Locus 96

Sequence ID pao.802
Location 1,436,537 – 1,436,662
Length 125
Max. P 0.996479
window491 window492 window493 window494

overview

Window 1

Location 1,436,537 – 1,436,650
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.48
Mean single sequence MFE -37.69
Consensus MFE -27.69
Energy contribution -27.83
Covariance contribution 0.14
Combinations/Pair 1.11
Mean z-score -2.36
Structure conservation index 0.73
SVM decision value 2.38
SVM RNA-class probability 0.993176
Prediction RNA

Download alignment: ClustalW | MAF

>pao.802 1436537 113 + 6264404
CCGCCGC-AGCAUUAUUACCGCCAUUCCAGCUA--UGGCGGGUUAGCCAGCGUCC---ACUCCGAACCCGCCCUCGAGGCGGGUUCUU-CGUUCUGUCUCCUGGGCCAAAACCACCGAAC
..(((.(-((........(((((((.......)--))))))..............---.....(((((((((.....)))))))))..-...........)))))).............. ( -38.00)
>pst.2260 4311668 98 + 6397126
CGGCCAG-AUUAUUAUUACCGUCAUUCCAGUCA--UGGCGGGUUAGCCGACGUUU---GCAAAAAACCCGCCCUGGAGGCGGGUUUUU----UCUGUCUCCUGGGC-AA-----------
((((..(-((....))).(((((((.......)--))))))....))))..((((---.....))))..((((.(((((((((.....----))))))))).))))-..----------- ( -38.40)
>pss.989 4213940 98 - 6093698
CGGCCAG-AUUAUUAUUACCGUCAUUCCAGUCA--UGGCGGGUUAGCCGACGUUU---GCCAAAAACCCGCCCUGGAGGCGGGUUUCU----UCUGUCUCCCGGGC-AA-----------
((((..(-((....))).(((((((.......)--))))))....))))..((((---.....))))..((((.(((((((((.....----))))))))).))))-..----------- ( -38.40)
>pel.1698 2767291 101 - 5888780
CCGCCAGCAUUAUUAUUACCGCCAUUAUCGGUU--UGGCGGGCUAGCGCGUACGU---GCACCGAACCCGCCCUGGAGGCGGGUUUUUUCUCUCUGACUCCUGGGC--------------
...((((...........((((((.........--))))))....((((....))---))...(((((((((.....)))))))))..............))))..-------------- ( -36.70)
>pf5.1854 3504933 99 - 7074893
CCAGCCA-AGCAUUAUUACCGCCAUUCC--UUA-UUGGCGGGCUUGCUGACGACU---GCACCCAACCCGCCCUGGAGGCGGGUUUUUUCUCUCUGUCUCCCGGGC--------------
.((((.(-(((.......((((((....--...-.))))))))))))))......---...........((((.(((((((((.........))))))))).))))-------------- ( -39.71)
>pfo.1531 2997812 103 + 6438405
CCAGCCA-AGCAUUAUUACCGCCAUUCC--UCAUUUGGCGGGCUAGCUCACGACUGCAGCACCCAACCCGCCCUAGAGGCGGGUUUUUAUUUUCUGUCUCCGGGGU--------------
.......-..........((((((....--.....))))))(((.((........))))).........((((..((((((((.........))))))))..))))-------------- ( -34.90)
>consensus
CCGCCAG_AGCAUUAUUACCGCCAUUCCAGUCA__UGGCGGGCUAGCCGACGUCU___GCACCAAACCCGCCCUGGAGGCGGGUUUUU_CU_UCUGUCUCCUGGGC______________
..................((((((...........))))))............................((((.(((((((((.........))))))))).)))).............. (-27.69 = -27.83 +   0.14)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,436,537 – 1,436,650
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 72.48
Mean single sequence MFE -40.25
Consensus MFE -23.64
Energy contribution -23.95
Covariance contribution 0.31
Combinations/Pair 1.11
Mean z-score -2.29
Structure conservation index 0.59
SVM decision value 2.23
SVM RNA-class probability 0.990782
Prediction RNA

Download alignment: ClustalW | MAF

>pao.802 1436537 113 - 6264404
GUUCGGUGGUUUUGGCCCAGGAGACAGAACG-AAGAACCCGCCUCGAGGGCGGGUUCGGAGU---GGACGCUGGCUAACCCGCCA--UAGCUGGAAUGGCGGUAAUAAUGCU-GCGGCGG
(((.(.((((.((.((((.(....)......-..(((((((((.....))))))))))).))---.)).)))).).)))(((((.--...(......)((((((....))))-))))))) ( -46.80)
>pst.2260 4311668 98 - 6397126
-----------UU-GCCCAGGAGACAGA----AAAAACCCGCCUCCAGGGCGGGUUUUUUGC---AAACGUCGGCUAACCCGCCA--UGACUGGAAUGACGGUAAUAAUAAU-CUGGCCG
-----------((-((...(....)..(----(((((((((((.....))))))))))))))---))....((((((........--..((((......)))).........-.)))))) ( -35.25)
>pss.989 4213940 98 + 6093698
-----------UU-GCCCGGGAGACAGA----AGAAACCCGCCUCCAGGGCGGGUUUUUGGC---AAACGUCGGCUAACCCGCCA--UGACUGGAAUGACGGUAAUAAUAAU-CUGGCCG
-----------((-(((..(....)...----(((((((((((.....))))))))))))))---))....((((((........--..((((......)))).........-.)))))) ( -37.45)
>pel.1698 2767291 101 + 5888780
--------------GCCCAGGAGUCAGAGAGAAAAAACCCGCCUCCAGGGCGGGUUCGGUGC---ACGUACGCGCUAGCCCGCCA--AACCGAUAAUGGCGGUAAUAAUAAUGCUGGCGG
--------------((((.....((.....))...((((((((.....)))))))).)).))---.......(((((((((((((--.........))))))..........))))))). ( -38.40)
>pf5.1854 3504933 99 + 7074893
--------------GCCCGGGAGACAGAGAGAAAAAACCCGCCUCCAGGGCGGGUUGGGUGC---AGUCGUCAGCAAGCCCGCCAA-UAA--GGAAUGGCGGUAAUAAUGCU-UGGCUGG
--------------((((.(....)..........((((((((.....)))))))))))).(---(((((..((((...((((((.-...--....))))))......))))-)))))). ( -42.90)
>pfo.1531 2997812 103 - 6438405
--------------ACCCCGGAGACAGAAAAUAAAAACCCGCCUCUAGGGCGGGUUGGGUGCUGCAGUCGUGAGCUAGCCCGCCAAAUGA--GGAAUGGCGGUAAUAAUGCU-UGGCUGG
--------------((((.(....)..........((((((((.....))))))))))))....(((((..((((....((((((.....--....)))))).......)))-)))))). ( -40.70)
>consensus
______________GCCCAGGAGACAGA_AG_AAAAACCCGCCUCCAGGGCGGGUUCGGUGC___AGACGUCGGCUAACCCGCCA__UAACUGGAAUGGCGGUAAUAAUAAU_CUGGCGG
..............(((..(....)..........((((((((.....)))))))).......................((((((...........)))))).............))).. (-23.64 = -23.95 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,436,548 – 1,436,662
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 71.07
Mean single sequence MFE -36.12
Consensus MFE -27.69
Energy contribution -27.83
Covariance contribution 0.14
Combinations/Pair 1.11
Mean z-score -2.83
Structure conservation index 0.77
SVM decision value 2.29
SVM RNA-class probability 0.991760
Prediction RNA

Download alignment: ClustalW | MAF

>pao.802 1436548 114 + 6264404
UUAUUACCGCCAUUCCAGCUA--UGGCGGGUUAGCCAGCGUCC---ACUCCGAACCCGCCCUCGAGGCGGGUUCUU-CGUUCUGUCUCCUGGGCCAAAACCACCGAACCGGGAGAACAGC
......(((((((.......)--))))))..............---.....(((((((((.....)))))))))..-....(((((((((((..(.........)..))))))).)))). ( -46.40)
>pst.2260 4311679 87 + 6397126
UUAUUACCGUCAUUCCAGUCA--UGGCGGGUUAGCCGACGUUU---GCAAAAAACCCGCCCUGGAGGCGGGUUUUU----UCUGUCUCCUGGGC-AA-----------------------
......(((((((.......)--))))))((.(((....))).---)).........((((.(((((((((.....----))))))))).))))-..----------------------- ( -33.70)
>pss.989 4213951 87 - 6093698
UUAUUACCGUCAUUCCAGUCA--UGGCGGGUUAGCCGACGUUU---GCCAAAAACCCGCCCUGGAGGCGGGUUUCU----UCUGUCUCCCGGGC-AA-----------------------
......(((((((.......)--))))))..........((((---.....))))..((((.(((((((((.....----))))))))).))))-..----------------------- ( -33.70)
>pel.1698 2767303 89 - 5888780
UUAUUACCGCCAUUAUCGGUU--UGGCGGGCUAGCGCGUACGU---GCACCGAACCCGCCCUGGAGGCGGGUUUUUUCUCUCUGACUCCUGGGC--------------------------
......((((((.........--))))))(((.((((....))---))...(((((((((.....))))))))).................)))-------------------------- ( -33.50)
>pf5.1854 3504944 88 - 7074893
UUAUUACCGCCAUUCC--UUA-UUGGCGGGCUUGCUGACGACU---GCACCCAACCCGCCCUGGAGGCGGGUUUUUUCUCUCUGUCUCCCGGGC--------------------------
......((((((....--...-.))))))...(((........---)))........((((.(((((((((.........))))))))).))))-------------------------- ( -34.50)
>pfo.1531 2997823 92 + 6438405
UUAUUACCGCCAUUCC--UCAUUUGGCGGGCUAGCUCACGACUGCAGCACCCAACCCGCCCUAGAGGCGGGUUUUUAUUUUCUGUCUCCGGGGU--------------------------
......((((((....--.....))))))(((.((........))))).........((((..((((((((.........))))))))..))))-------------------------- ( -34.90)
>consensus
UUAUUACCGCCAUUCCAGUCA__UGGCGGGCUAGCCGACGUCU___GCACCAAACCCGCCCUGGAGGCGGGUUUUU_CU_UCUGUCUCCUGGGC__________________________
......((((((...........))))))............................((((.(((((((((.........))))))))).)))).......................... (-27.69 = -27.83 +   0.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,436,548 – 1,436,662
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 71.07
Mean single sequence MFE -36.55
Consensus MFE -22.40
Energy contribution -22.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.61
SVM decision value 2.70
SVM RNA-class probability 0.996479
Prediction RNA

Download alignment: ClustalW | MAF

>pao.802 1436548 114 - 6264404
GCUGUUCUCCCGGUUCGGUGGUUUUGGCCCAGGAGACAGAACG-AAGAACCCGCCUCGAGGGCGGGUUCGGAGU---GGACGCUGGCUAACCCGCCA--UAGCUGGAAUGGCGGUAAUAA
(((((..(.((((((.(((((..((((((..(....)...((.-..(((((((((.....)))))))))...))---.......)))))).))))).--.)))))).)..)))))..... ( -50.20)
>pst.2260 4311679 87 - 6397126
-----------------------UU-GCCCAGGAGACAGA----AAAAACCCGCCUCCAGGGCGGGUUUUUUGC---AAACGUCGGCUAACCCGCCA--UGACUGGAAUGACGGUAAUAA
-----------------------((-((...(....)..(----(((((((((((.....))))))))))))))---)).(((.(((......))))--))((((......))))..... ( -32.50)
>pss.989 4213951 87 + 6093698
-----------------------UU-GCCCGGGAGACAGA----AGAAACCCGCCUCCAGGGCGGGUUUUUGGC---AAACGUCGGCUAACCCGCCA--UGACUGGAAUGACGGUAAUAA
-----------------------((-(((..(....)...----(((((((((((.....))))))))))))))---)).(((.(((......))))--))((((......))))..... ( -34.70)
>pel.1698 2767303 89 + 5888780
--------------------------GCCCAGGAGUCAGAGAGAAAAAACCCGCCUCCAGGGCGGGUUCGGUGC---ACGUACGCGCUAGCCCGCCA--AACCGAUAAUGGCGGUAAUAA
--------------------------((((.((((.(.(.(........)).).)))).))))(((((.(((((---......))))))))))((((--.........))))........ ( -31.70)
>pf5.1854 3504944 88 + 7074893
--------------------------GCCCGGGAGACAGAGAGAAAAAACCCGCCUCCAGGGCGGGUUGGGUGC---AGUCGUCAGCAAGCCCGCCAA-UAA--GGAAUGGCGGUAAUAA
--------------------------((((.(....)..........((((((((.....))))))))))))((---........))....((((((.-...--....))))))...... ( -34.50)
>pfo.1531 2997823 92 - 6438405
--------------------------ACCCCGGAGACAGAAAAUAAAAACCCGCCUCUAGGGCGGGUUGGGUGCUGCAGUCGUGAGCUAGCCCGCCAAAUGA--GGAAUGGCGGUAAUAA
--------------------------((((.(....)..........((((((((.....))))))))))))(((((........)).)))((((((.....--....))))))...... ( -35.70)
>consensus
__________________________GCCCAGGAGACAGA_AG_AAAAACCCGCCUCCAGGGCGGGUUCGGUGC___AGACGUCGGCUAACCCGCCA__UAACUGGAAUGGCGGUAAUAA
...............................(....)..........((((((((.....)))))))).......................((((((...........))))))...... (-22.40 = -22.73 +   0.33)

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 21:12:15 2007