sRNA21 INTArna Interactions

8/21/2019 sRNA21 INTArna Interactions

1/7

3/22/2014 RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cg i?page=3&tempdir=eieAZ18dVl

History:Version 1.33 online

= Post Processing =

Post Processing of selected Interactions:

No GO-terms available for NC_009085, no GO analysis possible.

Detailed View for selected Interactions:

Interaction1

Energy [kJ/mol] z-

Score Interaction [dot-bracket]

mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA

[End] Gene Annotation

Locus

Tag

Genomic

Coordinates Acces sion Replicon

-7.68 0.94 ((((((.((((&)))).)))))) -190 -180 115 125 " ben zo at e d io xyg en as e larg e s ub un it A 1S" A 1S_ 1861c2165314-

2164713 NC_009085 chromosom

Asso ciated GO-

terms No GO-terms available

download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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Detailed Interaction(as ASCII):

mRNA: 5'-

sRNA: 3'-

GAUGGCCGUAG

|||||| ||||

UUACCGCCGUC

-3'

-5'

Interaction2

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-8.89 0.53 (((((((((......(((((.

((((&)))).))))).........))))))))) -178 -154 117 144 " bet a ket oad ip yl Co A t hio las e A 1S" A 1S_ 1849

2149442-


Asso ciated GO-


download:mRNA

sequence

download:

sRNA sequence

Accessiblity

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window)

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mRNA: 5'-

sRNA: 3'-

GCCGGUGAGAUACCG---UAAUG-U

||||||||| || || |

CGGCUAUUCAUAACUCCAAU-UACC

-3'

-5'

Interaction3

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-8.87 0.54 (((((((((......(((((.

((((&)))).))))).........))))))))) -177 -153 117 144 " bet a ket oad ip yl Co A t hio las e A 1S" A 1S_ 1891

c2193519-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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window)

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window)


mRNA: 5'-

sRNA: 3'-

GCCGGUGAGAUACCG---UAAUG-U

||||||||| || || |

CGGCUAUUCAUAACUCCAAU-UACC

-3'

-5'

Interaction4
http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2815.&b=10&e=20&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2815..fastahttp://rna.tbi.univie.ac.at/RNApredator2/introduction.htmlhttp://rna.tbi.univie.ac.at/RNApredator2/target_search.cgihttp://rna.tbi.univie.ac.at/RNApredator2/target_search.cgihttp://rna.tbi.univie.ac.at/RNApredator2/help.htmlhttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=ATTTATGGCTGTGCGAATCACAGCCGGTGAGATACCGTAATGTCGGCCGTATGTCAGCTTTACTTGCTGGTTTATCTTATCAAGTGCCAGCAACCACCATTAACCGTTTATGCGGTTCATCACTCGATGCCATTGCCATTGCTGCCCGTGCTATTAAAGCAGGTGAAGCCAACTTGGTAATTGCTGGTGGTGTGGAAAGCATGAGCCGTGCGCCCTATGTGATGGGTAAGTCTGACAGTGCCTTTGGCCGTAGCCAGAAGATTGAAGACACCACCATGGGCTGGCGTTTCATTAACCCTAAACTTAAAGAATTGTATGGTGTAGACACTATGCCCCAGACTGAACAAAACGTTGCTGAACAGTTTAACATCAATCGTGCAGATCAGGACCAGTTTGCCTTGGTGAGCCAACAACGCACCGCAAGCGCGCAAGCCAAAGGCTTTTTTTCTAAAGAAATCGTGGCAGTTGAAATCCCTCAGCGTAAGGGTGATGCTGTGGTGATTGATACCGATGAGCATCCTCGTGCATCGACCACGCTTGAAGGCTTAAGCAAACTTAAACCTGTTGTGAAAGCAGATGGCACAGTTACTGCGGGTAATGCTTCAGGTATTAATGATGGTGCAGCAGCTCTACTGATTGCTTCTGATGATGCAGTTCAGGCATACAACTTAAAACCGCGTGCCAAGATCATTGCCTCAACAGCCGTGGGCGTAGAACCACGCATTATGGGTTTTGCTCCGGCACCAGCGATTAAAAAATTACTTAAACAAGCCAACCTGACTTTAGAGCAAATGGATGTAATTGAGCTGAACGAAGCCTTTGCTGCACAGGCTTTGGCCGTCACCCGTGATTTAGGTTTGCCAGACAACTCTGACAAGGTAAATCCAAACGGTGGTGCCATTGCTTTGGGCCATCCACTTGGGGCATCAGGTGCACGTCTTGTGACTACAGCCTTAAACCAGCTTGAACAAACAGGCGGTCGTTATGCCTTGTGTTCAATGTGTATTGGTGTAGGTCAAGGCATCGCATTGATTATTGAGAGAGTCTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2383.&b=23&e=47&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2383..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=TTTATGGCTGTGCGAATCACAGCCGGTGAGATACCGTAATGTCGGCCGTATGTCAGCTTTACTTGCTGGTTTATCTTATCAAGTGCCAGCAACCACCATTAACCGTTTATGCGGTTCATCACTCGATGCCATTGCCATTGCTGCCCGTGCTATTAAAGCAGGTGAAGCCAACTTGGTAATTGCTGGTGGTGTGGAAAGCATGAGCCGTGCGCCCTATGTGATGGGTAAGTCTGACAGTGCCTTTGGCCGTAGCCAGAAGATTGAAGACACCACCATGGGCTGGCGTTTCATTAACCCTAAACTTAAAGAATTGTATGGTGTAGACACTATGCCCCAGACTGAACAAAACGTTGCTGAACAGTTTAACATCAATCGTGCAGATCAGGACCAGTTTGCCTTGGTGAGCCAACAACGCACCGCAAGCGCGCAAGCCAAAGGCTTTTTTTCTAAAGAAATCGTGGCAGTTGAAATCCCTCAGCGTAAAGGTGATGCTGTGGTGATTGATACCGATGAGCATCCTCGTGCATCAACCACCCTTGAAGGTTTAAGCAAACTTAAACCTGTAGTTAAAGCAGATGGCACAGTCACTGCGGGGAATGCTTCAGGCATCAACGATGGTGCAGCAGCTCTACTGATTGCTTCTGATGATGCAGTTCAGGCTTACAACTTAAAACCGCGTGCCAAGATCATTGCTTCAACAGCCGTAGGTGTAGAACCACGCATTATGGGTTTTGCTCCGGCACCAGCGATTAAAAAATTACTTAAACAAGCCAACCTGACTTTAGAGCAAATGGATGTAATTGAGCTGAACGAAGCCTTTGCTGCACAGGCTTTGGCAGTGACCCGTGATTTAGGTTTGCCAGATGATTCTGACAAGGTAAATCCAAACGGTGGTGCCATTGCATTAGGCCATCCACTTGGTGCATCAGGTGCACGCTTAGTGACTACAGCCTTAAACCAGCTTGAACAGACAGGTGGTCGTTACGCTTTGTGTTCAATGTGTATTGGGGTAGGTCAAGGCATTGCTTTGATTATTGAACGTATTGAAGCACTTTAA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2372.&b=22&e=46&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2372..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=ACTTTTCAAGATGGCCGTAGTCATCTGAATGCGGCAAAGCTCAAGGTAAAGTTTCATAAGCAAACAGATGGAACATGGAAAATTAAACATTTCCAAACACAGAATATTTTCAGTCGTCCGGTATCGCATTGGCACAGTGAAGCCGAGTTGCCGGTACCTTCCCAGGAATGACCCAGGACATATTTAAAAGGACTATTGATATGAACAGTATTATCCCAACGCATAACATTGGCATTGATTATGATGCTTTAGTTAAAAGTGACCGTGCCCATACCTCTCTTTATAAAGATGAACGCATTTTTGATGAAGAAATGGAAAAAATCTTTTATAGCACTTGGGTGTGGGTTGCGCATGCTAGCGAAATTCCAGAAGCCGGAAGCTATAAAACCATTAATATCGGTAAACAGCCTGTTGTAGTGGTGCGTGACCGTAAAAAGAAAGTCCATGTACTTTTAAACCGTTGCCGTCACCGTGCAGCAACCGTATGTGAACATAAAAAAGGAAAACTAACAGTTTTGTATGCCCATATCACGGTTGGAGTTATGCACTTGATGGCAGTTTACGTGGCGTGCCATCTCCGGAAAGTTACGGCGATTGTTTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2815.&b=10&e=20&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2815..fastahttp://rna.tbi.univie.ac.at/RNApredator2/introduction.html#historyhttp://rna.tbi.univie.ac.at/RNApredator2/help.htmlhttp://rna.tbi.univie.ac.at/RNApredator2/target_search.cgihttp://rna.tbi.univie.ac.at/RNApredator2/available_genomes.cgihttp://rna.tbi.univie.ac.at/RNApredator2/introduction.html


2/7



Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-12.45 -0.65 ((((((((((&)))))))))) -174 -165 169 178 "23 dihydro 2;3 dihydroxybenzoate synth etase;

isochorismatase A1S" A1S_2580

c2984752-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

CACGGCCAGA

||||||||||GUGCCGGUCU

-3'

-5'

Interaction5

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-13.70 -1.06 (((((((((..((&))..))))))))) -153 -141 105 117 "p hydroxybenzoate hydroxylase transcriptional

activator A1S" A1S_1355

c1587350-


Asso ciated GO-


download:

mRNA

sequence

download:sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

CAGGAAUGAAAGG

||||||||| ||

GUCCUUACUCGCC

-3'

-5'

Interaction6

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-11.02 -0.17 ((((((((((&)))))))))) -93 -84 264 273 " po rin fo r b en zo at e t ran sp ort (Be nP) A 1S" A 1S_ 18682170698-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

AGUGCCGAGG

||||||||||

UCGCGGUUCC

-3'

-5'

Interaction7

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-7.83 0.89 ((((((.(.(((.((.(((((((&)).))))).)).)))).)))))) -92 -70 107 129 "3 ketoacyl CoA thiolase A1S" A1S_0305c332884-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

Plot:

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mRNA: 5'-

sRNA: 3'-

GGUUAAGGAGC-GA-CGUGA-AU

|||||| | || | |||| ||

CCAAUUAC-CGC-CG-UCCUUAC

-3'

-5'
http://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=GTGTTGCTGAATACGTTGCACTTTGCGACAAATATGCGCACTTAGGTAAGGCTTATGAAGCGCCACAAATGTTGCGCGACATGGCTGCTAACAACAAAAAATTCTACGGTTAAGGAGCGACGTGAATGGCTACTTTAAATCCACGTGACGTTGTGATTGTTGATGGCGTTCGTTCTGCCATGGGCAAATCTAAAAACGGTATGTTCCGTAATGTACGTGCCGACAGTTTATCTGCTGAACTTGTACGTGCGCTCATTGCCCGTAACCAGTTTGATGTAAATGAAGTTGAAGACCTGATTTGGGGCTGTGTAAACCAGACCCTAGAACAAGGTATGAACATTGGCCGCAACATCGGTTTATTGGCTGGCTTGCCTAAAACTGTGGCTGGTCAAACAGTTAACCGTCTTTGTGGTTCTTCTATGCAAGCGATCCACACTGCGGCTGCACAAATTGCAACAAACCAAGGTGATATCTTCATTATTGGTGGTGTAGAGCACATGGGCCACGTAGGTATGATGCACGGCATCGACCTTAACCCTGAAGCATCTAAACACTACGCTAAAGCATCTAATATGATGGGCTTAACTGCTGAAATGTTAGGTCGCATGAACGGCATTACCCGTGAAGAACAAGATACGTTCGGTGTTGAATCTCACCGTCGTGCTTGGGCTGCAACTCAAGAAGGCCGTTTCAAAAATGAAATCATTGGTGTTGAAGGCCACGATGCAAATGGCTTTAAAATCCTTTGTGACATCGATGAAGTGATTCGTCCAGATGCAAACCTTGAAGCGTTCAAAGCATTAAAACCTGTATTTGACCCTAAAGGTGGTTCAGTAACAGCAGCAACATCTTCTGCTCTTTCTGATGGCGCCTCTGCAATGTTGCTTATGTCTGCTGAACGTGCACAAGCATTAGGTTTAAAACCACGTGCCGTGATCCGCTCTATGGCGGTTGCTGGTTGTGATGCAGCAATCATGGGTTATGGTCCAGTTCCAGCAACTCAAAAAGCGCTTAAACGTGCTGGCTTATCAATTGCTGATATCCAGACTGTTGAGTTAAATGAAGCATTTGCTGCACAAGGCTTGTCTGTTCTTAAAGGCTTAGGTCTGTATGACAAACAAGACATCGTGAACTTAAATGGTGGTGCGATTGCTTTAGGTCACCCACTAGGCTGTTCAGGTGCTCGTATCACCACTACGTTGTTAAATGTAATGGAACAACAAGATACTCAAATCGGTCTTGCGACCATGTGTATCGGCCTTGGTCAAGGTATCGCAACAGTGATCGAACGTGTTTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2777.&b=108&e=130&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2777..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AGTGAAAGTATGAAGCTTGAAAAATTAAATTAATAGGTCTCACCAATTGCCAAAATGTACTCTCTAATTAAACGCTTAGAGAGTACCGAAATATTCAAAATTACGTAGTGCCGAGGACTGGCATACATCTGGGAAATGGATTATGGAATTATTTCACCGTTTTAAACCACACACTTTAGCCATTGCCACTTTATTACTTATGTGCAGCAACTCATGGGCCGCAAATCCAAATCAGCAAACTGAAGATGAATGGAAATTCACTTTAAAGAATGCCTATATCAACCGGGATTTTGATAATGATGCCTTAAAAGATACTGGCAGTTGGTCTCAAGCAGCATCATTATTTTATAAATCGAAAATGCATGAAACTCCACTAGTTATAGCAGACAAGCCGATTACGATTGGTGCCGATGCTTCTGTTCAATACGCCGTGCGCTTAAGTTCAGACAAACATGTCGCAGATACTGTTCTGCCTTTTAATAAAGAAACGCAATCTCAGGCTTCAGACTATTTAAAATACGGCGCGACTTTAAAGCTAGGCTATGACAAAACACTTTTAAGTGTCGGTGAACTCTGGCTAGATTTACCTGTCACTGCTGTAGATGCTAGTCGTCAGTTACTCACATCGTATTGGGGAACCAACTTAAAGTCTCAACTTTCAGATCAACTCTATGCTGAAATTGGCCGAGTGGAAAAGTGTCGCCACGAAATGAAGAAGACTTTAAAAAGTTTTCTTTCACATCCAATGGGGTTACTAAAGAATCTGATGGTTTGA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=1376.&b=107&e=116&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/1376..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=TTATCATTTAGTTTGTCCGAATAGCGGACAGAAACAACCAAAATAACAGGAATGAAAGGATGCCTTCTCTCGATGCTTTTCTAGAGCACCCGAACTCGCATGAGAAAATTCGTCAAGATGACTACATTGCAGGATTAGCAAAAGGCTTGGCTTTATTGGAAGCTTTTGGAACAGATCGGCAACGGCTTAATGTCACTCAAGTGGCAGAACGAACAGGTATTAGTCGTACAGCGGCAAGGCGTTACCTAAAAACTTTAAAATACTTAGGCTATTTAGAGACAGATGAACATTACTTTTGGCTCACTCATCGCGTGCTGCGCTTTTCAAGTTCTTATTTAAGCTCTGCTCATCTGCCTAAAGTTGCTCAGTCATTTTTAAATCTTTTGTGTGCGCAGACATCACTTACTTTTTCAATTGTGGTGTTAGACGATAACGAAGTGGTGCCGATTGCCCGTAGTTATCTACCACAGCAAGATAATTTGCGTGTCAGCCCTTATGGCATGCACTTAGGAAACCGTCTCCCTGCCCATGCCACTTCCACGGGTAAAGTATTGCTGGCAGCACTACCTGAAGAAGCCCAACATACGTGGGTAAAAAATTACGGTTTAAAACGCTTAACGCCTTTTACCATAGTAGATGAGTCAAAGTTTTTTGAAGTGCTTAAGGGTATTTCGTTATCGGATTATTGTCTTTCTAAAGAAGAACATGAACTTGGTGTAATTGCGATTGCCGTGCCCGTTTTTAATGCACAAGGTCAAGCAGTGGCAGCACTTAACTGCATGTCTCAAACCAACCGTGTACAAGAAGATTATTTGGTTCAGCAAATTTTGCCATTGCTGCGTAACACGGCAAATGAACTTAGAAATGTAATTTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=458.&b=47&e=59&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/458..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AAGCCCAATACAGCTTTACAGCATACACGGCCAGATTAATCCTTGAAGACACACACTTTATAACTAATACACGATATATAGGCATCACCATGGCAATTCCAAAAATTCAAAGCTATCCGCTTCCGTTTAAACAAGATTATCCAGCGGCAAAAGTGAAATGGAAAATTGAAAAGAATCGTGCGGCTTTATTGATCCACGATATGCAGGATTATTTCATTAATTTTTATGGTGAAGATTCTCCATTGATTCAGGAGGTGATTAACAATATCGCCCAAATGAAAGCATGGTGTGTAGAAAATCATATTCCTGTGTTTTACACGGCACAACCCGTAAAACAAAACGATGAAGATCGTGCCTTATTGAATGATATGTGGGGACCTGGTTTAACCGCATATCCTGAGCAAGCTGAAATTGTTCAGAAATTAGCGCCAACACAACACGATGTTGTACTGACCAAATGGCGCTATAGCGCTTTTTATCATTCAAATTTGCAAAACCAATTAAAAGAAATGGGAAAAGATCAGCTGATTATTTGTGGTGTCTACGCCCATATTGGTGTGCTTCAAACTGCTGCAGAGGCGTTTATGAATGGTATCCAGCCTTTTATGGTCGGGGATTCTGTAGCTGATTTTAGTCTTCAGGATCATCTATTTGCATTGCAGTATGTCCATCGTAACTTGGGGGTCGTTGAAGATGCTCAAAGTGTGATTGCTTCATA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=786.&b=26&e=35&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/786..fasta


3/7



Interaction8

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-6.21 1.42 ((((. ...((.((((.((((((&)))))))))).))..)))) -60 -39 246 264 " fructose 1;6 bisphosphatase A1S" A1S_25963005058-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

Plot:Calculate (new

window)

RNAup

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mRNA: 5'-

sRNA: 3'-

GGAAUUUU-GGGUAGCGCA

|||| | |||| |||

CCUUCU--UC-AGUC-GGU

-3'

-5'

Interaction9

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-16.12 -1.87 (((.(((((.(((((.

(((((((&))))))).)))))..))))).))) -43 -21 99 122

"putative ferredoxin reductase subun it of

phen ylpropionate dioxygenase A 1S" A1S_0950

1098146-


Asso ciated GO-


download:

mRNA

sequencedownload:

sRNA sequence

Accessiblity

Plot:

Calculate (new

window)

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mRNA: 5'-

sRNA: 3'-

GGCUGCAGGU-UGGGC-AGUUAG

||| ||||| |||| ||||||

CCGCCGUCCUUACUC-GCCAGUC

-3'

-5'

Interaction10

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-15.02 -1.5 (((((((((((.((((((&))).))). ..))))))))))) -33 -16 142 162 "LysR family transcriptional regulator A1S" A1S_15061752113-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

GAGGGGGAGCGU--CUG-

||||||||||| |||

CUCUCUCUCGCUUUGAUU

-3'

-5'

Interaction11

Energy [kJ/mol]

z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-10.82 -0.11 (((.(((.(.((((((..(((((((.

((&)).))))))))))))))))).))) -31 -4 253 276 "Beta ketoadipyl CoA thiolas e A1S" A1S_1848

2149080-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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window)

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mRNA: 5'-

sRNA: 3'-

UGAUGCGACUCAAGGGUAAGG-AA

||| ||| | |||||| ||| ||

ACUUCGC-G-GUUCCC--UUCUUC

-3'

-5'
http://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AAAGATTGTCGCTGAGCTGACTTATCCGGTAACGGGTAAGCACTGTGTGGACCGTATTTACACTGACCTGTGTGTGATTGATGTGACCAGAGATGGTTTAAAGGTGATTGAGAAAGTTGAAGGTCTTAGCTTTGATGAGTTACAGGCTTTAACAGGTGCAACTTTGATTGATGCGACTCAAGGGTAAGGAAGTAGGGAAATGACATTCAAAAACGCTTATATCATCGATGCCATCCGTACTCCATTTGGCCGTTACGCCGGTGGCCTTGCACCCGTCCGTGCCGATGACCTTGGCGCTGTGCCGCTTAAAGCCCTCATGCAGCGTAACCCAAATGTAGACTGGGAACAGGTCGATGATGTGATTTATGGCTGTGCGAATCACAGCCGGTGA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=1470.&b=169&e=196&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/1470..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AAATTTACATTACTTTTCAGTTTTTTCTGAAGAGAAGACACTTTCAGCTGCTGCAAGAAAGTTAGGTGTTGACCATGCTACTGTTGCAAGAAGAATTGCCCAGTTAGAAGATAATTTAAAACTAAAATTAGTGGACCGTAGACCTCGTACTTATATTTTAACTTCAGAGGGGGAGCGTCTGGCCAAAATCGTGACACGTATGATGGAAGAAACATTTTCTATTGAACGTCTAGCTCAGGCAGGACAACAGGAAATTAGTGGAGTAGTTTCGGTAAGTCTACCGCCAGCTACGGCTGCGCATTTAGTAATGCCTCATCTTGGTAAGTTTTATCGTCAATATCCTGAGCTACAATTGAGAATACTCGGTGATGTTCATTATGCCTCCTTACAGCATCGTGAAGCAGATATCGCAGTTCGCTTTGGACGCCCTAAAGATGATTATCTAATTGCGCGTAAAGCTGGTGAAGTTCCTTTTGGCATATATGCAGCCCAAGAATATTTGGATGCTATACAAGAAGAAAACTATGAATGGATTAGCGTTGAAGTTGGTGGAGTTCAAGGACAAAAACAGCAAAAGTTAAAACAACGGTTAAATTATAAAGAGCCTGTTATGGTTACGAATCATCCTGAGCTTCAATGGCGGGCTACTTGTGGAGCAGTTGGCTTAGCTGTACTACCTGATTTTTTAGGCCAGCAAGGTCATTTAGTAAAATTACCTGATGATGACCCAATGAGTGCTGAAATTTGGTTAGTAATTCATGAAGATCTGCGGAGTAGTCCTGCAGTAAGGGTAGTGATGGATTTTCTTTTAGATTGTTTTGAATCTTTTCGTGTTTAA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=230.&b=167&e=184&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/230..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=CACGTGTAGAAGAACATCGTCTAGAGCTTTTCACCGAGTGGGCGATTGAAGGTGGTCTTGATGACAAAACCCGCCGTCAGGTGAAGCCTGTGTAACAGGCATTGCTTTACAAGGAAGAAAGGCTATGGAAAAGATTGTAATTGTAGGGGCGGGGCAGGCTGCAGGTTGGGCAGTTAGTACCTTACGTCAAAATGGATATGTGGGTGAAATTCATGTGGTCTCAAATGAAGATCACGTGTTTTATGAGCGTCCGCCACTGTCTAAGCAAGTACTTTCAAAAGAAGCAAGTTATGAAAGTTTGAATCTGTTCTCTCCAGAACAGGTTCAAGAGTTCAACATTCAATGGCACAAACCGGAAATTGCAACAAAAGTCGATCGCGAGCAAAAGCAGGTTCATTTAGAAAGTGGTCAGATTTTGCCGTATGACAAATTGTTGATTGCAACAGGAAGCCGCGCCCGTGTACCCGTCAATACATGGCAGTTCATTCCAAATGTTGTGACTTTGCGAAATGTACGTGACTGTGACGTCTGGCTGAAATTTTAA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=118.&b=157&e=179&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/118..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=TTTTATGTCCAACCTCACATTGTCCCAATTTTTACAACAAGAAAAAGGGAATCTTACACCTGAGTTGGCTCAAGTCATCGACACAATTGCTGCGACTTGTAAAACCATTGATCAAGCCTTACAAAAAGGTGCCTTGGCTGGAATTTTGGGTAGCGCAGGTAACGAAAATGTTCAAGGTGAAACACAGAAAAAACTTGATGTGATTTCTAATGACTATTTAATCGATGCTTTAAAAGTCCATCCTCACGTCGGTGGTCTTGCATCTGAAGAACTTGATGATTTTACACTAGCACAAGAAAACGGCGAATACTTGGTTCTATTTGATCCATTAGATGGTTCAAGCAACATTGATATCAACATGTGTGTCGGAACAATCTTCTCGATTCTTCCTGCCAAAAATGCGGTTACACAAGCACAAGATTTCATGCAGGCAGGCACTCAACAAGTTGCTGCTGGCTATGTGTTATATGGCCCATCAACTATGATGGCTTTAACAGTTGGAAACGGTGTAGCTTTCTTTACGTTAGACCCAGAAACACAAACATTCTTACTTACTACAGAGAATGTTCAAGTATCAGCAGATACTCAAGAATTTGCTATTAATGCATCTAACCAACGCCATTGGGAACAACCAGTAAAACAATATATTGAAGAGTTACTTGCAGGTAAAACATCTGTACGTGAAAAAGACTTCAATATGCGTTGGGTCGCATGTATGGTGGGTGATGTTCACCGTATTTTATGCCGTGGCGGTATTTTCCTTTATCCATATGACTTAAAAGACCCGAAAAAAGCTGGTCGTTTACGTTTAATGTATGAAGCTAACCCAATGAGTATGCTCATTGAACAAGCAGGCGGCGCATCAACTACTGGCCGTGTACGCATTCTAGAGATTGAACCTACAGAACTTCATCAACGTGTTCCTGTAATTATCGGTTCTAAGAATGAAGTTGAACGCGTAACAAGCTATCATTAA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=3124.&b=140&e=161&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/3124..fasta


4/7



Interaction12

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-10.82 -0.11 (((.(((.(.((((((..(((((((.

((&)).))))))))))))))))).))) -30 -3 253 276 "Beta ketoadipyl CoA thiolas e A1S" A1S_1892

c2193881-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

AccessiblityPlot:

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window)

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mRNA: 5'-

sRNA: 3'-

UGAUGCGACUCAAGGGUAAGG-AA

||| ||| | |||||| ||| ||

ACUUCGC-G-GUUCCC--UUCUUC

-3'

-5'

Interaction13

Energy [kJ/mol]z-

Score Interaction [dot-bracket] mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

TagGenomic

CoordinatesAccess ion Replicon

-7.47 1.01 (((...(((((.(...(((((.

(((((((&))))))))))))))))))...))) -21 7 106 129 "2;3 dihydroxybenzoate 2;3 dehydrogenase A1S" A1S_2579

c2984107-


Asso ciated GO-


download:mRNA

sequence

download:

sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

GGUGACUGGCGUGAAUCAGGGCAU

||| ||||| | ||||| ||

CCAAUUACCGC-C---GUCCU-UA

-3'

-5'

Interaction14

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-13.86 -1.12 (((((.(((((((((.(&).))))))))).))))) -19 -3 90 106 "multidrug efflux MFS transporter putative A1S" A1S_1799

2095394-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

GGUCGAUAUUCGCGGUG

||||| ||||||||| |

CCAGUCGUAAGCGCCUC

-3'

-5'

Interaction15

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-15.91 -1.8 ((((..(((.(((..(((((((((&)))))))))))).)))...)))) -12 11 107 129 " ald o/ ket o redu ct as e A 1S" A1S_32663756550-

3757037NC_009085 ch romosom

Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

Plot:

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mRNA: 5'-

sRNA: 3'-

GGUUUA-GGU-UGCAUGGGAAUG

|||| || || ||||||||

CCAAUUACC-GCC--GUCCUUAC

-3'

-5'
http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=135.&b=188&e=211&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/135..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AAATTTAATAAGATAGTAGAGTACCGATCGGTACAGTTGAGCTTAATTACCGCTATAAGCATTAAGTTCATTTTAAAATTTAAGGTAAAAGATGAATATACGACCACTCATCGGTTTGGCAGGTGCAATTTTTGCAGCCATGACTGTCGAATTTAATAACCGAATTAGCAGCATTACCTTGGTCGATATTCGCGGTGAGATGGGTATTAGTGTCGACTCTGGTTATTGGGTCAGCAGTATTTATGCCAGTGCCATGATTATTGGGATGATCCTGTCCACCAGTTGGGCGGTTATTTTTTCTATGCGTCGGGTTCTTCTTTTTGCGATAGGACTTTGCCTCTTCTCTAGCGTTTTAATTCCTTTTAGCCCAAATATCGAAATATTTTATTTATTACGGGGCTTACAAGGACTCGCCAATGGTTTAACTATTCCTTTATTAATGGCATGTGCACTTAGATTCCTAGGACCTGAAATTCGTCTATGGGGCTTGGCCTGCTATGCATTGACAGCAACTTTTTTCCCAAACTTAAGCGCTGCGCTTGCTGCCTTTTATTTAGATGTGATTGGTTGGAAGATGATATTTTTCCAAACCATTCCTTTTTGTGCTTTAAGTGCTGCGTTAGTTTACTTCGGTATTCCGCAAGATCCGTTAAATTACTCAAGAATAAAAACTTACGATTGGACTGGCGCGATTCTAGCCATTATTGGTTTGGCAAGCCTTAGTACCATGCTTTTGCATGGCAATCATTTGGACTGGTTCCATTCAAAATTGATTTGTGTTTTGGCTTTAATAAGTGCCATTACCCTACCTTTATTTTTAATACATGAATGGCGCTATCCAACACCATTAATTAAACCGCAAATGCTCGAAATACGAAATTTTGGTTATGCTGTTATTGCGTTGTTCTGCTTTGTGGTTATTGGTATGTCAACCAGTACATTACCCCTTAATTACTTAAGCGCTGTGCATGGTTATAAGCCTACTCAAACCATGTGGATTGGCTTACAAATTGCCGCATTACAATTTATCTATATCCCGATTGTTATTAAAGTTTTGAACCAAGCTTGGGTTGATAGCCGATATGTACATGGATTTGGTTTACTTTTGGTTATGGTTGGCTGCTTAGGTGCAAGTCAACTTGATACGACTTGGAACCAAGACCAATTCTATTTTTGGCATGCAATCTCATGTTTAGGACAAACCTGTGTAGTGCTTTCGCTCCTCATGATGGGTACAAATAGTGTCCACCCAACTATGGCAATCTATGCTTCTCCTATGATTAACACCCCGCGTGCTATCAGCGGCGTACTTGGTGTGTGCCTTTTGGACTGGGTCAATCGAGTACGTGGTGAATACCATTCAACACGGCTGATTGAAAATACCGCACAACATGTTTTTCAAAATATTCAAGGTCCTGTTATTAATCCTCTTACCCCGCCTGTGCTGAGTGCAGATGGTACCGAACGTGTTTCCGGTGGTTTATCTGCCTTAAATTCTGCGATTCAGGCACAGCAATCGGTGTTAGTCATTAGTGATCAATATCTGATTTTAGCGGGACTTACTGCAATTTTATTTATCGTTATGCTGATTTTGCCAGTTAGAACTTATCCACCACGCATTGCTCTCATTAAGTTAATGAATAGTCATAACTCAGGAAAATCTTTATGA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=428.&b=181&e=197&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/428..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=ATCTATTTGCATTGCAGTATGTCCATCGTAACTTGGGGGTCGTTGAAGATGCTCAAAGTGTGATTGCTTCATAAATTTCAAGATCAATCGAAATTAGATAAGGAATTTTCATGAAAGAAGCAGAAACACAAGAGAAATCACCAACCCTCACTCATTCAGCTGATACCAAAATTGCATGGGTGACTGGCGTGAATCAGGGCATGGGTGCAGAAATTATGCAACGGCTGATTGCACAACATATATATGTCGTCGGTTTTGATTTATCAACGAATAACATTGTCGAAAGTGATCGTTACGAAGTTCATCAATGTGATGTTCGTGATGCTGTGCAGATTTCATCGCTCTGCCAAAAGCTTCTGAAAACTTCTCCACCAGATTATTTCATCAATACAGCTGGAGTACTGCATTTGGATGAACACGACACATTGCCAGAAGATGCATGGTTGCAAACCTTTGAAGTCAATACCTTTGCTCCATTTTATTTCTTAAAGCATTTAAGTCCATATTTTCGTGAAAAGAGAAATGGCAATATTGTCATGGTGTCGTCAAATTCTGCACATGTGCCTCGCATGAAGATGGCAGCCTATGGTGCATCTAAAGCCGCGCTGACCAGTTTTAGTAAAACTGTGGGGTTGGAACTCGCTGAATATGGCATCCGCGTCAATATTGTTTCACCTGGTTCAACCGCAACGCCTATGCTTCGCCAACTTTGGAAAGATGCTTCCGGCGAAAAACAGACCATTCACGGCAATTTAGCGCAGTACAAAGTTGGGATTCCTCTACAGAAAATTGCCTTAACCGAAGACATTGCCCATGCAGTGATGTTCCTCATCAGTGATCAAGCCTCGCATATCACCATGCACGATTTGGTGATTGATGGTGGCGCAACTTTAGGTCAATA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2878.&b=179&e=207&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2878..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=CAAAGATTGTCGCTGAGCTGACTTATCCGGTAACGGGTAAGCACTGTGTGGACCGTATTTACACTGACCTGTGTGTGATTGATGTGACCAGAGATGGTTTAAAGGTGATTGAGAAAGTTGAAGGTCTTAGCTTTGATGAGTTACAGGCTTTAACAGGTGCAACTTTGATTGATGCGACTCAAGGGTAAGGAAGTAGGGAAATGACATTCAAAAACGCTTATATCATCGATGCCATCCGTACTCCATTTGGCCGTTACGCCGGTGGCCTTGCACCCGTCCGTGCCGATGACCTTGGCGCTGTGCCGCTTAAAGCCCTCATGCAGCGTAACCCAAATGTAGACTGGGAACAGGTCGATGATGTGATTTATGGCTGTGCGAATCACAGCCGGTG&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=1469.&b=170&e=197&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/1469..fasta


5/7



Submit (new

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Interaction16

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-16.45 -1.98 ((((....((((.

(((((((((((((((((&)))))))))))..)))))).)))).)))) -11 18 94 122 "putative signal peptide A1S" A1S_3139

c3627123-


Asso ciated GO-


download:

mRNA

sequence

download:sRNA sequence

Accessiblity

Plot:

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window)

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mRNA: 5'-

sRNA: 3'-

GGCGACUUU-AGGCAU--GGGUUCAGCAU

|||| | || ||| |||||||||||

CCGCC---GUCC-UUACUCGCCAGUCGUA

-3'

-5'

Interaction17

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-11.22 -0.24 ((((((. .. .. ..(((((((((&))))))))).. .. .. ..)))))) -9 12 251 273 "LysR family transcriptional regulator A1S" A1S_3271c3761052-


Asso ciated GO-

terms

No GO-terms available

download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

Plot:

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window)

RNAup

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mRNA: 5'-

sRNA: 3'-

AGCGCUUAAACAU-GAGUCAGC

|||||| ||||||||

UCGCGGUUCCCUUCUUCAGUCG

-3'

-5'

Interaction18

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-9.19 0.43 ((((.....(((((&)))))...)))) -9 4 120 131 " fruc to se 1; 6 b is pho sp hat e ald olas e A 1S" A 1S_ 15441796550-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

Plot:

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window)

RNAup

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mRNA: 5'-

sRNA: 3'-

GAGGAUAUUAUG

|||| |||

CUCCAAU--UAC

-3'

-5'

Interaction19

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-7.68 0.94 (((((((.. .(((.((((.((&)).))))..))). .. .))))))) -3 17 259 281 "benzoate 12 dioxygenase beta subunit A1S" A1S_1214c1421349-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

Plot:

Calculate (new

window)


mRNA: 5'- CUGGAUGCCA-GCU--UGGG-

||||||| || || |

-3'
http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2814.&b=197&e=217&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2814..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=GCCAGTTTTAGATGAAAAGAATACAGATGTGGTTGAAGGTAGTGCATCTAGCGAGACGGCTGCTTCAGAAACGCATTAATTTGTTGTTTTTTGTTAAAAATTCCCTGCAAATGCAGGGATTTTTTTGAAATACTGTGATTTGTTGCTGAATTGAAATAAATGACAAGGTAGAATAAGCCGCACTACCTGGGAGGATATTATGGCACTCATTTCAATGCGCCAGCTCTTGGATCACGCTGCGGAACATAACTACGGCGTACCAGCATTTAACGTAAATAACTTAGAACAAATGCGTGCAATTATGCTTGCCGCAGATGCTACCAATTCACCTGTAATTGTTCAGGCATCTGCTGGAGCTCGCAAATATGCAGGCGCTCCATTCTTACGCCATCTTATTTTGGCTGCAATTGAAGAATGGCCACACATTCCAGTGGTAATGCACCAAGACCATGGTACAAGCCCTGATGTATGCCAACGTTCTATTCAACTTGGTTTTAGCTCAGTGATGATGGACGGTTCATTAGGCGCTGATGGTAAAACTCCTACAACTTACGATTACAACGTAGATGTAACTCGTCAAGTGGTAGCAATGGCTCATGCTTGTGGTGTATCTGTTGAAGGTGAGATCGGTTGCTTAGGTAGCCTTGAAACAGGTATGGCTGGAGAAGAAGACGGTGTGGGTGCAGAAGGTGTACTTGACCATTCTCAGCTTTTAACCTCTGTTGAAGAAGCAAAACAATTCGTTGCTGATACAAATGTTGATGCTTTAGCAATTGCTGTAGGTACTTCACACGGTGCTTATAAATTTACACGTCCACCTACAGGGGATATTTTAGCAATTGACCGTATTAAAGAAATTCATGCGGCATTGCCAAATACTCACCTTGTAATGCACGGTTCAAGCTCTGTACCACAAGAATGGTTAAAAGTAATTAACGAGTTTGGTGGTAATATTGGTGAGACTTATGGTGTACCAGTTGAACAGCTTGTAGAAGCGATTAAACATGGTGTACGTAAAATCAATATCGATACTGACTTGCGTTTAGCTTCAACAGGTGCAATTCGTCGTTTCATGGCGGAAAACCCAGCTGAATTTGACCCACGTAAGTATTTCGCTAAAACTGTCGATTCAATGAAACAAATTTGTATCGATCGTTATGAAGCTTTCGGTACAGCTGGTAATGCTGACAAGATTCGCCCAATTTCTTTAGAGAAAATGGTTGATCGTTATAAATAA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2237.&b=191&e=204&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2237..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=GAAAAAAGAGCAGGACCTAAAGGCATGCTGCATCGAGAAAATTCGATAAATTAAAATTAGCAATTTAAAAGGTATTTTTCTAATATATTTAATAATGGGACACGATATGTTTTATATATAACAATGGAACTCAGGCATATACGCTACTTTTTGGCAGTAGCAGAAGAAAAAAACTTTACCAAAGCTGCGCAGCGCTTAAACATGAGTCAGCCGCCTTTAAGTATGCAAATACGAGACTTAGAAGAAGAGCTCGGTGCAGATTTATTTATTCGTTCGCCTCATGGGGTGGAGCTGACCGAAGCGGGGCTTGCCTTTTTAAATGCAATTCAGCCAGTACAGCAGCGTGTAGAAGATGCAGCAAACCTTGTTAAGCAAGTGGCAAATGGCGAAGTAGGTCAATTACGATTAGGCTTTACAGGTACTTCAATGTTGAATCCTTTAATTCCTAAATGTGTTCGCTATTTCCAGCAGCAATACCCGAAAGTAAATTTAAAGCTTGAAGAAGCCAATACCTTACTGCTCATCGATTTATTGCTTGAAGACCGTTTAGATGTCGCAATTATTCGTTCGCCACGCAATATGCCGGATAGCCTCATTCTACAAGAATTATTGGCTGAGCCACTCATTGCTGCTTTACCTTCAGAGTCTTTTAATCTGGACGATGTATCACAAGAAATTGATTTAACTGCGCTGCGAGAGCTTGATTTTATTGTCTCGCCACCTTCAGTGAGTGCAGGGCTTTTTGATGCGATTAAACAGGCCTGCCATGAGCGTGGCTTTCAACCGAAAATTGGACAAAATGCCCCGCAAATTGTGTCAATTTTATCGTTGGTGTCTGCAAACTTAGGGGTGTCTTTGGTTCCCGAGTCGACCAAACAATTGCAAATACAGGGTGTGGCTTATCGCTCTTTGAAAGCGCCTGTACCTACGGTGGGTTTAGGGCTTGCTTATAAGAAACATGCCCCTTCACAGATGGCGATTAACTTTGCCAGTGTGGTGCAAGTGGCTTGTCACCACGCCAACGAAATAGATGAAATCGGCT&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=1282.&b=191&e=212&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/1282..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=TAGATTTTGAAGATTAATAATCTATTTAATTAGGCACAAAAATAGACGAAATTGATCTGTATTGTTACTAAATTCCGATATTTTTTTCATACCTTAGAGCTACCATAAAACGAAGATCTAATGAATTTGATCTAGCAATATTTGAGGTATAAAGCGATGAAAAAACAACGTTTGATGATAGCTTTGCTGGCGACTTTAGGCATGGGTTCAGCATTTGCATCAACCTCGAGTGAATACAATATTGCCAATGGCTTGCTTCCAGTTGAAAAAGATCAATCAATTTCTGTATTACAACCATTTCAGGGAAATTTTAGGATTTTAGGTTCAAAAATTTATCACAATGATGAGCAAGCCAAATTTTCACCGATTGATTATGCGGTAAGTTGGGGTTTATTTGCTCAACCTGAAATCGCACGACATATTTCAGTGAAACAATATGACCGCTATTTAAACTGGAAAATAGCAAAACTACCTGTACCAGCTGAGCAAGCGATGCAGATGGTATCGAATATGCACATTATTCCTGCAAACCCTGAAATCGCCCAACAAATTAAGCAAGTTAAACGTGGTGATTTGGTTTATTTAAAAGGTGATCTGGTTGAAATCAAAGATAAAGATTTAGTTTGGAAGTCATCTTTGACCCCAACTGATACCGGCGATGGTGCATGTGAACTCTTCCGTGTTCAATCAATTCACTGGGTTGAAAAACAAAATATTT&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=96.&b=189&e=218&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/96..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AAAATTCCGCGAAGACTGTGTAGCCTAAAAACAGATTGTTTGAATTTTATAATTATTGGTTTGAATGTTATACGTCAGTTTGAGCCAAAGCATTTTATAGTTTTTCTACTCAAGTGATTTTGCAAAAAGAGTGTGAAAAATGAAATATAGAACTTTAGGACAAACAGGCGAAAAAGTATCAGCACTTGGTTTAGGTTGCATGGGAATGAGCTTTGCCTATGGTGCCTCAGACGACACACAAAGCATTGCAACTCTAGAAAAGGCCTTAGACCTCGGCATTAACTTTTGGGACACTGCCGACATGTACGGCAACGGCGCAAACGAAGTGTTGCTCTCAAAAGTTTTAGAAAAACACCGTGACAAAGTGTTCTTGGCGACCAAATTTGGCTTCCGCTATAAAGAAGATAACCTCAACCCGAAAAATTCTTTAGAGTCTTATATCGACGGCTCACCTGAGTGGATTAAAGTCGCGGTCGAAAACAGCTGA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0


6/7



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sRNA: 3'- GACCUACUUCGCG-GUUC-CC-5'

Interaction20

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-9.12 0.46 (((((((..(((&)))..))))))) -1 10 220 231 "phosphopyruvate hydratase A1S" A1S_1898c2199259-


Asso ciated GO-


download:mRNA

sequence

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sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

GGGUGGUUGGUC

||||||| |||

CCCACUAGUUAG

-3'

-5'

Interaction21

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-15.37 -1.62 (((((((((((((((((((&))))))))).)))).)))))) 0 18 117 137 "alpha beta hydrolase family esterase A1S" A1S_2792

c3236080-


Asso ciated GO-


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mRNA

sequence

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sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

AGUGUU-AGGU-AGUGGUG

|||||| |||| |||||||

UCAUAACUCCAAUUACCGC

-3'

-5'

Interaction22

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-13.74 -1.08 (((((((((((&))))))))))) 0 10 115 125 " pu tative mo no oxyg en as e (Ds zA like) A 1S" A 1S_ 1486c1732080-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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mRNA: 5'-

sRNA: 3'-

AAUGGCGGCAG

|||||||||||

UUACCGCCGUC

-3'

-5'

Interaction23

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-10.47 0.01 (((((..((((((((&))))))))..))))) 7 21 252 266 "carbon s torage regulator A1S" A1S_1141c1331454-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

Plot:


mRNA: 5'- GGGGAUCAAGUCAGU-3'
http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/1637..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=ATCCACGTGATGAATCACATCGTTTTAACGAATTGAGCTATTGGACAGAACAGGCCAAAACTTTAGAAAATGGTTTATTTGATGGTTTGTTTATCGCTGATATTACAGGTGTGTATGACGTCTATCAAAACGGTATAGATCTCACTTTAAAAGAGTCCATTCAGCTTCCGAGCCATGACCCGTCTACACTCATTTCAGCAATGGCGGCAGTCACTCAAAACTTAAGTTTTGGGGTCACTGTGAACTTAAGCTATGAGCATCCATATCAATTTGCTCGCCGCTTTGCAAGTCTCGACCATTTAACTCAAGGTCGTATTGGCTGGAATATTGTTACAGGTTATCTAGATAGTGCGGAACGTCTAATTGGCCAAAAAGGTTTAAAAGACCACGATGCCCGCTATGAGCAAGCCGAAGAATTTTTAGAACTTTGCTATAAATATTGGGAAGGTTCATGGGAAAACGACGCAGTTAAAAAAGATAAAACACGGCGTGTTTTTACAGATCCATCTAAGGTGCATACCATTCACCACCATGGAAAGTATTACCAGAGTGAAGGCGTGTTTCAGGTATCTCCTTCTGTACAACGCACTCCAACCCTATTTCAAGCAGGTGCTTCACCTAAAGGTATGCAGTTTGCAACACGTCATGCTGAATGTGTATTTATTGGCGGTGACAAACCCGAAAAGATACGCGAACAAGTGAAAAAGATTCGTACTCTTGCCGAACAGCAAGGACGCTCAGCGAACGATATTAAAGTGTTTGTCGGCATAACTGTTGTTGTGGCCGAAACACATGATCTGGCTGTACAAAAACTTAATGAATATCGTCAGTATGCGAGCCCTGAAGCAGGCTTAGCGCATTATGCGAGTTCAACAGGCATTGACTTAAGTAAGTTTGCTGACGATGAAGCGATTCCTTACCAAAAAAGTAACAGCATTGTTTCGATTACCGAAAAGTTTAAAGAACAGCAAATCACAAAAAATGACTTAAAAGCTCAGCATGTTTTAGGTGGTCGTTATCCCCTTATTGTGGGTAGTGGCGAAGAGGTTGCTGAATACTTAATTCATCTTTTAGATGAGACTGATATTGATGGCTTTAATTTGACACGTACTGTTGCACCTGAGTCTCACCATGACTTTATTCGCTTGGTCATTCCAGAGCTACAACAACGTGGTCGCTATAAAACTGCATATAAAACGGGTTCACTACGGAACAAAATTTTTAATCGGGGTGATCAATTACCAGAACAGCACCCTGTTCAAGCGTTCCGATGTAGTCCCTATAACAACAGCAAAAACTTAACAAAAATTGAAGAAATAACCGCTTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=450.&b=200&e=210&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/450..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AAATTAACGTCATAGTGCAAAGATGGGCCATGAAACAGCTTAAATTGTGGGTTCTCGGACTTTCTATGGTGTTGGCCGGGTGCCAAACCACCTCACACTTATCTGCCTTAAAACCGCAAACGGCAGAGGCATACTCACGTTTCGTCGATCAGCCTTTTGCACAGCTTAAGAAGCAGCATAAGAAACCAGTAGTCGCATTAGTGTTAGGTAGTGGTGGTGCGCGAGGTTATGCACATATTGGTGTTATTGAAGTTTTAGAACAGCATGGTATCCGTCCTGATTTCATTGTTGGAACCAGTGCAGGAAGTATTGTCGGAGCAATTTATGCGAGTGGAAAAACGCCCGATGAACTTCGCGATACTGCATTGAAAATGAAAGCGGCTGATGTTCGTGACATCAGTATTGGTTTAAAAGGTTTTTTTGATGGTAAAAAAGTTGAAGACTATGTAAACCAGCAAGTAAATAACTTGCCGCTCGAAAAAATGAAAATTCCGATGTATGTGGTGGCAACAGAGCTCAAGCATGGCACCAAAACCGTATTTAATTATGGCAATACGGGGCAAGCCGTGAGAGCATCAGCCTCAATACCAAGCATGTTTGTGCCGACTAAAATTGGTAAATCTGAATATGTAGATGGCGGTTTAGTCAGTCCGGTACCTGTTGAAGTAGCCCGTGATTTAGGAGCCGATGTCATTATTGCTGTCGATATTCTGGCTCAACCCATTTATACGGAAACCTCCAATGTATGGGGACTCTTTAACCAGAATATTAATATTATGCAAGGACGTTTGGCTGCCGAAGAACTTCAATATGCAGATGTAGTAATTCAACCGGATTTAAGAGAAAAAGCACATATTTTTGATGTAAAAGGTCGTGAAGCAACCATGAAGGCAGGCATAGATGCAGCAAATGCAAAACTGTCTGATATTCAGTTTGCGATTGATGAAAAAATAGCTGAACAGAATCTATCTACTGACGGTTTAAGTGCGCAAACGCAATA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=196.&b=200&e=218&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/196..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=TCTTGGCACAACTAAAAGAATTGGATACTTTAGTTAAAGGATTCAAAAAGTTAGATACTCATTGATGCAGGAATTTGCATCGCGTTATTCATTCAACTGAGGAATTGTTCATGAGCCAAATCGTTGACATTCGTGCACGTGAAATTTTGGACTCTCGTGGTAACCCAACCATCGAAGCAGACGTCATCTTAGAATCTGGGGTGGTTGGTCGTGCATGTGCACCATCTGGTGCTTCAACTGGTTCTCGTGAAGCTTTAGAACTTCGTGACGGCGACAAATCTCGTTACTTAGGTAAAGGCGTTCGTACTGCTGTTCAGAATGTAAATAGCTCAATTCATGAATTGCTTGTTGGTCAAAGTGTTTTTGAACAAAAAGCACTTGATGAAAAAATGATTGCTTTTGATGGCACTGAAAACAAATCTAAATTAGGTGCTAATGCAACTTTGGCAGTATCTTTAGCAGCAGCTCACGCAGCAGCAGCTGAACAAAAACTTCCATTGTTCCAATACATTGCTAACTTACGTGGTCAAACTACTTTGACTATGCCTGTACCAATGATGAACATTTTGAACGGTGGTGCTCACGCAGATAACACTGTTGATATTCAAGAATTCATGATTGAGCCAGTTGGTTTCACTTCATTCGCTGAAGCATTACGTGCTGGTGCAGAAGTATTCCATTCTTTGAAATCAGTTCTTAAGAAACAAGGTTTGAACACAGCTGTAGGTGATGAAGGTGGTTTTGCGCCTAACCTTCGTTCAAATGAAGAAGCGATTACAGTAATTCTTCAAGCAATTGAGCAAACTGGTTATAAAGCTGGTTCAGATATTATGCTTGCACTTGACTGTGCATCTTCAGAATTCTACAAGAATGGTCAATATATTCTTGAAGGTGAAGGCAACAAGTCTTTTACAAGCAATCAATTTGCTGATTACTTAGCTGGTCTTGTTAAGCAGTATCCAATTATCTCTATTGAAGATGGTTTGGATGAGTCTGACTGGGAAGGCTGGAGTTACTTAACTTCAATTCTTGGTGATAAAATCCAATTGGTTGGTGACGATTTATTCGTAACTAATCCTAAGATTTTACAACGTGGTATTGATGAAAAAGTTGGTAACTCAATTTTGATCAAATATAACCAGATTGGTACATTGACTGAAACTTTAGATGCAATCTACCTTGCTAAAGCAAATGGTTATACTACTGTTATTTCTCACCGTTCTGGTGAAACAGAAGATTCAACTATTGCTGATTTAGCAGTAGGTACAGCAGCAGGTCAAATTAAGACTGGTTCACTTTGCCGTTCTGACCGTGTTTCTAAATATAACCAATTGCTTCGTATTGAAGAGTTAACTAAAGCGGTTTACCGCGGTAAAGCTGAATTCAAAGGTTTAAATTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=2276.&b=199&e=210&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/2276..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=CATCAATATTGGTTAAAAACCATGAAACACGCGATTGCATCAGAGAAAGAAATTGCTGATCAGGGAGAAACAGCATGAGTGCTCAAGACAAAGCAACTTTAGAAAATATTGCTCAGTTTCTTTATCGTGAAGCTCGCTTTTTAGATGATGAACAATGGGATGACTGGCTTGAATGCTATGCGCCAGAAGCTTCTTTCTGGATGCCAGCTTGGGATGACGACGATAGATTAACTGAAGATCCGCAATCTGAAATTTCACTTATTTATTATCCAGACCGTCAAGGTTTAGAAGATCGAGTGTTCCGTATTAAAACCGAACGCTCTTCTGCAACCATGCCGGACACACGCACAAGCCACAATATTGCCAACGTTGAAGTTCTCGATCGCGACGGCGACAAAGTCACTGTTCGCTTTAACTGGAATACCTTAAGTTTCCGTTATAAGACAAATTACAGCTATTTCGGTATGTCACGTTATGTGATCGATTTTTCAGGTGATCAACCAAAAATCTTGAGCAAGTATGTCGTTTTGAAAAATGACTATATCAATCAAGTCATTGATATCTACCACCTTTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0


7/7



Calculate (new

window)

RNAup

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sRNA: 3'-

||||| ||||||||

UCCCUUCUUCAGUCG -5'

Interaction24

Energy [kJ/mol] z-


mRNA

[Start]

mRNA

[End]

sRNA

[Start]

sRNA


Locus

Tag

Genomic


-15.40 -1.63 ((((.(((((.((((((((&))))))))))))))))) 863 881 258 274 "putative benzoate transport porin (BenP) A1S" A1S_1209c1415736-


Asso ciated GO-


download:

mRNA

sequence

download:

sRNA sequence

Accessiblity

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Calculate (new

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RNAup

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mRNA: 5'-

sRNA: 3'-

AAGCAGCCAAUGGGGAG

|||| ||||| ||||||

UUCG-CGGUU-CCCUUC

-3'

-5'

2010 - 2012 TBI - Contact- Publication
http://nar.oxfordjournals.org/content/early/2011/06/14/nar.gkr467.fullmailto:[email protected]://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=AACCATGTAATTTAGCAATAACTACATTATTCGGTTTATTAACTAGCTCAAGTTTATGGGCAGCAGACACCACTCAACAAAGCGAAGATGAATGGAAGTTCACGCTAAAAAATGCCTATATCAATCGTGATTTTGATAATGATGCACTCAAAGACACAGGCAGTTGGTCTCAGGCAGCCTCATTATTTTATAAGTCGAAAATGTATGACACTCCGTTAATCATAGCAGACAAGCCAATTACGATTGGTGCCGATGCTTCTGTTCAATACGCCGTGCGCTTGAGTTCAGACAAACATGTCGCAGATACAGTTTTGCCTTTTAATAAAGAAACGCAATCTCAAGCATCAGATTTCTTAAAATACGGTGCAACCTTAAAACTGGGCTATGACAAAACCCTGTTGAGTATCGGTGAACTCTGGCTGGATTTACCTGTAACGGCTGTCGATGCTAGCCGACAATTGCTTGCTTCTTATTGGGGAACCAACCTTAAATCGCAACTTTCAGATCAGCTTTATGCCGAAATTGGTCGGGTTGAAAAAGTTTCGCCACGAAATGAAGAGGACTTTAAAAAGTTTTCATTCACGGCAAATGGAATGACCAAAGAATCCGATGGCCTGAACTACATTGACCTACGTTATCAATTTACACCGTCACTCAAGGGTGAATATTACTTTGGTAACTTAGAAGACCTCTACAATAAACACTATGTAGGGCTTGAGCATACGTGGAAACAACCTAATTTTGCCCTCACCTCTAAGTTTAAATACTTCAATGCAAAAGATGATGGCAATACTTTTGATATTGATGCGCAAAACATCGGGGTGCTAGAAACACTTAAAGTAAAAAATCATACCTTTGGTTTGGGGTACCAGCAAATTATTGGTGAGTCGGCTTATCCATTACCGGATGGTTTTTTACCAGAAACCTATTTCATTAACTGGAATGCTACAGGTTTCTTTAAAGAAGATGAGAAGTCTTATCATGTGATGTATGGCTATGACTTTAAAGATTACGTTCCGGGCTTAAATGCAATGGTGAAATATGTTTACGGTCATGACTTTAAAGCAGCCAATGGGGAGAAAAACCACGAAACCGAGTCGAATGTGATTTTAAACTATGCGTTTCAACAGCCTTTCTTGAAAGGCTTTGCCCTGCAATATATTCGAATTGATTACAACGTAAAACATGGCAATGACTTTGGTGAAGATCGCTTGTTTGTAAACTACACTAAAAAGTTTTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=192.&b=1063&e=1081&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/sRNA.fastahttp://rna.tbi.univie.ac.at/RNApredator2/html/eieAZ18dVl/192..fastahttp://rna.tbi.univie.ac.at/cgi-bin/RNAup.cgi?PAGE=2&SCREEN=TTTTTATAGCGGCTCTGTTATATTAAACGGAAAGTTTTTTGGCAGTGATTATCAAAATATGACTTTGTTCTCATATTTCTGTTAGAATCTGACTGAAAACTGAGGTTGAGCTTTTTATTTGGGTACCAATATTGCAGTTTTAAGCGTTTAGCAAGGAGATAAACATGCTGATTCTGACCCGCCGTGTCGGGGAAACATTAATGATTGGGGATCAAGTCAGTGTTACTGTGCTTGGCGTCAAAGGAAACCAAGTTCGAATTGGTGTAAATGCACCAAAAGAGGTTTCTGTTCATCGCGAAGAAATTTATCAACGTATTCAACATGAACGTGCAATGCATGAACACCTTCAACATCTTGATCAAGATTATCAAGTTTCATATGAAGATGATAATTATGCACAGAAAAACTTCAATCGTTA&SCREEN2=GUCAUAAUUCACCUCUCCAGUAGGUGUUGAUUGAAAGUGCCGGGCUGGUUGUGGCCAGCCCGGUGCGCCUACAGGUACAGCCCCGCCGCCUCCGCGAAUGCUGACCGCUCAUUCCUGCCGCCAUUAACCUCAAUACUUAUCGGCUUAGUUUCGCUCUCUCUCAUAGGGUCUGGCCGUGAUACAAAAGCGGCUGUUUCUGUCUCUGCAUCGACCUCGGUCGAUUGAUCACCCAGCGGCGAAAUAAAUACCUGGCUGACUUCUUCCCUUGGCGCUUCAUCCAGGGCCGCCAAUGCGGCCAUGUAUGUUG&tempdir=eieAZ18dVl&page=0http://rna.tbi.univie.ac.at/RNApredator2/accessiblity_plot.cgi?s=1637.&b=207&e=221&tempdir=eieAZ18dVl&page=0

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