Locus 77

Sequence ID pao.506
Location 901,679 – 901,827
Length 148
Max. P 0.992278
window431 window432 window433 window434 window435

overview

Window 1

Location 901,679 – 901,757
Length 78
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 75.09
Mean single sequence MFE -35.77
Consensus MFE -20.74
Energy contribution -20.28
Covariance contribution -0.45
Combinations/Pair 1.27
Mean z-score -1.53
Structure conservation index 0.58
SVM decision value 0.33
SVM RNA-class probability 0.691071
Prediction RNA

Download alignment: ClustalW | MAF

>pao.506 901679 78 + 6264404
GGCGAUCCUGUUCUAUCUGACAGUCGUUUCGGGUUUACAGGCAUCCCCUAGCGACUGCU-----------------------------A-G----CCGCA-UUAAGCAGCUAG----
((.((((((((...((((((........))))))..))))).))).)).........((-----------------------------(-(----(.((.-....)).)))))---- ( -24.90)
>pss.2544 1093647 110 - 6093698
GACGAUCCUGUUCUAUAUGACAAUCAUUUCGGGUUUACAGGCAUCCCCUGAUGAUUGCUGGAGCCGAAGCUACCAGAAG-GAAGGCUAGCA----CCGC--UUACGCGGCGAGAGCG
.....((((...........((((((((..(((...........)))..))))))))(((((((....))).)))).))-))..(((..(.----((((--....)))).)..))). ( -37.40)
>pel.378 791534 110 + 5888780
GACGAUCCUGUUCUGUAUGACAAUCAUUUCGGGUUUACAGGCAUCCCCUGAUGAUUGCUGGAGCCGAAGCUACCAGGAG-AGCGGGCUCAG----CUGC--UUACGCAGCGAGAGCG
.......(((((((......((((((((..(((...........)))..))))))))(((((((....))).)))).))-)))))((((.(----((((--....)))))..)))). ( -44.60)
>ppk.2749 791616 115 - 6181863
GACGAUCCUGUUCUGUAUGACAAUCAGUUCGGGUUUACAGGCAUCCCCUAGUGAUUGCUGGAGCCGAAGCUACCAGAAGCAACGGGUCAAGAGGACUGC--UUACGCAGCCAGCUUG
...((.((((..(((.((....)))))..)))).)).(((((...(((...((....(((((((....))).))))...))..)))......((.((((--....)))))).))))) ( -36.20)
>pfo.416 878990 110 + 6438405
GGCGAUUCUGUUCUAUAUGACAAUCAUUUUGGGUUUACAGACAUCCCCUGAUGAUUGCUGGACCCGAAGGUACCAGGAG-UGCAUGUCA-G----CUGCAAUUAAGCAGCGAGAGC-
.........(((((...(((((....((((((((((((((.((((....)))).))).)))))))))))((((.....)-))).)))))-(----((((......))))).)))))- ( -38.00)
>pst.2683 1310716 106 - 6397126
GACGAUCCUGUUCUAUAUGACAAUCAUUUUGGGUUUACAGGCAUCCCCUGAUGAUUGCUGGAGCCGAAGCUACCAGAAG-UGCGGCUAG-G----CUGC--UUACGCAGCUAG---U
.......((((.((......((((((((..(((...........)))..))))))))(((((((....))).)))).))-.))))...(-(----((((--....))))))..---. ( -33.50)
>consensus
GACGAUCCUGUUCUAUAUGACAAUCAUUUCGGGUUUACAGGCAUCCCCUGAUGAUUGCUGGAGCCGAAGCUACCAGAAG_AGCGGGUAA_G____CUGC__UUACGCAGCGAGAGCG
....................((((((((..(((...........)))..))))))))(((((((....))).))))...................((((......))))........ (-20.74 = -20.28 +  -0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 901,679 – 901,757
Length 78
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 75.09
Mean single sequence MFE -37.31
Consensus MFE -23.44
Energy contribution -23.18
Covariance contribution -0.26
Combinations/Pair 1.22
Mean z-score -2.54
Structure conservation index 0.63
SVM decision value 2.32
SVM RNA-class probability 0.992278
Prediction RNA

Download alignment: ClustalW | MAF

>pao.506 901679 78 - 6264404
----CUAGCUGCUUAA-UGCGG----C-U-----------------------------AGCAGUCGCUAGGGGAUGCCUGUAAACCCGAAACGACUGUCAGAUAGAACAGGAUCGCC
----((((((((....-.))))----)-)-----------------------------))((((((...(((..((....))..)))....))))))...(((........)))... ( -26.80)
>pss.2544 1093647 110 + 6093698
CGCUCUCGCCGCGUAA--GCGG----UGCUAGCCUUC-CUUCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGCCUGUAAACCCGAAAUGAUUGUCAUAUAGAACAGGAUCGUC
.(((..((((((....--))))----))..)))..((-((.((((.(((....)))))))(((((((..(((..((....))..)))...)))))))...........))))..... ( -43.30)
>pel.378 791534 110 - 5888780
CGCUCUCGCUGCGUAA--GCAG----CUGAGCCCGCU-CUCCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGCCUGUAAACCCGAAAUGAUUGUCAUACAGAACAGGAUCGUC
.((((..(((((....--))))----).))))..((.-.((((((.(((....))).).((((((((..(((..((....))..)))...)))))))).........)))))..)). ( -43.50)
>ppk.2749 791616 115 + 6181863
CAAGCUGGCUGCGUAA--GCAGUCCUCUUGACCCGUUGCUUCUGGUAGCUUCGGCUCCAGCAAUCACUAGGGGAUGCCUGUAAACCCGAACUGAUUGUCAUACAGAACAGGAUCGUC
((((..((((((....--))))))..)))).(((..((.((((((.(((....))))))).)).))...)))(((.(((((........((.....))........))))))))... ( -40.69)
>pfo.416 878990 110 - 6438405
-GCUCUCGCUGCUUAAUUGCAG----C-UGACAUGCA-CUCCUGGUACCUUCGGGUCCAGCAAUCAUCAGGGGAUGUCUGUAAACCCAAAAUGAUUGUCAUAUAGAACAGAAUCGCC
-((....(((((......))))----)-((((.....-...((((.(((....))))))).((((((...(((...........)))...))))))))))..............)). ( -33.30)
>pst.2683 1310716 106 + 6397126
A---CUAGCUGCGUAA--GCAG----C-CUAGCCGCA-CUUCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGCCUGUAAACCCAAAAUGAUUGUCAUAUAGAACAGGAUCGUC
.---((((((((....--))))----.-))))((...-...((((.(((....)))))))(((((((..(((..((....))..)))...)))))))............))...... ( -36.30)
>consensus
CGCUCUCGCUGCGUAA__GCAG____C_UGACCCGCA_CUUCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGCCUGUAAACCCGAAAUGAUUGUCAUAUAGAACAGGAUCGUC
........((((......))))...................((((.(((....)))))))(((((((..(((..((....))..)))...))))))).................... (-23.44 = -23.18 +  -0.26)

alignment

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secondary structure

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dotplot

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Window 3

Location 901,719 – 901,787
Length 68
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 70.49
Mean single sequence MFE -35.75
Consensus MFE -16.43
Energy contribution -16.33
Covariance contribution -0.09
Combinations/Pair 1.16
Mean z-score -2.39
Structure conservation index 0.46
SVM decision value 2.16
SVM RNA-class probability 0.989431
Prediction RNA

Download alignment: ClustalW | MAF

>pao.506 901719 68 - 6264404
CU--UAUAGUUGCCAACGACGACAACUACGC---U---------CUAGCUGCUUAA-UGCGG----C-U-----------------------------AGCAGUCGCUAGGGGAUGC
..--....((((....))))..(..((((((---(---------((((((((....-.))))----)-)-----------------------------)).)).)).)))..).... ( -22.20)
>pel.378 791574 107 - 5888780
UUUCUAUAGUUGCCAAUGACGAAAACUACGA---GGGCUACGCUCUCGCUGCGUAA--GCAG----CUGAGCCCGCU-CUCCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGC
............((..(((.((.......((---((((...((((..(((((....--))))----).))))..)))-)))((((.(((....)))))))...)).)))..)).... ( -44.20)
>ppk.2749 791656 114 + 6181863
UUU-UAUAGUUGCCAAUGACGAAAACUACGGCGCGGAGUACAAGCUGGCUGCGUAA--GCAGUCCUCUUGACCCGUUGCUUCUGGUAGCUUCGGCUCCAGCAAUCACUAGGGGAUGC
...-....(((.((...............(((((((.((.((((..((((((....--))))))..))))))))).)))).((((.(((....))))))).........)).))).. ( -41.70)
>pfo.416 879030 105 - 6438405
UACUUAUAGUUGCCAAUGACGACCAAUACGG---UGCU---GCUCUCGCUGCUUAAUUGCAG----C-UGACAUGCA-CUCCUGGUACCUUCGGGUCCAGCAAUCAUCAGGGGAUGU
............((..(((.((.......((---((((---(.((..(((((......))))----)-.)))).)))-)).((((.(((....)))))))...)).)))..)).... ( -34.60)
>psp.2452 1124262 103 + 5928787
UUUCUAUAGUUGCCAAUGACGAAAACUACGG---UGCUCAA---CUAGCUGCGUAA--GCAG----C-CUAGCCGCA-CUUCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGU
............((..(((.((.......((---(((....---((((((((....--))))----.-))))..)))-)).((((.(((....)))))))...)).)))..)).... ( -35.90)
>pst.2683 1310756 103 + 6397126
UUUCUAUAGUUGCCAAUGACGAAAACUACGG---UGCUCAA---CUAGCUGCGUAA--GCAG----C-CUAGCCGCA-CUUCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGC
............((..(((.((.......((---(((....---((((((((....--))))----.-))))..)))-)).((((.(((....)))))))...)).)))..)).... ( -35.90)
>consensus
UUUCUAUAGUUGCCAAUGACGAAAACUACGG___UGCU_A____CUAGCUGCGUAA__GCAG____C_UGACCCGCA_CUUCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGC
........(((.((..(((.............................((((......))))...................((((.(((....)))))))...)))...)).))).. (-16.43 = -16.33 +  -0.09)

alignment

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secondary structure

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dotplot

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Window 4

Location 901,738 – 901,827
Length 89
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.00
Mean single sequence MFE -35.13
Consensus MFE -20.28
Energy contribution -19.65
Covariance contribution -0.63
Combinations/Pair 1.23
Mean z-score -1.90
Structure conservation index 0.58
SVM decision value 1.00
SVM RNA-class probability 0.898194
Prediction RNA

Download alignment: ClustalW | MAF

>pao.506 901738 89 + 6264404
-----------A-G----CCGCA-UUAAGCAGCUAG---------A---GCGUAGUUGUCGUCGUUGGCAACUAUA--AGUUUGCAGCAGCGAAUUUACGAGUUCUGCUACCAGCUCGGC
-----------.-(----(((..-...((((((.((---------(---((((((((((((....))))))))))(--(((((((....))))))))....))))))))....))))))) ( -32.50)
>pel.378 791613 108 + 5888780
AGCGGGCU---CAG----CUGC--UUACGCAGCGAGAGCGUAGCCC---UCGUAGUUUUCGUCAUUGGCAACUAUAGAAAGUUGCAACAGUGGAUUUACGAGUUCUGUUACCAACUCGGC
.((.((((---(.(----((((--....)))))..))))(((((.(---((((((......((((((((((((......))))))..))))))..)))))))....))))).....).)) ( -39.40)
>ppk.2749 791696 114 - 6181863
AACGGGUC---AAGAGGACUGC--UUACGCAGCCAGCUUGUACUCCGCGCCGUAGUUUUCGUCAUUGGCAACUAUA-AAAGUUGCAACAGUGGAUUUACGAGUUCUGUUACCAACUCGGC
..((((((---(((.((.((((--....))))))..)))).)).))).(((((((......((((((((((((...-..))))))..))))))..))))(((((........)))))))) ( -37.40)
>pf5.484 938531 110 + 7074893
GGAAGGGCUAAG-G----CUGC--UUACGCAGCGAGAGCGUAAUCC---CCGUAGGUUUCGUCAUUGGCAACUAUAGGAAGUUGCAACAGUGGAUUUACGAGUUCUGUUACCAACUCGGC
(((.(.(((...-(----((((--....)))))...))).)..)))---(((((((((....(((((((((((......))))))..))))))))))))(((((........))))))). ( -34.20)
>pfo.416 879069 106 + 6438405
UGCAUGUC---A-G----CUGCAAUUAAGCAGCGAGAGC---AGCA---CCGUAUUGGUCGUCAUUGGCAACUAUAAGUAGUUGCAACAGUGGAUUUACGACUUCUGUUACCAAGUCGGC
(((.(((.---.-(----((((......)))))....))---))))---(((..(((((........(((((((....)))))))(((((.((........)).))))))))))..))). ( -34.50)
>pst.2683 1310795 104 - 6397126
UGCGGCUA---G-G----CUGC--UUACGCAGCUAG---UUGAGCA---CCGUAGUUUUCGUCAUUGGCAACUAUAGAAAGUUGCAACAGUGGAUUUACGAGUUCUGUUACCAACUCGGC
..((((((---(-.----((((--....))))))))---)))....---((((((......((((((((((((......))))))..))))))..))))(((((........))))))). ( -32.80)
>consensus
AGCGGGUC___A_G____CUGC__UUACGCAGCGAGAGCGUAAGCA___CCGUAGUUUUCGUCAUUGGCAACUAUAGAAAGUUGCAACAGUGGAUUUACGAGUUCUGUUACCAACUCGGC
..................((((......)))).............................((((((((((((......))))))..)))))).....((((((........)))))).. (-20.28 = -19.65 +  -0.63)

alignment

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secondary structure

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dotplot

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Window 5

Location 901,738 – 901,827
Length 89
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.00
Mean single sequence MFE -33.74
Consensus MFE -15.74
Energy contribution -15.55
Covariance contribution -0.19
Combinations/Pair 1.15
Mean z-score -2.28
Structure conservation index 0.47
SVM decision value 1.08
SVM RNA-class probability 0.912338
Prediction RNA

Download alignment: ClustalW | MAF

>pao.506 901738 89 - 6264404
GCCGAGCUGGUAGCAGAACUCGUAAAUUCGCUGCUGCAAACU--UAUAGUUGCCAACGACGACAACUACGC---U---------CUAGCUGCUUAA-UGCGG----C-U-----------
...((((..(((((((....((......))))))))).....--..((((((.(......).)))))).))---)---------).((((((....-.))))----)-)----------- ( -29.20)
>pel.378 791613 108 - 5888780
GCCGAGUUGGUAACAGAACUCGUAAAUCCACUGUUGCAACUUUCUAUAGUUGCCAAUGACGAAAACUACGA---GGGCUACGCUCUCGCUGCGUAA--GCAG----CUG---AGCCCGCU
(((...(((....)))..((((((.......((((((((((......))))))....)))).....)))))---))))...((((..(((((....--))))----).)---)))..... ( -35.90)
>ppk.2749 791696 114 + 6181863
GCCGAGUUGGUAACAGAACUCGUAAAUCCACUGUUGCAACUUU-UAUAGUUGCCAAUGACGAAAACUACGGCGCGGAGUACAAGCUGGCUGCGUAA--GCAGUCCUCUU---GACCCGUU
((((((((.(((((((..............)))))((((((..-...)))))).....))...)))).))))((((.((.((((..((((((....--))))))..)))---))))))). ( -41.64)
>pf5.484 938531 110 - 7074893
GCCGAGUUGGUAACAGAACUCGUAAAUCCACUGUUGCAACUUCCUAUAGUUGCCAAUGACGAAACCUACGG---GGAUUACGCUCUCGCUGCGUAA--GCAG----C-CUUAGCCCUUCC
..((((((........))))))..(((((.((((.((((((......))))))..............))))---)))))..(((...(((((....--))))----)-...)))...... ( -33.06)
>pfo.416 879069 106 - 6438405
GCCGACUUGGUAACAGAAGUCGUAAAUCCACUGUUGCAACUACUUAUAGUUGCCAAUGACGACCAAUACGG---UGCU---GCUCUCGCUGCUUAAUUGCAG----C-U---GACAUGCA
((((..((((((((((..(........)..)))))(((((((....)))))))........)))))..)))---)(((---(.((..(((((......))))----)-.---)))).)). ( -32.30)
>pst.2683 1310795 104 + 6397126
GCCGAGUUGGUAACAGAACUCGUAAAUCCACUGUUGCAACUUUCUAUAGUUGCCAAUGACGAAAACUACGG---UGCUCAA---CUAGCUGCGUAA--GCAG----C-C---UAGCCGCA
((((((((.(((((((..............)))))((((((......)))))).....))...)))).)))---)((....---((((((((....--))))----.-)---)))..)). ( -30.34)
>consensus
GCCGAGUUGGUAACAGAACUCGUAAAUCCACUGUUGCAACUUUCUAUAGUUGCCAAUGACGAAAACUACGG___GGAUUACGCUCUCGCUGCGUAA__GCAG____C_U___GACCCGCA
..((((((........))))))......((.((..((((((......)))))))).))..............................((((......)))).................. (-15.74 = -15.55 +  -0.19)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:11:14 2007