----(((((.(((......(((((.......)-))))....)))))))).....((((((((.-.......))))))))))))--))....(((...)))... ( -34.10)
>pfo.3001 5723911 103 - 6438405
GGGUGGU-----GUCAAUGCAGCUAACCUCAGGUUUUUAAAUGAGAAAAUGCUUGACAGAGGUUUGGCAUG-GUAUAGAAUGCCGGCCUGA--UUAGGAGGGGUUCCCGAG
(((...(-----(((((.(((......((((..(....)..))))....))))))))).(((((.(((((.-.......))))))))))..--............)))... ( -29.10)
>psp.2682 5244545 107 - 5928787
GGGUGGU-AGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAGGUUGACAGAAGGGUGGCAUGAGUUGAGAAUGCUGCCUCGC--UUAGGAGGGGUUCCCGAG
(.(.(((-((((.(((((.(((((.((((...(((...((-(........))).)))....)))).))))).)))))...))))))).).)--......(((...)))... ( -34.80)
>pst.387 5722721 108 + 6397126
AAGCGGUUAGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAGGUUGACAGAAGGGUAGCAUAAGUUGAGAAUGCUGCCUCGC--UUAGGAGGGGUUCCCGAG
(((((.......((((((.(.......(((((.......)-)))).....)))))))....(((((((((.........))))))))))))--))....(((...)))... ( -32.90)
>consensus
AGGUGGU_____GUCAACGCA_CUAACCUCAGGUUUUUAA_UGAGAAAAAGCUUGACAGAAGGGUGGCAUA_GUAGAGAAUGCCGCCCCGC__UUAGGAGGGGUUCCCGAG
............(((((..........(((............))).......))))).....((((((((.........))))))))............(((...)))... (-15.82 = -14.88 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,785,898 – 4,786,000
Length 102
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 69.72
Mean single sequence MFE -29.00
Consensus MFE -4.89
Energy contribution -5.59
Covariance contribution 0.69
Combinations/Pair 1.14
Mean z-score -2.54
Structure conservation index 0.17
SVM decision value 0.37
SVM RNA-class probability 0.707437
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2544 4785898 102 + 6264404
UCUGCCACCUUGCUGUCAAGAGUUUUCUCU-UAAAAAACCUGAACUUAG--GUUUCAAC-----AGCAACUUCAUGGUAGGAGUCUUUCAGCC-UUCCCCCUGCGAAGCGG
(((((((..(((((((.(((((....))))-)...(((((((....)))--))))..))-----))))).....))))))).(.(((((((..-......))).))))).. ( -27.50)
>pss.2760 5420623 102 + 6093698
CAUGCUACCCUUCUGUCAACCUUUUUCUCA-GUAAAAACCUGAGGUUACAUGCGUUGACUACU-ACCACUUCGUUCGUGAGACUUUC-------ACCUCACUGCGAAGCGG
..............(((((((....(((((-(.......))))))......).))))))....-.((.((((((..(((((......-------..))))).)))))).)) ( -29.70)
>pf5.3377 6380888 103 + 7074893
CAUGCCACCCUUCUGUCAAGCAUUUUCUCA-AUAAAAUCUUGAGGUUAGCUGCGUUGAC-----CUCGCUUCGCGACGCCGACUUCGUGAA--GUCUUCGCUGCGGAGCGG
..............((((((((...(((((-(.......)))))).....))).)))))-----..(((((((((.((..(((((....))--)))..)).))))))))). ( -34.20)
>pfo.3001 5723948 104 + 6438405
CAUGCCAAACCUCUGUCAAGCAUUUUCUCAUUUAAAAACCUGAGGUUAGCUGCAUUGAC-----ACCACCCCACUGCAUCAACCUUUUCAG--GUCUUCGCUGUGGAGCGG
.............(((((((((...(((((..........))))).....))).)))))-----)((.(.((((.((....((((....))--))....)).)))).).)) ( -25.10)
>psp.2682 5244583 102 + 5928787
CAUGCCACCCUUCUGUCAACCUUUUUCUCA-GUAAAAACCUGAGGUUACAUGCGUUGACUACU-ACCACCCCAUUCGCGAGACUUUC-------ACCUCGCUGCGAAGCGG
.......((((((.(((((((....(((((-(.......))))))......).))))))....-............(((((......-------..)))))...)))).)) ( -26.30)
>pst.387 5722759 103 - 6397126
UAUGCUACCCUUCUGUCAACCUUUUUCUCA-GUAAAAACCUGAGGUUACAUGCGUUGACUACUAACCGCUUCGUUCGCGAGACUUUC-------ACCUCACUGCGAAGCGG
..............(((((((....(((((-(.......))))))......).))))))......(((((((((..(.(((......-------..))).).))))))))) ( -31.20)
>consensus
CAUGCCACCCUUCUGUCAACCUUUUUCUCA_GUAAAAACCUGAGGUUACAUGCGUUGAC_____ACCACCUCGUUCGCGAGACUUUC_______ACCUCGCUGCGAAGCGG
..............((((((.....((((............))))........)))))).........................................((((...)))) ( -4.89 =  -5.59 +   0.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,785,898 – 4,786,000
Length 102
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 69.72
Mean single sequence MFE -34.09
Consensus MFE -10.68
Energy contribution -11.22
Covariance contribution 0.53
Combinations/Pair 1.61
Mean z-score -2.36
Structure conservation index 0.31
SVM decision value 1.27
SVM RNA-class probability 0.939020
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2544 4785898 102 - 6264404
CCGCUUCGCAGGGGGAA-GGCUGAAAGACUCCUACCAUGAAGUUGCU-----GUUGAAAC--CUAAGUUCAGGUUUUUUA-AGAGAAAACUCUUGACAGCAAGGUGGCAGA
(((((....(((((...-..........))))).........(((((-----((((((((--((......)))))))..(-((((....)))))))))))))))))).... ( -29.32)
>pss.2760 5420623 102 - 6093698
CCGCUUCGCAGUGAGGU-------GAAAGUCUCACGAACGAAGUGGU-AGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAGGUUGACAGAAGGGUAGCAUG
((((((((..(((((((-------....)))))))...)))))))).-....((((((.(.......(((((.......)-)))).....))))))).............. ( -33.30)
>pf5.3377 6380888 103 - 7074893
CCGCUCCGCAGCGAAGAC--UUCACGAAGUCGGCGUCGCGAAGCGAG-----GUCAACGCAGCUAACCUCAAGAUUUUAU-UGAGAAAAUGCUUGACAGAAGGGUGGCAUG
(((((((((.((((.(((--((....)))))....))))...)))..-----(((((.(((......(((((.......)-))))....))))))))....)))))).... ( -35.50)
>pfo.3001 5723948 104 - 6438405
CCGCUCCACAGCGAAGAC--CUGAAAAGGUUGAUGCAGUGGGGUGGU-----GUCAAUGCAGCUAACCUCAGGUUUUUAAAUGAGAAAAUGCUUGACAGAGGUUUGGCAUG
(((((((((.(((..(((--((....)))))..))).))))))))).-----....((((....((((((..(((.....((......))....))).))))))..)))). ( -39.80)
>psp.2682 5244583 102 - 5928787
CCGCUUCGCAGCGAGGU-------GAAAGUCUCGCGAAUGGGGUGGU-AGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAGGUUGACAGAAGGGUGGCAUG
((((((((..(((((((-------....)))))))...)))))))).-....((((((.(.......(((((.......)-)))).....))))))).............. ( -31.80)
>pst.387 5722759 103 + 6397126
CCGCUUCGCAGUGAGGU-------GAAAGUCUCGCGAACGAAGCGGUUAGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAGGUUGACAGAAGGGUAGCAUA
((((((((..(((((((-------....)))))))...))))))))......((((((.(.......(((((.......)-)))).....))))))).............. ( -34.80)
>consensus
CCGCUUCGCAGCGAGGA_______GAAAGUCUCACGAACGAAGUGGU_____GUCAACGCAUCUAACCUCAGGUUUUUAC_UGAGAAAAAGCUUGACAGAAGGGUGGCAUG
((((((((....((((.............)))).....))))))))......(((((..........((((.((....)).)))).......))))).............. (-10.68 = -11.22 +   0.53)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,785,918 – 4,786,020
Length 102
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 69.71
Mean single sequence MFE -33.13
Consensus MFE -10.10
Energy contribution -10.64
Covariance contribution 0.53
Combinations/Pair 1.64
Mean z-score -2.37
Structure conservation index 0.30
SVM decision value 1.25
SVM RNA-class probability 0.936421
Prediction RNA

Download alignment: ClustalW | MAF

>pao.2544 4785918 102 - 6264404
UGGUUUGCAUAGAAUGGCGCCCGCUUCGCAGGGGGAA-GGCUGAAAGACUCCUACCAUGAAGUUGCU-----GUUGAAAC--CUAAGUUCAGGUUUUUUA-AGAGAAAACU
.(((((.(....(((((((...((((((..((((((.-(.........))))).)).))))))))))-----)))(((((--((......)))))))...-...).))))) ( -22.20)
>pss.2760 5420643 99 - 6093698
---UUUACAUAGAAUGGCGCCCGCUUCGCAGUGAGGU-------GAAAGUCUCACGAACGAAGUGGU-AGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAG
---.((((((.(..((((..((((((((..(((((((-------....)))))))...)))))))).-....))))...))))))).(((((.......)-))))...... ( -34.30)
>pf5.3377 6380908 101 - 7074893
--GGUUGCAUAGAAUGGCGCCCGCUCCGCAGCGAAGAC--UUCACGAAGUCGGCGUCGCGAAGCGAG-----GUCAACGCAGCUAACCUCAAGAUUUUAU-UGAGAAAAUG
--((((((......((((.(.((((.(((.(((..(((--((....)))))..))).))).)))).)-----))))..))))))...(((((.......)-))))...... ( -35.40)
>pfo.3001 5723968 100 - 6438405
----UUGCAUAGAAUGGCGCCCGCUCCACAGCGAAGAC--CUGAAAAGGUUGAUGCAGUGGGGUGGU-----GUCAAUGCAGCUAACCUCAGGUUUUUAAAUGAGAAAAUG
----((((((....(((((((.(((((((.(((..(((--((....)))))..))).))))))))))-----)))))))))).....((((..(....)..))))...... ( -40.40)
>psp.2682 5244603 97 - 5928787
-----UACAUAGAAUGGCGCCCGCUUCGCAGCGAGGU-------GAAAGUCUCGCGAAUGGGGUGGU-AGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAG
-----(((((.(..((((..((((((((..(((((((-------....)))))))...)))))))).-....))))...))))))..(((((.......)-))))...... ( -32.00)
>pst.387 5722779 98 + 6397126
-----UACAUAGAAUGGCGCCCGCUUCGCAGUGAGGU-------GAAAGUCUCGCGAACGAAGCGGUUAGUAGUCAACGCAUGUAACCUCAGGUUUUUAC-UGAGAAAAAG
-----(((((.(..((((((((((((((..(((((((-------....)))))))...))))))))...)).))))...))))))..(((((.......)-))))...... ( -34.50)
>consensus
____UUACAUAGAAUGGCGCCCGCUUCGCAGCGAGGA_______GAAAGUCUCACGAACGAAGUGGU_____GUCAACGCAUCUAACCUCAGGUUUUUAC_UGAGAAAAAG
..............((((..((((((((....((((.............)))).....))))))))......))))...........((((.((....)).))))...... (-10.10 = -10.64 +   0.53)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:10:35 2007