Locus 171

Sequence ID pao.225
Location 406,498 – 406,618
Length 120
Max. P 0.935718
window733 window734 window735 window736

overview

Window 3

Location 406,498 – 406,612
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 63.98
Mean single sequence MFE -46.77
Consensus MFE -22.23
Energy contribution -23.07
Covariance contribution 0.84
Combinations/Pair 1.14
Mean z-score -1.86
Structure conservation index 0.48
SVM decision value 1.25
SVM RNA-class probability 0.935718
Prediction RNA

Download alignment: ClustalW | MAF

>pao.225 406498 114 + 6264404
CUAACAACUCCAACCGCGACGGACAGCCACGGCAUCGG-UAACGGGAAUAGCGGAAUUGUGCCGCAUCGGCGCCCGCAGUGCACGCGGGAC-GCCG----ACGGGAGGCCGGCGGAGAGA
.......(((...((((..(((.(..((.(((((.(((-(..((.......))..)))))))))(.(((((((((((.......))))).)-))))----).)))..)))))))).))). ( -49.60)
>pau.231 421252 112 + 6537648
--AACAACUCCAACCGCGACGGACAGCCACGGCAUCGG-UAACGGGAAUAGCGGAAUUGUGCCGCAUCGGCGCCCGCAGUGCACGCGGGGC-GCCG----ACGGGAGGCCGGCGAAGAGA
--.....(((....(((..(((.(..((.(((((.(((-(..((.......))..)))))))))(.(((((((((((.......)).))))-))))----).)))..)))))))..))). ( -46.00)
>pfo.3157 429187 85 - 6438405
-----AACUCCAGCCGGGGCGGGGAGCCCGGGCGC-UA-UGAAUCAAUGCGCGCAAUUGUGCCGCAUUGGCGCCCGUAGUGCACGCGGGCGC----------------------------
-----.......(((.((((.....)))).)))..-..-.....((((((((((....))).)))))))((((((((.......))))))))---------------------------- ( -44.80)
>ppk.2978 336200 89 - 6181863
------ACUCCGGCCGGGGCUCACAGCCCGGGCAUGUU-CAACGCAAUGGGCACAAUUGUGCCGCAUUCGCGCCCGCAGUGCACGCGGGCGCGACA------------------------
------......(((.((((.....)))).))).....-.......((((((((....))))).)))((((((((((.......))))))))))..------------------------ ( -47.90)
>pel.151 303916 90 + 5888780
------ACUCCGGCCGGGGCGUCGGGCCCGGGCAUGUUUCAAAGCGACAAGCGCAAUUGUGCCGGAUUCGCGCCCGCAGUGCACGCGGGCGCGACA------------------------
------..(((((((.((((.....)))).))).................((((....)))))))).((((((((((.......))))))))))..------------------------ ( -47.80)
>pf5.3537 400626 106 - 7074893
------ACUCCGGCCUGGGCGGCAGGCCCGGGCAUGUA-AAAACGAAUGCGCGCAAUUGUGCCGUAUUGACGCCCACAGUGCACGCGGGCGCGAUGGCUGACGUCAGG----CG-AGG--
------.(((((((((((((.....)))))))).....-....((..((((.(((.(((((.(((....)))..)))))))).))))..))))..(.(((....))).----))-)).-- ( -44.50)
>consensus
______ACUCCAGCCGGGGCGGACAGCCCGGGCAUGUA_UAAAGCAAUGAGCGCAAUUGUGCCGCAUUGGCGCCCGCAGUGCACGCGGGCGCGACG________________________
........(((.(((.((((.....)))).))).................(((..((((((.(((....)))..))))))...))))))............................... (-22.23 = -23.07 +   0.84)

alignment

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secondary structure

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dotplot

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Window 4

Location 406,498 – 406,612
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 63.98
Mean single sequence MFE -45.87
Consensus MFE -25.29
Energy contribution -25.60
Covariance contribution 0.31
Combinations/Pair 1.32
Mean z-score -1.64
Structure conservation index 0.55
SVM decision value 1.08
SVM RNA-class probability 0.911293
Prediction RNA

Download alignment: ClustalW | MAF

>pao.225 406498 114 - 6264404
UCUCUCCGCCGGCCUCCCGU----CGGC-GUCCCGCGUGCACUGCGGGCGCCGAUGCGGCACAAUUCCGCUAUUCCCGUUA-CCGAUGCCGUGGCUGUCCGUCGCGGUUGGAGUUGUUAG
.......((((......(((----((((-(.((((((.....))))))))))))))))))((((((((........((...-.))..((((((((.....)))))))).))))))))... ( -52.30)
>pau.231 421252 112 - 6537648
UCUCUUCGCCGGCCUCCCGU----CGGC-GCCCCGCGUGCACUGCGGGCGCCGAUGCGGCACAAUUCCGCUAUUCCCGUUA-CCGAUGCCGUGGCUGUCCGUCGCGGUUGGAGUUGUU--
.......((((......(((----((((-((((.(((.....))))))))))))))))))((((((((........((...-.))..((((((((.....)))))))).)))))))).-- ( -52.30)
>pfo.3157 429187 85 + 6438405
----------------------------GCGCCCGCGUGCACUACGGGCGCCAAUGCGGCACAAUUGCGCGCAUUGAUUCA-UA-GCGCCCGGGCUCCCCGCCCCGGCUGGAGUU-----
----------------------------(((((((.........)))))))((((((((((....))).)))))))((((.-..-..(((.((((.....)))).)))..)))).----- ( -40.60)
>ppk.2978 336200 89 + 6181863
------------------------UGUCGCGCCCGCGUGCACUGCGGGCGCGAAUGCGGCACAAUUGUGCCCAUUGCGUUG-AACAUGCCCGGGCUGUGAGCCCCGGCCGGAGU------
------------------------..(((((((((((.....)))))))))))(((.(((((....)))))))).......-.....(((.((((.....)))).)))......------ ( -46.00)
>pel.151 303916 90 - 5888780
------------------------UGUCGCGCCCGCGUGCACUGCGGGCGCGAAUCCGGCACAAUUGCGCUUGUCGCUUUGAAACAUGCCCGGGCCCGACGCCCCGGCCGGAGU------
------------------------..(((((((((((.....))))))))))).((((((.(((..(((.....))).)))........(.((((.....)))).)))))))..------ ( -45.30)
>pf5.3537 400626 106 + 7074893
--CCU-CG----CCUGACGUCAGCCAUCGCGCCCGCGUGCACUGUGGGCGUCAAUACGGCACAAUUGCGCGCAUUCGUUUU-UACAUGCCCGGGCCUGCCGCCCAGGCCGGAGU------
--.((-((----((((.((.(((((...(((((((((.....)))))))))......((((.((..(((......)))..)-)...))))..)).))).))..)))))..))).------ ( -38.70)
>consensus
________________________CGUCGCGCCCGCGUGCACUGCGGGCGCCAAUGCGGCACAAUUGCGCUCAUCCCGUUA_AACAUGCCCGGGCUGUCCGCCCCGGCCGGAGU______
............................(((((((((.....)))))))))......(((........)))................(((.((((.....)))).)))............ (-25.29 = -25.60 +   0.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 406,504 – 406,618
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 63.98
Mean single sequence MFE -47.45
Consensus MFE -22.23
Energy contribution -23.07
Covariance contribution 0.84
Combinations/Pair 1.14
Mean z-score -1.71
Structure conservation index 0.47
SVM decision value 0.90
SVM RNA-class probability 0.877592
Prediction RNA

Download alignment: ClustalW | MAF

>pao.225 406504 114 + 6264404
ACUCCAACCGCGACGGACAGCCACGGCAUCGG-UAACGGGAAUAGCGGAAUUGUGCCGCAUCGGCGCCCGCAGUGCACGCGGGAC-GCCG----ACGGGAGGCCGGCGGAGAGACGCGGA
..(((..(((..((.((..((....)).)).)-)..))).....(((...((...((((.(((((((((((.......))))).)-))))----)(((....))))))).))..)))))) ( -51.50)
>pau.231 421256 112 + 6537648
ACUCCAACCGCGACGGACAGCCACGGCAUCGG-UAACGGGAAUAGCGGAAUUGUGCCGCAUCGGCGCCCGCAGUGCACGCGGGGC-GCCG----ACGGGAGGCCGGCGAAGAGACGCG--
.((((..(((..((.((..((....)).)).)-)..))).....((((.......)))).(((((((((((.......)).))))-))))----)..))))....(((......))).-- ( -48.20)
>pfo.3157 429188 84 - 6438405
ACUCCAGCCGGGGCGGGGAGCCCGGGCGC-UA-UGAAUCAAUGCGCGCAAUUGUGCCGCAUUGGCGCCCGUAGUGCACGCGGGCGC----------------------------------
......(((.((((.....)))).)))..-..-.....((((((((((....))).)))))))((((((((.......))))))))---------------------------------- ( -44.80)
>ppk.2978 336200 89 - 6181863
ACUCCGGCCGGGGCUCACAGCCCGGGCAUGUU-CAACGCAAUGGGCACAAUUGUGCCGCAUUCGCGCCCGCAGUGCACGCGGGCGCGACA------------------------------
......(((.((((.....)))).))).....-.......((((((((....))))).)))((((((((((.......))))))))))..------------------------------ ( -47.90)
>pel.151 303916 90 + 5888780
ACUCCGGCCGGGGCGUCGGGCCCGGGCAUGUUUCAAAGCGACAAGCGCAAUUGUGCCGGAUUCGCGCCCGCAGUGCACGCGGGCGCGACA------------------------------
..(((((((.((((.....)))).))).................((((....)))))))).((((((((((.......))))))))))..------------------------------ ( -47.80)
>pf5.3537 400626 106 - 7074893
ACUCCGGCCUGGGCGGCAGGCCCGGGCAUGUA-AAAACGAAUGCGCGCAAUUGUGCCGUAUUGACGCCCACAGUGCACGCGGGCGCGAUGGCUGACGUCAGG----CG-AGG--------
.(((((((((((((.....)))))))).....-....((..((((.(((.(((((.(((....)))..)))))))).))))..))))..(.(((....))).----))-)).-------- ( -44.50)
>consensus
ACUCCAGCCGGGGCGGACAGCCCGGGCAUGUA_UAAAGCAAUGAGCGCAAUUGUGCCGCAUUGGCGCCCGCAGUGCACGCGGGCGCGACG______________________________
..(((.(((.((((.....)))).))).................(((..((((((.(((....)))..))))))...))))))..................................... (-22.23 = -23.07 +   0.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 406,504 – 406,618
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 63.98
Mean single sequence MFE -44.97
Consensus MFE -25.29
Energy contribution -25.60
Covariance contribution 0.31
Combinations/Pair 1.32
Mean z-score -1.19
Structure conservation index 0.56
SVM decision value 0.15
SVM RNA-class probability 0.605958
Prediction RNA

Download alignment: ClustalW | MAF

>pao.225 406504 114 - 6264404
UCCGCGUCUCUCCGCCGGCCUCCCGU----CGGC-GUCCCGCGUGCACUGCGGGCGCCGAUGCGGCACAAUUCCGCUAUUCCCGUUA-CCGAUGCCGUGGCUGUCCGUCGCGGUUGGAGU
.........((((((((((.((..((----((((-(.((((((.....)))))))))))))((((.......))))...........-..)).)))(((((.....))))))).))))). ( -50.30)
>pau.231 421256 112 - 6537648
--CGCGUCUCUUCGCCGGCCUCCCGU----CGGC-GCCCCGCGUGCACUGCGGGCGCCGAUGCGGCACAAUUCCGCUAUUCCCGUUA-CCGAUGCCGUGGCUGUCCGUCGCGGUUGGAGU
--.(((......)))..(((...(((----((((-((((.(((.....)))))))))))))).)))...(((((........((...-.))..((((((((.....)))))))).))))) ( -49.00)
>pfo.3157 429188 84 + 6438405
----------------------------------GCGCCCGCGUGCACUACGGGCGCCAAUGCGGCACAAUUGCGCGCAUUGAUUCA-UA-GCGCCCGGGCUCCCCGCCCCGGCUGGAGU
----------------------------------(((((((.........)))))))((((((((((....))).)))))))((((.-..-..(((.((((.....)))).)))..)))) ( -40.50)
>ppk.2978 336200 89 + 6181863
------------------------------UGUCGCGCCCGCGUGCACUGCGGGCGCGAAUGCGGCACAAUUGUGCCCAUUGCGUUG-AACAUGCCCGGGCUGUGAGCCCCGGCCGGAGU
------------------------------..(((((((((((.....)))))))))))(((.(((((....)))))))).......-.....(((.((((.....)))).)))...... ( -46.00)
>pel.151 303916 90 - 5888780
------------------------------UGUCGCGCCCGCGUGCACUGCGGGCGCGAAUCCGGCACAAUUGCGCUUGUCGCUUUGAAACAUGCCCGGGCCCGACGCCCCGGCCGGAGU
------------------------------..(((((((((((.....))))))))))).((((((.(((..(((.....))).)))........(.((((.....)))).))))))).. ( -45.30)
>pf5.3537 400626 106 + 7074893
--------CCU-CG----CCUGACGUCAGCCAUCGCGCCCGCGUGCACUGUGGGCGUCAAUACGGCACAAUUGCGCGCAUUCGUUUU-UACAUGCCCGGGCCUGCCGCCCAGGCCGGAGU
--------.((-((----((((.((.(((((...(((((((((.....)))))))))......((((.((..(((......)))..)-)...))))..)).))).))..)))))..))). ( -38.70)
>consensus
______________________________CGUCGCGCCCGCGUGCACUGCGGGCGCCAAUGCGGCACAAUUGCGCUCAUCCCGUUA_AACAUGCCCGGGCUGUCCGCCCCGGCCGGAGU
..................................(((((((((.....)))))))))......(((........)))................(((.((((.....)))).)))...... (-25.29 = -25.60 +   0.31)

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 21:16:33 2007