Locus 217

Sequence ID pao.1177
Location 2,141,565 – 2,141,684
Length 119
Max. P 0.946718
window833 window834 window835

overview

Window 3

Location 2,141,565 – 2,141,669
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 48.60
Mean single sequence MFE -37.82
Consensus MFE -9.80
Energy contribution -10.68
Covariance contribution 0.88
Combinations/Pair 1.54
Mean z-score -1.30
Structure conservation index 0.26
SVM decision value 0.42
SVM RNA-class probability 0.727914
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.1177 2141565 104 + 6264404
UUCCUUGUCAAUCAAGGGCUUGGAGGUGAGCGCCGGGGGAACCUGGCGGACAGUGUUGCAUCCGUGCAACAGCAGGCCCGCCG-ACCAU-GGGGUCAAGCCU-------GCCG-------
..(((((.....)))))((((......))))((((((....))))))......(((((((....)))))))((((((.....(-(((..-..))))..))))-------))..------- ( -46.90)
>pel.1680 2799203 93 - 5888780
AUUCUUGAGAAUCAAUGGGUUGCGUUGCAAAGGUGAGGGCGCCAGGAAUCCGCUGUUUCAGCGAUGAGACAG------------ACGCU-CGGGCAAUGCGA-------GCCU-------
((((....))))....((.(((((((((...((((....))))......(((((((((((....))))))))------------.....-))))))))))))-------.)).------- ( -34.20)
>pau.1848 3045006 104 - 6537648
UUCCUUGUCCAUCAAGGACUUGGCCGUGAGUGCCGGGGGAACCUGGCGGACAGUGUUGCAUCCGUGCAACAGCAGGCCCGCCA-ACCAG-GGGGCGAAGCCU-------GCCG-------
....((((((.(((.((......)).)))..((((((....))))))))))))(((((((....)))))))((((((.((((.-.....-..))))..))))-------))..------- ( -51.10)
>ppk.1650 3261333 111 + 6181863
UACGUUUCAGAUCAGAUAGUUAGGAAAAGAGGUUGAUAAAAUGCGGCGCAUGCUGUCUCAGGCUUGAAACAGCUUGCC--CUGCGCGUUGCCGGCAAAGUCA-------GCUGUGGCCUU
.....................(((..(...(((((((.....((((.(((.(((((.((......)).))))).))).--))))((.......))...))))-------))).)..))). ( -31.10)
>pfo.1518 2976933 112 + 6438405
AUCUUUAAAUUUCAAUGCGUUGGGUUUGACGAGUGCAGGCCUGAUACAAAAGCUGUUUCAUCGUUGAAACAAGUCAUUGUCUUCGCAAC-CCCUUAAUGCCAUUGCAAAGCUC-------
.........(((((((((((((((.(((.((((.((((((((........)).(((((((....))))))).)))..))).))))))).-)))..)))).))))).)))....------- ( -25.80)
>consensus
UUCCUUGAAAAUCAAGGAGUUGGGUGUGAAGGCUGAGGGAACCAGGCGGACGCUGUUUCAUCCGUGAAACAGCAGGCC__CCG_ACCAU_CGGGCAAAGCCA_______GCCG_______
...............................((((((....))))))......(((((((....)))))))................................................. ( -9.80 = -10.68 +   0.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,141,605 – 2,141,684
Length 79
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 44.90
Mean single sequence MFE -33.76
Consensus MFE -7.94
Energy contribution -8.86
Covariance contribution 0.92
Combinations/Pair 1.53
Mean z-score -1.27
Structure conservation index 0.24
SVM decision value 1.01
SVM RNA-class probability 0.899751
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.1177 2141605 79 + 6264404
ACCUGGCGGACAGUGUUGCAUCCGUGCAACAGCAGGCCCGCCG-ACCAU-GGGGUCAAGCCU-------GCCG----------GGGA--AGCGCCC--------------------GGAG
....(((((.(..(((((((....)))))))....).)))))(-(((..-..))))......-------.(((----------((..--....)))--------------------)).. ( -34.20)
>pel.1680 2799243 89 - 5888780
GCCAGGAAUCCGCUGUUUCAGCGAUGAGACAG------------ACGCU-CGGGCAAUGCGA-------GCCU---------CGGGG--AGUGUUUACCCCCUCAAACGGGCUUGCGGGG
(((..((...((((((((((....))))))))------------.)).)-).)))..(((((-------((((---------.((((--.((....))))))......)))))))))... ( -36.70)
>pau.1848 3045046 79 - 6537648
ACCUGGCGGACAGUGUUGCAUCCGUGCAACAGCAGGCCCGCCA-ACCAG-GGGGCGAAGCCU-------GCCG----------GGGA--CGCGCCU--------------------GGAG
.((.((((.....(((((((....)))))))((((((.((((.-.....-..))))..))))-------))((----------....--)))))).--------------------)).. ( -39.20)
>ppk.1650 3261373 93 + 6181863
AUGCGGCGCAUGCUGUCUCAGGCUUGAAACAGCUUGCC--CUGCGCGUUGCCGGCAAAGUCA-------GCUGUGGCCUUGAUGGGA--AGGGUUU----------------UUGCAAGU
.((((((.(.(.(((((..(((((....((((((.((.--.(((.((....)))))..)).)-------)))))))))).))))).)--.).))..----------------.))))... ( -30.50)
>pfo.1518 2976973 94 + 6438405
CUGAUACAAAAGCUGUUUCAUCGUUGAAACAAGUCAUUGUCUUCGCAAC-CCCUUAAUGCCAUUGCAAAGCUC---------UGGAACAAGGGUUU----------------GCGCGCAG
(((..((((..(((((((((....)))))).)))..))))...(((((.-(((((....(((..((...))..---------)))...))))).))----------------)))..))) ( -28.20)
>consensus
ACCAGGCGGACGCUGUUUCAUCCGUGAAACAGCAGGCC__CCG_ACCAU_CGGGCAAAGCCA_______GCCG__________GGGA__AGCGUUU__________________GCGGAG
...((((......(((((((....)))))))....((((............))))..............))))............................................... ( -7.94 =  -8.86 +   0.92)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,141,605 – 2,141,684
Length 79
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 44.90
Mean single sequence MFE -33.36
Consensus MFE -7.92
Energy contribution -8.60
Covariance contribution 0.68
Combinations/Pair 1.50
Mean z-score -1.63
Structure conservation index 0.24
SVM decision value 1.37
SVM RNA-class probability 0.946718
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.1177 2141605 79 - 6264404
CUCC--------------------GGGCGCU--UCCC----------CGGC-------AGGCUUGACCCC-AUGGU-CGGCGGGCCUGCUGUUGCACGGAUGCAACACUGUCCGCCAGGU
((((--------------------(((....--..))----------))).-------))((((((((..-..)))-)(((((((..(.(((((((....)))))))).))))))))))) ( -38.20)
>pel.1680 2799243 89 + 5888780
CCCCGCAAGCCCGUUUGAGGGGGUAAACACU--CCCCG---------AGGC-------UCGCAUUGCCCG-AGCGU------------CUGUCUCAUCGCUGAAACAGCGGAUUCCUGGC
........(((....((((((((........--))))(---------(.((-------(((.......))-))).)------------)...))))((((((...))))))......))) ( -30.70)
>pau.1848 3045046 79 + 6537648
CUCC--------------------AGGCGCG--UCCC----------CGGC-------AGGCUUCGCCCC-CUGGU-UGGCGGGCCUGCUGUUGCACGGAUGCAACACUGUCCGCCAGGU
..((--------------------(((.(((--...(----------(...-------.))...)))..)-))))(-((((((((..(.(((((((....)))))))).))))))))).. ( -37.40)
>ppk.1650 3261373 93 - 6181863
ACUUGCAA----------------AAACCCU--UCCCAUCAAGGCCACAGC-------UGACUUUGCCGGCAACGCGCAG--GGCAAGCUGUUUCAAGCCUGAGACAGCAUGCGCCGCAU
...(((..----------------....(((--(......)))).......-------......(((((....)).)))(--((((.(((((((((....))))))))).))).))))). ( -31.90)
>pfo.1518 2976973 94 - 6438405
CUGCGCGC----------------AAACCCUUGUUCCA---------GAGCUUUGCAAUGGCAUUAAGGG-GUUGCGAAGACAAUGACUUGUUUCAACGAUGAAACAGCUUUUGUAUCAG
((...(((----------------((.((((((..(((---------..((...))..)))...))))))-.))))).))((((....((((((((....))))))))...))))..... ( -28.60)
>consensus
CUCCGC__________________AAACCCU__UCCC__________CGGC_______UGGCUUUGCCCG_AUCGU_CAG__GGCCAGCUGUUUCAAGGAUGAAACAGCGUCCGCCAGGU
..................................................................................(((..(((((((((....)))))))))....))).... ( -7.92 =  -8.60 +   0.68)

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 21:18:19 2007